Starting phenix.real_space_refine on Fri Mar 1 01:01:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msm_23969/03_2024/7msm_23969_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msm_23969/03_2024/7msm_23969.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msm_23969/03_2024/7msm_23969_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msm_23969/03_2024/7msm_23969_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msm_23969/03_2024/7msm_23969_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msm_23969/03_2024/7msm_23969.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msm_23969/03_2024/7msm_23969.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msm_23969/03_2024/7msm_23969_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msm_23969/03_2024/7msm_23969_updated.pdb" } resolution = 2.79 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= 0.012 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 445 5.21 5 S 102 5.16 5 C 76294 2.51 5 N 28462 2.21 5 O 42285 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 "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 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 "M PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 134": "NH1" <-> "NH2" 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 ARG 14": "NH1" <-> "NH2" Residue "W ARG 73": "NH1" <-> "NH2" Residue "c PHE 129": "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 "g ARG 112": "NH1" <-> "NH2" 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 ARG 3": "NH1" <-> "NH2" Residue "x ARG 12": "NH1" <-> "NH2" Residue "x ARG 233": "NH1" <-> "NH2" Residue "x TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 257": "NH1" <-> "NH2" Residue "x ARG 265": "NH1" <-> "NH2" Residue "x ARG 302": "NH1" <-> "NH2" Residue "x ARG 346": "NH1" <-> "NH2" Residue "x ARG 393": "NH1" <-> "NH2" Residue "x ARG 399": "NH1" <-> "NH2" Residue "x ARG 539": "NH1" <-> "NH2" Residue "x ARG 553": "NH1" <-> "NH2" Residue "x ARG 557": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 152436 Number of models: 1 Model: "" Number of chains: 69 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: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 186 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 1, 'TRANS': 20} 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': 160, 'rna3p': 1, 'rna3p_pur': 1483, 'rna3p_pyr': 1174} Link IDs: {'rna2p': 460, 'rna3p': 2657} 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': 6, 'rna3p_pur': 54, 'rna3p_pyr': 47} Link IDs: {'rna2p': 13, 'rna3p': 101} Chain breaks: 1 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: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 549 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} 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': 117, 'rna2p_pyr': 93, 'rna3p': 6, 'rna3p_pur': 733, 'rna3p_pyr': 569} Link IDs: {'rna2p': 211, 'rna3p': 1307} 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: 4312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4312 Classifications: {'peptide': 553} Link IDs: {'PTRANS': 23, 'TRANS': 529} 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': 4, 'rna3p_pur': 31, 'rna3p_pyr': 34} Link IDs: {'rna2p': 11, 'rna3p': 65} 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': 2, 'rna3p': 4} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 302 Unusual residues: {' MG': 302} Classifications: {'undetermined': 302} Link IDs: {None: 301} 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: 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: "W" 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: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 130 Unusual residues: {' MG': 130} Classifications: {'undetermined': 130} Link IDs: {None: 129} 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: "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 15 115.867 178.561 187.780 1.00 47.48 S ATOM 519 SG CYS 1 18 115.992 181.867 186.012 1.00 48.97 S ATOM 734 SG CYS 1 42 119.294 180.773 187.053 1.00 43.92 S ATOM 755 SG CYS 1 45 117.321 182.626 189.979 1.00 45.82 S ATOM 1778 SG CYS 4 11 184.423 97.945 136.839 1.00 85.72 S ATOM 1801 SG CYS 4 14 184.906 101.224 135.423 1.00 81.38 S ATOM 1911 SG CYS 4 27 186.386 98.761 133.196 1.00 75.54 S ATOM 2121 SG CYS 6 16 112.373 112.454 224.095 1.00 89.46 S ATOM 2280 SG CYS 6 38 115.967 112.075 224.074 1.00 86.15 S ATOM 2301 SG CYS 6 41 113.888 109.433 222.777 1.00 88.03 S ATOM 94958 SG CYS X 5 91.650 200.418 123.003 1.00 44.36 S ATOM 94980 SG CYS X 8 93.432 202.725 125.374 1.00 46.64 S ATOM 95323 SG CYS X 52 91.259 199.572 126.587 1.00 45.86 S ATOM 95342 SG CYS X 55 89.606 202.818 126.442 1.00 49.22 S ATOM A0VVK SG CYS n 24 89.637 55.260 169.131 1.00 58.99 S ATOM A0VW5 SG CYS n 27 91.508 56.536 165.957 1.00 59.14 S ATOM A0VZ3 SG CYS n 40 88.549 58.813 167.471 1.00 56.80 S ATOM A0VZS SG CYS n 43 87.719 55.865 165.493 1.00 58.55 S ATOM A0XXZ SG CYS r 20 35.020 120.361 106.946 1.00 72.82 S ATOM A0XYN SG CYS r 23 34.971 119.134 103.119 1.00 75.59 S ATOM A0Y68 SG CYS r 57 38.399 119.622 104.383 1.00 60.23 S Time building chain proxies: 58.15, per 1000 atoms: 0.38 Number of scatterers: 152436 At special positions: 0 Unit cell: (241.301, 270.002, 243.427, 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 445 11.99 O 42285 8.00 N 28462 7.00 C 76294 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: 59.06 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 42 " pdb="ZN ZN 1 101 " - pdb=" SG CYS 1 18 " pdb="ZN ZN 1 101 " - pdb=" SG CYS 1 45 " pdb="ZN ZN 1 101 " - pdb=" SG CYS 1 15 " pdb=" ZN 4 101 " pdb="ZN ZN 4 101 " - pdb=" ND1 HIS 4 32 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 11 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 27 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 14 " pdb=" ZN 6 101 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 41 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 16 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 38 " pdb=" ZN X 101 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 8 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 52 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 55 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 5 " pdb=" ZN n 101 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 43 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 24 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 27 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 40 " pdb=" ZN r 101 " pdb="ZN ZN r 101 " - pdb=" ND1 HIS r 60 " pdb="ZN ZN r 101 " - pdb=" SG CYS r 23 " pdb="ZN ZN r 101 " - pdb=" SG CYS r 57 " pdb="ZN ZN r 101 " - pdb=" SG CYS r 20 " Number of angles added : 24 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11260 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: 179 helices and 78 sheets defined 37.0% alpha, 18.5% beta 1256 base pairs and 2738 stacking pairs defined. Time for finding SS restraints: 75.25 Creating SS restraints... Processing helix chain '0' and resid 9 through 21 removed outlier: 3.526A pdb=" N SER 0 15 " --> pdb=" O SER 0 11 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG 0 16 " --> pdb=" O ASN 0 12 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLN 0 19 " --> pdb=" O SER 0 15 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TRP 0 20 " --> pdb=" O ARG 0 16 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N LYS 0 21 " --> pdb=" O ARG 0 17 " (cutoff:3.500A) Processing helix chain '0' and resid 40 through 50 removed outlier: 3.808A pdb=" N LEU 0 44 " --> pdb=" O PRO 0 40 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LYS 0 45 " --> pdb=" O ARG 0 41 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ALA 0 46 " --> pdb=" O ARG 0 42 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG 0 48 " --> pdb=" O LEU 0 44 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU 0 49 " --> pdb=" O LYS 0 45 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY 0 50 " --> pdb=" O ALA 0 46 " (cutoff:3.500A) Processing helix chain '1' and resid 28 through 33 Proline residue: 1 33 - end of helix No H-bonds generated for 'chain '1' and resid 28 through 33' Processing helix chain '2' and resid 11 through 19 removed outlier: 3.560A pdb=" N VAL 2 18 " --> pdb=" O ARG 2 14 " (cutoff:3.500A) Processing helix chain '2' and resid 20 through 28 removed outlier: 4.639A pdb=" N ARG 2 26 " --> pdb=" O ARG 2 22 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N THR 2 27 " --> pdb=" O LEU 2 23 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ARG 2 28 " --> pdb=" O ARG 2 24 " (cutoff:3.500A) Processing helix chain '2' and resid 29 through 41 Processing helix chain '3' and resid 7 through 14 removed outlier: 3.875A pdb=" N LYS 3 12 " --> pdb=" O SER 3 8 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG 3 13 " --> pdb=" O GLY 3 9 " (cutoff:3.500A) Processing helix chain '3' and resid 37 through 45 removed outlier: 3.760A pdb=" N ARG 3 43 " --> pdb=" O THR 3 39 " (cutoff:3.500A) Processing helix chain '3' and resid 51 through 63 removed outlier: 5.369A pdb=" N LYS 3 56 " --> pdb=" O ALA 3 52 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ARG 3 57 " --> pdb=" O ASN 3 53 " (cutoff:3.500A) Processing helix chain '6' and resid 42 through 47 removed outlier: 3.952A pdb=" N THR 6 46 " --> pdb=" O HIS 6 42 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLY 6 47 " --> pdb=" O PRO 6 43 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 42 through 47' Processing helix chain '6' and resid 56 through 65 removed outlier: 3.594A pdb=" N ARG 6 60 " --> pdb=" O GLY 6 56 " (cutoff:3.500A) Processing helix chain '7' and resid 2 through 12 removed outlier: 3.701A pdb=" N ARG 7 11 " --> pdb=" O LYS 7 7 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LYS 7 12 " --> pdb=" O LYS 7 8 " (cutoff:3.500A) Processing helix chain '8' and resid 5 through 16 removed outlier: 6.521A pdb=" N ARG 8 9 " --> pdb=" O SER 8 5 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ALA 8 10 " --> pdb=" O LYS 8 6 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA 8 11 " --> pdb=" O ALA 8 7 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS 8 14 " --> pdb=" O ALA 8 10 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ASP 8 16 " --> pdb=" O ALA 8 12 " (cutoff:3.500A) Processing helix chain '8' and resid 22 through 38 removed outlier: 3.798A pdb=" N ALA 8 27 " --> pdb=" O PRO 8 23 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS 8 31 " --> pdb=" O ALA 8 27 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N THR 8 36 " --> pdb=" O GLU 8 32 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LYS 8 37 " --> pdb=" O THR 8 33 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLN 8 38 " --> pdb=" O SER 8 34 " (cutoff:3.500A) Processing helix chain '8' and resid 81 through 91 removed outlier: 4.301A pdb=" N ASP 8 85 " --> pdb=" O GLY 8 81 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA 8 86 " --> pdb=" O GLU 8 82 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA 8 87 " --> pdb=" O LYS 8 83 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL 8 88 " --> pdb=" O ALA 8 84 " (cutoff:3.500A) Processing helix chain '8' and resid 97 through 107 removed outlier: 3.973A pdb=" N ILE 8 101 " --> pdb=" O SER 8 97 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU 8 102 " --> pdb=" O ASP 8 98 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG 8 103 " --> pdb=" O ASP 8 99 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY 8 106 " --> pdb=" O GLU 8 102 " (cutoff:3.500A) Processing helix chain '8' and resid 120 through 132 removed outlier: 4.343A pdb=" N VAL 8 124 " --> pdb=" O GLN 8 120 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY 8 125 " --> pdb=" O MET 8 121 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG 8 126 " --> pdb=" O ALA 8 122 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ARG 8 129 " --> pdb=" O GLY 8 125 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N VAL 8 130 " --> pdb=" O ARG 8 126 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU 8 131 " --> pdb=" O ILE 8 127 " (cutoff:3.500A) Processing helix chain '8' and resid 151 through 159 removed outlier: 4.015A pdb=" N ASP 8 155 " --> pdb=" O LYS 8 151 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS 8 157 " --> pdb=" O VAL 8 153 " (cutoff:3.500A) Processing helix chain '8' and resid 181 through 200 removed outlier: 4.309A pdb=" N GLU 8 187 " --> pdb=" O LYS 8 183 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN 8 188 " --> pdb=" O LEU 8 184 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG 8 198 " --> pdb=" O ASP 8 194 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU 8 199 " --> pdb=" O GLU 8 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 137 removed outlier: 3.745A 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: 3.990A pdb=" N MET C 212 " --> pdb=" O LYS C 208 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 227 removed outlier: 4.537A pdb=" N MET C 226 " --> pdb=" O ARG C 222 " (cutoff:3.500A) removed outlier: 5.287A 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: 3.776A pdb=" N ILE C 268 " --> pdb=" O SER C 264 " (cutoff:3.500A) removed outlier: 5.721A 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: 3.549A pdb=" N GLY D 68 " --> pdb=" O LYS D 64 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN D 69 " --> pdb=" O PRO D 65 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA D 73 " --> pdb=" O GLN D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 95 removed outlier: 5.485A pdb=" N GLU D 94 " --> pdb=" O ASP D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 130 removed outlier: 3.599A pdb=" N HIS D 130 " --> pdb=" O THR D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 107 removed outlier: 3.961A pdb=" N ILE D 105 " --> pdb=" O THR D 102 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE D 106 " --> pdb=" O ALA D 103 " (cutoff:3.500A) removed outlier: 5.277A 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: 3.510A 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: 3.649A pdb=" N ALA E 50 " --> pdb=" O ALA E 46 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG E 52 " --> pdb=" O ARG E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 128 removed outlier: 3.590A pdb=" N ALA E 115 " --> pdb=" O LYS E 111 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA E 116 " --> pdb=" O MET E 112 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG E 118 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY E 119 " --> pdb=" O ALA E 115 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN E 127 " --> pdb=" O ASP E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 155 removed outlier: 3.504A pdb=" N SER E 153 " --> pdb=" O ALA E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 177 removed outlier: 3.517A pdb=" N ALA E 172 " --> pdb=" O ASP E 168 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL E 175 " --> pdb=" O GLY E 171 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG E 176 " --> pdb=" O ALA E 172 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ASN E 177 " --> pdb=" O LYS E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 198 removed outlier: 5.388A pdb=" N ASP E 198 " --> pdb=" O VAL E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 215 removed outlier: 3.506A pdb=" N ALA E 209 " --> pdb=" O GLU E 205 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA E 213 " --> pdb=" O ALA E 209 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN E 214 " --> pdb=" O TYR E 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 27 removed outlier: 3.622A pdb=" N GLU F 18 " --> pdb=" O ARG F 14 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ARG F 20 " --> pdb=" O ARG F 16 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ASP F 21 " --> pdb=" O SER F 17 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU F 23 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG F 24 " --> pdb=" O ARG F 20 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS F 25 " --> pdb=" O ASP F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 54 removed outlier: 5.502A pdb=" N ASP F 53 " --> pdb=" O GLU F 49 " (cutoff:3.500A) removed outlier: 4.144A 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 55 through 69 removed outlier: 5.145A pdb=" N GLY F 59 " --> pdb=" O LYS F 55 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL F 61 " --> pdb=" O ILE F 57 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASN F 62 " --> pdb=" O ASN F 58 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ASP F 63 " --> pdb=" O GLY F 59 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU F 64 " --> pdb=" O ALA F 60 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU F 66 " --> pdb=" O ASN F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 112 removed outlier: 3.738A pdb=" N TRP F 104 " --> pdb=" O GLY F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 118 removed outlier: 4.837A pdb=" N ARG F 117 " --> pdb=" O ILE F 113 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ILE F 118 " --> pdb=" O ALA F 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 113 through 118' Processing helix chain 'F' and resid 169 through 181 removed outlier: 3.817A pdb=" N LEU F 176 " --> pdb=" O GLU F 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 82 removed outlier: 3.595A pdb=" N SER G 64 " --> pdb=" O ARG G 60 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU G 65 " --> pdb=" O ARG G 61 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG G 70 " --> pdb=" O HIS G 66 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR G 71 " --> pdb=" O GLY G 67 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL G 73 " --> pdb=" O SER G 69 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN G 75 " --> pdb=" O THR G 71 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY G 79 " --> pdb=" O ASN G 75 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR G 81 " --> pdb=" O VAL G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 153 removed outlier: 3.627A pdb=" N ILE G 145 " --> pdb=" O LYS G 141 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU G 152 " --> pdb=" O ASN G 148 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ARG G 153 " --> pdb=" O ILE G 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 29 removed outlier: 5.926A pdb=" N GLY H 26 " --> pdb=" O LYS H 22 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ARG H 27 " --> pdb=" O ASP H 23 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE H 29 " --> pdb=" O TYR H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 47 removed outlier: 5.443A pdb=" N GLN H 44 " --> pdb=" O SER H 40 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA H 47 " --> pdb=" O ALA H 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.508A pdb=" N VAL J 30 " --> pdb=" O GLY J 26 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU J 35 " --> pdb=" O ALA J 31 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG J 37 " --> pdb=" O ALA J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 72 removed outlier: 3.528A pdb=" N LEU J 69 " --> pdb=" O SER J 65 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN J 70 " --> pdb=" O GLY J 66 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N HIS J 71 " --> pdb=" O ASP J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 96 removed outlier: 3.950A pdb=" N GLN J 94 " --> pdb=" O GLY J 90 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ARG J 95 " --> pdb=" O GLU J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 110 removed outlier: 3.835A pdb=" N VAL J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU J 102 " --> pdb=" O ASP J 98 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE J 105 " --> pdb=" O VAL J 101 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY J 107 " --> pdb=" O LYS J 103 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) removed outlier: 3.612A 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: 4.086A pdb=" N ARG J 116 " --> pdb=" O ASN J 112 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN J 117 " --> pdb=" O ARG J 113 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG J 120 " --> pdb=" O ARG J 116 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LYS J 121 " --> pdb=" O GLN J 117 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU J 122 " --> pdb=" O ILE J 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 110 removed outlier: 4.493A pdb=" N GLU K 108 " --> pdb=" O ARG K 104 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS K 109 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG K 110 " --> pdb=" O LEU K 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 104 through 110' Processing helix chain 'K' and resid 111 through 118 Processing helix chain 'L' and resid 38 through 43 removed outlier: 4.300A pdb=" N ARG L 42 " --> pdb=" O GLY L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 60 removed outlier: 4.052A pdb=" N LEU L 60 " --> pdb=" O ILE L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 86 removed outlier: 3.540A pdb=" N ILE L 82 " --> pdb=" O ASN L 78 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN L 83 " --> pdb=" O VAL L 79 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG L 84 " --> pdb=" O GLY L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 93 through 101 removed outlier: 3.518A pdb=" N LEU L 97 " --> pdb=" O GLY L 93 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL L 98 " --> pdb=" O VAL L 94 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY L 101 " --> pdb=" O LEU L 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 129 through 140 removed outlier: 3.937A pdb=" N ARG L 133 " --> pdb=" O SER L 129 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA L 134 " --> pdb=" O GLY L 130 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS L 135 " --> pdb=" O SER L 131 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA L 139 " --> pdb=" O LYS L 135 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY L 140 " --> pdb=" O ILE L 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 59 removed outlier: 3.515A pdb=" N ILE M 47 " --> pdb=" O THR M 43 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE M 52 " --> pdb=" O GLU M 48 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA M 53 " --> pdb=" O SER M 49 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE M 54 " --> pdb=" O ALA M 50 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG M 56 " --> pdb=" O ILE M 52 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N HIS M 57 " --> pdb=" O ALA M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 126 removed outlier: 3.698A pdb=" N THR M 119 " --> pdb=" O ARG M 115 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG M 120 " --> pdb=" O ALA M 116 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA M 121 " --> pdb=" O ALA M 117 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LYS M 124 " --> pdb=" O ARG M 120 " (cutoff:3.500A) removed outlier: 3.780A 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: 3.600A pdb=" N GLN N 17 " --> pdb=" O SER N 13 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS N 18 " --> pdb=" O SER N 14 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA N 19 " --> pdb=" O SER N 15 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA N 25 " --> pdb=" O LEU N 21 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 58 removed outlier: 3.778A pdb=" N LEU N 44 " --> pdb=" O LYS N 40 " (cutoff:3.500A) Proline residue: N 46 - end of helix removed outlier: 4.423A pdb=" N LYS N 50 " --> pdb=" O PRO N 46 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU N 51 " --> pdb=" O TYR N 47 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR N 53 " --> pdb=" O GLU N 49 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N HIS N 54 " --> pdb=" O LYS N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 70 removed outlier: 4.124A pdb=" N LYS N 69 " --> pdb=" O GLU N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 89 removed outlier: 3.604A pdb=" N THR N 78 " --> pdb=" O ASP N 74 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE N 83 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N GLY N 84 " --> pdb=" O PHE N 80 " (cutoff:3.500A) Proline residue: N 85 - end of helix removed outlier: 3.891A pdb=" N ALA N 88 " --> pdb=" O GLY N 84 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ASP N 89 " --> pdb=" O PRO N 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 24 removed outlier: 4.438A pdb=" N THR O 8 " --> pdb=" O SER O 4 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG O 10 " --> pdb=" O SER O 6 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE O 11 " --> pdb=" O ALA O 7 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR O 18 " --> pdb=" O LEU O 14 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N LYS O 23 " --> pdb=" O ARG O 19 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU O 24 " --> pdb=" O LEU O 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 68 removed outlier: 3.732A pdb=" N GLY O 67 " --> pdb=" O ALA O 63 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL O 68 " --> pdb=" O ASP O 64 " (cutoff:3.500A) Processing helix chain 'O' and resid 71 through 91 removed outlier: 3.613A pdb=" N ARG O 75 " --> pdb=" O ASP O 71 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA O 84 " --> pdb=" O GLY O 80 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS O 88 " --> pdb=" O ALA O 84 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA O 89 " --> pdb=" O GLU O 85 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA O 90 " --> pdb=" O ARG O 86 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 119 removed outlier: 3.506A pdb=" N GLU O 117 " --> pdb=" O ASP O 113 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASN O 118 " --> pdb=" O ALA O 114 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY O 119 " --> pdb=" O ALA O 115 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 12 removed outlier: 3.657A pdb=" N ASP P 8 " --> pdb=" O LEU P 4 " (cutoff:3.500A) removed outlier: 3.902A 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 12' Processing helix chain 'P' and resid 97 through 103 removed outlier: 4.789A pdb=" N GLU P 101 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ARG P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 97 through 103' Processing helix chain 'Q' and resid 6 through 22 removed outlier: 4.608A pdb=" N LYS Q 12 " --> pdb=" O VAL Q 8 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LYS Q 13 " --> pdb=" O ASN Q 9 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG Q 14 " --> pdb=" O ALA Q 10 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG Q 15 " --> pdb=" O HIS Q 11 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER Q 16 " --> pdb=" O LYS Q 12 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG Q 22 " --> pdb=" O LEU Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 4.054A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 36 through 73 removed outlier: 3.743A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLY Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE Q 57 " --> pdb=" O ARG Q 53 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG Q 58 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS Q 59 " --> pdb=" O GLY Q 55 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA Q 63 " --> pdb=" O LYS Q 59 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU Q 71 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASN Q 72 " --> pdb=" O ALA Q 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 removed outlier: 3.695A pdb=" N GLN Q 81 " --> pdb=" O ASN Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 102 removed outlier: 3.694A pdb=" N ALA Q 99 " --> pdb=" O LEU Q 95 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILE Q 100 " --> pdb=" O ALA Q 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 117 removed outlier: 3.749A pdb=" N THR Q 107 " --> pdb=" O PRO Q 103 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA Q 108 " --> pdb=" O ALA Q 104 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL Q 112 " --> pdb=" O ALA Q 108 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA Q 115 " --> pdb=" O ASP Q 111 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU Q 117 " --> pdb=" O ALA Q 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 60 removed outlier: 3.666A pdb=" N ALA R 57 " --> pdb=" O ALA R 53 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL R 59 " --> pdb=" O ALA R 55 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N ALA R 60 " --> pdb=" O LEU R 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 23 through 35 removed outlier: 4.173A pdb=" N VAL S 30 " --> pdb=" O LYS S 26 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU S 33 " --> pdb=" O ARG S 29 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL S 34 " --> pdb=" O VAL S 30 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG S 35 " --> pdb=" O ILE S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 38 through 49 removed outlier: 4.014A pdb=" N ASP S 44 " --> pdb=" O SER S 40 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE S 45 " --> pdb=" O ASP S 41 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG S 47 " --> pdb=" O LEU S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 51 through 71 removed outlier: 4.669A pdb=" N GLY S 55 " --> pdb=" O GLN S 51 " (cutoff:3.500A) Proline residue: S 56 - end of helix removed outlier: 3.884A pdb=" N VAL S 60 " --> pdb=" O PRO S 56 " (cutoff:3.500A) Processing helix chain 'T' and resid 6 through 12 removed outlier: 4.491A pdb=" N ILE T 10 " --> pdb=" O ASP T 6 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE T 11 " --> pdb=" O PRO T 7 " (cutoff:3.500A) removed outlier: 5.719A 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: 3.888A pdb=" N GLY T 22 " --> pdb=" O GLU T 18 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP T 25 " --> pdb=" O TYR T 21 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ASP T 26 " --> pdb=" O GLY T 22 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN T 27 " --> pdb=" O LEU T 23 " (cutoff:3.500A) Processing helix chain 'T' and resid 38 through 50 removed outlier: 3.591A pdb=" N LYS T 43 " --> pdb=" O LYS T 39 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU T 47 " --> pdb=" O LYS T 43 " (cutoff:3.500A) Processing helix chain 'U' and resid 67 through 72 removed outlier: 4.314A pdb=" N VAL U 71 " --> pdb=" O HIS U 67 " (cutoff:3.500A) removed outlier: 5.679A 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: 3.606A pdb=" N ALA V 25 " --> pdb=" O ALA V 21 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG V 27 " --> pdb=" O ARG V 23 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA V 28 " --> pdb=" O ARG V 24 " (cutoff:3.500A) Processing helix chain 'V' and resid 48 through 59 removed outlier: 5.320A pdb=" N TYR V 52 " --> pdb=" O PRO V 48 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU V 56 " --> pdb=" O TYR V 52 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG V 57 " --> pdb=" O ALA V 53 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER V 59 " --> pdb=" O VAL V 55 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 59 removed outlier: 3.861A pdb=" N ALA X 58 " --> pdb=" O SER X 54 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLY X 59 " --> pdb=" O CYS X 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 6 through 13 removed outlier: 3.867A pdb=" N LEU Y 10 " --> pdb=" O SER Y 6 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG Y 11 " --> pdb=" O PRO Y 7 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLU Y 12 " --> pdb=" O GLY Y 8 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LEU Y 13 " --> pdb=" O GLU Y 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 6 through 13' Processing helix chain 'Y' and resid 14 through 39 removed outlier: 5.758A pdb=" N LEU Y 18 " --> pdb=" O THR Y 14 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA Y 19 " --> pdb=" O ASP Y 15 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU Y 20 " --> pdb=" O GLU Y 16 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG Y 23 " --> pdb=" O ALA Y 19 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR Y 38 " --> pdb=" O PHE Y 34 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 67 removed outlier: 4.707A pdb=" N ARG Y 48 " --> pdb=" O ASN Y 44 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG Y 56 " --> pdb=" O GLN Y 52 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE Y 57 " --> pdb=" O GLU Y 53 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL Y 60 " --> pdb=" O ARG Y 56 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU Y 65 " --> pdb=" O LEU Y 61 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY Y 67 " --> pdb=" O GLU Y 63 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 removed outlier: 3.514A pdb=" N SER Z 22 " --> pdb=" O LYS Z 18 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU Z 26 " --> pdb=" O SER Z 22 " (cutoff:3.500A) Processing helix chain 'Z' and resid 40 through 51 removed outlier: 3.883A pdb=" N GLY Z 45 " --> pdb=" O ALA Z 41 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU Z 46 " --> pdb=" O ALA Z 42 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA Z 48 " --> pdb=" O ARG Z 44 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL Z 49 " --> pdb=" O GLY Z 45 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL Z 50 " --> pdb=" O LEU Z 46 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 removed outlier: 3.644A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU c 12 " --> pdb=" O HIS c 8 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 46 removed outlier: 3.643A pdb=" N TYR c 31 " --> pdb=" O GLN c 27 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA c 37 " --> pdb=" O LYS c 33 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU c 41 " --> pdb=" O ALA c 37 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER c 43 " --> pdb=" O ARG c 39 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N GLY c 45 " --> pdb=" O LEU c 41 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LEU c 46 " --> pdb=" O LEU c 42 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 77 removed outlier: 4.429A pdb=" N VAL c 75 " --> pdb=" O ARG c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 95 removed outlier: 4.961A pdb=" N ASP c 84 " --> pdb=" O GLY c 80 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ARG c 85 " --> pdb=" O THR c 81 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG c 87 " --> pdb=" O ALA c 83 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS c 92 " --> pdb=" O ALA c 88 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR c 94 " --> pdb=" O LEU c 90 " (cutoff:3.500A) Processing helix chain 'c' and resid 107 through 112 removed outlier: 3.898A pdb=" N GLN c 111 " --> pdb=" O ASN c 107 " (cutoff:3.500A) removed outlier: 7.199A 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: 3.967A pdb=" N GLN c 117 " --> pdb=" O GLN c 113 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA c 120 " --> pdb=" O ALA c 116 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN c 122 " --> pdb=" O GLY c 118 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN c 125 " --> pdb=" O GLU c 121 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG c 126 " --> pdb=" O GLN c 122 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 144 removed outlier: 3.634A pdb=" N ILE c 137 " --> pdb=" O MET c 133 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER c 139 " --> pdb=" O LYS c 135 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG c 142 " --> pdb=" O GLN c 138 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLN c 143 " --> pdb=" O SER c 139 " (cutoff:3.500A) Proline residue: c 144 - end of helix Processing helix chain 'd' and resid 7 through 16 removed outlier: 3.950A pdb=" N LYS d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER d 12 " --> pdb=" O VAL d 8 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG d 14 " --> pdb=" O ARG d 10 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LEU d 15 " --> pdb=" O LYS d 11 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG d 16 " --> pdb=" O SER d 12 " (cutoff:3.500A) Processing helix chain 'd' and resid 23 through 30 removed outlier: 4.739A pdb=" N GLU d 27 " --> pdb=" O ASP d 23 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS d 28 " --> pdb=" O GLN d 24 " (cutoff:3.500A) removed outlier: 3.778A 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: 3.868A pdb=" N GLU d 52 " --> pdb=" O LEU d 48 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS d 55 " --> pdb=" O GLN d 51 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA d 56 " --> pdb=" O GLU d 52 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE d 58 " --> pdb=" O GLN d 54 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR d 60 " --> pdb=" O ALA d 56 " (cutoff:3.500A) Processing helix chain 'd' and resid 63 through 78 removed outlier: 3.963A pdb=" N ARG d 69 " --> pdb=" O LYS d 65 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR d 70 " --> pdb=" O GLN d 66 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU d 73 " --> pdb=" O ARG d 69 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ARG d 76 " --> pdb=" O GLU d 72 " (cutoff:3.500A) Proline residue: d 78 - end of helix Processing helix chain 'd' and resid 80 through 92 removed outlier: 4.580A pdb=" N GLU d 84 " --> pdb=" O LYS d 80 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU d 86 " --> pdb=" O GLY d 82 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER d 91 " --> pdb=" O LYS d 87 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ARG d 92 " --> pdb=" O ILE d 88 " (cutoff:3.500A) Processing helix chain 'd' and resid 93 through 101 Processing helix chain 'd' and resid 105 through 116 removed outlier: 3.517A pdb=" N ALA d 109 " --> pdb=" O THR d 105 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG d 110 " --> pdb=" O ARG d 106 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL d 113 " --> pdb=" O ALA d 109 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLY d 116 " --> pdb=" O LEU d 112 " (cutoff:3.500A) Processing helix chain 'd' and resid 147 through 157 removed outlier: 4.989A pdb=" N ALA d 153 " --> pdb=" O PRO d 149 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG d 154 " --> pdb=" O PHE d 150 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLU d 155 " --> pdb=" O GLN d 151 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR d 156 " --> pdb=" O ILE d 152 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ALA d 157 " --> pdb=" O ALA d 153 " (cutoff:3.500A) Processing helix chain 'd' and resid 192 through 201 removed outlier: 3.939A pdb=" N VAL d 196 " --> pdb=" O GLU d 192 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU d 197 " --> pdb=" O GLN d 193 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR d 199 " --> pdb=" O ILE d 195 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER d 200 " --> pdb=" O VAL d 196 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LYS d 201 " --> pdb=" O GLU d 197 " (cutoff:3.500A) Processing helix chain 'e' and resid 86 through 102 removed outlier: 3.562A pdb=" N ALA e 92 " --> pdb=" O PRO e 88 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS e 93 " --> pdb=" O ALA e 89 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS e 100 " --> pdb=" O GLU e 96 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER e 101 " --> pdb=" O GLU e 97 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE e 102 " --> pdb=" O ALA e 98 " (cutoff:3.500A) Processing helix chain 'e' and resid 140 through 150 removed outlier: 4.075A pdb=" N ALA e 144 " --> pdb=" O GLY e 140 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL e 145 " --> pdb=" O ALA e 141 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU e 146 " --> pdb=" O ALA e 142 " (cutoff:3.500A) Processing helix chain 'e' and resid 163 through 179 removed outlier: 3.500A pdb=" N VAL e 168 " --> pdb=" O ALA e 164 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU e 178 " --> pdb=" O ALA e 174 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N GLN e 179 " --> pdb=" O LEU e 175 " (cutoff:3.500A) Processing helix chain 'e' and resid 180 through 189 removed outlier: 3.848A pdb=" N ALA e 185 " --> pdb=" O PRO e 181 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA e 186 " --> pdb=" O GLU e 182 " (cutoff:3.500A) Processing helix chain 'e' and resid 191 through 196 removed outlier: 3.761A pdb=" N VAL e 195 " --> pdb=" O PRO e 191 " (cutoff:3.500A) Processing helix chain 'e' and resid 197 through 209 removed outlier: 3.594A pdb=" N LYS e 202 " --> pdb=" O ALA e 198 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA e 203 " --> pdb=" O GLY e 199 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG e 204 " --> pdb=" O MET e 200 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG e 205 " --> pdb=" O LEU e 201 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER e 207 " --> pdb=" O ALA e 203 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU e 208 " --> pdb=" O ARG e 204 " (cutoff:3.500A) Processing helix chain 'f' and resid 15 through 32 removed outlier: 4.231A pdb=" N VAL f 19 " --> pdb=" O ASP f 15 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ALA f 20 " --> pdb=" O GLU f 16 " (cutoff:3.500A) Proline residue: f 21 - end of helix removed outlier: 3.717A pdb=" N GLU f 24 " --> pdb=" O ALA f 20 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N THR f 25 " --> pdb=" O PRO f 21 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE f 26 " --> pdb=" O SER f 22 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL f 29 " --> pdb=" O THR f 25 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL f 30 " --> pdb=" O PHE f 26 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG f 31 " --> pdb=" O LEU f 27 " (cutoff:3.500A) Processing helix chain 'f' and resid 68 through 83 removed outlier: 3.542A pdb=" N VAL f 72 " --> pdb=" O ALA f 68 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER f 73 " --> pdb=" O PRO f 69 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU f 74 " --> pdb=" O ALA f 70 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG f 77 " --> pdb=" O SER f 73 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU f 81 " --> pdb=" O ARG f 77 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN f 82 " --> pdb=" O GLN f 78 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N GLU f 83 " --> pdb=" O LEU f 79 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 removed outlier: 3.892A pdb=" N THR g 24 " --> pdb=" O SER g 20 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN g 28 " --> pdb=" O THR g 24 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS g 29 " --> pdb=" O GLN g 25 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 55 removed outlier: 3.721A pdb=" N ASP g 52 " --> pdb=" O GLU g 48 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS g 53 " --> pdb=" O GLN g 49 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 3.710A pdb=" N THR g 61 " --> pdb=" O ASP g 57 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN g 68 " --> pdb=" O ARG g 64 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL g 69 " --> pdb=" O ALA g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 112 removed outlier: 3.688A pdb=" N THR g 97 " --> pdb=" O PRO g 93 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR g 98 " --> pdb=" O ASP g 94 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP g 103 " --> pdb=" O LEU g 99 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG g 109 " --> pdb=" O VAL g 105 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLN g 110 " --> pdb=" O GLY g 106 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG g 111 " --> pdb=" O TYR g 107 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ARG g 112 " --> pdb=" O SER g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 Processing helix chain 'g' and resid 132 through 149 removed outlier: 3.649A pdb=" N ARG g 138 " --> pdb=" O SER g 134 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN g 148 " --> pdb=" O MET g 144 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ARG g 149 " --> pdb=" O ALA g 145 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 removed outlier: 3.516A pdb=" N ALA h 17 " --> pdb=" O ARG h 13 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA h 20 " --> pdb=" O ASN h 16 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 44 removed outlier: 3.532A pdb=" N ASN h 35 " --> pdb=" O LYS h 31 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN h 38 " --> pdb=" O ALA h 34 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE h 39 " --> pdb=" O ASN h 35 " (cutoff:3.500A) Processing helix chain 'h' and resid 114 through 122 removed outlier: 3.711A pdb=" N GLN h 121 " --> pdb=" O GLN h 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 55 through 61 Proline residue: i 61 - end of helix Processing helix chain 'i' and resid 62 through 77 removed outlier: 3.603A pdb=" N GLN i 66 " --> pdb=" O ASN i 62 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU i 68 " --> pdb=" O VAL i 64 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS i 70 " --> pdb=" O GLN i 66 " (cutoff:3.500A) Proline residue: i 72 - end of helix removed outlier: 3.608A pdb=" N THR i 75 " --> pdb=" O ALA i 71 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL i 76 " --> pdb=" O PRO i 72 " (cutoff:3.500A) Processing helix chain 'i' and resid 92 through 112 removed outlier: 3.512A pdb=" N ALA i 97 " --> pdb=" O PRO i 93 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU i 102 " --> pdb=" O GLY i 98 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE i 109 " --> pdb=" O ALA i 105 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU i 110 " --> pdb=" O ARG i 106 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL i 111 " --> pdb=" O ALA i 107 " (cutoff:3.500A) Processing helix chain 'i' and resid 115 through 123 removed outlier: 3.503A pdb=" N LYS i 121 " --> pdb=" O PRO i 117 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA i 122 " --> pdb=" O ALA i 118 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 24 removed outlier: 3.831A pdb=" N ILE j 18 " --> pdb=" O ASP j 14 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASP j 19 " --> pdb=" O HIS j 15 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ALA j 20 " --> pdb=" O GLU j 16 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER j 21 " --> pdb=" O ALA j 17 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS j 24 " --> pdb=" O ALA j 20 " (cutoff:3.500A) Processing helix chain 'j' and resid 26 through 33 removed outlier: 5.142A pdb=" N VAL j 30 " --> pdb=" O VAL j 26 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG j 31 " --> pdb=" O GLU j 27 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY j 33 " --> pdb=" O VAL j 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 26 through 33' Processing helix chain 'j' and resid 80 through 90 removed outlier: 4.266A pdb=" N ASP j 85 " --> pdb=" O PRO j 81 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA j 86 " --> pdb=" O LYS j 82 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU j 87 " --> pdb=" O THR j 83 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ILE j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 56 through 61 removed outlier: 5.084A pdb=" N GLY k 61 " --> pdb=" O SER k 57 " (cutoff:3.500A) Processing helix chain 'k' and resid 69 through 88 removed outlier: 3.610A pdb=" N ALA k 73 " --> pdb=" O THR k 69 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU k 78 " --> pdb=" O GLN k 74 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS k 83 " --> pdb=" O ASN k 79 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASP k 86 " --> pdb=" O ARG k 82 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N HIS k 87 " --> pdb=" O LYS k 83 " (cutoff:3.500A) Processing helix chain 'k' and resid 102 through 114 removed outlier: 4.777A pdb=" N ALA k 106 " --> pdb=" O GLY k 102 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE k 107 " --> pdb=" O ARG k 103 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER k 109 " --> pdb=" O THR k 105 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU k 110 " --> pdb=" O ALA k 106 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN k 111 " --> pdb=" O ILE k 107 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA k 112 " --> pdb=" O ARG k 108 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA k 113 " --> pdb=" O SER k 109 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY k 114 " --> pdb=" O LEU k 110 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 10 removed outlier: 3.861A pdb=" N LEU l 7 " --> pdb=" O THR l 3 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 22 removed outlier: 3.801A pdb=" N LEU m 19 " --> pdb=" O MET m 15 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N THR m 20 " --> pdb=" O GLU m 16 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TYR m 21 " --> pdb=" O VAL m 17 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ILE m 22 " --> pdb=" O ALA m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 removed outlier: 3.506A pdb=" N GLU m 32 " --> pdb=" O THR m 28 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLY m 38 " --> pdb=" O LEU m 34 " (cutoff:3.500A) Processing helix chain 'm' and resid 44 through 49 removed outlier: 4.120A pdb=" N LEU m 48 " --> pdb=" O ARG m 44 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N THR m 49 " --> pdb=" O THR m 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 44 through 49' Processing helix chain 'm' and resid 50 through 63 removed outlier: 3.581A pdb=" N ILE m 54 " --> pdb=" O GLU m 50 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N HIS m 55 " --> pdb=" O GLU m 51 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU m 56 " --> pdb=" O GLN m 52 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP m 58 " --> pdb=" O ILE m 54 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR m 59 " --> pdb=" O HIS m 55 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE m 60 " --> pdb=" O LEU m 56 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLU m 61 " --> pdb=" O ARG m 57 " (cutoff:3.500A) Processing helix chain 'm' and resid 67 through 85 removed outlier: 5.775A pdb=" N ARG m 71 " --> pdb=" O GLU m 67 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLU m 73 " --> pdb=" O ASP m 69 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA m 76 " --> pdb=" O ARG m 72 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE m 82 " --> pdb=" O ILE m 78 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU m 83 " --> pdb=" O ARG m 79 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE m 84 " --> pdb=" O ARG m 80 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY m 85 " --> pdb=" O LYS m 81 " (cutoff:3.500A) Processing helix chain 'm' and resid 86 through 95 removed outlier: 3.642A pdb=" N ARG m 94 " --> pdb=" O LEU m 90 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY m 95 " --> pdb=" O ARG m 91 " (cutoff:3.500A) Processing helix chain 'm' and resid 107 through 112 removed outlier: 4.600A pdb=" N GLY m 112 " --> pdb=" O ARG m 108 " (cutoff:3.500A) Processing helix chain 'n' and resid 3 through 13 removed outlier: 3.539A pdb=" N GLY n 12 " --> pdb=" O ASN n 8 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N LYS n 13 " --> pdb=" O LYS n 9 " (cutoff:3.500A) Processing helix chain 'n' and resid 40 through 51 removed outlier: 3.846A pdb=" N ARG n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 16 removed outlier: 4.042A pdb=" N LYS o 9 " --> pdb=" O ALA o 5 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLU o 10 " --> pdb=" O GLU o 6 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE o 11 " --> pdb=" O GLN o 7 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER o 14 " --> pdb=" O GLU o 10 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 47 removed outlier: 3.707A pdb=" N GLU o 41 " --> pdb=" O ALA o 37 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS o 42 " --> pdb=" O ASP o 38 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL o 45 " --> pdb=" O GLU o 41 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N HIS o 46 " --> pdb=" O HIS o 42 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS o 47 " --> pdb=" O LEU o 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.769A pdb=" N ARG o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN o 72 " --> pdb=" O LYS o 68 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP o 74 " --> pdb=" O ILE o 70 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 removed outlier: 4.717A pdb=" N ARG o 84 " --> pdb=" O SER o 80 " (cutoff:3.500A) Processing helix chain 'p' and resid 52 through 63 removed outlier: 5.869A pdb=" N ALA p 56 " --> pdb=" O ASN p 52 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLN p 57 " --> pdb=" O SER p 53 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR p 58 " --> pdb=" O GLU p 54 " (cutoff:3.500A) Processing helix chain 'p' and resid 67 through 78 removed outlier: 3.812A pdb=" N LYS p 72 " --> pdb=" O GLU p 68 " (cutoff:3.500A) Processing helix chain 'p' and resid 79 through 85 removed outlier: 3.667A pdb=" N PHE p 83 " --> pdb=" O ASP p 79 " (cutoff:3.500A) Processing helix chain 'p' and resid 101 through 114 removed outlier: 3.747A pdb=" N PHE p 106 " --> pdb=" O LYS p 102 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU p 110 " --> pdb=" O PHE p 106 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA p 113 " --> pdb=" O ALA p 109 " (cutoff:3.500A) Processing helix chain 'r' and resid 20 through 26 removed outlier: 4.693A pdb=" N LYS r 26 " --> pdb=" O PHE r 22 " (cutoff:3.500A) Processing helix chain 'r' and resid 34 through 42 removed outlier: 3.865A pdb=" N LEU r 38 " --> pdb=" O ASP r 34 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ARG r 39 " --> pdb=" O THR r 35 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N THR r 40 " --> pdb=" O ALA r 36 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N TYR r 41 " --> pdb=" O LEU r 37 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE r 42 " --> pdb=" O LEU r 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 34 through 42' Processing helix chain 'r' and resid 50 through 55 removed outlier: 3.758A pdb=" N THR r 54 " --> pdb=" O ALA r 50 " (cutoff:3.500A) Processing helix chain 'r' and resid 57 through 75 removed outlier: 3.596A pdb=" N LYS r 69 " --> pdb=" O ALA r 65 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU r 73 " --> pdb=" O LYS r 69 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 26 removed outlier: 3.827A pdb=" N LYS s 18 " --> pdb=" O HIS s 14 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N VAL s 21 " --> pdb=" O LYS s 17 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN s 22 " --> pdb=" O LYS s 18 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU s 24 " --> pdb=" O ASP s 20 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LYS s 25 " --> pdb=" O VAL s 21 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN s 26 " --> pdb=" O GLN s 22 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 76 removed outlier: 4.902A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.826A 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 8 through 41 removed outlier: 3.662A pdb=" N ARG t 12 " --> pdb=" O GLN t 8 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR t 13 " --> pdb=" O LYS t 9 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU t 15 " --> pdb=" O ASN t 11 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA t 23 " --> pdb=" O LEU t 19 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR t 30 " --> pdb=" O SER t 26 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE t 35 " --> pdb=" O ALA t 31 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA t 41 " --> pdb=" O GLU t 37 " (cutoff:3.500A) Processing helix chain 't' and resid 44 through 65 removed outlier: 4.001A pdb=" N ALA t 48 " --> pdb=" O LYS t 44 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU t 49 " --> pdb=" O ALA t 45 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA t 52 " --> pdb=" O ALA t 48 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER t 53 " --> pdb=" O GLU t 49 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG t 56 " --> pdb=" O ALA t 52 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS t 60 " --> pdb=" O ARG t 56 " (cutoff:3.500A) Processing helix chain 't' and resid 68 through 86 removed outlier: 3.659A pdb=" N SER t 77 " --> pdb=" O ALA t 73 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN t 84 " --> pdb=" O ALA t 80 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS t 85 " --> pdb=" O GLN t 81 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU t 86 " --> pdb=" O ALA t 82 " (cutoff:3.500A) Processing helix chain 'x' and resid 43 through 53 removed outlier: 3.582A pdb=" N LEU x 48 " --> pdb=" O LYS x 44 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE x 50 " --> pdb=" O SER x 46 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY x 53 " --> pdb=" O ARG x 49 " (cutoff:3.500A) Processing helix chain 'x' and resid 83 through 92 removed outlier: 3.951A pdb=" N VAL x 89 " --> pdb=" O VAL x 85 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLU x 90 " --> pdb=" O ARG x 86 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N GLU x 91 " --> pdb=" O GLY x 87 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLY x 92 " --> pdb=" O ASN x 88 " (cutoff:3.500A) Processing helix chain 'x' and resid 94 through 113 removed outlier: 4.649A pdb=" N ILE x 98 " --> pdb=" O GLY x 94 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LYS x 99 " --> pdb=" O ASP x 95 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE x 103 " --> pdb=" O LYS x 99 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU x 105 " --> pdb=" O ASP x 101 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N GLU x 108 " --> pdb=" O ASN x 104 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET x 110 " --> pdb=" O VAL x 106 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ALA x 111 " --> pdb=" O ALA x 107 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR x 112 " --> pdb=" O GLU x 108 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP x 113 " --> pdb=" O LEU x 109 " (cutoff:3.500A) Processing helix chain 'x' and resid 116 through 133 removed outlier: 4.873A pdb=" N GLU x 120 " --> pdb=" O ASP x 116 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU x 121 " --> pdb=" O GLU x 117 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU x 125 " --> pdb=" O GLU x 121 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU x 127 " --> pdb=" O GLY x 123 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLU x 128 " --> pdb=" O ARG x 124 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU x 129 " --> pdb=" O LEU x 125 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ASP x 130 " --> pdb=" O GLN x 126 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N HIS x 131 " --> pdb=" O GLU x 127 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ALA x 132 " --> pdb=" O GLU x 128 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASP x 133 " --> pdb=" O LEU x 129 " (cutoff:3.500A) Processing helix chain 'x' and resid 136 through 149 removed outlier: 4.117A pdb=" N LEU x 141 " --> pdb=" O LEU x 137 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU x 142 " --> pdb=" O ASP x 138 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN x 143 " --> pdb=" O ALA x 139 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP x 146 " --> pdb=" O GLU x 142 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU x 148 " --> pdb=" O ALA x 144 " (cutoff:3.500A) Processing helix chain 'x' and resid 161 through 177 removed outlier: 3.782A pdb=" N ARG x 166 " --> pdb=" O GLY x 162 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG x 167 " --> pdb=" O GLY x 163 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS x 172 " --> pdb=" O VAL x 168 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU x 173 " --> pdb=" O ALA x 169 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU x 175 " --> pdb=" O CYS x 171 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER x 176 " --> pdb=" O LYS x 172 " (cutoff:3.500A) Processing helix chain 'x' and resid 191 through 205 removed outlier: 3.847A pdb=" N GLN x 196 " --> pdb=" O ALA x 192 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN x 200 " --> pdb=" O GLN x 196 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER x 204 " --> pdb=" O GLN x 200 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N TYR x 205 " --> pdb=" O HIS x 201 " (cutoff:3.500A) Processing helix chain 'x' and resid 215 through 223 removed outlier: 4.134A pdb=" N LEU x 219 " --> pdb=" O ASP x 215 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP x 220 " --> pdb=" O ARG x 216 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN x 221 " --> pdb=" O TYR x 217 " (cutoff:3.500A) Processing helix chain 'x' and resid 240 through 276 removed outlier: 6.307A pdb=" N TYR x 244 " --> pdb=" O ASN x 240 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU x 245 " --> pdb=" O TYR x 241 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU x 246 " --> pdb=" O SER x 242 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN x 255 " --> pdb=" O ARG x 251 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG x 257 " --> pdb=" O ALA x 253 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS x 258 " --> pdb=" O VAL x 254 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN x 263 " --> pdb=" O ASP x 259 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N TRP x 272 " --> pdb=" O GLU x 268 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG x 274 " --> pdb=" O LEU x 270 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER x 275 " --> pdb=" O ALA x 271 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N GLY x 276 " --> pdb=" O TRP x 272 " (cutoff:3.500A) Processing helix chain 'x' and resid 284 through 302 removed outlier: 4.160A pdb=" N ARG x 290 " --> pdb=" O ALA x 286 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU x 293 " --> pdb=" O GLN x 289 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA x 296 " --> pdb=" O GLU x 292 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU x 299 " --> pdb=" O ALA x 295 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS x 300 " --> pdb=" O ALA x 296 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N THR x 301 " --> pdb=" O GLU x 297 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ARG x 302 " --> pdb=" O ALA x 298 " (cutoff:3.500A) Processing helix chain 'x' and resid 359 through 369 removed outlier: 3.517A pdb=" N PHE x 364 " --> pdb=" O LYS x 360 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE x 367 " --> pdb=" O LEU x 363 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY x 369 " --> pdb=" O LYS x 365 " (cutoff:3.500A) Processing helix chain 'x' and resid 401 through 408 removed outlier: 4.036A pdb=" N VAL x 406 " --> pdb=" O VAL x 402 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASP x 408 " --> pdb=" O GLU x 404 " (cutoff:3.500A) Processing helix chain 'x' and resid 421 through 430 removed outlier: 3.504A pdb=" N ALA x 428 " --> pdb=" O ALA x 424 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE x 429 " --> pdb=" O TYR x 425 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY x 430 " --> pdb=" O VAL x 426 " (cutoff:3.500A) Processing helix chain 'x' and resid 439 through 444 removed outlier: 3.627A pdb=" N LEU x 443 " --> pdb=" O PRO x 439 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N SER x 444 " --> pdb=" O ALA x 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 439 through 444' Processing helix chain 'x' and resid 445 through 460 removed outlier: 4.045A pdb=" N ARG x 450 " --> pdb=" O GLY x 446 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU x 453 " --> pdb=" O ASN x 449 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LYS x 458 " --> pdb=" O ALA x 454 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N GLN x 459 " --> pdb=" O LEU x 455 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N GLY x 460 " --> pdb=" O THR x 456 " (cutoff:3.500A) Processing helix chain 'x' and resid 474 through 488 removed outlier: 3.658A pdb=" N ALA x 484 " --> pdb=" O SER x 480 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU x 486 " --> pdb=" O GLU x 482 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN x 487 " --> pdb=" O ASN x 483 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE x 488 " --> pdb=" O ALA x 484 " (cutoff:3.500A) Processing helix chain 'x' and resid 498 through 506 removed outlier: 4.844A pdb=" N ARG x 504 " --> pdb=" O TRP x 500 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR x 505 " --> pdb=" O PHE x 501 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N CYS x 506 " --> pdb=" O LEU x 502 " (cutoff:3.500A) Processing helix chain 'x' and resid 528 through 540 removed outlier: 3.700A pdb=" N GLU x 534 " --> pdb=" O GLY x 530 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL x 537 " --> pdb=" O GLU x 533 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU x 538 " --> pdb=" O GLU x 534 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU x 540 " --> pdb=" O LYS x 536 " (cutoff:3.500A) Processing helix chain 'x' and resid 433 through 438 removed outlier: 3.650A pdb=" N GLN x 437 " --> pdb=" O PRO x 434 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS x 438 " --> pdb=" O ASP x 435 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '0' and resid 28 through 31 Processing sheet with id= 2, first strand: chain '1' and resid 10 through 13 removed outlier: 3.782A pdb=" N TYR 1 23 " --> pdb=" O LEU 1 13 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '1' and resid 37 through 40 Processing sheet with id= 4, first strand: chain '4' and resid 1 through 5 removed outlier: 3.607A pdb=" N GLY 4 37 " --> pdb=" O ASN 4 4 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N VAL 4 23 " --> pdb=" O GLN 4 36 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '6' and resid 11 through 16 removed outlier: 4.866A pdb=" N ASN 6 20 " --> pdb=" O CYS 6 16 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain '8' and resid 59 through 64 removed outlier: 6.257A pdb=" N VAL 8 59 " --> pdb=" O VAL 8 165 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL 8 63 " --> pdb=" O ILE 8 161 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE 8 161 " --> pdb=" O VAL 8 63 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain '8' and resid 75 through 78 Processing sheet with id= 8, first strand: chain '8' and resid 169 through 175 removed outlier: 6.691A pdb=" N ALA 8 169 " --> pdb=" O LEU 8 48 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL 8 42 " --> pdb=" O ILE 8 175 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS 8 211 " --> pdb=" O ARG 8 47 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'C' and resid 33 through 36 No H-bonds generated for sheet with id= 9 Processing sheet with id= 10, first strand: chain 'C' and resid 76 through 79 removed outlier: 4.577A pdb=" N ASP C 115 " --> pdb=" O VAL C 79 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'C' and resid 81 through 84 removed outlier: 3.740A pdb=" N HIS C 81 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ARG C 91 " --> pdb=" O ALA C 107 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'C' and resid 139 through 143 removed outlier: 4.456A pdb=" N THR C 140 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C 165 " --> pdb=" O THR C 140 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER C 174 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLU C 181 " --> pdb=" O MET C 177 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'D' and resid 4 through 8 removed outlier: 5.861A pdb=" N LYS D 4 " --> pdb=" O SER D 210 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL D 175 " --> pdb=" O GLY D 116 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ASP D 173 " --> pdb=" O SER D 118 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'D' and resid 12 through 18 removed outlier: 3.687A pdb=" N GLY D 12 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ARG D 22 " --> pdb=" O ASP D 18 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS D 184 " --> pdb=" O LEU D 193 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'D' and resid 48 through 54 removed outlier: 5.667A pdb=" N SER D 48 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'D' and resid 110 through 113 removed outlier: 4.401A pdb=" N SER D 110 " --> pdb=" O VAL D 182 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'E' and resid 9 through 13 removed outlier: 5.779A pdb=" N LEU E 9 " --> pdb=" O LEU E 26 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY E 22 " --> pdb=" O VAL E 13 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'E' and resid 129 through 132 removed outlier: 3.534A pdb=" N LEU E 184 " --> pdb=" O VAL E 162 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE E 164 " --> pdb=" O LEU E 184 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'F' and resid 72 through 76 removed outlier: 4.902A pdb=" N VAL F 92 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL F 94 " --> pdb=" O MET F 45 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS F 40 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLY F 46 " --> pdb=" O GLY F 158 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N GLY F 158 " --> pdb=" O GLY F 46 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ARG F 157 " --> pdb=" O GLU F 141 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU F 141 " --> pdb=" O ARG F 157 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N MET F 159 " --> pdb=" O LEU F 139 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'G' and resid 15 through 19 removed outlier: 3.564A pdb=" N ILE G 24 " --> pdb=" O LEU G 35 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU G 35 " --> pdb=" O ILE G 24 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL G 26 " --> pdb=" O LEU G 33 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'G' and resid 83 through 90 removed outlier: 5.723A pdb=" N THR G 130 " --> pdb=" O ILE G 90 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LYS G 131 " --> pdb=" O GLN G 127 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'G' and resid 95 through 99 removed outlier: 3.833A pdb=" N ARG G 96 " --> pdb=" O ALA G 107 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU G 104 " --> pdb=" O ILE G 116 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'H' and resid 1 through 4 Processing sheet with id= 24, first strand: chain 'J' and resid 52 through 57 removed outlier: 5.088A 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: 7.266A pdb=" N GLY J 83 " --> pdb=" O SER J 78 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'K' and resid 18 through 21 removed outlier: 4.806A pdb=" N SER K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ASN K 82 " --> pdb=" O ARG K 7 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLU K 81 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL K 66 " --> pdb=" O GLU K 81 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'K' and resid 38 through 42 Processing sheet with id= 28, first strand: chain 'K' and resid 68 through 71 removed outlier: 3.679A pdb=" N ILE K 77 " --> pdb=" O ARG K 69 " (cutoff:3.500A) removed outlier: 4.258A 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 Processing sheet with id= 30, first strand: chain 'L' and resid 121 through 124 removed outlier: 3.705A pdb=" N SER L 142 " --> pdb=" O VAL L 121 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'M' and resid 62 through 66 removed outlier: 4.042A pdb=" N PHE M 104 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LYS M 128 " --> pdb=" O LEU M 37 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'N' and resid 33 through 37 removed outlier: 4.325A pdb=" N MET N 110 " --> pdb=" O ILE N 100 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'O' and resid 31 through 37 removed outlier: 6.589A pdb=" N ARG O 32 " --> pdb=" O VAL O 47 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE O 42 " --> pdb=" O SER O 60 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA O 56 " --> pdb=" O LEU O 46 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'P' and resid 37 through 44 removed outlier: 6.569A pdb=" N THR P 24 " --> pdb=" O VAL P 86 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS P 28 " --> pdb=" O HIS P 82 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N HIS P 82 " --> pdb=" O HIS P 28 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'P' and resid 48 through 51 removed outlier: 3.806A pdb=" N ARG P 48 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR P 57 " --> pdb=" O GLN P 50 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N GLU P 56 " --> pdb=" O VAL P 75 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'R' and resid 14 through 17 removed outlier: 3.810A pdb=" N LEU R 42 " --> pdb=" O ILE R 7 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL R 43 " --> pdb=" O THR R 50 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR R 50 " --> pdb=" O VAL R 43 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR R 48 " --> pdb=" O ASP R 45 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'R' and resid 20 through 24 removed outlier: 4.086A pdb=" N ASP R 21 " --> pdb=" O VAL R 100 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL R 97 " --> pdb=" O LEU R 66 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N THR R 62 " --> pdb=" O THR R 101 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL R 36 " --> pdb=" O GLY R 63 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'R' and resid 70 through 80 No H-bonds generated for sheet with id= 38 Processing sheet with id= 39, first strand: chain 'S' and resid 11 through 18 removed outlier: 6.758A pdb=" N VAL S 116 " --> pdb=" O ALA S 82 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'S' and resid 83 through 89 removed outlier: 5.079A pdb=" N THR S 110 " --> pdb=" O GLY S 89 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'S' and resid 91 through 98 removed outlier: 4.285A pdb=" N ARG S 102 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'T' and resid 28 through 33 removed outlier: 4.486A pdb=" N LYS T 80 " --> pdb=" O VAL T 33 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LYS T 65 " --> pdb=" O ARG T 76 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N SER T 78 " --> pdb=" O GLN T 63 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLN T 63 " --> pdb=" O SER T 78 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS T 80 " --> pdb=" O ASN T 61 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASN T 61 " --> pdb=" O LYS T 80 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA T 82 " --> pdb=" O THR T 59 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR T 59 " --> pdb=" O ALA T 82 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL T 84 " --> pdb=" O VAL T 57 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL T 57 " --> pdb=" O VAL T 84 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'U' and resid 8 through 11 removed outlier: 3.530A pdb=" N VAL U 11 " --> pdb=" O ALA U 19 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ALA U 19 " --> pdb=" O VAL U 11 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'U' and resid 25 through 28 removed outlier: 3.992A pdb=" N GLN U 25 " --> pdb=" O LEU U 34 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'V' and resid 7 through 10 removed outlier: 4.578A pdb=" N ASN V 7 " --> pdb=" O VAL V 64 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU V 9 " --> pdb=" O THR V 66 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LEU V 75 " --> pdb=" O VAL V 98 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU V 96 " --> pdb=" O LEU V 77 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'V' and resid 88 through 91 removed outlier: 4.273A pdb=" N THR V 89 " --> pdb=" O HIS V 84 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N HIS V 82 " --> pdb=" O GLN V 91 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'V' and resid 119 through 125 removed outlier: 8.068A pdb=" N ASP V 119 " --> pdb=" O ALA V 182 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N VAL V 176 " --> pdb=" O GLU V 125 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'V' and resid 127 through 132 removed outlier: 5.914A pdb=" N ASN V 127 " --> pdb=" O VAL V 110 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL V 144 " --> pdb=" O VAL V 111 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'V' and resid 79 through 82 removed outlier: 3.678A pdb=" N ALA V 80 " --> pdb=" O ASP V 94 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N HIS V 92 " --> pdb=" O HIS V 82 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'W' and resid 66 through 71 Processing sheet with id= 51, first strand: chain 'X' and resid 12 through 19 removed outlier: 3.540A pdb=" N GLY X 15 " --> pdb=" O ARG X 27 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG X 27 " --> pdb=" O GLY X 15 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER X 19 " --> pdb=" O ARG X 23 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ARG X 23 " --> pdb=" O SER X 19 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'X' and resid 35 through 39 Processing sheet with id= 53, first strand: chain 'Z' and resid 32 through 38 removed outlier: 4.371A pdb=" N HIS Z 33 " --> pdb=" O GLN Z 8 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N LEU Z 53 " --> pdb=" O VAL Z 9 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'c' and resid 53 through 58 removed outlier: 4.006A pdb=" N ASP c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) removed outlier: 6.220A 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 169 removed outlier: 3.619A pdb=" N GLY c 194 " --> pdb=" O THR c 191 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ASP c 181 " --> pdb=" O LYS c 204 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'd' and resid 135 through 139 removed outlier: 4.420A pdb=" N ASP d 136 " --> pdb=" O ILE d 177 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE d 177 " --> pdb=" O ASP d 136 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'e' and resid 42 through 47 removed outlier: 6.920A 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: 5.924A pdb=" N VAL e 124 " --> pdb=" O LEU e 159 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA e 130 " --> pdb=" O ASP e 153 " (cutoff:3.500A) removed outlier: 6.697A 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: 4.976A pdb=" N GLY e 82 " --> pdb=" O ALA e 66 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N MET e 76 " --> pdb=" O ASP e 72 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'f' and resid 35 through 38 removed outlier: 7.521A pdb=" N ASP f 64 " --> pdb=" O GLU f 38 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N GLU f 57 " --> pdb=" O PRO f 12 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ILE f 6 " --> pdb=" O ILE f 63 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL f 65 " --> pdb=" O TYR f 4 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG f 87 " --> pdb=" O ILE f 9 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'f' and resid 39 through 44 removed outlier: 3.799A pdb=" N LYS f 39 " --> pdb=" O ASP f 64 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP f 64 " --> pdb=" O LYS f 39 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR f 60 " --> pdb=" O TRP f 43 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'f' and resid 45 through 48 removed outlier: 6.955A pdb=" N ALA f 56 " --> pdb=" O LEU f 48 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'g' and resid 72 through 79 removed outlier: 6.342A pdb=" N ALA g 72 " --> pdb=" O VAL g 91 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG g 78 " --> pdb=" O TYR g 85 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'h' and resid 23 through 29 removed outlier: 6.310A pdb=" N ASP h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N LYS h 58 " --> pdb=" O HIS h 29 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'h' and resid 125 through 128 removed outlier: 6.234A pdb=" N VAL h 103 " --> pdb=" O VAL h 131 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA h 129 " --> pdb=" O ILE h 105 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'i' and resid 27 through 32 removed outlier: 4.541A pdb=" N ILE i 27 " --> pdb=" O LEU i 42 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU i 42 " --> pdb=" O ILE i 27 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS i 87 " --> pdb=" O ARG i 39 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE i 85 " --> pdb=" O ARG i 41 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'j' and resid 42 through 52 removed outlier: 5.026A pdb=" N LYS j 71 " --> pdb=" O PRO j 43 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL j 51 " --> pdb=" O GLU j 63 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU j 10 " --> pdb=" O ARG j 72 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG j 7 " --> pdb=" O GLN j 101 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG j 9 " --> pdb=" O ASN j 99 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASN j 99 " --> pdb=" O ARG j 9 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'k' and resid 39 through 46 removed outlier: 3.893A pdb=" N ASN k 39 " --> pdb=" O THR k 36 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'l' and resid 29 through 33 removed outlier: 3.554A pdb=" N GLY l 32 " --> pdb=" O VAL l 80 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LEU l 81 " --> pdb=" O ILE l 98 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'l' and resid 35 through 41 removed outlier: 4.960A pdb=" N ARG l 36 " --> pdb=" O ARG l 54 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'p' and resid 5 through 11 removed outlier: 5.124A pdb=" N GLN p 17 " --> pdb=" O LEU p 10 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'q' and resid 59 through 63 removed outlier: 3.635A pdb=" N ARG q 60 " --> pdb=" O LEU q 113 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N SER q 112 " --> pdb=" O VAL q 128 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'q' and resid 71 through 82 No H-bonds generated for sheet with id= 73 Processing sheet with id= 74, first strand: chain 's' and resid 46 through 52 removed outlier: 4.594A pdb=" N HIS s 47 " --> pdb=" O VAL s 62 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'x' and resid 6 through 9 removed outlier: 3.713A pdb=" N LEU x 26 " --> pdb=" O MET x 8 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'x' and resid 70 through 73 removed outlier: 3.577A pdb=" N GLY x 71 " --> pdb=" O LEU x 180 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA x 32 " --> pdb=" O GLY x 207 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP x 225 " --> pdb=" O LYS x 33 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU x 228 " --> pdb=" O TYR x 235 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG x 233 " --> pdb=" O ASP x 230 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'x' and resid 322 through 325 removed outlier: 4.410A 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: 4.027A pdb=" N ASP x 467 " --> pdb=" O VAL x 389 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY x 348 " --> pdb=" O GLY x 490 " (cutoff:3.500A) 1506 hydrogen bonds defined for protein. 4461 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3080 hydrogen bonds 4978 hydrogen bond angles 0 basepair planarities 1256 basepair parallelities 2738 stacking parallelities Total time for adding SS restraints: 266.26 Time building geometry restraints manager: 64.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.31: 15890 1.31 - 1.46: 83337 1.46 - 1.61: 65666 1.61 - 1.76: 59 1.76 - 1.91: 177 Bond restraints: 165129 Sorted by residual: bond pdb=" C5 5MU A2177 " pdb=" C6 5MU A2177 " ideal model delta sigma weight residual 1.155 1.439 -0.284 2.00e-02 2.50e+03 2.02e+02 bond pdb=" C4 5MU A2177 " pdb=" C5 5MU A2177 " ideal model delta sigma weight residual 1.802 1.591 0.211 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C1' ADP x 603 " pdb=" C2' ADP x 603 " 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 601 " pdb=" C2' ADP x 601 " ideal model delta sigma weight residual 1.306 1.510 -0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C1' ADP x 603 " pdb=" O4' ADP x 603 " ideal model delta sigma weight residual 1.615 1.418 0.197 2.00e-02 2.50e+03 9.73e+01 ... (remaining 165124 not shown) Histogram of bond angle deviations from ideal: 97.65 - 105.79: 26603 105.79 - 113.92: 104107 113.92 - 122.05: 79926 122.05 - 130.19: 34415 130.19 - 138.32: 2104 Bond angle restraints: 247155 Sorted by residual: angle pdb=" C1' G7M a 518 " pdb=" N9 G7M a 518 " pdb=" C8 G7M a 518 " ideal model delta sigma weight residual 94.96 128.47 -33.51 3.00e+00 1.11e-01 1.25e+02 angle pdb=" C1' OMG A2791 " pdb=" N9 OMG A2791 " pdb=" C4 OMG A2791 " ideal model delta sigma weight residual 108.29 132.85 -24.56 3.00e+00 1.11e-01 6.70e+01 angle pdb=" C1' OMG A2791 " pdb=" N9 OMG A2791 " pdb=" C8 OMG A2791 " ideal model delta sigma weight residual 142.82 118.90 23.92 3.00e+00 1.11e-01 6.36e+01 angle pdb=" C1' 2MG a 959 " pdb=" N9 2MG a 959 " pdb=" C8 2MG a 959 " ideal model delta sigma weight residual 110.07 129.36 -19.29 3.00e+00 1.11e-01 4.13e+01 angle pdb=" C GLY n 28 " pdb=" N ARG n 29 " pdb=" CA ARG n 29 " ideal model delta sigma weight residual 120.94 132.81 -11.87 1.90e+00 2.77e-01 3.90e+01 ... (remaining 247150 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 94742 35.86 - 71.72: 10143 71.72 - 107.58: 1315 107.58 - 143.44: 3 143.44 - 179.30: 24 Dihedral angle restraints: 106227 sinusoidal: 88697 harmonic: 17530 Sorted by residual: dihedral pdb=" O4' U a1254 " pdb=" C1' U a1254 " pdb=" N1 U a1254 " pdb=" C2 U a1254 " ideal model delta sinusoidal sigma weight residual -160.00 16.96 -176.96 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 200.00 23.29 176.71 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U a 223 " pdb=" C1' U a 223 " pdb=" N1 U a 223 " pdb=" C2 U a 223 " ideal model delta sinusoidal sigma weight residual -160.00 14.23 -174.23 1 1.50e+01 4.44e-03 8.51e+01 ... (remaining 106224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 29447 0.089 - 0.177: 1959 0.177 - 0.266: 99 0.266 - 0.355: 9 0.355 - 0.443: 2 Chirality restraints: 31516 Sorted by residual: chirality pdb=" CB VAL g 75 " pdb=" CA VAL g 75 " pdb=" CG1 VAL g 75 " pdb=" CG2 VAL g 75 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.91e+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 -2.26 -0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" C1' G A 877 " pdb=" O4' G A 877 " pdb=" C2' G A 877 " pdb=" N9 G A 877 " both_signs ideal model delta sigma weight residual False 2.46 2.13 0.33 2.00e-01 2.50e+01 2.65e+00 ... (remaining 31513 not shown) Planarity restraints: 13409 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a 959 " 0.011 2.00e-02 2.50e+03 5.38e-01 6.50e+03 pdb=" C4' 2MG a 959 " 0.423 2.00e-02 2.50e+03 pdb=" O4' 2MG a 959 " 0.605 2.00e-02 2.50e+03 pdb=" C3' 2MG a 959 " -0.588 2.00e-02 2.50e+03 pdb=" O3' 2MG a 959 " -0.490 2.00e-02 2.50e+03 pdb=" C2' 2MG a 959 " -0.243 2.00e-02 2.50e+03 pdb=" O2' 2MG a 959 " 0.843 2.00e-02 2.50e+03 pdb=" C1' 2MG a 959 " 0.239 2.00e-02 2.50e+03 pdb=" N9 2MG a 959 " -0.801 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG A2791 " 0.015 2.00e-02 2.50e+03 5.10e-01 5.86e+03 pdb=" C4' OMG A2791 " 0.407 2.00e-02 2.50e+03 pdb=" O4' OMG A2791 " 0.534 2.00e-02 2.50e+03 pdb=" C3' OMG A2791 " -0.584 2.00e-02 2.50e+03 pdb=" O3' OMG A2791 " -0.454 2.00e-02 2.50e+03 pdb=" C2' OMG A2791 " -0.249 2.00e-02 2.50e+03 pdb=" O2' OMG A2791 " 0.819 2.00e-02 2.50e+03 pdb=" C1' OMG A2791 " 0.251 2.00e-02 2.50e+03 pdb=" N9 OMG A2791 " -0.740 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC a 960 " -0.031 2.00e-02 2.50e+03 4.69e-01 4.96e+03 pdb=" C4' 5MC a 960 " 0.413 2.00e-02 2.50e+03 pdb=" O4' 5MC a 960 " 0.481 2.00e-02 2.50e+03 pdb=" C3' 5MC a 960 " -0.546 2.00e-02 2.50e+03 pdb=" O3' 5MC a 960 " -0.370 2.00e-02 2.50e+03 pdb=" C2' 5MC a 960 " -0.276 2.00e-02 2.50e+03 pdb=" O2' 5MC a 960 " 0.734 2.00e-02 2.50e+03 pdb=" C1' 5MC a 960 " 0.271 2.00e-02 2.50e+03 pdb=" N1 5MC a 960 " -0.677 2.00e-02 2.50e+03 ... (remaining 13406 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 2341 2.59 - 3.17: 107051 3.17 - 3.75: 281585 3.75 - 4.32: 411354 4.32 - 4.90: 554257 Nonbonded interactions: 1356588 Sorted by model distance: nonbonded pdb=" OP2 U A2920 " pdb="MG MG A3342 " model vdw 2.013 2.170 nonbonded pdb=" O6 G A 905 " pdb="MG MG A3203 " model vdw 2.016 2.170 nonbonded pdb=" OP2 G A1318 " pdb="MG MG A3287 " model vdw 2.017 2.170 nonbonded pdb=" OP1 A A2686 " pdb="MG MG A3206 " model vdw 2.022 2.170 nonbonded pdb=" OP2 A A 511 " pdb="MG MG A3360 " model vdw 2.024 2.170 ... (remaining 1356583 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: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 13.480 Check model and map are aligned: 1.740 Set scattering table: 1.160 Process input model: 587.150 Find NCS groups from input model: 3.040 Set up NCS constraints: 0.420 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 621.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 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 : 0.009 0.284 165129 Z= 0.533 Angle : 0.882 33.511 247155 Z= 0.436 Chirality : 0.047 0.443 31516 Planarity : 0.012 0.538 13409 Dihedral : 22.183 179.296 94967 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.77 % Favored : 93.07 % Rotamer: Outliers : 0.18 % Allowed : 3.37 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -4.70 (0.08), residues: 6072 helix: -4.62 (0.05), residues: 1806 sheet: -1.93 (0.14), residues: 1109 loop : -2.59 (0.09), residues: 3157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP Q 61 HIS 0.028 0.003 HIS M 13 PHE 0.049 0.004 PHE E 90 TYR 0.043 0.003 TYR E 104 ARG 0.025 0.001 ARG 4 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1258 residues out of total 5038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1249 time to evaluate : 6.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 39 ASP cc_start: 0.7521 (p0) cc_final: 0.7303 (p0) REVERT: 8 54 LYS cc_start: 0.8323 (mppt) cc_final: 0.7836 (mmpt) REVERT: 8 58 MET cc_start: 0.8160 (tpt) cc_final: 0.7656 (tmm) REVERT: 8 85 ASP cc_start: 0.9156 (m-30) cc_final: 0.8916 (m-30) REVERT: 8 93 ASP cc_start: 0.7682 (p0) cc_final: 0.7091 (t0) REVERT: 8 99 ASP cc_start: 0.8589 (p0) cc_final: 0.8361 (t70) REVERT: 8 123 LYS cc_start: 0.5781 (ptpt) cc_final: 0.5486 (ptpp) REVERT: 8 124 VAL cc_start: 0.8236 (t) cc_final: 0.8028 (m) REVERT: 8 225 ASP cc_start: 0.8337 (t0) cc_final: 0.8111 (t0) REVERT: C 78 LYS cc_start: 0.7744 (ttmm) cc_final: 0.7454 (ttmt) REVERT: C 161 SER cc_start: 0.8959 (p) cc_final: 0.8643 (m) REVERT: D 83 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7923 (mt-10) REVERT: F 16 ARG cc_start: 0.7851 (ptp90) cc_final: 0.7550 (ptt180) REVERT: F 52 ARG cc_start: 0.7497 (mpp-170) cc_final: 0.7246 (mpp-170) REVERT: F 108 ASP cc_start: 0.7393 (t0) cc_final: 0.7109 (t0) REVERT: J 60 ASP cc_start: 0.8044 (p0) cc_final: 0.7793 (p0) REVERT: J 108 MET cc_start: 0.8988 (mtt) cc_final: 0.8647 (mtt) REVERT: K 53 LYS cc_start: 0.8472 (mmtm) cc_final: 0.8101 (mptt) REVERT: L 63 LEU cc_start: 0.8825 (mt) cc_final: 0.8528 (mt) REVERT: M 115 ARG cc_start: 0.8109 (ttm-80) cc_final: 0.7897 (ttm-80) REVERT: Q 21 SER cc_start: 0.8717 (m) cc_final: 0.8485 (m) REVERT: T 34 ARG cc_start: 0.8393 (ttp-170) cc_final: 0.8150 (ttp-170) REVERT: Z 9 VAL cc_start: 0.8461 (t) cc_final: 0.8213 (m) REVERT: c 133 MET cc_start: 0.8382 (mtp) cc_final: 0.8035 (mtm) REVERT: d 19 LEU cc_start: 0.8354 (mt) cc_final: 0.7962 (mt) REVERT: d 99 ARG cc_start: 0.7934 (mmt180) cc_final: 0.7381 (mtt-85) REVERT: d 126 ASN cc_start: 0.8542 (p0) cc_final: 0.8287 (p0) REVERT: e 83 LYS cc_start: 0.8225 (ptmm) cc_final: 0.7760 (pttm) REVERT: e 165 ILE cc_start: 0.8905 (mt) cc_final: 0.8680 (mp) REVERT: f 89 LYS cc_start: 0.9046 (tppt) cc_final: 0.8834 (tptt) REVERT: g 89 VAL cc_start: 0.9116 (m) cc_final: 0.8839 (p) REVERT: h 93 ASN cc_start: 0.8045 (p0) cc_final: 0.7794 (p0) REVERT: k 57 SER cc_start: 0.8722 (t) cc_final: 0.8511 (p) REVERT: l 44 LYS cc_start: 0.7717 (tppt) cc_final: 0.6981 (tptt) REVERT: r 44 GLU cc_start: 0.7884 (mp0) cc_final: 0.7586 (mp0) REVERT: t 21 ASN cc_start: 0.8881 (m-40) cc_final: 0.8640 (m110) REVERT: t 60 LYS cc_start: 0.8286 (mtpp) cc_final: 0.8041 (mtpp) REVERT: t 66 VAL cc_start: 0.9021 (t) cc_final: 0.8801 (t) REVERT: x 159 ASN cc_start: 0.8283 (m-40) cc_final: 0.7967 (m-40) REVERT: x 226 ILE cc_start: 0.8481 (mt) cc_final: 0.8193 (mm) REVERT: x 237 TYR cc_start: 0.8283 (p90) cc_final: 0.7812 (p90) REVERT: x 240 ASN cc_start: 0.7969 (p0) cc_final: 0.7492 (p0) REVERT: x 255 GLN cc_start: 0.8074 (tp-100) cc_final: 0.6994 (tp-100) REVERT: x 259 ASP cc_start: 0.7556 (m-30) cc_final: 0.6985 (m-30) REVERT: x 338 LYS cc_start: 0.8773 (tttp) cc_final: 0.8402 (tttm) REVERT: x 387 SER cc_start: 0.8484 (t) cc_final: 0.8169 (p) REVERT: x 533 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7783 (mm-30) outliers start: 9 outliers final: 4 residues processed: 1257 average time/residue: 2.5190 time to fit residues: 4378.0550 Evaluate side-chains 827 residues out of total 5038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 823 time to evaluate : 6.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain S residue 80 VAL Chi-restraints excluded: chain x residue 389 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1075 random chunks: chunk 907 optimal weight: 8.9990 chunk 814 optimal weight: 9.9990 chunk 452 optimal weight: 3.9990 chunk 278 optimal weight: 2.9990 chunk 549 optimal weight: 9.9990 chunk 435 optimal weight: 0.0770 chunk 842 optimal weight: 8.9990 chunk 326 optimal weight: 6.9990 chunk 512 optimal weight: 0.9980 chunk 627 optimal weight: 5.9990 chunk 976 optimal weight: 8.9990 overall best weight: 2.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 20 HIS 3 63 ASN 7 17 ASN 8 172 HIS 8 231 ASN C 96 HIS C 113 GLN C 130 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 GLN F 146 HIS F 162 ASN G 66 HIS ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 147 GLN M 57 HIS O 17 HIS O 36 HIS P 28 HIS P 50 GLN P 82 HIS Q 94 ASN Q 122 ASN S 71 ASN S 88 GLN ** T 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 58 ASN U 62 GLN V 44 HIS ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 127 ASN W 19 GLN W 40 GLN d 121 ASN d 173 GLN d 179 GLN e 163 ASN ** h 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 52 ASN i 65 HIS j 70 HIS k 79 ASN k 85 GLN o 51 HIS p 15 ASN s 57 HIS t 71 GLN x 40 ASN x 59 ASN ** x 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 165129 Z= 0.227 Angle : 0.632 20.030 247155 Z= 0.323 Chirality : 0.037 0.310 31516 Planarity : 0.006 0.121 13409 Dihedral : 23.000 178.678 82987 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.81 % Favored : 94.02 % Rotamer: Outliers : 2.70 % Allowed : 12.88 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.42 (0.09), residues: 6072 helix: -2.91 (0.09), residues: 1851 sheet: -1.33 (0.15), residues: 1098 loop : -2.17 (0.10), residues: 3123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP S 48 HIS 0.015 0.001 HIS M 13 PHE 0.017 0.002 PHE i 85 TYR 0.019 0.001 TYR C 104 ARG 0.008 0.001 ARG l 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1045 residues out of total 5038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 909 time to evaluate : 6.386 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: 8 58 MET cc_start: 0.8237 (tpt) cc_final: 0.7899 (tmm) REVERT: 8 85 ASP cc_start: 0.9247 (m-30) cc_final: 0.8694 (p0) REVERT: 8 121 MET cc_start: 0.6382 (OUTLIER) cc_final: 0.5717 (pmt) REVERT: 8 131 LEU cc_start: 0.5626 (OUTLIER) cc_final: 0.5305 (tm) REVERT: 8 197 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8255 (mt) REVERT: C 78 LYS cc_start: 0.7911 (ttmm) cc_final: 0.7644 (ttmt) REVERT: C 161 SER cc_start: 0.8946 (p) cc_final: 0.8615 (m) REVERT: D 83 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7717 (mt-10) REVERT: F 160 ASP cc_start: 0.7172 (p0) cc_final: 0.6825 (p0) REVERT: H 12 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7212 (tm) REVERT: J 60 ASP cc_start: 0.8022 (p0) cc_final: 0.7773 (p0) REVERT: J 99 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7034 (ttp-170) REVERT: J 108 MET cc_start: 0.8928 (mtt) cc_final: 0.8715 (mtt) REVERT: K 53 LYS cc_start: 0.8501 (mmtm) cc_final: 0.8266 (mptt) REVERT: L 54 MET cc_start: 0.8332 (tpp) cc_final: 0.8069 (tpt) REVERT: L 63 LEU cc_start: 0.8831 (mt) cc_final: 0.8545 (mt) REVERT: M 18 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7365 (ptp90) REVERT: M 106 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8366 (tp) REVERT: O 23 LYS cc_start: 0.8675 (ttmm) cc_final: 0.8442 (ttmt) REVERT: Q 21 SER cc_start: 0.8661 (m) cc_final: 0.8381 (m) REVERT: R 24 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8372 (mttm) REVERT: T 63 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.7862 (mp10) REVERT: V 166 VAL cc_start: 0.7858 (t) cc_final: 0.7594 (m) REVERT: c 133 MET cc_start: 0.8317 (mtp) cc_final: 0.7832 (mtp) REVERT: d 19 LEU cc_start: 0.8350 (mt) cc_final: 0.8112 (mt) REVERT: d 76 ARG cc_start: 0.7330 (ttp-170) cc_final: 0.7051 (mmm-85) REVERT: d 83 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6916 (mm-30) REVERT: d 120 VAL cc_start: 0.7807 (OUTLIER) cc_final: 0.7573 (t) REVERT: d 126 ASN cc_start: 0.8489 (p0) cc_final: 0.8238 (p0) REVERT: e 83 LYS cc_start: 0.8095 (ptmm) cc_final: 0.7717 (pttm) REVERT: f 40 VAL cc_start: 0.7731 (OUTLIER) cc_final: 0.7478 (p) REVERT: h 93 ASN cc_start: 0.8020 (p0) cc_final: 0.7753 (p0) REVERT: h 96 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.6912 (tpt170) REVERT: i 63 LYS cc_start: 0.8416 (mppt) cc_final: 0.8183 (mmtp) REVERT: k 129 ASN cc_start: 0.6632 (OUTLIER) cc_final: 0.6363 (m110) REVERT: l 25 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8622 (mttt) REVERT: l 44 LYS cc_start: 0.7865 (tppt) cc_final: 0.7130 (tptt) REVERT: m 79 ARG cc_start: 0.7727 (ttm110) cc_final: 0.7399 (ttp-170) REVERT: o 64 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.8079 (ttp-110) REVERT: q 82 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7937 (mtt-85) REVERT: t 21 ASN cc_start: 0.8807 (m-40) cc_final: 0.8605 (m110) REVERT: x 159 ASN cc_start: 0.8326 (m-40) cc_final: 0.8045 (m-40) REVERT: x 196 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7628 (tt0) REVERT: x 226 ILE cc_start: 0.8439 (mt) cc_final: 0.8168 (mm) REVERT: x 237 TYR cc_start: 0.8222 (p90) cc_final: 0.7771 (p90) REVERT: x 238 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7169 (pt0) REVERT: x 331 TYR cc_start: 0.8193 (m-80) cc_final: 0.7719 (m-80) REVERT: x 519 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7468 (tm-30) outliers start: 136 outliers final: 53 residues processed: 981 average time/residue: 2.1879 time to fit residues: 3089.5496 Evaluate side-chains 877 residues out of total 5038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 806 time to evaluate : 6.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 27 LEU Chi-restraints excluded: chain 1 residue 25 THR Chi-restraints excluded: chain 2 residue 44 THR Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 16 LEU Chi-restraints excluded: chain 4 residue 22 ARG Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 39 SER Chi-restraints excluded: chain 8 residue 4 THR Chi-restraints excluded: chain 8 residue 56 ASP Chi-restraints excluded: chain 8 residue 121 MET Chi-restraints excluded: chain 8 residue 131 LEU Chi-restraints excluded: chain 8 residue 197 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 108 GLU Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 107 SER Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain S residue 40 SER Chi-restraints excluded: chain S residue 80 VAL Chi-restraints excluded: chain S residue 95 ILE Chi-restraints excluded: chain T residue 37 SER Chi-restraints excluded: chain T residue 63 GLN Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain c residue 56 ILE Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain e residue 154 ILE Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 88 THR Chi-restraints excluded: chain g residue 149 ARG Chi-restraints excluded: chain h residue 96 ARG Chi-restraints excluded: chain i residue 68 LEU Chi-restraints excluded: chain i residue 76 VAL Chi-restraints excluded: chain i residue 88 LEU Chi-restraints excluded: chain i residue 94 SER Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain k residue 68 SER Chi-restraints excluded: chain k residue 129 ASN Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 25 LYS Chi-restraints excluded: chain m residue 5 VAL Chi-restraints excluded: chain m residue 64 LEU Chi-restraints excluded: chain o residue 64 ARG Chi-restraints excluded: chain o residue 71 SER Chi-restraints excluded: chain q residue 82 ARG Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain x residue 64 LEU Chi-restraints excluded: chain x residue 82 ASP Chi-restraints excluded: chain x residue 161 SER Chi-restraints excluded: chain x residue 196 GLN Chi-restraints excluded: chain x residue 212 VAL Chi-restraints excluded: chain x residue 238 GLU Chi-restraints excluded: chain x residue 321 VAL Chi-restraints excluded: chain x residue 386 LEU Chi-restraints excluded: chain x residue 389 VAL Chi-restraints excluded: chain x residue 435 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1075 random chunks: chunk 542 optimal weight: 7.9990 chunk 302 optimal weight: 8.9990 chunk 812 optimal weight: 9.9990 chunk 664 optimal weight: 10.0000 chunk 269 optimal weight: 8.9990 chunk 977 optimal weight: 9.9990 chunk 1056 optimal weight: 2.9990 chunk 870 optimal weight: 10.0000 chunk 969 optimal weight: 10.0000 chunk 333 optimal weight: 6.9990 chunk 784 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 44 ASN 4 34 GLN 8 105 GLN C 113 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 GLN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 117 GLN S 51 GLN S 88 GLN U 62 GLN ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 143 GLN c 176 HIS i 66 GLN s 47 HIS t 71 GLN x 59 ASN x 75 GLN x 88 ASN x 281 GLN x 449 ASN x 508 HIS ** x 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.145 165129 Z= 0.507 Angle : 0.748 20.294 247155 Z= 0.373 Chirality : 0.045 0.307 31516 Planarity : 0.006 0.129 13409 Dihedral : 22.904 178.987 82987 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.95 % Favored : 92.92 % Rotamer: Outliers : 4.47 % Allowed : 14.81 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.87 (0.10), residues: 6072 helix: -2.08 (0.10), residues: 1870 sheet: -1.13 (0.15), residues: 1137 loop : -2.06 (0.10), residues: 3065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP x 522 HIS 0.015 0.002 HIS S 112 PHE 0.033 0.003 PHE X 14 TYR 0.027 0.002 TYR C 104 ARG 0.014 0.001 ARG 1 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1024 residues out of total 5038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 799 time to evaluate : 6.964 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: 8 58 MET cc_start: 0.8211 (tpt) cc_final: 0.7943 (tmm) REVERT: 8 85 ASP cc_start: 0.9251 (m-30) cc_final: 0.8936 (m-30) REVERT: 8 121 MET cc_start: 0.6701 (OUTLIER) cc_final: 0.5602 (pmm) REVERT: 8 197 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8227 (mp) REVERT: 8 207 ARG cc_start: 0.7117 (ptp-110) cc_final: 0.6756 (ttp-110) REVERT: C 23 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.6933 (pm20) REVERT: C 78 LYS cc_start: 0.8037 (ttmm) cc_final: 0.7703 (ttmt) REVERT: C 161 SER cc_start: 0.8926 (p) cc_final: 0.8627 (m) REVERT: D 13 MET cc_start: 0.8576 (mtp) cc_final: 0.8281 (mtp) REVERT: D 83 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7783 (mt-10) REVERT: H 12 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7288 (tm) REVERT: J 70 GLN cc_start: 0.8539 (mm-40) cc_final: 0.8285 (mt0) REVERT: J 99 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7187 (ttp-170) REVERT: L 63 LEU cc_start: 0.8846 (mt) cc_final: 0.8570 (mt) REVERT: M 18 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7376 (ptp90) REVERT: M 45 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.7018 (mtt90) REVERT: M 106 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8499 (tp) REVERT: O 21 ARG cc_start: 0.8424 (mmm160) cc_final: 0.8190 (mmm160) REVERT: P 93 ARG cc_start: 0.9257 (OUTLIER) cc_final: 0.6893 (mtp85) REVERT: P 103 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7377 (mtt-85) REVERT: Q 21 SER cc_start: 0.8693 (m) cc_final: 0.8409 (m) REVERT: R 24 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8393 (mttm) REVERT: T 63 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.7846 (mp10) REVERT: U 39 ASN cc_start: 0.8063 (p0) cc_final: 0.7717 (p0) REVERT: U 83 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8573 (tt) REVERT: V 23 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8651 (mmm-85) REVERT: X 27 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.6587 (ppp80) REVERT: c 133 MET cc_start: 0.8344 (mtp) cc_final: 0.8012 (mtp) REVERT: d 19 LEU cc_start: 0.8429 (mt) cc_final: 0.8184 (mt) REVERT: d 120 VAL cc_start: 0.7820 (OUTLIER) cc_final: 0.7604 (t) REVERT: d 126 ASN cc_start: 0.8574 (p0) cc_final: 0.8324 (p0) REVERT: d 141 ARG cc_start: 0.7781 (mmt90) cc_final: 0.7478 (mmt90) REVERT: e 176 LYS cc_start: 0.8907 (mttm) cc_final: 0.8693 (mttp) REVERT: f 40 VAL cc_start: 0.7860 (t) cc_final: 0.7575 (p) REVERT: g 64 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7462 (mtm110) REVERT: g 134 SER cc_start: 0.8972 (t) cc_final: 0.8747 (p) REVERT: g 137 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8114 (tpt90) REVERT: h 93 ASN cc_start: 0.8196 (p0) cc_final: 0.7844 (p0) REVERT: h 96 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.7070 (tpt170) REVERT: j 88 MET cc_start: 0.7572 (mmm) cc_final: 0.7116 (mmm) REVERT: k 129 ASN cc_start: 0.6833 (OUTLIER) cc_final: 0.6540 (m110) REVERT: l 7 LEU cc_start: 0.8831 (mt) cc_final: 0.8600 (mm) REVERT: l 44 LYS cc_start: 0.7943 (tppt) cc_final: 0.7280 (tptt) REVERT: m 79 ARG cc_start: 0.7903 (ttm110) cc_final: 0.7582 (ttp-110) REVERT: n 19 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8770 (mtt180) REVERT: n 53 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8149 (pp) REVERT: o 64 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.8136 (ttp-110) REVERT: p 28 ARG cc_start: 0.8352 (ptm-80) cc_final: 0.7979 (ptm160) REVERT: p 39 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.7930 (ptt90) REVERT: q 57 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8697 (mtt180) REVERT: q 82 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7959 (mtt-85) REVERT: x 159 ASN cc_start: 0.8408 (m-40) cc_final: 0.8124 (m-40) REVERT: x 196 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7686 (tt0) REVERT: x 226 ILE cc_start: 0.8580 (mt) cc_final: 0.8259 (mm) outliers start: 225 outliers final: 111 residues processed: 932 average time/residue: 2.1686 time to fit residues: 2921.7952 Evaluate side-chains 889 residues out of total 5038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 751 time to evaluate : 6.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 27 LEU Chi-restraints excluded: chain 1 residue 25 THR Chi-restraints excluded: chain 2 residue 44 THR Chi-restraints excluded: chain 3 residue 60 SER Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 16 LEU Chi-restraints excluded: chain 4 residue 22 ARG Chi-restraints excluded: chain 6 residue 5 ILE Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 39 SER Chi-restraints excluded: chain 8 residue 41 THR Chi-restraints excluded: chain 8 residue 56 ASP Chi-restraints excluded: chain 8 residue 121 MET Chi-restraints excluded: chain 8 residue 124 VAL Chi-restraints excluded: chain 8 residue 197 LEU Chi-restraints excluded: chain 8 residue 216 THR Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 266 LYS Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain K residue 108 GLU Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 45 ARG Chi-restraints excluded: chain M residue 59 LYS Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 107 SER Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain P residue 103 ARG Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain S residue 80 VAL Chi-restraints excluded: chain S residue 95 ILE Chi-restraints excluded: chain T residue 37 SER Chi-restraints excluded: chain T residue 63 GLN Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain V residue 23 ARG Chi-restraints excluded: chain V residue 96 LEU Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain W residue 59 LEU Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain X residue 27 ARG Chi-restraints excluded: chain X residue 35 THR Chi-restraints excluded: chain Y residue 53 GLU Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain c residue 56 ILE Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 147 LYS Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain e residue 100 LYS Chi-restraints excluded: chain e residue 154 ILE Chi-restraints excluded: chain e residue 158 SER Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 88 THR Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 64 ARG Chi-restraints excluded: chain g residue 89 VAL Chi-restraints excluded: chain g residue 137 ARG Chi-restraints excluded: chain g residue 149 ARG Chi-restraints excluded: chain h residue 50 ARG Chi-restraints excluded: chain h residue 96 ARG Chi-restraints excluded: chain h residue 132 TRP Chi-restraints excluded: chain i residue 76 VAL Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain k residue 68 SER Chi-restraints excluded: chain k residue 129 ASN Chi-restraints excluded: chain m residue 5 VAL Chi-restraints excluded: chain m residue 9 LEU Chi-restraints excluded: chain m residue 15 MET Chi-restraints excluded: chain m residue 64 LEU Chi-restraints excluded: chain n residue 19 ARG Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain n residue 46 GLU Chi-restraints excluded: chain n residue 53 LEU Chi-restraints excluded: chain o residue 64 ARG Chi-restraints excluded: chain o residue 71 SER Chi-restraints excluded: chain p residue 39 ARG Chi-restraints excluded: chain q residue 57 ARG Chi-restraints excluded: chain q residue 68 LYS Chi-restraints excluded: chain q residue 82 ARG Chi-restraints excluded: chain q residue 116 THR Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain x residue 24 VAL Chi-restraints excluded: chain x residue 64 LEU Chi-restraints excluded: chain x residue 82 ASP Chi-restraints excluded: chain x residue 161 SER Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain x residue 196 GLN Chi-restraints excluded: chain x residue 210 LEU Chi-restraints excluded: chain x residue 212 VAL Chi-restraints excluded: chain x residue 254 VAL Chi-restraints excluded: chain x residue 300 LYS Chi-restraints excluded: chain x residue 321 VAL Chi-restraints excluded: chain x residue 341 SER Chi-restraints excluded: chain x residue 377 SER Chi-restraints excluded: chain x residue 386 LEU Chi-restraints excluded: chain x residue 470 THR Chi-restraints excluded: chain x residue 551 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1075 random chunks: chunk 966 optimal weight: 3.9990 chunk 735 optimal weight: 6.9990 chunk 507 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 466 optimal weight: 5.9990 chunk 656 optimal weight: 3.9990 chunk 981 optimal weight: 10.0000 chunk 1039 optimal weight: 6.9990 chunk 512 optimal weight: 4.9990 chunk 930 optimal weight: 9.9990 chunk 280 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 44 ASN 3 63 ASN C 113 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN E 214 ASN F 34 GLN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 147 GLN Q 77 ASN U 62 GLN ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 126 GLN o 72 GLN p 41 HIS s 22 GLN t 21 ASN t 71 GLN t 84 ASN x 59 ASN ** x 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 165129 Z= 0.305 Angle : 0.630 19.211 247155 Z= 0.321 Chirality : 0.038 0.280 31516 Planarity : 0.005 0.125 13409 Dihedral : 22.852 179.307 82986 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.16 % Favored : 93.71 % Rotamer: Outliers : 3.85 % Allowed : 16.79 % Favored : 79.36 % 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: -2.42 (0.10), residues: 6072 helix: -1.51 (0.11), residues: 1882 sheet: -0.87 (0.15), residues: 1108 loop : -1.92 (0.10), residues: 3082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP x 225 HIS 0.010 0.001 HIS S 112 PHE 0.018 0.002 PHE i 85 TYR 0.016 0.002 TYR C 104 ARG 0.009 0.001 ARG m 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 971 residues out of total 5038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 777 time to evaluate : 6.743 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: 0.8720 (OUTLIER) cc_final: 0.7977 (ttm-80) REVERT: 3 32 LEU cc_start: 0.8902 (mt) cc_final: 0.8654 (mt) REVERT: 8 58 MET cc_start: 0.8231 (tpt) cc_final: 0.7955 (tmm) REVERT: 8 85 ASP cc_start: 0.9245 (m-30) cc_final: 0.8933 (m-30) REVERT: 8 121 MET cc_start: 0.6725 (OUTLIER) cc_final: 0.6150 (pmm) REVERT: 8 134 ARG cc_start: 0.6159 (OUTLIER) cc_final: 0.5925 (mpt90) REVERT: 8 197 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8187 (mp) REVERT: 8 205 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8453 (mmpt) REVERT: 8 207 ARG cc_start: 0.7088 (ptp-110) cc_final: 0.6877 (ttp-110) REVERT: C 23 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.6938 (pm20) REVERT: C 78 LYS cc_start: 0.8052 (ttmm) cc_final: 0.7724 (ttmt) REVERT: C 161 SER cc_start: 0.8896 (p) cc_final: 0.8602 (m) REVERT: D 83 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7749 (mt-10) REVERT: F 70 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8116 (pt0) REVERT: H 12 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7383 (tm) REVERT: J 70 GLN cc_start: 0.8512 (mm-40) cc_final: 0.8284 (mt0) REVERT: J 99 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7070 (ttp-170) REVERT: K 3 GLN cc_start: 0.8432 (pt0) cc_final: 0.8118 (pt0) REVERT: L 54 MET cc_start: 0.8343 (tpp) cc_final: 0.8076 (tpt) REVERT: L 63 LEU cc_start: 0.8823 (mt) cc_final: 0.8558 (mt) REVERT: M 18 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7380 (ptp90) REVERT: M 45 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.6974 (mtt90) REVERT: M 106 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8459 (tp) REVERT: N 75 VAL cc_start: 0.8797 (OUTLIER) cc_final: 0.8574 (t) REVERT: O 21 ARG cc_start: 0.8390 (mmm160) cc_final: 0.8173 (mmm160) REVERT: P 1 MET cc_start: 0.7757 (ptm) cc_final: 0.7381 (ptp) REVERT: P 93 ARG cc_start: 0.9217 (OUTLIER) cc_final: 0.6842 (mtp85) REVERT: Q 21 SER cc_start: 0.8684 (m) cc_final: 0.8406 (m) REVERT: R 24 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8325 (mttm) REVERT: T 63 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.7848 (mp10) REVERT: U 39 ASN cc_start: 0.7910 (p0) cc_final: 0.7651 (p0) REVERT: U 83 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8499 (tt) REVERT: V 23 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.8840 (mmm-85) REVERT: V 166 VAL cc_start: 0.7870 (t) cc_final: 0.7583 (m) REVERT: X 27 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.6582 (ppp80) REVERT: c 133 MET cc_start: 0.8275 (mtp) cc_final: 0.8046 (mtt) REVERT: d 19 LEU cc_start: 0.8440 (mt) cc_final: 0.8212 (mt) REVERT: d 120 VAL cc_start: 0.7771 (OUTLIER) cc_final: 0.7511 (t) REVERT: d 126 ASN cc_start: 0.8530 (p0) cc_final: 0.8289 (p0) REVERT: d 147 THR cc_start: 0.6272 (OUTLIER) cc_final: 0.6029 (p) REVERT: f 7 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8195 (ttm) REVERT: f 40 VAL cc_start: 0.7836 (OUTLIER) cc_final: 0.7579 (p) REVERT: g 64 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7519 (mtm110) REVERT: g 137 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7979 (tpt90) REVERT: h 93 ASN cc_start: 0.8081 (p0) cc_final: 0.7799 (p0) REVERT: h 96 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.7102 (tpt170) REVERT: k 129 ASN cc_start: 0.6755 (OUTLIER) cc_final: 0.6503 (m110) REVERT: l 44 LYS cc_start: 0.7914 (tppt) cc_final: 0.7289 (tptt) REVERT: m 79 ARG cc_start: 0.8083 (ttm110) cc_final: 0.7669 (ttp-110) REVERT: n 19 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8706 (mtt180) REVERT: n 53 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8110 (pp) REVERT: o 53 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7978 (ttp-170) REVERT: o 64 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8104 (ttp-110) REVERT: p 28 ARG cc_start: 0.8349 (ptm-80) cc_final: 0.7986 (ptm160) REVERT: q 82 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7933 (mtt-85) REVERT: x 83 LYS cc_start: 0.8101 (tppp) cc_final: 0.7810 (tppt) REVERT: x 119 MET cc_start: 0.7150 (ttm) cc_final: 0.6922 (ttm) REVERT: x 159 ASN cc_start: 0.8379 (m-40) cc_final: 0.8107 (m-40) REVERT: x 196 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7631 (tt0) REVERT: x 226 ILE cc_start: 0.8508 (mt) cc_final: 0.8193 (mm) REVERT: x 365 LYS cc_start: 0.8660 (mtmp) cc_final: 0.7968 (mtmp) REVERT: x 372 THR cc_start: 0.8168 (m) cc_final: 0.7894 (p) outliers start: 194 outliers final: 112 residues processed: 881 average time/residue: 2.1974 time to fit residues: 2817.5621 Evaluate side-chains 896 residues out of total 5038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 751 time to evaluate : 6.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 27 LEU Chi-restraints excluded: chain 1 residue 25 THR Chi-restraints excluded: chain 2 residue 28 ARG Chi-restraints excluded: chain 2 residue 44 THR Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 16 LEU Chi-restraints excluded: chain 4 residue 22 ARG Chi-restraints excluded: chain 6 residue 5 ILE Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 39 SER Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 8 residue 41 THR Chi-restraints excluded: chain 8 residue 56 ASP Chi-restraints excluded: chain 8 residue 121 MET Chi-restraints excluded: chain 8 residue 124 VAL Chi-restraints excluded: chain 8 residue 134 ARG Chi-restraints excluded: chain 8 residue 197 LEU Chi-restraints excluded: chain 8 residue 205 LYS Chi-restraints excluded: chain 8 residue 216 THR Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 266 LYS Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 70 GLN Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 108 GLU Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 127 LYS Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 45 ARG Chi-restraints excluded: chain M residue 59 LYS Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 107 SER Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain Q residue 77 ASN Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain S residue 40 SER Chi-restraints excluded: chain S residue 80 VAL Chi-restraints excluded: chain S residue 95 ILE Chi-restraints excluded: chain T residue 37 SER Chi-restraints excluded: chain T residue 63 GLN Chi-restraints excluded: chain U residue 72 MET Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain V residue 23 ARG Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain W residue 59 LEU Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain X residue 27 ARG Chi-restraints excluded: chain X residue 35 THR Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain c residue 56 ILE Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 147 LYS Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 147 THR Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain e residue 154 ILE Chi-restraints excluded: chain e residue 158 SER Chi-restraints excluded: chain f residue 7 MET Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain g residue 64 ARG Chi-restraints excluded: chain g residue 89 VAL Chi-restraints excluded: chain g residue 137 ARG Chi-restraints excluded: chain g residue 149 ARG Chi-restraints excluded: chain h residue 96 ARG Chi-restraints excluded: chain h residue 132 TRP Chi-restraints excluded: chain i residue 76 VAL Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain k residue 68 SER Chi-restraints excluded: chain k residue 129 ASN Chi-restraints excluded: chain l residue 79 MET Chi-restraints excluded: chain m residue 5 VAL Chi-restraints excluded: chain m residue 9 LEU Chi-restraints excluded: chain m residue 15 MET Chi-restraints excluded: chain m residue 64 LEU Chi-restraints excluded: chain n residue 19 ARG Chi-restraints excluded: chain n residue 46 GLU Chi-restraints excluded: chain n residue 53 LEU Chi-restraints excluded: chain o residue 20 THR Chi-restraints excluded: chain o residue 44 LYS Chi-restraints excluded: chain o residue 45 VAL Chi-restraints excluded: chain o residue 53 ARG Chi-restraints excluded: chain o residue 64 ARG Chi-restraints excluded: chain o residue 71 SER Chi-restraints excluded: chain q residue 68 LYS Chi-restraints excluded: chain q residue 82 ARG Chi-restraints excluded: chain q residue 116 THR Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 57 LYS Chi-restraints excluded: chain x residue 25 THR Chi-restraints excluded: chain x residue 64 LEU Chi-restraints excluded: chain x residue 82 ASP Chi-restraints excluded: chain x residue 161 SER Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain x residue 196 GLN Chi-restraints excluded: chain x residue 210 LEU Chi-restraints excluded: chain x residue 212 VAL Chi-restraints excluded: chain x residue 254 VAL Chi-restraints excluded: chain x residue 321 VAL Chi-restraints excluded: chain x residue 337 ILE Chi-restraints excluded: chain x residue 470 THR Chi-restraints excluded: chain x residue 540 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1075 random chunks: chunk 865 optimal weight: 4.9990 chunk 589 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 chunk 773 optimal weight: 20.0000 chunk 428 optimal weight: 6.9990 chunk 886 optimal weight: 6.9990 chunk 718 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 530 optimal weight: 8.9990 chunk 932 optimal weight: 8.9990 chunk 262 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 44 ASN 3 63 ASN C 113 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 GLN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 62 GLN ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 40 GLN c 122 GLN ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 126 GLN o 72 GLN t 21 ASN t 84 ASN x 59 ASN x 417 GLN ** x 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 165129 Z= 0.331 Angle : 0.637 19.530 247155 Z= 0.323 Chirality : 0.038 0.285 31516 Planarity : 0.005 0.126 13409 Dihedral : 22.809 179.456 82986 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.51 % Favored : 93.36 % Rotamer: Outliers : 4.62 % Allowed : 17.23 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 6072 helix: -1.13 (0.12), residues: 1886 sheet: -0.70 (0.16), residues: 1109 loop : -1.82 (0.10), residues: 3077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP x 512 HIS 0.011 0.001 HIS S 112 PHE 0.035 0.002 PHE W 45 TYR 0.019 0.002 TYR x 237 ARG 0.009 0.001 ARG m 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1000 residues out of total 5038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 767 time to evaluate : 6.783 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: 0.8753 (OUTLIER) cc_final: 0.8008 (ttm-80) REVERT: 3 32 LEU cc_start: 0.8899 (mt) cc_final: 0.8663 (mt) REVERT: 8 58 MET cc_start: 0.8199 (tpt) cc_final: 0.7921 (tmm) REVERT: 8 85 ASP cc_start: 0.9257 (m-30) cc_final: 0.8970 (m-30) REVERT: 8 121 MET cc_start: 0.6754 (OUTLIER) cc_final: 0.5703 (pmm) REVERT: 8 155 ASP cc_start: 0.7978 (m-30) cc_final: 0.7407 (t0) REVERT: 8 197 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8171 (mp) REVERT: C 23 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.6922 (pm20) REVERT: C 78 LYS cc_start: 0.8073 (ttmm) cc_final: 0.7748 (ttmt) REVERT: C 161 SER cc_start: 0.8891 (p) cc_final: 0.8602 (m) REVERT: C 261 ASN cc_start: 0.9133 (p0) cc_final: 0.8906 (p0) REVERT: D 30 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7638 (ttmt) REVERT: D 83 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7790 (mt-10) REVERT: F 45 MET cc_start: 0.7994 (mmm) cc_final: 0.7540 (mtt) REVERT: F 70 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8170 (pt0) REVERT: H 12 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7472 (tm) REVERT: J 99 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7129 (ttp-170) REVERT: J 123 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.6153 (mmt90) REVERT: L 54 MET cc_start: 0.8355 (tpp) cc_final: 0.8024 (tpt) REVERT: L 63 LEU cc_start: 0.8833 (mt) cc_final: 0.8572 (mt) REVERT: M 18 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7375 (ptp90) REVERT: M 45 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.6976 (mtt90) REVERT: M 106 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8490 (tp) REVERT: N 75 VAL cc_start: 0.8822 (OUTLIER) cc_final: 0.8586 (t) REVERT: N 117 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.5649 (mtp85) REVERT: P 93 ARG cc_start: 0.9217 (OUTLIER) cc_final: 0.6982 (mtp85) REVERT: P 103 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7405 (mtt-85) REVERT: Q 21 SER cc_start: 0.8701 (m) cc_final: 0.8417 (m) REVERT: R 24 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8352 (mttm) REVERT: T 63 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.7826 (mp10) REVERT: U 39 ASN cc_start: 0.7985 (p0) cc_final: 0.7741 (p0) REVERT: U 83 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8501 (tt) REVERT: V 19 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7949 (ttpp) REVERT: V 134 GLU cc_start: 0.6366 (OUTLIER) cc_final: 0.6099 (tp30) REVERT: V 166 VAL cc_start: 0.7859 (t) cc_final: 0.7622 (m) REVERT: W 24 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.7584 (mmtt) REVERT: X 27 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.6478 (ppp80) REVERT: Z 5 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.7925 (tttp) REVERT: d 15 LEU cc_start: 0.8016 (mp) cc_final: 0.7653 (tt) REVERT: d 19 LEU cc_start: 0.8429 (mt) cc_final: 0.8204 (mt) REVERT: d 120 VAL cc_start: 0.7735 (OUTLIER) cc_final: 0.7474 (t) REVERT: d 141 ARG cc_start: 0.7723 (mmt90) cc_final: 0.7471 (mmt90) REVERT: d 147 THR cc_start: 0.6196 (OUTLIER) cc_final: 0.5969 (p) REVERT: e 83 LYS cc_start: 0.7954 (ptmm) cc_final: 0.7653 (pttm) REVERT: f 40 VAL cc_start: 0.7810 (OUTLIER) cc_final: 0.7542 (p) REVERT: g 89 VAL cc_start: 0.8917 (OUTLIER) cc_final: 0.8679 (t) REVERT: g 137 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7971 (tpt90) REVERT: h 93 ASN cc_start: 0.8119 (p0) cc_final: 0.7804 (p0) REVERT: h 96 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.7081 (tpt170) REVERT: j 88 MET cc_start: 0.7615 (mmm) cc_final: 0.7189 (mmm) REVERT: k 129 ASN cc_start: 0.6804 (OUTLIER) cc_final: 0.6563 (m110) REVERT: l 44 LYS cc_start: 0.7890 (tppt) cc_final: 0.7299 (tptt) REVERT: m 79 ARG cc_start: 0.8062 (ttm110) cc_final: 0.7689 (ttp-110) REVERT: n 19 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8698 (mtt180) REVERT: n 53 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8125 (pp) REVERT: o 53 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.8005 (ttp-170) REVERT: o 64 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.8117 (ttp-110) REVERT: p 28 ARG cc_start: 0.8401 (ptm-80) cc_final: 0.8039 (ptm160) REVERT: p 39 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7929 (ptt90) REVERT: q 68 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.8010 (ptpp) REVERT: x 159 ASN cc_start: 0.8369 (m-40) cc_final: 0.8084 (m-40) REVERT: x 196 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7627 (tt0) REVERT: x 226 ILE cc_start: 0.8547 (mt) cc_final: 0.8241 (mm) REVERT: x 229 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8468 (mt) REVERT: x 365 LYS cc_start: 0.8661 (mtmp) cc_final: 0.7977 (mtmp) REVERT: x 372 THR cc_start: 0.7944 (m) cc_final: 0.7711 (p) REVERT: x 482 GLU cc_start: 0.8051 (tt0) cc_final: 0.7798 (tt0) outliers start: 233 outliers final: 137 residues processed: 903 average time/residue: 2.2030 time to fit residues: 2882.8444 Evaluate side-chains 921 residues out of total 5038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 745 time to evaluate : 6.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 27 LEU Chi-restraints excluded: chain 1 residue 25 THR Chi-restraints excluded: chain 2 residue 28 ARG Chi-restraints excluded: chain 2 residue 44 THR Chi-restraints excluded: chain 3 residue 3 LYS Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 8 LYS Chi-restraints excluded: chain 4 residue 16 LEU Chi-restraints excluded: chain 4 residue 22 ARG Chi-restraints excluded: chain 6 residue 5 ILE Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 39 SER Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 8 residue 41 THR Chi-restraints excluded: chain 8 residue 56 ASP Chi-restraints excluded: chain 8 residue 121 MET Chi-restraints excluded: chain 8 residue 124 VAL Chi-restraints excluded: chain 8 residue 197 LEU Chi-restraints excluded: chain 8 residue 216 THR Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 266 LYS Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 70 GLN Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain J residue 119 GLN Chi-restraints excluded: chain J residue 123 ARG Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 54 ARG Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 108 GLU Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 45 ARG Chi-restraints excluded: chain M residue 59 LYS Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 107 SER Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 117 ARG Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain P residue 103 ARG Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain S residue 80 VAL Chi-restraints excluded: chain S residue 95 ILE Chi-restraints excluded: chain T residue 37 SER Chi-restraints excluded: chain T residue 63 GLN Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain V residue 19 LYS Chi-restraints excluded: chain V residue 96 LEU Chi-restraints excluded: chain V residue 134 GLU Chi-restraints excluded: chain W residue 24 LYS Chi-restraints excluded: chain W residue 59 LEU Chi-restraints excluded: chain W residue 68 GLU Chi-restraints excluded: chain X residue 27 ARG Chi-restraints excluded: chain X residue 35 THR Chi-restraints excluded: chain Z residue 5 LYS Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain c residue 56 ILE Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 147 LYS Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 147 THR Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain e residue 100 LYS Chi-restraints excluded: chain e residue 154 ILE Chi-restraints excluded: chain e residue 158 SER Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 56 THR Chi-restraints excluded: chain g residue 64 ARG Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 89 VAL Chi-restraints excluded: chain g residue 137 ARG Chi-restraints excluded: chain g residue 149 ARG Chi-restraints excluded: chain h residue 96 ARG Chi-restraints excluded: chain h residue 132 TRP Chi-restraints excluded: chain i residue 76 VAL Chi-restraints excluded: chain i residue 110 LEU Chi-restraints excluded: chain j residue 30 VAL Chi-restraints excluded: chain j residue 40 VAL Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain k residue 68 SER Chi-restraints excluded: chain k residue 129 ASN Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 79 MET Chi-restraints excluded: chain m residue 5 VAL Chi-restraints excluded: chain m residue 9 LEU Chi-restraints excluded: chain m residue 15 MET Chi-restraints excluded: chain m residue 64 LEU Chi-restraints excluded: chain n residue 19 ARG Chi-restraints excluded: chain n residue 46 GLU Chi-restraints excluded: chain n residue 53 LEU Chi-restraints excluded: chain o residue 20 THR Chi-restraints excluded: chain o residue 44 LYS Chi-restraints excluded: chain o residue 45 VAL Chi-restraints excluded: chain o residue 53 ARG Chi-restraints excluded: chain o residue 64 ARG Chi-restraints excluded: chain o residue 71 SER Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 39 ARG Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain q residue 68 LYS Chi-restraints excluded: chain q residue 116 THR Chi-restraints excluded: chain r residue 73 GLU Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 57 LYS Chi-restraints excluded: chain x residue 25 THR Chi-restraints excluded: chain x residue 64 LEU Chi-restraints excluded: chain x residue 82 ASP Chi-restraints excluded: chain x residue 106 VAL Chi-restraints excluded: chain x residue 161 SER Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain x residue 196 GLN Chi-restraints excluded: chain x residue 210 LEU Chi-restraints excluded: chain x residue 212 VAL Chi-restraints excluded: chain x residue 229 LEU Chi-restraints excluded: chain x residue 254 VAL Chi-restraints excluded: chain x residue 321 VAL Chi-restraints excluded: chain x residue 337 ILE Chi-restraints excluded: chain x residue 470 THR Chi-restraints excluded: chain x residue 551 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1075 random chunks: chunk 349 optimal weight: 10.0000 chunk 935 optimal weight: 0.0770 chunk 205 optimal weight: 30.0000 chunk 610 optimal weight: 5.9990 chunk 256 optimal weight: 5.9990 chunk 1040 optimal weight: 0.6980 chunk 863 optimal weight: 4.9990 chunk 481 optimal weight: 0.9980 chunk 86 optimal weight: 60.0000 chunk 344 optimal weight: 7.9990 chunk 546 optimal weight: 6.9990 overall best weight: 2.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 44 ASN 3 63 ASN C 113 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 ASN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 62 GLN ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 126 GLN o 72 GLN t 21 ASN t 84 ASN x 59 ASN x 417 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 165129 Z= 0.200 Angle : 0.599 19.418 247155 Z= 0.307 Chirality : 0.035 0.266 31516 Planarity : 0.005 0.124 13409 Dihedral : 22.845 179.851 82986 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.27 % Favored : 93.61 % Rotamer: Outliers : 4.23 % Allowed : 18.08 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.92 (0.10), residues: 6072 helix: -0.90 (0.12), residues: 1888 sheet: -0.65 (0.16), residues: 1110 loop : -1.73 (0.10), residues: 3074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP x 512 HIS 0.007 0.001 HIS S 112 PHE 0.016 0.001 PHE W 45 TYR 0.020 0.001 TYR x 237 ARG 0.017 0.001 ARG 8 207 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 967 residues out of total 5038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 754 time to evaluate : 6.763 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: 2 28 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.7996 (ttm-80) REVERT: 3 32 LEU cc_start: 0.8895 (mt) cc_final: 0.8656 (mt) REVERT: 8 58 MET cc_start: 0.8218 (tpt) cc_final: 0.7925 (tmm) REVERT: 8 121 MET cc_start: 0.6663 (OUTLIER) cc_final: 0.5535 (pmm) REVERT: 8 155 ASP cc_start: 0.7974 (m-30) cc_final: 0.7402 (t0) REVERT: 8 197 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8178 (mp) REVERT: 8 207 ARG cc_start: 0.6845 (ttp-110) cc_final: 0.6633 (tpp80) REVERT: C 23 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.6948 (pm20) REVERT: C 78 LYS cc_start: 0.8059 (ttmm) cc_final: 0.7733 (ttmt) REVERT: C 161 SER cc_start: 0.8864 (p) cc_final: 0.8591 (m) REVERT: C 261 ASN cc_start: 0.9123 (p0) cc_final: 0.8884 (p0) REVERT: D 30 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7622 (ttmt) REVERT: D 83 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7790 (mt-10) REVERT: F 70 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8141 (pt0) REVERT: H 12 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7464 (tm) REVERT: J 99 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7033 (ttp-170) REVERT: L 54 MET cc_start: 0.8343 (tpp) cc_final: 0.8108 (tpt) REVERT: L 63 LEU cc_start: 0.8812 (mt) cc_final: 0.8552 (mt) REVERT: M 18 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7368 (ptp90) REVERT: M 45 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.6943 (mtt90) REVERT: M 106 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8456 (tp) REVERT: N 75 VAL cc_start: 0.8798 (OUTLIER) cc_final: 0.8566 (t) REVERT: N 117 ARG cc_start: 0.7035 (OUTLIER) cc_final: 0.5673 (mtp85) REVERT: Q 21 SER cc_start: 0.8690 (m) cc_final: 0.8408 (m) REVERT: R 24 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8317 (mttm) REVERT: T 63 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.7845 (mp10) REVERT: V 166 VAL cc_start: 0.7856 (t) cc_final: 0.7647 (m) REVERT: X 27 ARG cc_start: 0.9142 (OUTLIER) cc_final: 0.6560 (ppp80) REVERT: Z 5 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.7871 (tttp) REVERT: d 19 LEU cc_start: 0.8418 (mt) cc_final: 0.8206 (mt) REVERT: d 120 VAL cc_start: 0.7729 (OUTLIER) cc_final: 0.7468 (t) REVERT: d 141 ARG cc_start: 0.7774 (mmt90) cc_final: 0.7497 (mmt90) REVERT: d 147 THR cc_start: 0.6214 (OUTLIER) cc_final: 0.5977 (p) REVERT: f 40 VAL cc_start: 0.7862 (OUTLIER) cc_final: 0.7595 (p) REVERT: g 64 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7561 (mtm110) REVERT: g 89 VAL cc_start: 0.8901 (OUTLIER) cc_final: 0.8669 (t) REVERT: g 137 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7975 (tpt90) REVERT: h 93 ASN cc_start: 0.8096 (p0) cc_final: 0.7782 (p0) REVERT: h 96 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.7043 (tpt170) REVERT: j 88 MET cc_start: 0.7612 (mmm) cc_final: 0.7171 (mmm) REVERT: k 129 ASN cc_start: 0.6768 (OUTLIER) cc_final: 0.6525 (m110) REVERT: l 44 LYS cc_start: 0.7866 (tppt) cc_final: 0.7273 (tptt) REVERT: m 79 ARG cc_start: 0.8050 (ttm110) cc_final: 0.7566 (ttp-110) REVERT: n 19 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8695 (mtt180) REVERT: o 53 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7972 (ttp-170) REVERT: o 64 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.8099 (ttp-110) REVERT: p 28 ARG cc_start: 0.8389 (ptm-80) cc_final: 0.8012 (ptm160) REVERT: p 39 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7945 (ptt90) REVERT: q 68 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.8024 (ptpp) REVERT: x 83 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7794 (tppt) REVERT: x 159 ASN cc_start: 0.8356 (m-40) cc_final: 0.8074 (m-40) REVERT: x 196 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7613 (tt0) REVERT: x 226 ILE cc_start: 0.8535 (mt) cc_final: 0.8228 (mm) REVERT: x 229 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8460 (mt) REVERT: x 365 LYS cc_start: 0.8645 (mtmp) cc_final: 0.7933 (mtmp) REVERT: x 482 GLU cc_start: 0.8010 (tt0) cc_final: 0.7781 (tt0) outliers start: 213 outliers final: 132 residues processed: 876 average time/residue: 2.1830 time to fit residues: 2771.6919 Evaluate side-chains 905 residues out of total 5038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 740 time to evaluate : 9.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 27 LEU Chi-restraints excluded: chain 1 residue 25 THR Chi-restraints excluded: chain 2 residue 28 ARG Chi-restraints excluded: chain 2 residue 44 THR Chi-restraints excluded: chain 3 residue 3 LYS Chi-restraints excluded: chain 3 residue 48 THR Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 22 ARG Chi-restraints excluded: chain 6 residue 5 ILE Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 8 residue 41 THR Chi-restraints excluded: chain 8 residue 56 ASP Chi-restraints excluded: chain 8 residue 121 MET Chi-restraints excluded: chain 8 residue 124 VAL Chi-restraints excluded: chain 8 residue 197 LEU Chi-restraints excluded: chain 8 residue 216 THR Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 266 LYS Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 70 GLN Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 54 ARG Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 108 GLU Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 45 ARG Chi-restraints excluded: chain M residue 59 LYS Chi-restraints excluded: chain M residue 67 ASN Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 107 SER Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 117 ARG Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain S residue 80 VAL Chi-restraints excluded: chain S residue 95 ILE Chi-restraints excluded: chain T residue 37 SER Chi-restraints excluded: chain T residue 56 SER Chi-restraints excluded: chain T residue 63 GLN Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain V residue 122 VAL Chi-restraints excluded: chain W residue 59 LEU Chi-restraints excluded: chain W residue 68 GLU Chi-restraints excluded: chain X residue 27 ARG Chi-restraints excluded: chain X residue 35 THR Chi-restraints excluded: chain Z residue 5 LYS Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 147 LYS Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 147 THR Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain e residue 154 ILE Chi-restraints excluded: chain e residue 158 SER Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 56 THR Chi-restraints excluded: chain g residue 64 ARG Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 89 VAL Chi-restraints excluded: chain g residue 137 ARG Chi-restraints excluded: chain g residue 149 ARG Chi-restraints excluded: chain h residue 96 ARG Chi-restraints excluded: chain h residue 132 TRP Chi-restraints excluded: chain i residue 76 VAL Chi-restraints excluded: chain i residue 94 SER Chi-restraints excluded: chain i residue 110 LEU Chi-restraints excluded: chain j residue 40 VAL Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain k residue 68 SER Chi-restraints excluded: chain k residue 129 ASN Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 79 MET Chi-restraints excluded: chain m residue 5 VAL Chi-restraints excluded: chain m residue 9 LEU Chi-restraints excluded: chain m residue 15 MET Chi-restraints excluded: chain m residue 64 LEU Chi-restraints excluded: chain n residue 19 ARG Chi-restraints excluded: chain n residue 46 GLU Chi-restraints excluded: chain o residue 20 THR Chi-restraints excluded: chain o residue 44 LYS Chi-restraints excluded: chain o residue 45 VAL Chi-restraints excluded: chain o residue 53 ARG Chi-restraints excluded: chain o residue 64 ARG Chi-restraints excluded: chain o residue 71 SER Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 39 ARG Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain q residue 68 LYS Chi-restraints excluded: chain q residue 116 THR Chi-restraints excluded: chain r residue 73 GLU Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 57 LYS Chi-restraints excluded: chain x residue 25 THR Chi-restraints excluded: chain x residue 59 ASN Chi-restraints excluded: chain x residue 64 LEU Chi-restraints excluded: chain x residue 82 ASP Chi-restraints excluded: chain x residue 83 LYS Chi-restraints excluded: chain x residue 106 VAL Chi-restraints excluded: chain x residue 161 SER Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain x residue 196 GLN Chi-restraints excluded: chain x residue 210 LEU Chi-restraints excluded: chain x residue 212 VAL Chi-restraints excluded: chain x residue 229 LEU Chi-restraints excluded: chain x residue 254 VAL Chi-restraints excluded: chain x residue 321 VAL Chi-restraints excluded: chain x residue 337 ILE Chi-restraints excluded: chain x residue 341 SER Chi-restraints excluded: chain x residue 377 SER Chi-restraints excluded: chain x residue 540 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1075 random chunks: chunk 1002 optimal weight: 8.9990 chunk 117 optimal weight: 7.9990 chunk 592 optimal weight: 0.7980 chunk 759 optimal weight: 60.0000 chunk 588 optimal weight: 10.0000 chunk 875 optimal weight: 6.9990 chunk 580 optimal weight: 9.9990 chunk 1036 optimal weight: 5.9990 chunk 648 optimal weight: 8.9990 chunk 631 optimal weight: 0.0010 chunk 478 optimal weight: 0.8980 overall best weight: 2.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 44 ASN 3 63 ASN C 113 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 ASN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 62 GLN ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 126 GLN o 72 GLN t 84 ASN x 417 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 165129 Z= 0.225 Angle : 0.587 19.187 247155 Z= 0.301 Chirality : 0.035 0.270 31516 Planarity : 0.005 0.124 13409 Dihedral : 22.817 179.798 82986 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.11 % Favored : 93.76 % Rotamer: Outliers : 4.07 % Allowed : 18.66 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.77 (0.10), residues: 6072 helix: -0.73 (0.12), residues: 1896 sheet: -0.55 (0.16), residues: 1123 loop : -1.69 (0.10), residues: 3053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP x 512 HIS 0.007 0.001 HIS S 112 PHE 0.019 0.001 PHE W 45 TYR 0.021 0.001 TYR x 237 ARG 0.009 0.000 ARG d 160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 964 residues out of total 5038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 759 time to evaluate : 6.790 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: 0.8747 (OUTLIER) cc_final: 0.8001 (ttm-80) REVERT: 3 32 LEU cc_start: 0.8894 (mt) cc_final: 0.8653 (mt) REVERT: 8 58 MET cc_start: 0.8235 (tpt) cc_final: 0.7939 (tmm) REVERT: 8 85 ASP cc_start: 0.9226 (m-30) cc_final: 0.8696 (p0) REVERT: 8 121 MET cc_start: 0.6685 (OUTLIER) cc_final: 0.5551 (pmm) REVERT: 8 155 ASP cc_start: 0.7951 (m-30) cc_final: 0.7398 (t0) REVERT: 8 197 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8165 (mp) REVERT: C 23 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.6953 (pm20) REVERT: C 78 LYS cc_start: 0.8060 (ttmm) cc_final: 0.7734 (ttmt) REVERT: C 161 SER cc_start: 0.8854 (p) cc_final: 0.8580 (m) REVERT: C 261 ASN cc_start: 0.9121 (p0) cc_final: 0.8873 (p0) REVERT: D 83 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7766 (mt-10) REVERT: F 45 MET cc_start: 0.7993 (mmm) cc_final: 0.7535 (mtt) REVERT: F 70 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.8136 (pt0) REVERT: F 157 ARG cc_start: 0.8905 (ptp90) cc_final: 0.8688 (ptp90) REVERT: H 12 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7460 (tm) REVERT: J 99 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7038 (ttp-170) REVERT: J 123 ARG cc_start: 0.9119 (OUTLIER) cc_final: 0.6130 (mmt90) REVERT: L 54 MET cc_start: 0.8364 (tpp) cc_final: 0.8154 (tpt) REVERT: L 63 LEU cc_start: 0.8808 (mt) cc_final: 0.8549 (mt) REVERT: M 18 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7356 (ptp90) REVERT: M 45 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.6969 (mtt90) REVERT: M 106 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8451 (tp) REVERT: N 75 VAL cc_start: 0.8790 (OUTLIER) cc_final: 0.8560 (t) REVERT: N 117 ARG cc_start: 0.7024 (OUTLIER) cc_final: 0.5669 (mtp85) REVERT: P 103 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7388 (mtt-85) REVERT: Q 21 SER cc_start: 0.8693 (m) cc_final: 0.8412 (m) REVERT: R 24 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8300 (mttm) REVERT: T 63 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.7848 (mp10) REVERT: V 23 ARG cc_start: 0.8988 (tpp80) cc_final: 0.8694 (mmm-85) REVERT: V 166 VAL cc_start: 0.7859 (t) cc_final: 0.7654 (m) REVERT: Z 5 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.7873 (tttp) REVERT: d 15 LEU cc_start: 0.8009 (mp) cc_final: 0.7651 (tt) REVERT: d 120 VAL cc_start: 0.7723 (OUTLIER) cc_final: 0.7452 (t) REVERT: d 141 ARG cc_start: 0.7828 (mmt90) cc_final: 0.7533 (mmt90) REVERT: d 147 THR cc_start: 0.6173 (OUTLIER) cc_final: 0.5232 (p) REVERT: d 154 ARG cc_start: 0.6724 (tpt-90) cc_final: 0.6278 (mtp85) REVERT: f 40 VAL cc_start: 0.7795 (OUTLIER) cc_final: 0.7529 (p) REVERT: g 89 VAL cc_start: 0.8913 (OUTLIER) cc_final: 0.8683 (t) REVERT: g 137 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7914 (tpt90) REVERT: h 93 ASN cc_start: 0.8099 (p0) cc_final: 0.7803 (p0) REVERT: h 96 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.7040 (tpt170) REVERT: k 129 ASN cc_start: 0.6770 (OUTLIER) cc_final: 0.6529 (m110) REVERT: l 44 LYS cc_start: 0.7864 (tppt) cc_final: 0.7252 (tptt) REVERT: l 94 ARG cc_start: 0.8048 (mtt-85) cc_final: 0.7744 (mtp85) REVERT: m 79 ARG cc_start: 0.8058 (ttm110) cc_final: 0.7591 (ttp-110) REVERT: m 96 MET cc_start: 0.8254 (mmp) cc_final: 0.7967 (tpp) REVERT: n 19 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8694 (mtt180) REVERT: o 53 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7983 (ttp-170) REVERT: o 64 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.8104 (ttp-110) REVERT: p 39 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7953 (ptt90) REVERT: t 25 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7287 (mtmp) REVERT: x 83 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7797 (tppt) REVERT: x 159 ASN cc_start: 0.8318 (m-40) cc_final: 0.8044 (m-40) REVERT: x 196 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7613 (tt0) REVERT: x 226 ILE cc_start: 0.8492 (mt) cc_final: 0.8182 (mm) REVERT: x 229 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8456 (mt) REVERT: x 365 LYS cc_start: 0.8616 (mtmp) cc_final: 0.7909 (mtmp) REVERT: x 415 VAL cc_start: 0.8887 (p) cc_final: 0.8578 (t) outliers start: 205 outliers final: 135 residues processed: 873 average time/residue: 2.2033 time to fit residues: 2786.0009 Evaluate side-chains 909 residues out of total 5038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 742 time to evaluate : 6.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 27 LEU Chi-restraints excluded: chain 1 residue 25 THR Chi-restraints excluded: chain 2 residue 28 ARG Chi-restraints excluded: chain 2 residue 44 THR Chi-restraints excluded: chain 3 residue 3 LYS Chi-restraints excluded: chain 3 residue 48 THR Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 22 ARG Chi-restraints excluded: chain 6 residue 5 ILE Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 8 residue 41 THR Chi-restraints excluded: chain 8 residue 121 MET Chi-restraints excluded: chain 8 residue 124 VAL Chi-restraints excluded: chain 8 residue 197 LEU Chi-restraints excluded: chain 8 residue 216 THR Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 70 GLN Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain J residue 123 ARG Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 54 ARG Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 108 GLU Chi-restraints excluded: chain K residue 114 ILE 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 36 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 45 ARG Chi-restraints excluded: chain M residue 67 ASN Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 107 SER Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 117 ARG Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 103 ARG Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain S residue 80 VAL Chi-restraints excluded: chain S residue 95 ILE Chi-restraints excluded: chain T residue 37 SER Chi-restraints excluded: chain T residue 56 SER Chi-restraints excluded: chain T residue 63 GLN Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 41 ILE Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain V residue 122 VAL Chi-restraints excluded: chain V residue 126 THR Chi-restraints excluded: chain W residue 59 LEU Chi-restraints excluded: chain W residue 68 GLU Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain X residue 35 THR Chi-restraints excluded: chain Z residue 5 LYS Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 53 ASP Chi-restraints excluded: chain c residue 56 ILE Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 147 LYS Chi-restraints excluded: chain c residue 190 LYS Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 129 SER Chi-restraints excluded: chain d residue 147 THR Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain e residue 154 ILE Chi-restraints excluded: chain e residue 158 SER Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 56 THR Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 89 VAL Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain g residue 137 ARG Chi-restraints excluded: chain g residue 149 ARG Chi-restraints excluded: chain h residue 96 ARG Chi-restraints excluded: chain h residue 132 TRP Chi-restraints excluded: chain i residue 76 VAL Chi-restraints excluded: chain i residue 94 SER Chi-restraints excluded: chain j residue 40 VAL Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain k residue 68 SER Chi-restraints excluded: chain k residue 129 ASN Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 14 ASP Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 79 MET Chi-restraints excluded: chain m residue 5 VAL Chi-restraints excluded: chain m residue 9 LEU Chi-restraints excluded: chain m residue 15 MET Chi-restraints excluded: chain m residue 64 LEU Chi-restraints excluded: chain n residue 19 ARG Chi-restraints excluded: chain n residue 46 GLU Chi-restraints excluded: chain o residue 20 THR Chi-restraints excluded: chain o residue 44 LYS Chi-restraints excluded: chain o residue 45 VAL Chi-restraints excluded: chain o residue 53 ARG Chi-restraints excluded: chain o residue 64 ARG Chi-restraints excluded: chain o residue 71 SER Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 39 ARG Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain q residue 116 THR Chi-restraints excluded: chain r residue 73 GLU Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain t residue 25 LYS Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 57 LYS Chi-restraints excluded: chain x residue 25 THR Chi-restraints excluded: chain x residue 64 LEU Chi-restraints excluded: chain x residue 82 ASP Chi-restraints excluded: chain x residue 83 LYS Chi-restraints excluded: chain x residue 106 VAL Chi-restraints excluded: chain x residue 161 SER Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain x residue 196 GLN Chi-restraints excluded: chain x residue 210 LEU Chi-restraints excluded: chain x residue 212 VAL Chi-restraints excluded: chain x residue 229 LEU Chi-restraints excluded: chain x residue 254 VAL Chi-restraints excluded: chain x residue 321 VAL Chi-restraints excluded: chain x residue 341 SER Chi-restraints excluded: chain x residue 470 THR Chi-restraints excluded: chain x residue 540 LEU Chi-restraints excluded: chain x residue 551 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1075 random chunks: chunk 641 optimal weight: 0.6980 chunk 413 optimal weight: 0.0980 chunk 618 optimal weight: 20.0000 chunk 312 optimal weight: 10.0000 chunk 203 optimal weight: 10.0000 chunk 200 optimal weight: 6.9990 chunk 658 optimal weight: 10.0000 chunk 705 optimal weight: 20.0000 chunk 512 optimal weight: 0.3980 chunk 96 optimal weight: 40.0000 chunk 814 optimal weight: 10.0000 overall best weight: 3.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 44 ASN 3 63 ASN C 113 GLN D 34 ASN E 214 ASN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 39 ASN U 62 GLN ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 126 GLN o 72 GLN t 21 ASN t 84 ASN x 417 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 165129 Z= 0.267 Angle : 0.599 19.206 247155 Z= 0.305 Chirality : 0.036 0.275 31516 Planarity : 0.005 0.124 13409 Dihedral : 22.778 179.517 82986 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.21 % Favored : 93.66 % Rotamer: Outliers : 3.97 % Allowed : 19.06 % Favored : 76.97 % 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: -1.64 (0.10), residues: 6072 helix: -0.55 (0.12), residues: 1891 sheet: -0.52 (0.16), residues: 1125 loop : -1.64 (0.10), residues: 3056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP x 512 HIS 0.009 0.001 HIS S 112 PHE 0.029 0.002 PHE W 45 TYR 0.020 0.001 TYR x 237 ARG 0.015 0.001 ARG U 100 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 951 residues out of total 5038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 751 time to evaluate : 6.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 28 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8003 (ttm-80) REVERT: 3 32 LEU cc_start: 0.8892 (mt) cc_final: 0.8650 (mt) REVERT: 8 58 MET cc_start: 0.8229 (tpt) cc_final: 0.7947 (tmm) REVERT: 8 121 MET cc_start: 0.6886 (OUTLIER) cc_final: 0.5488 (pmm) REVERT: 8 155 ASP cc_start: 0.7979 (m-30) cc_final: 0.7424 (t0) REVERT: 8 197 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8157 (mp) REVERT: 8 207 ARG cc_start: 0.7180 (tpp80) cc_final: 0.6880 (ttp-110) REVERT: C 23 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.6953 (pm20) REVERT: C 78 LYS cc_start: 0.8075 (ttmm) cc_final: 0.7748 (ttmt) REVERT: C 161 SER cc_start: 0.8855 (p) cc_final: 0.8592 (m) REVERT: C 261 ASN cc_start: 0.9122 (p0) cc_final: 0.8865 (p0) REVERT: D 30 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7629 (ttmt) REVERT: D 83 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7764 (mt-10) REVERT: F 45 MET cc_start: 0.7989 (mmm) cc_final: 0.7549 (mtt) REVERT: F 70 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.8127 (pt0) REVERT: F 157 ARG cc_start: 0.8898 (ptp90) cc_final: 0.8671 (ptp90) REVERT: J 99 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7019 (ttp-170) REVERT: J 123 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.6119 (mmt90) REVERT: L 54 MET cc_start: 0.8369 (tpp) cc_final: 0.8061 (tpt) REVERT: L 63 LEU cc_start: 0.8814 (mt) cc_final: 0.8554 (mt) REVERT: L 145 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6236 (mp0) REVERT: M 18 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7370 (ptp90) REVERT: M 45 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.6980 (mtt90) REVERT: M 106 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8462 (tp) REVERT: N 75 VAL cc_start: 0.8802 (OUTLIER) cc_final: 0.8572 (t) REVERT: N 117 ARG cc_start: 0.7037 (OUTLIER) cc_final: 0.5872 (mtp180) REVERT: P 103 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7386 (mtt-85) REVERT: Q 21 SER cc_start: 0.8695 (m) cc_final: 0.8417 (m) REVERT: T 63 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.7863 (mp10) REVERT: V 23 ARG cc_start: 0.9063 (tpp80) cc_final: 0.8692 (mmm-85) REVERT: V 166 VAL cc_start: 0.7860 (t) cc_final: 0.7655 (m) REVERT: X 27 ARG cc_start: 0.9147 (OUTLIER) cc_final: 0.6543 (ppp80) REVERT: Z 5 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.7878 (tttp) REVERT: Z 51 ARG cc_start: 0.8091 (tpp80) cc_final: 0.7878 (tpp80) REVERT: c 87 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.6947 (ttm170) REVERT: d 15 LEU cc_start: 0.8000 (mp) cc_final: 0.7636 (tt) REVERT: d 120 VAL cc_start: 0.7717 (OUTLIER) cc_final: 0.7436 (t) REVERT: d 141 ARG cc_start: 0.7897 (mmt90) cc_final: 0.7601 (mmt90) REVERT: e 83 LYS cc_start: 0.7965 (ptmm) cc_final: 0.7576 (pttm) REVERT: f 40 VAL cc_start: 0.7817 (OUTLIER) cc_final: 0.7562 (p) REVERT: g 89 VAL cc_start: 0.8916 (OUTLIER) cc_final: 0.8689 (t) REVERT: g 137 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7941 (tpt90) REVERT: h 93 ASN cc_start: 0.8109 (p0) cc_final: 0.7815 (p0) REVERT: h 96 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.7126 (tpt170) REVERT: j 88 MET cc_start: 0.7630 (mmm) cc_final: 0.7284 (mmm) REVERT: k 129 ASN cc_start: 0.6770 (OUTLIER) cc_final: 0.6537 (m110) REVERT: l 44 LYS cc_start: 0.7872 (tppt) cc_final: 0.7265 (tptt) REVERT: l 94 ARG cc_start: 0.8047 (mtt-85) cc_final: 0.7755 (mtp85) REVERT: m 79 ARG cc_start: 0.8049 (ttm110) cc_final: 0.7609 (ttp-110) REVERT: m 96 MET cc_start: 0.8255 (mmp) cc_final: 0.7975 (tpp) REVERT: n 19 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8691 (mtt180) REVERT: n 53 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8122 (pp) REVERT: o 53 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7989 (ttp-170) REVERT: o 64 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8128 (ttp-110) REVERT: p 28 ARG cc_start: 0.8475 (ptm-80) cc_final: 0.8095 (ptm160) REVERT: p 39 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7974 (ptt90) REVERT: q 71 LYS cc_start: 0.8375 (mtmt) cc_final: 0.8039 (ttpt) REVERT: t 25 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7289 (mtmp) REVERT: x 83 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7809 (tppt) REVERT: x 159 ASN cc_start: 0.8299 (m-40) cc_final: 0.8031 (m-40) REVERT: x 226 ILE cc_start: 0.8503 (mt) cc_final: 0.8205 (mm) REVERT: x 365 LYS cc_start: 0.8610 (mtmp) cc_final: 0.7903 (mtmp) REVERT: x 415 VAL cc_start: 0.8879 (p) cc_final: 0.8571 (t) outliers start: 200 outliers final: 141 residues processed: 865 average time/residue: 2.2303 time to fit residues: 2781.7049 Evaluate side-chains 911 residues out of total 5038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 738 time to evaluate : 6.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 27 LEU Chi-restraints excluded: chain 1 residue 25 THR Chi-restraints excluded: chain 2 residue 28 ARG Chi-restraints excluded: chain 2 residue 44 THR Chi-restraints excluded: chain 3 residue 3 LYS Chi-restraints excluded: chain 3 residue 48 THR Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 22 ARG Chi-restraints excluded: chain 6 residue 5 ILE Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 39 SER Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 8 residue 41 THR Chi-restraints excluded: chain 8 residue 56 ASP Chi-restraints excluded: chain 8 residue 121 MET Chi-restraints excluded: chain 8 residue 124 VAL Chi-restraints excluded: chain 8 residue 174 VAL Chi-restraints excluded: chain 8 residue 197 LEU Chi-restraints excluded: chain 8 residue 216 THR Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 70 GLN Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain J residue 119 GLN Chi-restraints excluded: chain J residue 123 ARG Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 54 ARG Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 108 GLU Chi-restraints excluded: chain K residue 114 ILE 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 36 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 45 ARG Chi-restraints excluded: chain M residue 67 ASN Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 107 SER Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 117 ARG Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 103 ARG Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain S residue 80 VAL Chi-restraints excluded: chain S residue 95 ILE Chi-restraints excluded: chain T residue 37 SER Chi-restraints excluded: chain T residue 56 SER Chi-restraints excluded: chain T residue 63 GLN Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 39 ASN Chi-restraints excluded: chain U residue 41 ILE Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain V residue 122 VAL Chi-restraints excluded: chain W residue 59 LEU Chi-restraints excluded: chain W residue 68 GLU Chi-restraints excluded: chain X residue 27 ARG Chi-restraints excluded: chain X residue 35 THR Chi-restraints excluded: chain Z residue 5 LYS Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 53 ASP Chi-restraints excluded: chain c residue 56 ILE Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 87 ARG Chi-restraints excluded: chain c residue 137 ILE Chi-restraints excluded: chain c residue 147 LYS Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 129 SER Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain e residue 154 ILE Chi-restraints excluded: chain e residue 158 SER Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 56 THR Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 89 VAL Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain g residue 137 ARG Chi-restraints excluded: chain g residue 149 ARG Chi-restraints excluded: chain h residue 96 ARG Chi-restraints excluded: chain h residue 132 TRP Chi-restraints excluded: chain i residue 76 VAL Chi-restraints excluded: chain j residue 40 VAL Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain k residue 68 SER Chi-restraints excluded: chain k residue 129 ASN Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 79 MET Chi-restraints excluded: chain m residue 5 VAL Chi-restraints excluded: chain m residue 9 LEU Chi-restraints excluded: chain m residue 15 MET Chi-restraints excluded: chain m residue 64 LEU Chi-restraints excluded: chain n residue 19 ARG Chi-restraints excluded: chain n residue 46 GLU Chi-restraints excluded: chain n residue 53 LEU Chi-restraints excluded: chain o residue 20 THR Chi-restraints excluded: chain o residue 44 LYS Chi-restraints excluded: chain o residue 45 VAL Chi-restraints excluded: chain o residue 53 ARG Chi-restraints excluded: chain o residue 64 ARG Chi-restraints excluded: chain o residue 71 SER Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 39 ARG Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain q residue 116 THR Chi-restraints excluded: chain r residue 73 GLU Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain t residue 25 LYS Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 57 LYS Chi-restraints excluded: chain x residue 25 THR Chi-restraints excluded: chain x residue 64 LEU Chi-restraints excluded: chain x residue 82 ASP Chi-restraints excluded: chain x residue 83 LYS Chi-restraints excluded: chain x residue 106 VAL Chi-restraints excluded: chain x residue 161 SER Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain x residue 210 LEU Chi-restraints excluded: chain x residue 212 VAL Chi-restraints excluded: chain x residue 254 VAL Chi-restraints excluded: chain x residue 321 VAL Chi-restraints excluded: chain x residue 337 ILE Chi-restraints excluded: chain x residue 341 SER Chi-restraints excluded: chain x residue 377 SER Chi-restraints excluded: chain x residue 390 ASP Chi-restraints excluded: chain x residue 470 THR Chi-restraints excluded: chain x residue 540 LEU Chi-restraints excluded: chain x residue 551 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1075 random chunks: chunk 942 optimal weight: 0.2980 chunk 992 optimal weight: 10.0000 chunk 905 optimal weight: 3.9990 chunk 965 optimal weight: 1.9990 chunk 581 optimal weight: 0.8980 chunk 420 optimal weight: 0.5980 chunk 758 optimal weight: 20.0000 chunk 296 optimal weight: 10.0000 chunk 872 optimal weight: 4.9990 chunk 913 optimal weight: 0.9980 chunk 962 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 44 ASN 3 63 ASN C 113 GLN E 214 ASN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 13 HIS P 79 ASN ** Q 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 62 GLN ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 54 GLN d 95 ASN k 126 GLN o 72 GLN t 84 ASN x 417 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.099 165129 Z= 0.129 Angle : 0.550 18.696 247155 Z= 0.284 Chirality : 0.033 0.445 31516 Planarity : 0.005 0.121 13409 Dihedral : 22.830 178.820 82986 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.67 % Favored : 94.22 % Rotamer: Outliers : 2.72 % Allowed : 20.46 % Favored : 76.82 % Cbeta Deviations : 0.02 % 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: -1.43 (0.10), residues: 6072 helix: -0.33 (0.12), residues: 1900 sheet: -0.37 (0.16), residues: 1117 loop : -1.56 (0.10), residues: 3055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP x 512 HIS 0.004 0.001 HIS 1 51 PHE 0.022 0.001 PHE i 85 TYR 0.017 0.001 TYR c 23 ARG 0.035 0.000 ARG U 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 5038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 754 time to evaluate : 6.787 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: 3 32 LEU cc_start: 0.8880 (mt) cc_final: 0.8640 (mt) REVERT: 8 58 MET cc_start: 0.8213 (tpt) cc_final: 0.7944 (tmm) REVERT: 8 121 MET cc_start: 0.6895 (OUTLIER) cc_final: 0.5509 (pmm) REVERT: 8 155 ASP cc_start: 0.7978 (m-30) cc_final: 0.7420 (t70) REVERT: 8 197 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8135 (mp) REVERT: 8 207 ARG cc_start: 0.7173 (tpp80) cc_final: 0.6877 (ttp-110) REVERT: C 23 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.6920 (pm20) REVERT: C 78 LYS cc_start: 0.8041 (ttmm) cc_final: 0.7717 (ttmt) REVERT: C 161 SER cc_start: 0.8806 (p) cc_final: 0.8562 (m) REVERT: C 261 ASN cc_start: 0.9101 (p0) cc_final: 0.8822 (p0) REVERT: D 83 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7735 (mt-10) REVERT: F 45 MET cc_start: 0.7949 (mmm) cc_final: 0.7563 (mtt) REVERT: F 70 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.8101 (pt0) REVERT: J 99 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.6936 (ttp-170) REVERT: L 54 MET cc_start: 0.8380 (tpp) cc_final: 0.8102 (tpt) REVERT: L 63 LEU cc_start: 0.8779 (mt) cc_final: 0.8521 (mt) REVERT: M 18 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7342 (ptp90) REVERT: M 45 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.6799 (mtt90) REVERT: M 94 VAL cc_start: 0.8522 (OUTLIER) cc_final: 0.8258 (m) REVERT: N 14 SER cc_start: 0.8988 (t) cc_final: 0.8751 (t) REVERT: N 75 VAL cc_start: 0.8756 (OUTLIER) cc_final: 0.8535 (t) REVERT: N 117 ARG cc_start: 0.6936 (OUTLIER) cc_final: 0.5767 (mtp180) REVERT: O 34 VAL cc_start: 0.8510 (t) cc_final: 0.8205 (m) REVERT: P 103 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7380 (mtt-85) REVERT: Q 21 SER cc_start: 0.8680 (m) cc_final: 0.8404 (m) REVERT: T 63 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.7854 (mp10) REVERT: V 23 ARG cc_start: 0.9073 (tpp80) cc_final: 0.8683 (mmm-85) REVERT: Z 51 ARG cc_start: 0.8061 (tpp80) cc_final: 0.7855 (tpp80) REVERT: d 15 LEU cc_start: 0.7957 (mp) cc_final: 0.7601 (tt) REVERT: d 141 ARG cc_start: 0.7864 (mmt90) cc_final: 0.7598 (mmt90) REVERT: e 83 LYS cc_start: 0.7974 (ptmm) cc_final: 0.7596 (pttm) REVERT: f 40 VAL cc_start: 0.7790 (OUTLIER) cc_final: 0.7529 (p) REVERT: g 76 ARG cc_start: 0.7972 (ttp80) cc_final: 0.7672 (ttp-170) REVERT: g 89 VAL cc_start: 0.8885 (OUTLIER) cc_final: 0.8669 (t) REVERT: h 93 ASN cc_start: 0.8057 (p0) cc_final: 0.7793 (p0) REVERT: i 70 LYS cc_start: 0.8626 (ptpt) cc_final: 0.8386 (ptpt) REVERT: j 88 MET cc_start: 0.7631 (mmm) cc_final: 0.7290 (mmm) REVERT: k 129 ASN cc_start: 0.6723 (OUTLIER) cc_final: 0.6496 (m110) REVERT: l 44 LYS cc_start: 0.7984 (tppt) cc_final: 0.7313 (tptt) REVERT: l 94 ARG cc_start: 0.8013 (mtt-85) cc_final: 0.7725 (mtp85) REVERT: m 79 ARG cc_start: 0.8045 (ttm110) cc_final: 0.7594 (ttp-110) REVERT: m 96 MET cc_start: 0.8226 (mmp) cc_final: 0.7956 (tpp) REVERT: o 53 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7945 (ttp-170) REVERT: o 64 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.8107 (ttp-110) REVERT: p 39 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8010 (ptt90) REVERT: q 71 LYS cc_start: 0.8392 (mtmt) cc_final: 0.7975 (ttpt) REVERT: x 83 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7866 (ttmt) REVERT: x 159 ASN cc_start: 0.8272 (m-40) cc_final: 0.8000 (m-40) REVERT: x 226 ILE cc_start: 0.8452 (mt) cc_final: 0.8169 (mm) REVERT: x 229 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8421 (mt) REVERT: x 365 LYS cc_start: 0.8595 (mtmp) cc_final: 0.8342 (mtmt) outliers start: 137 outliers final: 91 residues processed: 832 average time/residue: 2.2439 time to fit residues: 2685.7725 Evaluate side-chains 845 residues out of total 5038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 734 time to evaluate : 5.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 25 THR Chi-restraints excluded: chain 3 residue 3 LYS Chi-restraints excluded: chain 3 residue 48 THR Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 6 residue 5 ILE Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 8 residue 41 THR Chi-restraints excluded: chain 8 residue 121 MET Chi-restraints excluded: chain 8 residue 124 VAL Chi-restraints excluded: chain 8 residue 174 VAL Chi-restraints excluded: chain 8 residue 197 LEU Chi-restraints excluded: chain 8 residue 216 THR Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 70 GLN Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 108 GLU Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 45 ARG Chi-restraints excluded: chain M residue 67 ASN Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 117 ARG Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 103 ARG Chi-restraints excluded: chain S residue 80 VAL Chi-restraints excluded: chain S residue 95 ILE Chi-restraints excluded: chain T residue 56 SER Chi-restraints excluded: chain T residue 63 GLN Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 122 VAL Chi-restraints excluded: chain W residue 59 LEU Chi-restraints excluded: chain W residue 68 GLU Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain c residue 53 ASP Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 147 LYS Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain e residue 154 ILE Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 64 ASP Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain g residue 56 THR Chi-restraints excluded: chain g residue 89 VAL Chi-restraints excluded: chain i residue 76 VAL Chi-restraints excluded: chain i residue 94 SER Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 68 SER Chi-restraints excluded: chain k residue 129 ASN Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain m residue 5 VAL Chi-restraints excluded: chain m residue 9 LEU Chi-restraints excluded: chain m residue 15 MET Chi-restraints excluded: chain m residue 64 LEU Chi-restraints excluded: chain n residue 46 GLU Chi-restraints excluded: chain o residue 45 VAL Chi-restraints excluded: chain o residue 53 ARG Chi-restraints excluded: chain o residue 64 ARG Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 39 ARG Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain q residue 116 THR Chi-restraints excluded: chain r residue 73 GLU Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain t residue 57 LYS Chi-restraints excluded: chain x residue 25 THR Chi-restraints excluded: chain x residue 64 LEU Chi-restraints excluded: chain x residue 82 ASP Chi-restraints excluded: chain x residue 83 LYS Chi-restraints excluded: chain x residue 106 VAL Chi-restraints excluded: chain x residue 161 SER Chi-restraints excluded: chain x residue 212 VAL Chi-restraints excluded: chain x residue 229 LEU Chi-restraints excluded: chain x residue 262 LEU Chi-restraints excluded: chain x residue 310 GLN Chi-restraints excluded: chain x residue 341 SER Chi-restraints excluded: chain x residue 390 ASP Chi-restraints excluded: chain x residue 470 THR Chi-restraints excluded: chain x residue 540 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1075 random chunks: chunk 634 optimal weight: 4.9990 chunk 1020 optimal weight: 0.0270 chunk 623 optimal weight: 8.9990 chunk 484 optimal weight: 0.8980 chunk 709 optimal weight: 10.0000 chunk 1070 optimal weight: 10.0000 chunk 985 optimal weight: 5.9990 chunk 852 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 chunk 658 optimal weight: 10.0000 chunk 522 optimal weight: 10.0000 overall best weight: 4.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 44 ASN 3 63 ASN C 113 GLN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 62 GLN ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 40 GLN i 52 ASN k 126 GLN o 72 GLN t 84 ASN x 417 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 165129 Z= 0.302 Angle : 0.612 18.821 247155 Z= 0.310 Chirality : 0.037 0.274 31516 Planarity : 0.005 0.125 13409 Dihedral : 22.745 179.556 82986 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.18 % Favored : 93.69 % Rotamer: Outliers : 2.52 % Allowed : 20.78 % Favored : 76.70 % 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: -1.44 (0.10), residues: 6072 helix: -0.32 (0.12), residues: 1887 sheet: -0.43 (0.16), residues: 1122 loop : -1.55 (0.10), residues: 3063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP x 512 HIS 0.009 0.001 HIS S 112 PHE 0.028 0.002 PHE W 45 TYR 0.017 0.001 TYR x 237 ARG 0.014 0.001 ARG U 100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 883 residues out of total 5038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 756 time to evaluate : 6.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 32 LEU cc_start: 0.8898 (mt) cc_final: 0.8651 (mt) REVERT: 8 58 MET cc_start: 0.8220 (tpt) cc_final: 0.7944 (tmm) REVERT: 8 85 ASP cc_start: 0.9242 (m-30) cc_final: 0.8925 (m-30) REVERT: 8 121 MET cc_start: 0.6842 (OUTLIER) cc_final: 0.5488 (pmm) REVERT: 8 155 ASP cc_start: 0.7993 (m-30) cc_final: 0.7455 (t0) REVERT: 8 197 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8120 (mp) REVERT: 8 207 ARG cc_start: 0.7286 (tpp80) cc_final: 0.6966 (ttp-110) REVERT: C 23 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.6935 (pm20) REVERT: C 78 LYS cc_start: 0.8084 (ttmm) cc_final: 0.7764 (ttmt) REVERT: C 161 SER cc_start: 0.8839 (p) cc_final: 0.8590 (m) REVERT: C 261 ASN cc_start: 0.9125 (p0) cc_final: 0.8877 (p0) REVERT: D 83 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7766 (mt-10) REVERT: F 45 MET cc_start: 0.7972 (mmm) cc_final: 0.7588 (mtt) REVERT: F 70 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8118 (pt0) REVERT: J 99 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7025 (ttp-170) REVERT: L 63 LEU cc_start: 0.8818 (mt) cc_final: 0.8558 (mt) REVERT: L 145 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6289 (mp0) REVERT: M 18 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7394 (ptp90) REVERT: M 45 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.6979 (mtt90) REVERT: M 94 VAL cc_start: 0.8594 (OUTLIER) cc_final: 0.8349 (m) REVERT: N 75 VAL cc_start: 0.8811 (OUTLIER) cc_final: 0.8574 (t) REVERT: P 103 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7408 (mtt-85) REVERT: Q 21 SER cc_start: 0.8694 (m) cc_final: 0.8420 (m) REVERT: Q 59 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8291 (ttmm) REVERT: T 63 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.7871 (mp10) REVERT: V 23 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8863 (mmm-85) REVERT: X 27 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.6508 (ppp80) REVERT: Z 51 ARG cc_start: 0.8081 (tpp80) cc_final: 0.7869 (tpp80) REVERT: c 133 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.6940 (mpp) REVERT: d 15 LEU cc_start: 0.7986 (mp) cc_final: 0.7630 (tt) REVERT: d 141 ARG cc_start: 0.7937 (mmt90) cc_final: 0.7439 (mmt90) REVERT: e 83 LYS cc_start: 0.8013 (ptmm) cc_final: 0.7648 (pttm) REVERT: f 40 VAL cc_start: 0.7841 (OUTLIER) cc_final: 0.7569 (p) REVERT: g 76 ARG cc_start: 0.8007 (ttp80) cc_final: 0.7713 (ttp-170) REVERT: g 89 VAL cc_start: 0.8897 (OUTLIER) cc_final: 0.8686 (t) REVERT: h 93 ASN cc_start: 0.8128 (p0) cc_final: 0.7822 (p0) REVERT: j 88 MET cc_start: 0.7731 (mmm) cc_final: 0.7389 (mmm) REVERT: k 129 ASN cc_start: 0.6788 (OUTLIER) cc_final: 0.6557 (m110) REVERT: l 44 LYS cc_start: 0.7931 (tppt) cc_final: 0.7295 (tptt) REVERT: l 94 ARG cc_start: 0.8047 (mtt-85) cc_final: 0.7755 (mtp85) REVERT: m 79 ARG cc_start: 0.8067 (ttm110) cc_final: 0.7633 (ttp-110) REVERT: o 53 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7996 (ttp-170) REVERT: o 64 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8139 (ttp-110) REVERT: p 28 ARG cc_start: 0.8448 (ptm-80) cc_final: 0.8108 (ptm160) REVERT: p 39 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7991 (ptt90) REVERT: q 71 LYS cc_start: 0.8386 (mtmt) cc_final: 0.7970 (ttpt) REVERT: t 25 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7398 (mtmp) REVERT: x 83 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7902 (ttmt) REVERT: x 159 ASN cc_start: 0.8286 (m-40) cc_final: 0.8015 (m-40) REVERT: x 226 ILE cc_start: 0.8512 (mt) cc_final: 0.8205 (mm) REVERT: x 229 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8451 (mt) REVERT: x 365 LYS cc_start: 0.8605 (mtmp) cc_final: 0.7895 (mtmp) REVERT: x 415 VAL cc_start: 0.8867 (p) cc_final: 0.8562 (t) outliers start: 127 outliers final: 91 residues processed: 830 average time/residue: 2.2428 time to fit residues: 2689.0466 Evaluate side-chains 863 residues out of total 5038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 747 time to evaluate : 6.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 25 THR Chi-restraints excluded: chain 3 residue 3 LYS Chi-restraints excluded: chain 3 residue 48 THR Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 6 residue 5 ILE Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 39 SER Chi-restraints excluded: chain 8 residue 41 THR Chi-restraints excluded: chain 8 residue 121 MET Chi-restraints excluded: chain 8 residue 124 VAL Chi-restraints excluded: chain 8 residue 174 VAL Chi-restraints excluded: chain 8 residue 197 LEU Chi-restraints excluded: chain 8 residue 216 THR Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 70 GLN Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 108 GLU Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 45 ARG Chi-restraints excluded: chain M residue 67 ASN Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 103 ARG Chi-restraints excluded: chain Q residue 59 LYS Chi-restraints excluded: chain S residue 80 VAL Chi-restraints excluded: chain S residue 95 ILE Chi-restraints excluded: chain T residue 56 SER Chi-restraints excluded: chain T residue 63 GLN Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain V residue 23 ARG Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain V residue 122 VAL Chi-restraints excluded: chain V residue 126 THR Chi-restraints excluded: chain W residue 59 LEU Chi-restraints excluded: chain X residue 27 ARG Chi-restraints excluded: chain X residue 35 THR Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain c residue 53 ASP Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 133 MET Chi-restraints excluded: chain c residue 147 LYS Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain d residue 129 SER Chi-restraints excluded: chain e residue 154 ILE Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain g residue 56 THR Chi-restraints excluded: chain g residue 89 VAL Chi-restraints excluded: chain i residue 76 VAL Chi-restraints excluded: chain i residue 94 SER Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 68 SER Chi-restraints excluded: chain k residue 129 ASN Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain m residue 5 VAL Chi-restraints excluded: chain m residue 9 LEU Chi-restraints excluded: chain m residue 15 MET Chi-restraints excluded: chain m residue 64 LEU Chi-restraints excluded: chain n residue 46 GLU Chi-restraints excluded: chain o residue 45 VAL Chi-restraints excluded: chain o residue 53 ARG Chi-restraints excluded: chain o residue 64 ARG Chi-restraints excluded: chain p residue 39 ARG Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain q residue 116 THR Chi-restraints excluded: chain r residue 73 GLU Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain t residue 25 LYS Chi-restraints excluded: chain t residue 57 LYS Chi-restraints excluded: chain x residue 25 THR Chi-restraints excluded: chain x residue 64 LEU Chi-restraints excluded: chain x residue 82 ASP Chi-restraints excluded: chain x residue 83 LYS Chi-restraints excluded: chain x residue 106 VAL Chi-restraints excluded: chain x residue 161 SER Chi-restraints excluded: chain x residue 212 VAL Chi-restraints excluded: chain x residue 229 LEU Chi-restraints excluded: chain x residue 341 SER Chi-restraints excluded: chain x residue 390 ASP Chi-restraints excluded: chain x residue 470 THR Chi-restraints excluded: chain x residue 482 GLU Chi-restraints excluded: chain x residue 540 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1075 random chunks: chunk 677 optimal weight: 20.0000 chunk 908 optimal weight: 0.9980 chunk 261 optimal weight: 30.0000 chunk 786 optimal weight: 10.0000 chunk 125 optimal weight: 8.9990 chunk 236 optimal weight: 7.9990 chunk 854 optimal weight: 7.9990 chunk 357 optimal weight: 8.9990 chunk 877 optimal weight: 0.0000 chunk 108 optimal weight: 8.9990 chunk 157 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 44 ASN 3 63 ASN C 113 GLN E 214 ASN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 62 GLN ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 52 ASN k 126 GLN o 72 GLN t 21 ASN t 84 ASN x 417 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.112668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.074898 restraints weight = 216326.730| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 0.90 r_work: 0.2686 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 165129 Z= 0.357 Angle : 0.651 18.759 247155 Z= 0.329 Chirality : 0.039 0.285 31516 Planarity : 0.005 0.126 13409 Dihedral : 22.765 179.660 82986 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.44 % Favored : 93.45 % Rotamer: Outliers : 2.92 % Allowed : 20.46 % Favored : 76.62 % 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: -1.48 (0.10), residues: 6072 helix: -0.37 (0.12), residues: 1888 sheet: -0.42 (0.16), residues: 1113 loop : -1.58 (0.10), residues: 3071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP x 512 HIS 0.011 0.001 HIS S 112 PHE 0.032 0.002 PHE W 45 TYR 0.022 0.002 TYR x 237 ARG 0.011 0.001 ARG m 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 44942.74 seconds wall clock time: 781 minutes 29.94 seconds (46889.94 seconds total)