Starting phenix.real_space_refine on Fri Jun 28 03:30:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgt_19148/06_2024/8rgt_19148_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgt_19148/06_2024/8rgt_19148.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgt_19148/06_2024/8rgt_19148_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgt_19148/06_2024/8rgt_19148_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgt_19148/06_2024/8rgt_19148_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgt_19148/06_2024/8rgt_19148.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgt_19148/06_2024/8rgt_19148.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgt_19148/06_2024/8rgt_19148_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgt_19148/06_2024/8rgt_19148_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.007 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: 9 Type Number sf(0) Gaussians K 1 8.98 5 Fe 28 7.16 5 Zn 1 6.06 5 P 42 5.49 5 Mg 1 5.21 5 S 492 5.16 5 C 43408 2.51 5 N 11108 2.21 5 O 12042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "6 ASP 45": "OD1" <-> "OD2" Residue "6 PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 94": "OD1" <-> "OD2" Residue "6 GLU 119": "OE1" <-> "OE2" Residue "6 ASP 147": "OD1" <-> "OD2" Residue "6 ASP 153": "OD1" <-> "OD2" Residue "D GLU 226": "OE1" <-> "OE2" Residue "2 GLU 204": "OE1" <-> "OE2" Residue "1 TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 170": "OD1" <-> "OD2" Residue "1 ASP 292": "OD1" <-> "OD2" Residue "3 TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 441": "OE1" <-> "OE2" Residue "3 TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 86": "OE1" <-> "OE2" Residue "P PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 285": "OE1" <-> "OE2" Residue "Q GLU 15": "OE1" <-> "OE2" Residue "Q TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 51": "OE1" <-> "OE2" Residue "S GLU 56": "OE1" <-> "OE2" Residue "T ASP 13": "OD1" <-> "OD2" Residue "T ASP 43": "OD1" <-> "OD2" Residue "W ASP 26": "OD1" <-> "OD2" Residue "W GLU 29": "OE1" <-> "OE2" Residue "W GLU 67": "OE1" <-> "OE2" Residue "W ASP 82": "OD1" <-> "OD2" Residue "W GLU 91": "OE1" <-> "OE2" Residue "W GLU 113": "OE1" <-> "OE2" Residue "W ASP 119": "OD1" <-> "OD2" Residue "q ASP 32": "OD1" <-> "OD2" Residue "q PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 78": "OD1" <-> "OD2" Residue "q GLU 136": "OE1" <-> "OE2" Residue "A PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 24": "OE1" <-> "OE2" Residue "H GLU 143": "OE1" <-> "OE2" Residue "H PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 127": "OE1" <-> "OE2" Residue "J GLU 136": "OE1" <-> "OE2" Residue "J GLU 168": "OE1" <-> "OE2" Residue "K PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 60": "OE1" <-> "OE2" Residue "L TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 145": "OE1" <-> "OE2" Residue "L GLU 197": "OE1" <-> "OE2" Residue "L PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 46": "OD1" <-> "OD2" Residue "M GLU 47": "OE1" <-> "OE2" Residue "M ASP 59": "OD1" <-> "OD2" Residue "M ASP 87": "OD1" <-> "OD2" Residue "M GLU 123": "OE1" <-> "OE2" Residue "M ASP 187": "OD1" <-> "OD2" Residue "M TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 335": "OE1" <-> "OE2" Residue "N GLU 34": "OE1" <-> "OE2" Residue "N GLU 117": "OE1" <-> "OE2" Residue "N TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 162": "OE1" <-> "OE2" Residue "U GLU 49": "OE1" <-> "OE2" Residue "X ASP 51": "OD1" <-> "OD2" Residue "X ASP 120": "OD1" <-> "OD2" Residue "Y GLU 81": "OE1" <-> "OE2" Residue "Y TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 8": "OD1" <-> "OD2" Residue "Z TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 63": "OD1" <-> "OD2" Residue "a GLU 4": "OE1" <-> "OE2" Residue "a TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 35": "OE1" <-> "OE2" Residue "c GLU 6": "OE1" <-> "OE2" Residue "c GLU 37": "OE1" <-> "OE2" Residue "c TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 9": "OE1" <-> "OE2" Residue "d TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 87": "OD1" <-> "OD2" Residue "d ASP 100": "OD1" <-> "OD2" Residue "e ASP 14": "OD1" <-> "OD2" Residue "e PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 36": "OE1" <-> "OE2" Residue "e GLU 38": "OE1" <-> "OE2" Residue "e GLU 63": "OE1" <-> "OE2" Residue "e GLU 88": "OE1" <-> "OE2" Residue "f GLU 9": "OE1" <-> "OE2" Residue "f ASP 30": "OD1" <-> "OD2" Residue "f GLU 47": "OE1" <-> "OE2" Residue "f GLU 52": "OE1" <-> "OE2" Residue "g TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 107": "OE1" <-> "OE2" Residue "i GLU 16": "OE1" <-> "OE2" Residue "i ASP 24": "OD1" <-> "OD2" Residue "i GLU 26": "OE1" <-> "OE2" Residue "j ASP 43": "OD1" <-> "OD2" Residue "j ASP 55": "OD1" <-> "OD2" Residue "j ASP 61": "OD1" <-> "OD2" Residue "j GLU 63": "OE1" <-> "OE2" Residue "k GLU 20": "OE1" <-> "OE2" Residue "k GLU 30": "OE1" <-> "OE2" Residue "k GLU 35": "OE1" <-> "OE2" Residue "k ASP 48": "OD1" <-> "OD2" Residue "k TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 31": "OE1" <-> "OE2" Residue "l GLU 56": "OE1" <-> "OE2" Residue "l GLU 74": "OE1" <-> "OE2" Residue "m ASP 61": "OD1" <-> "OD2" Residue "m ASP 107": "OD1" <-> "OD2" Residue "m GLU 112": "OE1" <-> "OE2" Residue "n ASP 55": "OD1" <-> "OD2" Residue "n TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 133": "OD1" <-> "OD2" Residue "o ASP 11": "OD1" <-> "OD2" Residue "o ASP 27": "OD1" <-> "OD2" Residue "o ASP 56": "OD1" <-> "OD2" Residue "o TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 100": "OE1" <-> "OE2" Residue "o GLU 102": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 67123 Number of models: 1 Model: "" Number of chains: 67 Chain: "6" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1258 Classifications: {'peptide': 157} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 146} Chain: "C" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1730 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "D" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3371 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 25, 'TRANS': 392} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1660 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 192} Chain: "1" Number of atoms: 3321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3321 Classifications: {'peptide': 430} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 408} Chain: "3" Number of atoms: 5305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5305 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 31, 'TRANS': 658} Chain: "9" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1431 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 168} Chain: "P" Number of atoms: 2513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2513 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 15, 'TRANS': 298} Chain breaks: 2 Chain: "Q" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1022 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "7" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 758 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "S" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 671 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "T" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "V" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 923 Classifications: {'peptide': 113} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 104} Chain: "W" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 970 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "q" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1209 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 11, 'TRANS': 133} Chain: "r" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 781 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 11, 'TRANS': 85} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "s" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 351 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 3, 'TRANS': 38} Chain: "A" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 771 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'FME:plan-2': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 2 Chain: "H" Number of atoms: 2452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2452 Classifications: {'peptide': 306} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1240 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 737 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 4800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4800 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 26, 'TRANS': 579} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3632 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 2703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2703 Classifications: {'peptide': 345} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 324} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2607 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 16, 'TRANS': 303} Chain: "U" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 706 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "X" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1396 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 11, 'TRANS': 159} Chain: "Y" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1037 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "Z" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1167 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "a" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 572 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "b" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 643 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 11, 'TRANS': 70} Chain: "c" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 398 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "d" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 996 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 12, 'TRANS': 107} Chain: "e" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 877 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "f" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 456 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "g" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 850 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 8, 'TRANS': 92} Chain: "h" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1166 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 11, 'TRANS': 127} Chain: "i" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 897 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 94} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'SAC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 562 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 6, 'TRANS': 58} Chain: "k" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 626 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain: "l" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1323 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 18, 'TRANS': 138} Chain: "m" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1050 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 11, 'TRANS': 114} Chain: "n" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1541 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 16, 'TRANS': 161} Chain: "o" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1014 Classifications: {'peptide': 118} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 110} Chain: "p" Number of atoms: 1430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1430 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 10, 'TRANS': 158} Chain: "6" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'3PE': 1, 'PC1': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Chain: "2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "3" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' K': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "9" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 117 Unusual residues: {'PC1': 2, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "P" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Chain: "r" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 48 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "L" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 222 Unusual residues: {'3PE': 3, 'CDL': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "M" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 141 Unusual residues: {'3PE': 2, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "N" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 128 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Chain: "O" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'DGT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Chain: "d" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 130 Unusual residues: {'3PE': 2, 'CDL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 72 Chain: "h" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 121 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Chain: "i" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "m" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 766 SG CYS 6 129 63.291 129.958 108.942 1.00 68.05 S ATOM 269 SG CYS 6 65 58.049 127.363 105.862 1.00 53.74 S ATOM 263 SG CYS 6 64 59.673 124.586 111.197 1.00 60.80 S ATOM 996 SG CYS 6 159 57.628 130.641 111.526 1.00 70.01 S ATOM 7165 SG CYS 2 103 26.368 167.224 163.213 1.00 77.35 S ATOM 7199 SG CYS 2 108 23.933 166.377 165.569 1.00 58.72 S ATOM 7483 SG CYS 2 144 30.609 166.497 166.657 1.00103.20 S ATOM 7506 SG CYS 2 148 28.419 165.517 169.309 1.00 91.11 S ATOM 10744 SG CYS 1 365 43.203 158.245 157.182 1.00 59.36 S ATOM 11066 SG CYS 1 405 46.425 160.885 162.182 1.00 70.11 S ATOM 10724 SG CYS 1 362 48.640 158.017 156.424 1.00 57.41 S ATOM 10705 SG CYS 1 359 46.361 164.308 156.916 1.00 78.63 S ATOM 12170 SG CYS 3 114 55.209 153.342 137.256 1.00 62.26 S ATOM 12109 SG CYS 3 105 50.163 150.859 133.898 1.00 79.71 S ATOM 12130 SG CYS 3 108 52.480 156.862 132.628 1.00 39.48 S ATOM 12502 SG CYS 3 156 56.109 161.396 145.353 1.00 55.53 S ATOM 12479 SG CYS 3 153 50.237 163.328 142.823 1.00 43.48 S ATOM 12526 SG CYS 3 159 55.201 167.480 143.175 1.00 63.53 S ATOM 12855 SG CYS 3 203 55.591 162.338 139.193 1.00 60.32 S ATOM 11616 SG CYS 3 41 57.569 159.102 151.486 1.00 56.55 S ATOM 11702 SG CYS 3 52 55.992 155.792 150.314 1.00 61.40 S ATOM 11727 SG CYS 3 55 59.389 153.877 154.899 1.00 84.69 S ATOM 11828 SG CYS 3 69 60.295 157.304 155.067 1.00 84.74 S ATOM 17616 SG CYS 9 121 54.646 135.371 117.864 1.00 53.52 S ATOM 17590 SG CYS 9 118 54.656 137.727 111.707 1.00 58.28 S ATOM 17637 SG CYS 9 124 51.352 140.658 116.564 1.00 49.12 S ATOM 17364 SG CYS 9 89 57.914 140.792 116.329 1.00 71.77 S ATOM 17666 SG CYS 9 128 46.873 146.281 120.444 1.00 56.07 S ATOM 17336 SG CYS 9 85 53.134 146.509 118.615 1.00 67.56 S ATOM 17294 SG CYS 9 79 49.431 151.719 117.665 1.00 45.50 S ATOM 17313 SG CYS 9 82 50.828 149.469 123.849 1.00 50.47 S ATOM 22091 SG CYS 7 59 35.540 156.402 126.541 1.00 62.95 S ATOM 22267 SG CYS 7 84 39.299 157.244 126.242 1.00 59.92 S ATOM 22289 SG CYS 7 87 37.254 156.705 123.558 1.00 70.90 S Time building chain proxies: 26.62, per 1000 atoms: 0.40 Number of scatterers: 67123 At special positions: 0 Unit cell: (237.44, 210.94, 212, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 K 1 19.00 S 492 16.00 P 42 15.00 Mg 1 11.99 O 12042 8.00 N 11108 7.00 C 43408 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS X 45 " - pdb=" SG CYS X 55 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 17 " - pdb=" SG CYS Y 74 " distance=2.02 Simple disulfide: pdb=" SG CYS Y 94 " - pdb=" SG CYS Y 114 " distance=2.03 Simple disulfide: pdb=" SG CYS e 32 " - pdb=" SG CYS e 65 " distance=2.03 Simple disulfide: pdb=" SG CYS e 42 " - pdb=" SG CYS e 55 " distance=2.03 Simple disulfide: pdb=" SG CYS o 58 " - pdb=" SG CYS o 89 " distance=2.03 Simple disulfide: pdb=" SG CYS o 68 " - pdb=" SG CYS o 79 " distance=2.03 Simple disulfide: pdb=" SG CYS p 112 " - pdb=" SG CYS p 124 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 22.85 Conformation dependent library (CDL) restraints added in 8.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES 2 301 " pdb="FE1 FES 2 301 " - pdb=" SG CYS 2 103 " pdb="FE2 FES 2 301 " - pdb=" SG CYS 2 148 " pdb="FE2 FES 2 301 " - pdb=" SG CYS 2 144 " pdb="FE1 FES 2 301 " - pdb=" SG CYS 2 108 " pdb=" FES 3 803 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 55 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 52 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 69 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 41 " pdb=" SF4 1 502 " pdb="FE1 SF4 1 502 " - pdb=" SG CYS 1 365 " pdb="FE4 SF4 1 502 " - pdb=" SG CYS 1 359 " pdb="FE2 SF4 1 502 " - pdb=" SG CYS 1 405 " pdb="FE3 SF4 1 502 " - pdb=" SG CYS 1 362 " pdb=" SF4 3 801 " pdb="FE3 SF4 3 801 " - pdb=" NE2 HIS 3 101 " pdb="FE4 SF4 3 801 " - pdb=" SG CYS 3 108 " pdb="FE2 SF4 3 801 " - pdb=" SG CYS 3 105 " pdb="FE1 SF4 3 801 " - pdb=" SG CYS 3 114 " pdb=" SF4 3 802 " pdb="FE4 SF4 3 802 " - pdb=" SG CYS 3 203 " pdb="FE3 SF4 3 802 " - pdb=" SG CYS 3 159 " pdb="FE2 SF4 3 802 " - pdb=" SG CYS 3 153 " pdb="FE1 SF4 3 802 " - pdb=" SG CYS 3 156 " pdb=" SF4 6 201 " pdb="FE1 SF4 6 201 " - pdb=" SG CYS 6 129 " pdb="FE4 SF4 6 201 " - pdb=" SG CYS 6 159 " pdb="FE3 SF4 6 201 " - pdb=" SG CYS 6 64 " pdb="FE2 SF4 6 201 " - pdb=" SG CYS 6 65 " pdb=" SF4 9 201 " pdb="FE3 SF4 9 201 " - pdb=" SG CYS 9 124 " pdb="FE2 SF4 9 201 " - pdb=" SG CYS 9 118 " pdb="FE4 SF4 9 201 " - pdb=" SG CYS 9 89 " pdb="FE1 SF4 9 201 " - pdb=" SG CYS 9 121 " pdb=" SF4 9 202 " pdb="FE4 SF4 9 202 " - pdb=" SG CYS 9 82 " pdb="FE2 SF4 9 202 " - pdb=" SG CYS 9 85 " pdb="FE3 SF4 9 202 " - pdb=" SG CYS 9 79 " pdb="FE1 SF4 9 202 " - pdb=" SG CYS 9 128 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN 7 201 " pdb="ZN ZN 7 201 " - pdb=" NE2 HIS 7 68 " pdb="ZN ZN 7 201 " - pdb=" SG CYS 7 87 " pdb="ZN ZN 7 201 " - pdb=" SG CYS 7 84 " pdb="ZN ZN 7 201 " - pdb=" SG CYS 7 59 " Number of angles added : 3 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15348 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 333 helices and 28 sheets defined 52.8% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.55 Creating SS restraints... Processing helix chain '6' and resid 35 through 53 Processing helix chain '6' and resid 64 through 73 Processing helix chain '6' and resid 104 through 116 Proline residue: 6 108 - end of helix Processing helix chain '6' and resid 127 through 132 Processing helix chain '6' and resid 134 through 136 No H-bonds generated for 'chain '6' and resid 134 through 136' Processing helix chain '6' and resid 146 through 148 No H-bonds generated for 'chain '6' and resid 146 through 148' Processing helix chain '6' and resid 163 through 179 Processing helix chain '6' and resid 182 through 187 Processing helix chain 'C' and resid 16 through 32 Processing helix chain 'C' and resid 54 through 66 removed outlier: 3.632A pdb=" N VAL C 57 " --> pdb=" O PRO C 54 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ILE C 58 " --> pdb=" O ASP C 55 " (cutoff:3.500A) Proline residue: C 59 - end of helix removed outlier: 3.516A pdb=" N ASP C 66 " --> pdb=" O PHE C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 138 Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'D' and resid 8 through 14 removed outlier: 4.412A pdb=" N PHE D 14 " --> pdb=" O TRP D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 93 Processing helix chain 'D' and resid 96 through 106 Proline residue: D 101 - end of helix removed outlier: 4.033A pdb=" N ASP D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG D 105 " --> pdb=" O PRO D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 126 Processing helix chain 'D' and resid 132 through 161 Processing helix chain 'D' and resid 165 through 185 Processing helix chain 'D' and resid 207 through 229 removed outlier: 4.015A pdb=" N ASN D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N SER D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N LEU D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ARG D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 239 Processing helix chain 'D' and resid 247 through 253 Processing helix chain 'D' and resid 258 through 263 Processing helix chain 'D' and resid 269 through 272 No H-bonds generated for 'chain 'D' and resid 269 through 272' Processing helix chain 'D' and resid 293 through 316 Processing helix chain 'D' and resid 335 through 340 Processing helix chain 'D' and resid 342 through 353 Processing helix chain 'D' and resid 394 through 405 removed outlier: 4.699A pdb=" N ASP D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LYS D 404 " --> pdb=" O ALA D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 420 Processing helix chain 'D' and resid 425 through 429 Processing helix chain '2' and resid 25 through 37 Processing helix chain '2' and resid 43 through 58 removed outlier: 3.607A pdb=" N VAL 2 47 " --> pdb=" O ALA 2 44 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LEU 2 48 " --> pdb=" O ALA 2 45 " (cutoff:3.500A) Proline residue: 2 49 - end of helix Processing helix chain '2' and resid 63 through 73 Processing helix chain '2' and resid 77 through 86 Processing helix chain '2' and resid 106 through 110 Processing helix chain '2' and resid 113 through 124 Processing helix chain '2' and resid 166 through 178 Processing helix chain '1' and resid 33 through 39 Processing helix chain '1' and resid 45 through 51 Processing helix chain '1' and resid 53 through 63 Processing helix chain '1' and resid 75 through 82 removed outlier: 4.473A pdb=" N MET 1 82 " --> pdb=" O LYS 1 78 " (cutoff:3.500A) Processing helix chain '1' and resid 106 through 113 Processing helix chain '1' and resid 115 through 129 Processing helix chain '1' and resid 143 through 159 Processing helix chain '1' and resid 185 through 187 No H-bonds generated for 'chain '1' and resid 185 through 187' Processing helix chain '1' and resid 189 through 197 Processing helix chain '1' and resid 215 through 217 No H-bonds generated for 'chain '1' and resid 215 through 217' Processing helix chain '1' and resid 225 through 237 Proline residue: 1 232 - end of helix Processing helix chain '1' and resid 239 through 244 Processing helix chain '1' and resid 276 through 283 Processing helix chain '1' and resid 309 through 314 removed outlier: 4.785A pdb=" N THR 1 314 " --> pdb=" O SER 1 310 " (cutoff:3.500A) Processing helix chain '1' and resid 319 through 324 Processing helix chain '1' and resid 343 through 357 Processing helix chain '1' and resid 363 through 381 Processing helix chain '1' and resid 386 through 399 Processing helix chain '1' and resid 407 through 421 Proline residue: 1 414 - end of helix Processing helix chain '1' and resid 423 through 437 Processing helix chain '3' and resid 26 through 33 Processing helix chain '3' and resid 84 through 100 removed outlier: 4.133A pdb=" N ASN 3 100 " --> pdb=" O PHE 3 96 " (cutoff:3.500A) Processing helix chain '3' and resid 105 through 107 No H-bonds generated for 'chain '3' and resid 105 through 107' Processing helix chain '3' and resid 115 through 123 Processing helix chain '3' and resid 150 through 152 No H-bonds generated for 'chain '3' and resid 150 through 152' Processing helix chain '3' and resid 158 through 165 Processing helix chain '3' and resid 178 through 180 No H-bonds generated for 'chain '3' and resid 178 through 180' Processing helix chain '3' and resid 198 through 202 Processing helix chain '3' and resid 265 through 275 removed outlier: 5.016A pdb=" N TYR 3 271 " --> pdb=" O THR 3 267 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ASP 3 272 " --> pdb=" O ARG 3 268 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N GLY 3 273 " --> pdb=" O PHE 3 269 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU 3 274 " --> pdb=" O ALA 3 270 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LYS 3 275 " --> pdb=" O TYR 3 271 " (cutoff:3.500A) Processing helix chain '3' and resid 296 through 309 Processing helix chain '3' and resid 312 through 314 No H-bonds generated for 'chain '3' and resid 312 through 314' Processing helix chain '3' and resid 325 through 337 Processing helix chain '3' and resid 359 through 362 Processing helix chain '3' and resid 367 through 373 Processing helix chain '3' and resid 384 through 387 No H-bonds generated for 'chain '3' and resid 384 through 387' Processing helix chain '3' and resid 389 through 401 Processing helix chain '3' and resid 427 through 434 Processing helix chain '3' and resid 438 through 445 Processing helix chain '3' and resid 455 through 458 No H-bonds generated for 'chain '3' and resid 455 through 458' Processing helix chain '3' and resid 463 through 481 Processing helix chain '3' and resid 497 through 505 removed outlier: 4.650A pdb=" N ALA 3 501 " --> pdb=" O ALA 3 497 " (cutoff:3.500A) Processing helix chain '3' and resid 512 through 516 Processing helix chain '3' and resid 596 through 607 Processing helix chain '3' and resid 616 through 626 Processing helix chain '3' and resid 642 through 651 Processing helix chain '3' and resid 668 through 671 No H-bonds generated for 'chain '3' and resid 668 through 671' Processing helix chain '3' and resid 676 through 680 Processing helix chain '3' and resid 682 through 692 Processing helix chain '9' and resid 16 through 28 Processing helix chain '9' and resid 30 through 44 Processing helix chain '9' and resid 84 through 88 Processing helix chain '9' and resid 123 through 127 Processing helix chain '9' and resid 147 through 149 No H-bonds generated for 'chain '9' and resid 147 through 149' Processing helix chain '9' and resid 153 through 162 Processing helix chain '9' and resid 164 through 174 removed outlier: 4.666A pdb=" N ALA 9 169 " --> pdb=" O ALA 9 165 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 41 removed outlier: 4.218A pdb=" N TYR P 33 " --> pdb=" O PHE P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 59 removed outlier: 4.803A pdb=" N HIS P 58 " --> pdb=" O TYR P 54 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LEU P 59 " --> pdb=" O ASP P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 78 through 85 Processing helix chain 'P' and resid 106 through 110 Processing helix chain 'P' and resid 112 through 124 Processing helix chain 'P' and resid 144 through 159 Processing helix chain 'P' and resid 179 through 187 removed outlier: 4.279A pdb=" N ARG P 186 " --> pdb=" O PHE P 182 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N TRP P 187 " --> pdb=" O ALA P 183 " (cutoff:3.500A) Processing helix chain 'P' and resid 194 through 197 Processing helix chain 'P' and resid 207 through 219 Processing helix chain 'P' and resid 221 through 223 No H-bonds generated for 'chain 'P' and resid 221 through 223' Processing helix chain 'P' and resid 238 through 249 Processing helix chain 'P' and resid 281 through 288 Processing helix chain 'P' and resid 300 through 303 No H-bonds generated for 'chain 'P' and resid 300 through 303' Processing helix chain 'P' and resid 315 through 321 removed outlier: 3.503A pdb=" N ARG P 319 " --> pdb=" O ILE P 315 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ARG P 320 " --> pdb=" O GLU P 316 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N HIS P 321 " --> pdb=" O VAL P 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 315 through 321' Processing helix chain 'Q' and resid 20 through 23 No H-bonds generated for 'chain 'Q' and resid 20 through 23' Processing helix chain 'Q' and resid 27 through 31 removed outlier: 3.695A pdb=" N LYS Q 31 " --> pdb=" O GLU Q 28 " (cutoff:3.500A) Processing helix chain 'Q' and resid 89 through 99 Processing helix chain 'Q' and resid 118 through 122 Processing helix chain '7' and resid 23 through 25 No H-bonds generated for 'chain '7' and resid 23 through 25' Processing helix chain '7' and resid 40 through 45 Processing helix chain '7' and resid 64 through 66 No H-bonds generated for 'chain '7' and resid 64 through 66' Processing helix chain 'S' and resid 30 through 46 removed outlier: 6.217A pdb=" N VAL S 41 " --> pdb=" O VAL S 37 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N GLU S 42 " --> pdb=" O GLN S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 95 Processing helix chain 'T' and resid 8 through 21 Processing helix chain 'T' and resid 44 through 58 Processing helix chain 'T' and resid 64 through 69 removed outlier: 3.527A pdb=" N LYS T 69 " --> pdb=" O ILE T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 83 Processing helix chain 'V' and resid 19 through 36 removed outlier: 4.092A pdb=" N HIS V 36 " --> pdb=" O ASP V 32 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 60 Processing helix chain 'V' and resid 64 through 71 Processing helix chain 'V' and resid 76 through 96 Processing helix chain 'W' and resid 27 through 51 Proline residue: W 46 - end of helix Processing helix chain 'W' and resid 58 through 71 Processing helix chain 'W' and resid 78 through 96 Processing helix chain 'W' and resid 102 through 108 removed outlier: 4.442A pdb=" N PHE W 108 " --> pdb=" O HIS W 104 " (cutoff:3.500A) Processing helix chain 'W' and resid 120 through 126 Processing helix chain 'q' and resid 3 through 16 Processing helix chain 'q' and resid 20 through 29 Processing helix chain 'q' and resid 79 through 81 No H-bonds generated for 'chain 'q' and resid 79 through 81' Processing helix chain 'q' and resid 84 through 90 Processing helix chain 'r' and resid 5 through 15 Processing helix chain 'r' and resid 53 through 55 No H-bonds generated for 'chain 'r' and resid 53 through 55' Processing helix chain 'r' and resid 58 through 61 Processing helix chain 's' and resid 35 through 37 No H-bonds generated for 'chain 's' and resid 35 through 37' Processing helix chain 's' and resid 44 through 54 removed outlier: 4.618A pdb=" N LYS s 54 " --> pdb=" O LEU s 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 24 Processing helix chain 'A' and resid 53 through 78 Proline residue: A 74 - end of helix removed outlier: 5.741A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 107 Processing helix chain 'H' and resid 3 through 31 Proline residue: H 12 - end of helix Processing helix chain 'H' and resid 47 through 57 Processing helix chain 'H' and resid 68 through 87 Proline residue: H 75 - end of helix Processing helix chain 'H' and resid 101 through 122 Processing helix chain 'H' and resid 126 through 157 Processing helix chain 'H' and resid 163 through 169 Processing helix chain 'H' and resid 174 through 177 No H-bonds generated for 'chain 'H' and resid 174 through 177' Processing helix chain 'H' and resid 179 through 193 Processing helix chain 'H' and resid 217 through 242 Processing helix chain 'H' and resid 253 through 276 Processing helix chain 'H' and resid 282 through 311 removed outlier: 5.514A pdb=" N LEU H 294 " --> pdb=" O TRP H 290 " (cutoff:3.500A) Proline residue: H 295 - end of helix Proline residue: H 308 - end of helix Processing helix chain 'J' and resid 4 through 21 Processing helix chain 'J' and resid 25 through 46 Processing helix chain 'J' and resid 49 through 57 Processing helix chain 'J' and resid 63 through 73 Processing helix chain 'J' and resid 88 through 109 Processing helix chain 'J' and resid 138 through 143 Processing helix chain 'J' and resid 149 through 169 Processing helix chain 'K' and resid 3 through 20 Processing helix chain 'K' and resid 26 through 51 Processing helix chain 'K' and resid 58 through 85 Processing helix chain 'K' and resid 90 through 92 No H-bonds generated for 'chain 'K' and resid 90 through 92' Processing helix chain 'L' and resid 3 through 24 Proline residue: L 18 - end of helix Processing helix chain 'L' and resid 27 through 29 No H-bonds generated for 'chain 'L' and resid 27 through 29' Processing helix chain 'L' and resid 32 through 57 Proline residue: L 50 - end of helix Processing helix chain 'L' and resid 84 through 107 Processing helix chain 'L' and resid 114 through 133 Processing helix chain 'L' and resid 137 through 157 Processing helix chain 'L' and resid 162 through 193 Processing helix chain 'L' and resid 198 through 203 Processing helix chain 'L' and resid 210 through 224 Processing helix chain 'L' and resid 232 through 238 removed outlier: 4.637A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 250 removed outlier: 3.800A pdb=" N SER L 250 " --> pdb=" O LEU L 246 " (cutoff:3.500A) Processing helix chain 'L' and resid 255 through 262 Processing helix chain 'L' and resid 264 through 269 removed outlier: 4.507A pdb=" N ASN L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 294 removed outlier: 4.288A pdb=" N THR L 294 " --> pdb=" O ILE L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 318 Processing helix chain 'L' and resid 322 through 349 Processing helix chain 'L' and resid 356 through 358 No H-bonds generated for 'chain 'L' and resid 356 through 358' Processing helix chain 'L' and resid 362 through 365 No H-bonds generated for 'chain 'L' and resid 362 through 365' Processing helix chain 'L' and resid 367 through 381 Processing helix chain 'L' and resid 387 through 401 removed outlier: 3.680A pdb=" N TYR L 390 " --> pdb=" O THR L 387 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER L 391 " --> pdb=" O GLY L 388 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS L 392 " --> pdb=" O PHE L 389 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ASP L 393 " --> pdb=" O TYR L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 431 Processing helix chain 'L' and resid 448 through 471 Proline residue: L 453 - end of helix removed outlier: 5.945A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N PHE L 466 " --> pdb=" O ILE L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 484 through 487 No H-bonds generated for 'chain 'L' and resid 484 through 487' Processing helix chain 'L' and resid 489 through 509 Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 547 removed outlier: 3.847A pdb=" N PHE L 529 " --> pdb=" O LEU L 526 " (cutoff:3.500A) Proline residue: L 530 - end of helix removed outlier: 3.707A pdb=" N ILE L 533 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N HIS L 534 " --> pdb=" O SER L 531 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N THR L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 3.507A pdb=" N SER L 545 " --> pdb=" O LEU L 542 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU L 546 " --> pdb=" O ASN L 543 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS L 547 " --> pdb=" O LEU L 544 " (cutoff:3.500A) Processing helix chain 'L' and resid 549 through 553 Processing helix chain 'L' and resid 557 through 561 Processing helix chain 'L' and resid 563 through 577 Processing helix chain 'L' and resid 584 through 605 Processing helix chain 'M' and resid 5 through 17 removed outlier: 4.122A pdb=" N LEU M 12 " --> pdb=" O SER M 8 " (cutoff:3.500A) Proline residue: M 13 - end of helix Processing helix chain 'M' and resid 23 through 42 removed outlier: 4.249A pdb=" N THR M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LEU M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 80 Proline residue: M 74 - end of helix Processing helix chain 'M' and resid 89 through 111 Processing helix chain 'M' and resid 115 through 136 Proline residue: M 128 - end of helix Processing helix chain 'M' and resid 142 through 171 Proline residue: M 159 - end of helix Processing helix chain 'M' and resid 176 through 181 Processing helix chain 'M' and resid 190 through 206 removed outlier: 4.333A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 222 removed outlier: 4.411A pdb=" N LYS M 218 " --> pdb=" O LEU M 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 250 removed outlier: 5.748A pdb=" N LEU M 236 " --> pdb=" O ALA M 232 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LYS M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ILE M 248 " --> pdb=" O ILE M 244 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ILE M 249 " --> pdb=" O ARG M 245 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU M 250 " --> pdb=" O ILE M 246 " (cutoff:3.500A) Processing helix chain 'M' and resid 254 through 257 No H-bonds generated for 'chain 'M' and resid 254 through 257' Processing helix chain 'M' and resid 259 through 277 Processing helix chain 'M' and resid 282 through 303 Processing helix chain 'M' and resid 306 through 337 Processing helix chain 'M' and resid 348 through 351 No H-bonds generated for 'chain 'M' and resid 348 through 351' Processing helix chain 'M' and resid 353 through 366 Processing helix chain 'M' and resid 373 through 388 Processing helix chain 'M' and resid 390 through 414 removed outlier: 3.684A pdb=" N ILE M 393 " --> pdb=" O ASN M 390 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET M 408 " --> pdb=" O MET M 405 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR M 413 " --> pdb=" O MET M 410 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 449 Proline residue: M 443 - end of helix Processing helix chain 'M' and resid 451 through 454 removed outlier: 3.543A pdb=" N ILE M 454 " --> pdb=" O PRO M 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 451 through 454' Processing helix chain 'N' and resid 3 through 22 Proline residue: N 17 - end of helix Processing helix chain 'N' and resid 26 through 47 Proline residue: N 42 - end of helix removed outlier: 5.086A pdb=" N LYS N 47 " --> pdb=" O MET N 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 81 Processing helix chain 'N' and resid 92 through 106 Processing helix chain 'N' and resid 115 through 119 Processing helix chain 'N' and resid 124 through 133 Processing helix chain 'N' and resid 136 through 144 Processing helix chain 'N' and resid 146 through 148 No H-bonds generated for 'chain 'N' and resid 146 through 148' Processing helix chain 'N' and resid 151 through 171 Processing helix chain 'N' and resid 175 through 194 Processing helix chain 'N' and resid 198 through 222 Proline residue: N 214 - end of helix removed outlier: 4.202A pdb=" N ASN N 222 " --> pdb=" O ALA N 218 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 236 removed outlier: 4.222A pdb=" N LEU N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N TRP N 234 " --> pdb=" O ILE N 230 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS N 236 " --> pdb=" O LEU N 232 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 252 removed outlier: 3.537A pdb=" N LEU N 241 " --> pdb=" O PRO N 238 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR N 242 " --> pdb=" O ALA N 239 " (cutoff:3.500A) Processing helix chain 'N' and resid 259 through 272 removed outlier: 4.403A pdb=" N LYS N 263 " --> pdb=" O GLY N 259 " (cutoff:3.500A) Processing helix chain 'N' and resid 276 through 300 Processing helix chain 'N' and resid 311 through 316 Processing helix chain 'N' and resid 324 through 334 removed outlier: 3.908A pdb=" N THR N 328 " --> pdb=" O LEU N 324 " (cutoff:3.500A) Processing helix chain 'N' and resid 337 through 343 Proline residue: N 341 - end of helix Processing helix chain 'O' and resid 5 through 10 Processing helix chain 'O' and resid 14 through 17 No H-bonds generated for 'chain 'O' and resid 14 through 17' Processing helix chain 'O' and resid 35 through 46 Processing helix chain 'O' and resid 58 through 62 Processing helix chain 'O' and resid 79 through 84 Processing helix chain 'O' and resid 92 through 118 Processing helix chain 'O' and resid 128 through 130 No H-bonds generated for 'chain 'O' and resid 128 through 130' Processing helix chain 'O' and resid 132 through 140 Processing helix chain 'O' and resid 146 through 162 Proline residue: O 161 - end of helix Processing helix chain 'O' and resid 176 through 186 Processing helix chain 'O' and resid 196 through 215 removed outlier: 5.268A pdb=" N LEU O 211 " --> pdb=" O LYS O 207 " (cutoff:3.500A) Proline residue: O 212 - end of helix Processing helix chain 'O' and resid 233 through 239 Processing helix chain 'O' and resid 253 through 264 Processing helix chain 'O' and resid 266 through 269 No H-bonds generated for 'chain 'O' and resid 266 through 269' Processing helix chain 'O' and resid 272 through 274 No H-bonds generated for 'chain 'O' and resid 272 through 274' Processing helix chain 'O' and resid 286 through 297 Processing helix chain 'O' and resid 310 through 312 No H-bonds generated for 'chain 'O' and resid 310 through 312' Processing helix chain 'U' and resid 8 through 21 Processing helix chain 'U' and resid 44 through 58 Processing helix chain 'U' and resid 64 through 69 Processing helix chain 'U' and resid 73 through 84 Processing helix chain 'X' and resid 9 through 12 No H-bonds generated for 'chain 'X' and resid 9 through 12' Processing helix chain 'X' and resid 21 through 26 Processing helix chain 'X' and resid 28 through 34 Processing helix chain 'X' and resid 36 through 48 Processing helix chain 'X' and resid 52 through 54 No H-bonds generated for 'chain 'X' and resid 52 through 54' Processing helix chain 'X' and resid 56 through 76 Processing helix chain 'X' and resid 78 through 90 Processing helix chain 'X' and resid 96 through 98 No H-bonds generated for 'chain 'X' and resid 96 through 98' Processing helix chain 'X' and resid 101 through 112 Processing helix chain 'Y' and resid 2 through 7 Processing helix chain 'Y' and resid 17 through 42 Processing helix chain 'Y' and resid 48 through 80 Processing helix chain 'Y' and resid 86 through 104 Processing helix chain 'Y' and resid 107 through 130 Processing helix chain 'Z' and resid 31 through 98 Proline residue: Z 72 - end of helix removed outlier: 3.662A pdb=" N LYS Z 98 " --> pdb=" O ALA Z 94 " (cutoff:3.500A) Processing helix chain 'Z' and resid 120 through 124 Processing helix chain 'Z' and resid 129 through 141 removed outlier: 6.193A pdb=" N PHE Z 139 " --> pdb=" O ALA Z 135 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N THR Z 140 " --> pdb=" O ASN Z 136 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 30 removed outlier: 3.577A pdb=" N ILE a 5 " --> pdb=" O TRP a 2 " (cutoff:3.500A) Proline residue: a 7 - end of helix removed outlier: 4.386A pdb=" N ILE a 18 " --> pdb=" O CYS a 15 " (cutoff:3.500A) Proline residue: a 19 - end of helix removed outlier: 3.556A pdb=" N SER a 22 " --> pdb=" O PRO a 19 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 55 Processing helix chain 'a' and resid 66 through 68 No H-bonds generated for 'chain 'a' and resid 66 through 68' Processing helix chain 'b' and resid 3 through 14 Processing helix chain 'b' and resid 17 through 31 Processing helix chain 'b' and resid 38 through 47 removed outlier: 3.949A pdb=" N SER b 42 " --> pdb=" O THR b 38 " (cutoff:3.500A) Processing helix chain 'b' and resid 78 through 82 Processing helix chain 'c' and resid 14 through 46 Processing helix chain 'd' and resid 16 through 20 Processing helix chain 'd' and resid 29 through 48 Processing helix chain 'd' and resid 58 through 96 Processing helix chain 'e' and resid 5 through 9 Processing helix chain 'e' and resid 15 through 17 No H-bonds generated for 'chain 'e' and resid 15 through 17' Processing helix chain 'e' and resid 25 through 27 No H-bonds generated for 'chain 'e' and resid 25 through 27' Processing helix chain 'e' and resid 33 through 43 Processing helix chain 'e' and resid 47 through 54 Processing helix chain 'e' and resid 56 through 67 Processing helix chain 'e' and resid 69 through 88 Processing helix chain 'e' and resid 95 through 97 No H-bonds generated for 'chain 'e' and resid 95 through 97' Processing helix chain 'f' and resid 6 through 9 No H-bonds generated for 'chain 'f' and resid 6 through 9' Processing helix chain 'f' and resid 11 through 33 removed outlier: 3.637A pdb=" N ILE f 14 " --> pdb=" O TRP f 11 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU f 15 " --> pdb=" O VAL f 12 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N VAL f 16 " --> pdb=" O HIS f 13 " (cutoff:3.500A) Proline residue: f 17 - end of helix Processing helix chain 'g' and resid 35 through 38 No H-bonds generated for 'chain 'g' and resid 35 through 38' Processing helix chain 'g' and resid 49 through 63 Processing helix chain 'g' and resid 67 through 76 removed outlier: 4.106A pdb=" N THR g 72 " --> pdb=" O LEU g 68 " (cutoff:3.500A) Processing helix chain 'g' and resid 81 through 101 removed outlier: 3.558A pdb=" N GLN g 84 " --> pdb=" O TYR g 81 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N GLU g 85 " --> pdb=" O ARG g 82 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TRP g 86 " --> pdb=" O MET g 83 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN g 101 " --> pdb=" O ARG g 98 " (cutoff:3.500A) Processing helix chain 'g' and resid 113 through 115 No H-bonds generated for 'chain 'g' and resid 113 through 115' Processing helix chain 'h' and resid 16 through 46 Proline residue: h 35 - end of helix Processing helix chain 'h' and resid 64 through 66 No H-bonds generated for 'chain 'h' and resid 64 through 66' Processing helix chain 'h' and resid 70 through 79 Processing helix chain 'h' and resid 83 through 116 Processing helix chain 'h' and resid 130 through 132 No H-bonds generated for 'chain 'h' and resid 130 through 132' Processing helix chain 'i' and resid 5 through 24 Processing helix chain 'i' and resid 65 through 72 removed outlier: 3.908A pdb=" N PHE i 69 " --> pdb=" O ARG i 65 " (cutoff:3.500A) Processing helix chain 'i' and resid 75 through 88 Processing helix chain 'j' and resid 19 through 42 Processing helix chain 'j' and resid 61 through 64 No H-bonds generated for 'chain 'j' and resid 61 through 64' Processing helix chain 'k' and resid 24 through 26 No H-bonds generated for 'chain 'k' and resid 24 through 26' Processing helix chain 'k' and resid 33 through 44 removed outlier: 3.810A pdb=" N ARG k 44 " --> pdb=" O LYS k 40 " (cutoff:3.500A) Processing helix chain 'k' and resid 51 through 57 removed outlier: 4.988A pdb=" N TRP k 56 " --> pdb=" O ARG k 52 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ARG k 57 " --> pdb=" O ASN k 53 " (cutoff:3.500A) Processing helix chain 'k' and resid 60 through 62 No H-bonds generated for 'chain 'k' and resid 60 through 62' Processing helix chain 'k' and resid 68 through 72 Processing helix chain 'k' and resid 76 through 93 Processing helix chain 'l' and resid 16 through 25 Processing helix chain 'l' and resid 54 through 56 No H-bonds generated for 'chain 'l' and resid 54 through 56' Processing helix chain 'l' and resid 80 through 83 No H-bonds generated for 'chain 'l' and resid 80 through 83' Processing helix chain 'l' and resid 97 through 120 Processing helix chain 'l' and resid 133 through 141 removed outlier: 6.006A pdb=" N LEU l 139 " --> pdb=" O ASN l 135 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLU l 140 " --> pdb=" O ASN l 136 " (cutoff:3.500A) Processing helix chain 'm' and resid 19 through 21 No H-bonds generated for 'chain 'm' and resid 19 through 21' Processing helix chain 'm' and resid 26 through 51 Processing helix chain 'm' and resid 62 through 72 Processing helix chain 'm' and resid 83 through 117 Proline residue: m 96 - end of helix Processing helix chain 'n' and resid 11 through 30 Processing helix chain 'n' and resid 33 through 49 Processing helix chain 'n' and resid 57 through 72 Processing helix chain 'n' and resid 100 through 102 No H-bonds generated for 'chain 'n' and resid 100 through 102' Processing helix chain 'n' and resid 108 through 113 Processing helix chain 'n' and resid 115 through 141 removed outlier: 4.716A pdb=" N ASP n 133 " --> pdb=" O MET n 129 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ARG n 134 " --> pdb=" O GLU n 130 " (cutoff:3.500A) Processing helix chain 'n' and resid 167 through 170 No H-bonds generated for 'chain 'n' and resid 167 through 170' Processing helix chain 'o' and resid 2 through 9 Processing helix chain 'o' and resid 42 through 48 Processing helix chain 'o' and resid 59 through 71 Processing helix chain 'o' and resid 80 through 117 Processing helix chain 'p' and resid 28 through 57 removed outlier: 4.581A pdb=" N TRP p 42 " --> pdb=" O LEU p 38 " (cutoff:3.500A) Proline residue: p 43 - end of helix Processing helix chain 'p' and resid 81 through 123 removed outlier: 6.598A pdb=" N GLU p 118 " --> pdb=" O GLN p 114 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ASN p 119 " --> pdb=" O ARG p 115 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N TYR p 120 " --> pdb=" O GLU p 116 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLN p 121 " --> pdb=" O GLY p 117 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLN p 122 " --> pdb=" O GLU p 118 " (cutoff:3.500A) Processing helix chain 'p' and resid 125 through 142 Processing helix chain 'p' and resid 151 through 170 Processing sheet with id= A, first strand: chain '6' and resid 57 through 61 removed outlier: 6.203A pdb=" N VAL 6 95 " --> pdb=" O MET 6 58 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N PHE 6 60 " --> pdb=" O VAL 6 95 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ILE 6 97 " --> pdb=" O PHE 6 60 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N TYR 6 122 " --> pdb=" O MET 6 96 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL 6 98 " --> pdb=" O TYR 6 122 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL 6 124 " --> pdb=" O VAL 6 98 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE 6 154 " --> pdb=" O SER 6 125 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 74 through 82 removed outlier: 6.575A pdb=" N ASN C 95 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU C 78 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL C 93 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ALA C 80 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLU C 91 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU C 48 " --> pdb=" O ARG C 106 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LYS C 108 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE C 50 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N TYR C 110 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N ILE C 52 " --> pdb=" O TYR C 110 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 172 through 177 Processing sheet with id= D, first strand: chain 'D' and resid 47 through 51 removed outlier: 6.354A pdb=" N SER D 69 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL D 73 " --> pdb=" O SER D 69 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 361 through 369 Processing sheet with id= F, first strand: chain '2' and resid 137 through 142 removed outlier: 6.424A pdb=" N TYR 2 98 " --> pdb=" O THR 2 138 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE 2 140 " --> pdb=" O TYR 2 98 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE 2 100 " --> pdb=" O ILE 2 140 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL 2 142 " --> pdb=" O ILE 2 100 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N VAL 2 102 " --> pdb=" O VAL 2 142 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '1' and resid 220 through 224 removed outlier: 7.010A pdb=" N TYR 1 92 " --> pdb=" O THR 1 221 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N ALA 1 223 " --> pdb=" O TYR 1 92 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL 1 94 " --> pdb=" O ALA 1 223 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ALA 1 133 " --> pdb=" O LEU 1 93 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL 1 95 " --> pdb=" O ALA 1 133 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TYR 1 135 " --> pdb=" O VAL 1 95 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA 1 97 " --> pdb=" O TYR 1 135 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TYR 1 137 " --> pdb=" O ALA 1 97 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASP 1 174 " --> pdb=" O ALA 1 134 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ILE 1 136 " --> pdb=" O ASP 1 174 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N PHE 1 176 " --> pdb=" O ILE 1 136 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ILE 1 138 " --> pdb=" O PHE 1 176 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL 1 178 " --> pdb=" O ILE 1 138 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain '1' and resid 266 through 271 Processing sheet with id= I, first strand: chain '3' and resid 8 through 13 Processing sheet with id= J, first strand: chain '3' and resid 146 through 148 Processing sheet with id= K, first strand: chain '3' and resid 173 through 175 Processing sheet with id= L, first strand: chain '3' and resid 223 through 228 removed outlier: 6.295A pdb=" N ARG 3 243 " --> pdb=" O VAL 3 247 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N VAL 3 247 " --> pdb=" O ARG 3 243 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '3' and resid 283 through 285 Processing sheet with id= N, first strand: chain '3' and resid 343 through 345 removed outlier: 8.486A pdb=" N CYS 3 344 " --> pdb=" O VAL 3 315 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ALA 3 317 " --> pdb=" O CYS 3 344 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N MET 3 521 " --> pdb=" O ALA 3 316 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ILE 3 318 " --> pdb=" O MET 3 521 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N PHE 3 523 " --> pdb=" O ILE 3 318 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N PHE 3 542 " --> pdb=" O LEU 3 522 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N LEU 3 524 " --> pdb=" O PHE 3 542 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL 3 544 " --> pdb=" O LEU 3 524 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL 3 559 " --> pdb=" O TYR 3 545 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N GLY 3 547 " --> pdb=" O VAL 3 559 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N LEU 3 561 " --> pdb=" O GLY 3 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain '3' and resid 490 through 493 removed outlier: 8.256A pdb=" N ASN 3 491 " --> pdb=" O PRO 3 449 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL 3 451 " --> pdb=" O ASN 3 491 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU 3 493 " --> pdb=" O VAL 3 451 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU 3 453 " --> pdb=" O LEU 3 493 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL 3 376 " --> pdb=" O MET 3 450 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL 3 452 " --> pdb=" O VAL 3 376 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU 3 378 " --> pdb=" O VAL 3 452 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLY 3 454 " --> pdb=" O LEU 3 378 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL 3 380 " --> pdb=" O GLY 3 454 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LYS 3 405 " --> pdb=" O VAL 3 377 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N LEU 3 379 " --> pdb=" O LYS 3 405 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA 3 407 " --> pdb=" O LEU 3 379 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ASP 3 420 " --> pdb=" O LEU 3 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain '3' and resid 571 through 574 Processing sheet with id= Q, first strand: chain '9' and resid 66 through 69 Processing sheet with id= R, first strand: chain '9' and resid 94 through 100 removed outlier: 6.190A pdb=" N GLU 9 99 " --> pdb=" O THR 9 108 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N THR 9 108 " --> pdb=" O GLU 9 99 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'P' and resid 227 through 230 removed outlier: 6.627A pdb=" N ILE P 165 " --> pdb=" O PHE P 228 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N PHE P 230 " --> pdb=" O ILE P 165 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ARG P 167 " --> pdb=" O PHE P 230 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLN P 44 " --> pdb=" O ALA P 21 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL P 23 " --> pdb=" O GLN P 44 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE P 46 " --> pdb=" O VAL P 23 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'Q' and resid 102 through 105 Processing sheet with id= U, first strand: chain 'Q' and resid 64 through 66 Processing sheet with id= V, first strand: chain '7' and resid 50 through 52 Processing sheet with id= W, first strand: chain '7' and resid 56 through 59 Processing sheet with id= X, first strand: chain 'S' and resid 51 through 57 removed outlier: 6.636A pdb=" N ARG S 67 " --> pdb=" O ARG S 16 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE S 18 " --> pdb=" O TRP S 65 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TRP S 65 " --> pdb=" O ILE S 18 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL S 20 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LYS S 63 " --> pdb=" O VAL S 20 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'q' and resid 60 through 63 removed outlier: 6.588A pdb=" N GLU q 50 " --> pdb=" O LEU q 38 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU q 38 " --> pdb=" O GLU q 50 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'L' and resid 69 through 71 Processing sheet with id= AA, first strand: chain 'L' and resid 61 through 67 removed outlier: 6.834A pdb=" N MET L 78 " --> pdb=" O THR L 65 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'O' and resid 219 through 223 removed outlier: 6.433A pdb=" N VAL O 122 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N VAL O 27 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU O 124 " --> pdb=" O VAL O 27 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N GLY O 29 " --> pdb=" O LEU O 124 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LYS O 49 " --> pdb=" O VAL O 123 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLU O 125 " --> pdb=" O LYS O 49 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N TYR O 51 " --> pdb=" O GLU O 125 " (cutoff:3.500A) 2990 hydrogen bonds defined for protein. 8526 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 22.90 Time building geometry restraints manager: 25.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 28099 1.42 - 1.64: 39797 1.64 - 1.86: 804 1.86 - 2.09: 0 2.09 - 2.31: 80 Bond restraints: 68780 Sorted by residual: bond pdb=" C2' DGT O 401 " pdb=" C3' DGT O 401 " ideal model delta sigma weight residual 1.284 1.523 -0.239 2.00e-02 2.50e+03 1.42e+02 bond pdb=" C4' DGT O 401 " pdb=" O4' DGT O 401 " ideal model delta sigma weight residual 1.272 1.445 -0.173 2.00e-02 2.50e+03 7.52e+01 bond pdb=" C4 DGT O 401 " pdb=" N3 DGT O 401 " ideal model delta sigma weight residual 1.502 1.343 0.159 2.00e-02 2.50e+03 6.29e+01 bond pdb=" C13 ZMP T 201 " pdb=" N1 ZMP T 201 " ideal model delta sigma weight residual 1.487 1.337 0.150 2.00e-02 2.50e+03 5.62e+01 bond pdb=" C13 ZMP U 201 " pdb=" N1 ZMP U 201 " ideal model delta sigma weight residual 1.487 1.338 0.149 2.00e-02 2.50e+03 5.55e+01 ... (remaining 68775 not shown) Histogram of bond angle deviations from ideal: 68.78 - 82.52: 76 82.52 - 96.27: 2 96.27 - 110.01: 12040 110.01 - 123.75: 78598 123.75 - 137.50: 2307 Bond angle restraints: 93023 Sorted by residual: angle pdb=" PA NDP P 501 " pdb=" O3 NDP P 501 " pdb=" PN NDP P 501 " ideal model delta sigma weight residual 107.74 133.63 -25.89 1.95e+00 2.62e-01 1.75e+02 angle pdb=" C5B NDP P 501 " pdb=" O5B NDP P 501 " pdb=" PA NDP P 501 " ideal model delta sigma weight residual 103.84 118.15 -14.31 1.91e+00 2.73e-01 5.59e+01 angle pdb=" C5D NDP P 501 " pdb=" O5D NDP P 501 " pdb=" PN NDP P 501 " ideal model delta sigma weight residual 104.93 124.61 -19.68 2.66e+00 1.41e-01 5.48e+01 angle pdb=" C ASP n 55 " pdb=" N MET n 56 " pdb=" CA MET n 56 " ideal model delta sigma weight residual 121.54 135.17 -13.63 1.91e+00 2.74e-01 5.09e+01 angle pdb=" N ALA 1 97 " pdb=" CA ALA 1 97 " pdb=" C ALA 1 97 " ideal model delta sigma weight residual 112.59 104.18 8.41 1.22e+00 6.72e-01 4.75e+01 ... (remaining 93018 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.62: 40641 35.62 - 71.24: 968 71.24 - 106.86: 81 106.86 - 142.47: 3 142.47 - 178.09: 3 Dihedral angle restraints: 41696 sinusoidal: 17920 harmonic: 23776 Sorted by residual: dihedral pdb=" CB CYS X 45 " pdb=" SG CYS X 45 " pdb=" SG CYS X 55 " pdb=" CB CYS X 55 " ideal model delta sinusoidal sigma weight residual 93.00 165.70 -72.70 1 1.00e+01 1.00e-02 6.74e+01 dihedral pdb=" C10 FMN 1 501 " pdb=" C1' FMN 1 501 " pdb=" N10 FMN 1 501 " pdb=" C2' FMN 1 501 " ideal model delta sinusoidal sigma weight residual 257.59 79.50 178.09 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" CB CYS Y 17 " pdb=" SG CYS Y 17 " pdb=" SG CYS Y 74 " pdb=" CB CYS Y 74 " ideal model delta sinusoidal sigma weight residual -86.00 -141.85 55.85 1 1.00e+01 1.00e-02 4.21e+01 ... (remaining 41693 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.240: 10098 4.240 - 8.480: 0 8.480 - 12.720: 0 12.720 - 16.959: 0 16.959 - 21.199: 24 Chirality restraints: 10122 Sorted by residual: chirality pdb="FE2 SF4 6 201 " pdb=" S1 SF4 6 201 " pdb=" S3 SF4 6 201 " pdb=" S4 SF4 6 201 " both_signs ideal model delta sigma weight residual False 10.55 -10.64 21.20 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE1 SF4 9 201 " pdb=" S2 SF4 9 201 " pdb=" S3 SF4 9 201 " pdb=" S4 SF4 9 201 " both_signs ideal model delta sigma weight residual False -10.55 10.61 -21.16 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 9 201 " pdb=" S1 SF4 9 201 " pdb=" S2 SF4 9 201 " pdb=" S3 SF4 9 201 " both_signs ideal model delta sigma weight residual False 10.55 -10.60 21.15 2.00e-01 2.50e+01 1.12e+04 ... (remaining 10119 not shown) Planarity restraints: 11607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMN 1 501 " -0.144 2.00e-02 2.50e+03 6.10e-02 1.76e+02 pdb=" C10 FMN 1 501 " -0.038 2.00e-02 2.50e+03 pdb=" C2 FMN 1 501 " 0.057 2.00e-02 2.50e+03 pdb=" C4 FMN 1 501 " -0.017 2.00e-02 2.50e+03 pdb=" C4A FMN 1 501 " -0.049 2.00e-02 2.50e+03 pdb=" C5A FMN 1 501 " -0.035 2.00e-02 2.50e+03 pdb=" C6 FMN 1 501 " -0.010 2.00e-02 2.50e+03 pdb=" C7 FMN 1 501 " 0.028 2.00e-02 2.50e+03 pdb=" C7M FMN 1 501 " 0.060 2.00e-02 2.50e+03 pdb=" C8 FMN 1 501 " 0.037 2.00e-02 2.50e+03 pdb=" C8M FMN 1 501 " 0.068 2.00e-02 2.50e+03 pdb=" C9 FMN 1 501 " 0.011 2.00e-02 2.50e+03 pdb=" C9A FMN 1 501 " -0.024 2.00e-02 2.50e+03 pdb=" N1 FMN 1 501 " 0.003 2.00e-02 2.50e+03 pdb=" N10 FMN 1 501 " -0.040 2.00e-02 2.50e+03 pdb=" N3 FMN 1 501 " 0.040 2.00e-02 2.50e+03 pdb=" N5 FMN 1 501 " -0.056 2.00e-02 2.50e+03 pdb=" O2 FMN 1 501 " 0.149 2.00e-02 2.50e+03 pdb=" O4 FMN 1 501 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 6 135 " -0.042 2.00e-02 2.50e+03 3.93e-02 3.08e+01 pdb=" CG TYR 6 135 " 0.095 2.00e-02 2.50e+03 pdb=" CD1 TYR 6 135 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR 6 135 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR 6 135 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR 6 135 " -0.023 2.00e-02 2.50e+03 pdb=" CZ TYR 6 135 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR 6 135 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DGT O 401 " -0.064 2.00e-02 2.50e+03 2.79e-02 2.34e+01 pdb=" C2 DGT O 401 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DGT O 401 " 0.014 2.00e-02 2.50e+03 pdb=" C5 DGT O 401 " 0.015 2.00e-02 2.50e+03 pdb=" C6 DGT O 401 " -0.012 2.00e-02 2.50e+03 pdb=" C8 DGT O 401 " 0.028 2.00e-02 2.50e+03 pdb=" N1 DGT O 401 " -0.023 2.00e-02 2.50e+03 pdb=" N2 DGT O 401 " 0.033 2.00e-02 2.50e+03 pdb=" N3 DGT O 401 " 0.008 2.00e-02 2.50e+03 pdb=" N7 DGT O 401 " 0.029 2.00e-02 2.50e+03 pdb=" N9 DGT O 401 " 0.011 2.00e-02 2.50e+03 pdb=" O6 DGT O 401 " -0.036 2.00e-02 2.50e+03 ... (remaining 11604 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.78: 14808 2.78 - 3.37: 74490 3.37 - 3.96: 137047 3.96 - 4.55: 192996 4.55 - 5.14: 282628 Nonbonded interactions: 701969 Sorted by model distance: nonbonded pdb=" O1G DGT O 401 " pdb="MG MG O 402 " model vdw 2.192 2.170 nonbonded pdb=" OG1 THR L 574 " pdb=" O TRP N 167 " model vdw 2.193 2.440 nonbonded pdb=" O2B DGT O 401 " pdb="MG MG O 402 " model vdw 2.195 2.170 nonbonded pdb=" O1A DGT O 401 " pdb="MG MG O 402 " model vdw 2.199 2.170 nonbonded pdb=" O GLU 6 119 " pdb=" OH TYR P 54 " model vdw 2.220 2.440 ... (remaining 701964 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'T' and (resid 6 through 84 or (resid 201 and (name C1 or name C10 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or \ name C18 or name C19 or name C2 or name C20 or name C21 or name C3 or name C4 o \ r name C5 or name C6 or name C7 or name C8 or name C9 or name N1 or name N2 or n \ ame O1 or name O2 or name O3 or name O4 or name O5 or name O6 or name O7 or name \ P1 or name S1 )))) selection = (chain 'U' and (resid 6 through 84 or resid 201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 3.740 Check model and map are aligned: 0.380 Set scattering table: 0.480 Process input model: 162.880 Find NCS groups from input model: 2.080 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 172.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 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 : 0.006 0.239 68780 Z= 0.403 Angle : 0.868 25.886 93023 Z= 0.439 Chirality : 1.028 21.199 10122 Planarity : 0.006 0.081 11607 Dihedral : 15.617 178.093 26324 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.81 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.09), residues: 8031 helix: 0.56 (0.07), residues: 4473 sheet: -0.40 (0.24), residues: 393 loop : -0.68 (0.11), residues: 3165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP Q 124 HIS 0.017 0.001 HIS P 250 PHE 0.047 0.002 PHE J 56 TYR 0.095 0.002 TYR 6 135 ARG 0.015 0.001 ARG q 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1165 residues out of total 7149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1165 time to evaluate : 5.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 53 SER cc_start: 0.9202 (m) cc_final: 0.8990 (m) REVERT: C 49 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8446 (mt-10) REVERT: 1 436 GLN cc_start: 0.8979 (pt0) cc_final: 0.8627 (tm-30) REVERT: 3 54 MET cc_start: 0.9608 (tpt) cc_final: 0.9376 (tpt) REVERT: 3 122 MET cc_start: 0.9392 (mmt) cc_final: 0.9087 (mmt) REVERT: 3 447 LYS cc_start: 0.9225 (tppt) cc_final: 0.8850 (tppt) REVERT: 9 174 ASP cc_start: 0.9111 (t70) cc_final: 0.8907 (t70) REVERT: P 139 MET cc_start: 0.6269 (tpp) cc_final: 0.5871 (tpp) REVERT: P 180 ASN cc_start: 0.8713 (m-40) cc_final: 0.8335 (m-40) REVERT: P 184 ASN cc_start: 0.8776 (m-40) cc_final: 0.8524 (m-40) REVERT: S 38 GLN cc_start: 0.9283 (pp30) cc_final: 0.8629 (pp30) REVERT: S 81 LEU cc_start: 0.9155 (tp) cc_final: 0.8790 (tp) REVERT: T 47 GLN cc_start: 0.9168 (tm-30) cc_final: 0.8939 (tm-30) REVERT: T 56 ASP cc_start: 0.7606 (p0) cc_final: 0.7230 (p0) REVERT: T 74 GLN cc_start: 0.7835 (mm110) cc_final: 0.7554 (mm-40) REVERT: V 63 ASP cc_start: 0.8571 (t0) cc_final: 0.8002 (p0) REVERT: q 1 MET cc_start: 0.8339 (ptt) cc_final: 0.8041 (ptt) REVERT: q 72 ASN cc_start: 0.9248 (t0) cc_final: 0.9018 (t0) REVERT: s 51 ASP cc_start: 0.9235 (t0) cc_final: 0.8984 (t0) REVERT: H 61 MET cc_start: 0.7296 (tpp) cc_final: 0.6948 (tpp) REVERT: H 68 MET cc_start: 0.8350 (tpp) cc_final: 0.7949 (tpp) REVERT: J 108 TYR cc_start: 0.8079 (m-80) cc_final: 0.7817 (m-80) REVERT: J 127 GLU cc_start: 0.9098 (tt0) cc_final: 0.8800 (tp30) REVERT: K 36 MET cc_start: 0.9609 (mtm) cc_final: 0.9337 (mtm) REVERT: M 108 MET cc_start: 0.9438 (mtp) cc_final: 0.9086 (mtp) REVERT: M 114 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8044 (tm-30) REVERT: M 271 MET cc_start: 0.9247 (mmt) cc_final: 0.8593 (mmm) REVERT: O 272 TYR cc_start: 0.8904 (m-10) cc_final: 0.8580 (m-80) REVERT: U 29 LYS cc_start: 0.9298 (mmpt) cc_final: 0.8900 (ptpt) REVERT: Y 5 PHE cc_start: 0.8129 (m-10) cc_final: 0.7929 (m-80) REVERT: Y 82 LYS cc_start: 0.9261 (pttp) cc_final: 0.8905 (pttp) REVERT: Y 85 ASP cc_start: 0.9162 (t70) cc_final: 0.8708 (t0) REVERT: Z 9 MET cc_start: 0.7928 (mmm) cc_final: 0.7692 (mmm) REVERT: a 4 GLU cc_start: 0.9267 (tp30) cc_final: 0.9062 (tp30) REVERT: a 59 ARG cc_start: 0.8905 (mmm-85) cc_final: 0.8538 (mmm-85) REVERT: c 5 ARG cc_start: 0.8282 (ttp-110) cc_final: 0.7731 (ttm-80) REVERT: c 38 ASP cc_start: 0.9211 (m-30) cc_final: 0.8997 (m-30) REVERT: g 22 MET cc_start: 0.3816 (mmm) cc_final: 0.3307 (mmm) REVERT: g 32 ASP cc_start: 0.7776 (p0) cc_final: 0.7063 (p0) REVERT: j 7 ILE cc_start: 0.8116 (pt) cc_final: 0.7887 (pt) REVERT: k 18 LYS cc_start: 0.7352 (pptt) cc_final: 0.7142 (pptt) REVERT: k 47 ARG cc_start: 0.8799 (ttp-170) cc_final: 0.8479 (ttm-80) REVERT: l 31 GLU cc_start: 0.9259 (mp0) cc_final: 0.9031 (mp0) REVERT: m 109 ASP cc_start: 0.9104 (m-30) cc_final: 0.8733 (m-30) REVERT: o 43 GLN cc_start: 0.9044 (tp-100) cc_final: 0.8533 (tp40) REVERT: o 47 ASP cc_start: 0.9326 (m-30) cc_final: 0.9044 (m-30) outliers start: 0 outliers final: 0 residues processed: 1165 average time/residue: 0.6507 time to fit residues: 1277.5089 Evaluate side-chains 1004 residues out of total 7149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1004 time to evaluate : 5.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 669 optimal weight: 20.0000 chunk 601 optimal weight: 4.9990 chunk 333 optimal weight: 9.9990 chunk 205 optimal weight: 0.9990 chunk 405 optimal weight: 7.9990 chunk 321 optimal weight: 5.9990 chunk 621 optimal weight: 9.9990 chunk 240 optimal weight: 10.0000 chunk 377 optimal weight: 7.9990 chunk 462 optimal weight: 5.9990 chunk 720 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 13 GLN 3 110 GLN ** Q 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 47 ASN H 258 ASN L 56 HIS L 170 GLN L 580 GLN M 175 ASN U 74 GLN X 63 ASN ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 142 HIS Z 75 GLN e 28 ASN i 73 HIS ** j 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 74 GLN n 140 GLN p 103 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.255 68780 Z= 0.565 Angle : 1.568 50.922 93023 Z= 1.016 Chirality : 0.310 6.423 10122 Planarity : 0.005 0.069 11607 Dihedral : 11.155 172.835 10191 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.29 % Favored : 96.70 % Rotamer: Outliers : 0.84 % Allowed : 6.73 % Favored : 92.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.09), residues: 8031 helix: 1.26 (0.08), residues: 4492 sheet: -0.24 (0.24), residues: 406 loop : -0.40 (0.11), residues: 3133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP M 307 HIS 0.006 0.001 HIS L 332 PHE 0.033 0.001 PHE M 151 TYR 0.046 0.001 TYR 6 135 ARG 0.008 0.000 ARG S 88 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1107 residues out of total 7149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 1047 time to evaluate : 6.024 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: 6 53 SER cc_start: 0.9225 (m) cc_final: 0.8935 (p) REVERT: 6 72 MET cc_start: 0.9310 (tmm) cc_final: 0.9077 (ttt) REVERT: C 49 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8413 (mt-10) REVERT: 1 269 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8310 (tt0) REVERT: 1 436 GLN cc_start: 0.8926 (pt0) cc_final: 0.8603 (tm-30) REVERT: 3 54 MET cc_start: 0.9638 (tpt) cc_final: 0.9362 (tpt) REVERT: 3 122 MET cc_start: 0.9402 (mmt) cc_final: 0.9073 (mmt) REVERT: 3 192 MET cc_start: 0.8352 (mmm) cc_final: 0.8075 (mmm) REVERT: P 184 ASN cc_start: 0.8922 (m-40) cc_final: 0.8719 (m-40) REVERT: 7 30 ASP cc_start: 0.8937 (t0) cc_final: 0.8669 (t0) REVERT: S 38 GLN cc_start: 0.9113 (pp30) cc_final: 0.8467 (pp30) REVERT: S 42 GLU cc_start: 0.8827 (mp0) cc_final: 0.8562 (mp0) REVERT: S 50 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8686 (tt) REVERT: S 81 LEU cc_start: 0.9091 (tp) cc_final: 0.8838 (tp) REVERT: T 9 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7540 (p0) REVERT: T 13 ASP cc_start: 0.9258 (t0) cc_final: 0.8669 (p0) REVERT: T 43 ASP cc_start: 0.9379 (t0) cc_final: 0.9174 (t0) REVERT: T 47 GLN cc_start: 0.9095 (tm-30) cc_final: 0.8801 (tm-30) REVERT: T 52 MET cc_start: 0.7889 (ptm) cc_final: 0.7456 (mtm) REVERT: T 56 ASP cc_start: 0.7672 (p0) cc_final: 0.7287 (p0) REVERT: V 63 ASP cc_start: 0.8700 (t0) cc_final: 0.8165 (p0) REVERT: q 1 MET cc_start: 0.8381 (ptt) cc_final: 0.8092 (ptt) REVERT: q 72 ASN cc_start: 0.9249 (t0) cc_final: 0.9032 (t0) REVERT: s 51 ASP cc_start: 0.9235 (t0) cc_final: 0.9003 (t0) REVERT: H 68 MET cc_start: 0.8397 (tpp) cc_final: 0.7994 (tpp) REVERT: K 29 THR cc_start: 0.9528 (m) cc_final: 0.9277 (p) REVERT: K 36 MET cc_start: 0.9647 (mtm) cc_final: 0.9361 (mtm) REVERT: M 108 MET cc_start: 0.9452 (mtp) cc_final: 0.9142 (mtp) REVERT: M 114 GLU cc_start: 0.8472 (tm-30) cc_final: 0.7942 (tm-30) REVERT: M 148 TYR cc_start: 0.8806 (m-80) cc_final: 0.8574 (m-80) REVERT: M 271 MET cc_start: 0.9344 (mmp) cc_final: 0.8950 (mmp) REVERT: O 272 TYR cc_start: 0.9005 (m-10) cc_final: 0.8627 (m-80) REVERT: Y 5 PHE cc_start: 0.8089 (m-10) cc_final: 0.7857 (m-80) REVERT: Y 85 ASP cc_start: 0.9224 (t70) cc_final: 0.8953 (t70) REVERT: Z 50 MET cc_start: 0.9641 (ttp) cc_final: 0.9366 (ttp) REVERT: a 9 LEU cc_start: 0.8781 (mm) cc_final: 0.8566 (mm) REVERT: c 5 ARG cc_start: 0.8229 (ttp-110) cc_final: 0.7744 (ttm-80) REVERT: c 38 ASP cc_start: 0.9233 (m-30) cc_final: 0.9008 (m-30) REVERT: k 47 ARG cc_start: 0.8813 (ttp-170) cc_final: 0.8464 (ttm-80) REVERT: l 148 GLU cc_start: 0.9008 (tp30) cc_final: 0.8765 (tp30) REVERT: m 109 ASP cc_start: 0.9145 (m-30) cc_final: 0.8732 (m-30) REVERT: n 56 MET cc_start: 0.8085 (ptt) cc_final: 0.7789 (ttm) REVERT: n 140 GLN cc_start: 0.8793 (mm-40) cc_final: 0.8583 (tp40) REVERT: o 47 ASP cc_start: 0.9366 (m-30) cc_final: 0.9152 (m-30) outliers start: 60 outliers final: 41 residues processed: 1081 average time/residue: 0.6406 time to fit residues: 1173.6012 Evaluate side-chains 1046 residues out of total 7149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 1002 time to evaluate : 6.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 64 CYS Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain 2 residue 35 VAL Chi-restraints excluded: chain 1 residue 269 GLU Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 402 ASN Chi-restraints excluded: chain 3 residue 424 ASP Chi-restraints excluded: chain 3 residue 440 CYS Chi-restraints excluded: chain 3 residue 596 ASP Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain 9 residue 124 CYS Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain 7 residue 79 THR Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain r residue 24 GLN Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 71 SER Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain J residue 16 CYS Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain L residue 109 HIS Chi-restraints excluded: chain L residue 472 ILE Chi-restraints excluded: chain O residue 250 LYS Chi-restraints excluded: chain X residue 63 ASN Chi-restraints excluded: chain Y residue 128 LYS Chi-restraints excluded: chain Y residue 133 GLU Chi-restraints excluded: chain b residue 21 SER Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain e residue 41 GLU Chi-restraints excluded: chain g residue 41 ASP Chi-restraints excluded: chain i residue 59 MET Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 13 GLU Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain n residue 74 GLN Chi-restraints excluded: chain n residue 131 SER Chi-restraints excluded: chain o residue 37 VAL Chi-restraints excluded: chain p residue 24 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 400 optimal weight: 10.0000 chunk 223 optimal weight: 10.0000 chunk 599 optimal weight: 8.9990 chunk 490 optimal weight: 9.9990 chunk 198 optimal weight: 7.9990 chunk 721 optimal weight: 6.9990 chunk 779 optimal weight: 30.0000 chunk 642 optimal weight: 0.0670 chunk 715 optimal weight: 0.0980 chunk 245 optimal weight: 30.0000 chunk 578 optimal weight: 7.9990 overall best weight: 4.6324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 155 GLN P 203 GLN ** Q 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 47 ASN H 97 ASN ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 105 HIS e 28 ASN i 73 HIS ** j 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 74 GLN o 43 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.244 68780 Z= 0.554 Angle : 1.557 50.769 93023 Z= 1.011 Chirality : 0.311 6.431 10122 Planarity : 0.004 0.063 11607 Dihedral : 10.679 171.240 10191 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.51 % Favored : 96.48 % Rotamer: Outliers : 1.27 % Allowed : 8.70 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.06 (0.10), residues: 8031 helix: 1.51 (0.08), residues: 4461 sheet: -0.23 (0.24), residues: 413 loop : -0.27 (0.11), residues: 3157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP M 307 HIS 0.005 0.001 HIS L 332 PHE 0.030 0.001 PHE M 151 TYR 0.033 0.001 TYR 6 135 ARG 0.007 0.000 ARG S 88 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1123 residues out of total 7149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 1032 time to evaluate : 6.596 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: 6 53 SER cc_start: 0.9236 (m) cc_final: 0.8965 (p) REVERT: 6 72 MET cc_start: 0.9266 (tmm) cc_final: 0.8996 (ttt) REVERT: C 49 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8415 (mt-10) REVERT: 1 269 GLU cc_start: 0.9066 (OUTLIER) cc_final: 0.8648 (tt0) REVERT: 1 436 GLN cc_start: 0.8899 (pt0) cc_final: 0.8594 (tm-30) REVERT: 3 54 MET cc_start: 0.9596 (tpt) cc_final: 0.9345 (tpt) REVERT: 3 192 MET cc_start: 0.8326 (mmm) cc_final: 0.8124 (mmm) REVERT: 3 436 ARG cc_start: 0.8355 (ptp90) cc_final: 0.8122 (ptp90) REVERT: 9 174 ASP cc_start: 0.9123 (t70) cc_final: 0.8893 (t70) REVERT: P 185 TYR cc_start: 0.7177 (OUTLIER) cc_final: 0.6312 (m-80) REVERT: P 248 MET cc_start: 0.8535 (mmm) cc_final: 0.8294 (mtp) REVERT: 7 30 ASP cc_start: 0.8894 (t0) cc_final: 0.8571 (t0) REVERT: S 38 GLN cc_start: 0.9130 (pp30) cc_final: 0.8613 (pp30) REVERT: S 42 GLU cc_start: 0.8748 (mp0) cc_final: 0.8491 (mp0) REVERT: S 81 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8632 (tp) REVERT: T 9 ASP cc_start: 0.7890 (p0) cc_final: 0.7624 (p0) REVERT: T 13 ASP cc_start: 0.9235 (t0) cc_final: 0.8625 (p0) REVERT: T 47 GLN cc_start: 0.9122 (tm-30) cc_final: 0.8804 (tm-30) REVERT: T 52 MET cc_start: 0.7951 (ptm) cc_final: 0.7455 (mtm) REVERT: T 56 ASP cc_start: 0.7739 (p0) cc_final: 0.7343 (p0) REVERT: T 74 GLN cc_start: 0.8079 (mm-40) cc_final: 0.7799 (mm-40) REVERT: V 63 ASP cc_start: 0.8694 (t0) cc_final: 0.8247 (p0) REVERT: q 72 ASN cc_start: 0.9246 (t0) cc_final: 0.9032 (t0) REVERT: q 76 ASP cc_start: 0.9085 (t0) cc_final: 0.8838 (t0) REVERT: s 51 ASP cc_start: 0.9246 (t0) cc_final: 0.8976 (t0) REVERT: s 68 ARG cc_start: 0.7729 (mpt-90) cc_final: 0.7489 (mpt-90) REVERT: A 10 ASN cc_start: 0.9152 (m-40) cc_final: 0.8895 (m110) REVERT: H 68 MET cc_start: 0.8339 (tpp) cc_final: 0.7964 (tpp) REVERT: K 29 THR cc_start: 0.9447 (m) cc_final: 0.9220 (p) REVERT: K 36 MET cc_start: 0.9652 (mtm) cc_final: 0.9421 (mtm) REVERT: M 108 MET cc_start: 0.9429 (mtp) cc_final: 0.9168 (mtp) REVERT: M 114 GLU cc_start: 0.8504 (tm-30) cc_final: 0.7978 (tm-30) REVERT: M 148 TYR cc_start: 0.8816 (m-80) cc_final: 0.8579 (m-80) REVERT: M 271 MET cc_start: 0.9377 (mmp) cc_final: 0.8974 (mmp) REVERT: M 310 MET cc_start: 0.9210 (tmm) cc_final: 0.8975 (tmm) REVERT: O 272 TYR cc_start: 0.9019 (m-10) cc_final: 0.8625 (m-80) REVERT: U 29 LYS cc_start: 0.9476 (OUTLIER) cc_final: 0.9269 (mmpt) REVERT: Y 1 VAL cc_start: 0.6831 (m) cc_final: 0.5866 (m) REVERT: Y 5 PHE cc_start: 0.8102 (m-10) cc_final: 0.7846 (m-80) REVERT: c 5 ARG cc_start: 0.8275 (ttp-110) cc_final: 0.7773 (ttm-80) REVERT: c 38 ASP cc_start: 0.9238 (m-30) cc_final: 0.8995 (m-30) REVERT: e 41 GLU cc_start: 0.9316 (OUTLIER) cc_final: 0.8814 (mp0) REVERT: f 8 ARG cc_start: 0.7830 (mpt180) cc_final: 0.7273 (mpt180) REVERT: h 68 LYS cc_start: 0.9308 (tmtt) cc_final: 0.9067 (tptp) REVERT: i 6 ASP cc_start: 0.8817 (m-30) cc_final: 0.8363 (m-30) REVERT: i 16 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8835 (tm-30) REVERT: k 19 MET cc_start: 0.8122 (tpp) cc_final: 0.7833 (tpp) REVERT: k 35 GLU cc_start: 0.9063 (tm-30) cc_final: 0.8849 (tm-30) REVERT: k 47 ARG cc_start: 0.8815 (ttp-170) cc_final: 0.8467 (ttm-80) REVERT: l 148 GLU cc_start: 0.9045 (tp30) cc_final: 0.8748 (tp30) REVERT: m 109 ASP cc_start: 0.9182 (m-30) cc_final: 0.8742 (m-30) REVERT: n 56 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7718 (tpp) REVERT: n 122 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8459 (mm-30) REVERT: n 140 GLN cc_start: 0.8793 (mm-40) cc_final: 0.8578 (tp40) REVERT: o 43 GLN cc_start: 0.9082 (tp40) cc_final: 0.8675 (tp-100) REVERT: o 47 ASP cc_start: 0.9357 (m-30) cc_final: 0.9137 (m-30) outliers start: 91 outliers final: 63 residues processed: 1081 average time/residue: 0.6427 time to fit residues: 1179.9600 Evaluate side-chains 1083 residues out of total 7149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 1013 time to evaluate : 5.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 64 CYS Chi-restraints excluded: chain 6 residue 177 ILE Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain 2 residue 171 GLU Chi-restraints excluded: chain 1 residue 105 CYS Chi-restraints excluded: chain 1 residue 269 GLU Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 402 ASN Chi-restraints excluded: chain 3 residue 424 ASP Chi-restraints excluded: chain 3 residue 440 CYS Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain 9 residue 85 CYS Chi-restraints excluded: chain 9 residue 124 CYS Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 185 TYR Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain 7 residue 79 THR Chi-restraints excluded: chain S residue 77 SER Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 95 SER Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain q residue 12 GLN Chi-restraints excluded: chain r residue 24 GLN Chi-restraints excluded: chain r residue 71 SER Chi-restraints excluded: chain s residue 30 THR Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain J residue 16 CYS Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain L residue 109 HIS Chi-restraints excluded: chain L residue 338 MET Chi-restraints excluded: chain L residue 404 THR Chi-restraints excluded: chain L residue 472 ILE Chi-restraints excluded: chain L residue 544 LEU Chi-restraints excluded: chain M residue 459 MET Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain O residue 250 LYS Chi-restraints excluded: chain U residue 29 LYS Chi-restraints excluded: chain X residue 63 ASN Chi-restraints excluded: chain Y residue 128 LYS Chi-restraints excluded: chain Y residue 133 GLU Chi-restraints excluded: chain Z residue 19 ASP Chi-restraints excluded: chain Z residue 95 ILE Chi-restraints excluded: chain Z residue 134 ASN Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain b residue 21 SER Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain c residue 24 SER Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain e residue 41 GLU Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 13 GLU Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain n residue 56 MET Chi-restraints excluded: chain n residue 74 GLN Chi-restraints excluded: chain n residue 122 GLU Chi-restraints excluded: chain n residue 130 GLU Chi-restraints excluded: chain n residue 131 SER Chi-restraints excluded: chain n residue 149 MET Chi-restraints excluded: chain o residue 37 VAL Chi-restraints excluded: chain p residue 60 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 712 optimal weight: 9.9990 chunk 542 optimal weight: 8.9990 chunk 374 optimal weight: 0.0030 chunk 79 optimal weight: 0.9990 chunk 344 optimal weight: 2.9990 chunk 484 optimal weight: 20.0000 chunk 724 optimal weight: 6.9990 chunk 766 optimal weight: 10.0000 chunk 378 optimal weight: 10.0000 chunk 686 optimal weight: 20.0000 chunk 206 optimal weight: 10.0000 overall best weight: 3.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 55 GLN ** Q 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN ** L 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 270 ASN X 63 ASN ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 105 HIS ** e 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 73 HIS j 24 GLN l 62 GLN n 52 ASN n 74 GLN p 54 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.243 68780 Z= 0.546 Angle : 1.552 50.770 93023 Z= 1.009 Chirality : 0.310 6.432 10122 Planarity : 0.004 0.057 11607 Dihedral : 10.324 170.626 10191 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.39 % Favored : 96.60 % Rotamer: Outliers : 1.50 % Allowed : 10.02 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.24 (0.10), residues: 8031 helix: 1.66 (0.08), residues: 4442 sheet: -0.22 (0.24), residues: 412 loop : -0.16 (0.11), residues: 3177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP M 307 HIS 0.004 0.001 HIS L 332 PHE 0.029 0.001 PHE M 151 TYR 0.023 0.001 TYR 6 135 ARG 0.007 0.000 ARG S 88 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1152 residues out of total 7149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 1045 time to evaluate : 5.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 53 SER cc_start: 0.9249 (m) cc_final: 0.8976 (p) REVERT: 6 72 MET cc_start: 0.9276 (tmm) cc_final: 0.9003 (ttt) REVERT: C 49 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8404 (mt-10) REVERT: 1 269 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8632 (tt0) REVERT: 1 436 GLN cc_start: 0.8862 (pt0) cc_final: 0.8557 (tm-30) REVERT: 3 19 MET cc_start: 0.9180 (mmp) cc_final: 0.8971 (mmp) REVERT: 3 54 MET cc_start: 0.9591 (tpt) cc_final: 0.9327 (tpt) REVERT: 3 192 MET cc_start: 0.8379 (mmm) cc_final: 0.8177 (mmm) REVERT: 3 436 ARG cc_start: 0.8410 (ptp90) cc_final: 0.7976 (ptp90) REVERT: 3 447 LYS cc_start: 0.9165 (tppt) cc_final: 0.8950 (mmmt) REVERT: 3 651 LEU cc_start: 0.8635 (tp) cc_final: 0.8426 (tp) REVERT: P 185 TYR cc_start: 0.7079 (OUTLIER) cc_final: 0.6240 (m-80) REVERT: P 248 MET cc_start: 0.8583 (mmm) cc_final: 0.8343 (mtp) REVERT: 7 30 ASP cc_start: 0.8905 (t0) cc_final: 0.8561 (t0) REVERT: S 38 GLN cc_start: 0.9149 (pp30) cc_final: 0.8492 (pp30) REVERT: S 42 GLU cc_start: 0.8780 (mp0) cc_final: 0.8505 (mp0) REVERT: S 81 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8594 (tp) REVERT: T 9 ASP cc_start: 0.7879 (p0) cc_final: 0.7653 (p0) REVERT: T 13 ASP cc_start: 0.9220 (t0) cc_final: 0.8578 (p0) REVERT: T 47 GLN cc_start: 0.9048 (tm-30) cc_final: 0.8686 (tm-30) REVERT: T 52 MET cc_start: 0.7878 (ptm) cc_final: 0.7380 (mtm) REVERT: T 56 ASP cc_start: 0.7759 (p0) cc_final: 0.7342 (p0) REVERT: V 63 ASP cc_start: 0.8716 (t0) cc_final: 0.8296 (p0) REVERT: q 72 ASN cc_start: 0.9240 (t0) cc_final: 0.9026 (t0) REVERT: q 76 ASP cc_start: 0.9080 (t0) cc_final: 0.8841 (t0) REVERT: s 51 ASP cc_start: 0.9222 (t0) cc_final: 0.8941 (t0) REVERT: A 10 ASN cc_start: 0.9180 (m-40) cc_final: 0.8909 (m110) REVERT: J 91 PHE cc_start: 0.7722 (m-10) cc_final: 0.7464 (m-10) REVERT: K 29 THR cc_start: 0.9462 (m) cc_final: 0.9246 (p) REVERT: L 503 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8351 (mm-30) REVERT: L 579 ASN cc_start: 0.7956 (t0) cc_final: 0.7646 (t0) REVERT: M 108 MET cc_start: 0.9430 (mtp) cc_final: 0.9168 (mtp) REVERT: M 114 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8035 (tm-30) REVERT: M 148 TYR cc_start: 0.8862 (m-80) cc_final: 0.8583 (m-80) REVERT: M 271 MET cc_start: 0.9369 (mmp) cc_final: 0.8946 (mmp) REVERT: O 272 TYR cc_start: 0.9012 (m-10) cc_final: 0.8620 (m-80) REVERT: Y 1 VAL cc_start: 0.6913 (m) cc_final: 0.5999 (m) REVERT: Y 5 PHE cc_start: 0.8030 (m-10) cc_final: 0.7824 (m-80) REVERT: Y 82 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.9069 (pttp) REVERT: a 4 GLU cc_start: 0.9255 (tp30) cc_final: 0.9032 (tp30) REVERT: c 5 ARG cc_start: 0.8276 (ttp-110) cc_final: 0.7756 (ttm-80) REVERT: c 11 LYS cc_start: 0.9290 (mmmt) cc_final: 0.9072 (mmmt) REVERT: c 38 ASP cc_start: 0.9238 (m-30) cc_final: 0.8996 (m-30) REVERT: f 8 ARG cc_start: 0.7825 (mpt180) cc_final: 0.7229 (mpt180) REVERT: i 6 ASP cc_start: 0.8821 (m-30) cc_final: 0.8365 (m-30) REVERT: i 12 GLN cc_start: 0.9115 (tt0) cc_final: 0.8884 (tm-30) REVERT: k 19 MET cc_start: 0.8130 (tpp) cc_final: 0.7825 (tpp) REVERT: k 35 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8737 (tm-30) REVERT: l 148 GLU cc_start: 0.9019 (tp30) cc_final: 0.8741 (tp30) REVERT: n 56 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7607 (tpp) REVERT: n 122 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8412 (mm-30) REVERT: n 140 GLN cc_start: 0.8772 (mm-40) cc_final: 0.8536 (tp40) REVERT: o 43 GLN cc_start: 0.9091 (tp40) cc_final: 0.8671 (tp-100) REVERT: o 47 ASP cc_start: 0.9351 (m-30) cc_final: 0.9127 (m-30) outliers start: 107 outliers final: 76 residues processed: 1106 average time/residue: 0.6474 time to fit residues: 1216.0379 Evaluate side-chains 1095 residues out of total 7149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 1013 time to evaluate : 5.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 64 CYS Chi-restraints excluded: chain 6 residue 95 VAL Chi-restraints excluded: chain 6 residue 177 ILE Chi-restraints excluded: chain 6 residue 181 GLN Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain 2 residue 171 GLU Chi-restraints excluded: chain 1 residue 105 CYS Chi-restraints excluded: chain 1 residue 269 GLU Chi-restraints excluded: chain 1 residue 327 THR Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 267 THR Chi-restraints excluded: chain 3 residue 402 ASN Chi-restraints excluded: chain 3 residue 424 ASP Chi-restraints excluded: chain 3 residue 596 ASP Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 185 TYR Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain 7 residue 79 THR Chi-restraints excluded: chain S residue 77 SER Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 85 GLU Chi-restraints excluded: chain S residue 95 SER Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain q residue 12 GLN Chi-restraints excluded: chain r residue 24 GLN Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 71 SER Chi-restraints excluded: chain s residue 30 THR Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 97 ASN Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain J residue 16 CYS Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain L residue 109 HIS Chi-restraints excluded: chain L residue 472 ILE Chi-restraints excluded: chain L residue 544 LEU Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 459 MET Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain O residue 250 LYS Chi-restraints excluded: chain Y residue 82 LYS Chi-restraints excluded: chain Y residue 128 LYS Chi-restraints excluded: chain Y residue 133 GLU Chi-restraints excluded: chain Z residue 19 ASP Chi-restraints excluded: chain Z residue 95 ILE Chi-restraints excluded: chain Z residue 134 ASN Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain b residue 21 SER Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain e residue 41 GLU Chi-restraints excluded: chain f residue 14 ILE Chi-restraints excluded: chain g residue 41 ASP Chi-restraints excluded: chain h residue 18 ASP Chi-restraints excluded: chain i residue 59 MET Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 13 GLU Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 70 MET Chi-restraints excluded: chain l residue 96 SER Chi-restraints excluded: chain n residue 56 MET Chi-restraints excluded: chain n residue 74 GLN Chi-restraints excluded: chain n residue 122 GLU Chi-restraints excluded: chain n residue 130 GLU Chi-restraints excluded: chain n residue 131 SER Chi-restraints excluded: chain n residue 149 MET Chi-restraints excluded: chain o residue 37 VAL Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 60 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 638 optimal weight: 6.9990 chunk 435 optimal weight: 20.0000 chunk 11 optimal weight: 2.9990 chunk 570 optimal weight: 9.9990 chunk 316 optimal weight: 7.9990 chunk 654 optimal weight: 9.9990 chunk 529 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 391 optimal weight: 8.9990 chunk 688 optimal weight: 9.9990 chunk 193 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 184 ASN ** Q 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 170 GLN ** L 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 270 ASN M 48 ASN M 51 ASN N 222 ASN O 287 HIS U 33 ASN X 63 ASN ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 73 HIS n 13 GLN n 74 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.239 68780 Z= 0.600 Angle : 1.572 50.807 93023 Z= 1.017 Chirality : 0.311 6.442 10122 Planarity : 0.004 0.055 11607 Dihedral : 10.263 169.026 10191 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.81 % Favored : 96.18 % Rotamer: Outliers : 1.86 % Allowed : 11.12 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.19 (0.10), residues: 8031 helix: 1.61 (0.08), residues: 4449 sheet: -0.19 (0.25), residues: 392 loop : -0.18 (0.11), residues: 3190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP M 307 HIS 0.005 0.001 HIS L 570 PHE 0.031 0.002 PHE M 151 TYR 0.024 0.001 TYR 6 135 ARG 0.008 0.000 ARG r 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1154 residues out of total 7149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 1021 time to evaluate : 5.906 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: 6 53 SER cc_start: 0.9242 (m) cc_final: 0.9008 (p) REVERT: 6 72 MET cc_start: 0.9340 (tmm) cc_final: 0.8972 (ttt) REVERT: 1 269 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8674 (tt0) REVERT: 1 436 GLN cc_start: 0.8875 (pt0) cc_final: 0.8530 (tm-30) REVERT: 3 54 MET cc_start: 0.9537 (tpt) cc_final: 0.9323 (tpt) REVERT: 3 436 ARG cc_start: 0.8470 (ptp90) cc_final: 0.7821 (ptp90) REVERT: 3 447 LYS cc_start: 0.9235 (tppt) cc_final: 0.8985 (mmmt) REVERT: 3 651 LEU cc_start: 0.8671 (tp) cc_final: 0.8460 (tp) REVERT: P 185 TYR cc_start: 0.7224 (OUTLIER) cc_final: 0.6194 (m-80) REVERT: 7 30 ASP cc_start: 0.8899 (t0) cc_final: 0.8555 (t0) REVERT: S 38 GLN cc_start: 0.9129 (pp30) cc_final: 0.8510 (pp30) REVERT: S 42 GLU cc_start: 0.8743 (mp0) cc_final: 0.8434 (mp0) REVERT: S 81 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8413 (tp) REVERT: T 13 ASP cc_start: 0.9233 (t0) cc_final: 0.8601 (p0) REVERT: T 37 MET cc_start: 0.8910 (mpp) cc_final: 0.8033 (mpt) REVERT: T 47 GLN cc_start: 0.9042 (tm-30) cc_final: 0.8679 (tm-30) REVERT: T 52 MET cc_start: 0.7981 (ptm) cc_final: 0.7575 (mtm) REVERT: T 56 ASP cc_start: 0.7854 (p0) cc_final: 0.7399 (p0) REVERT: V 63 ASP cc_start: 0.8758 (t0) cc_final: 0.8294 (p0) REVERT: W 77 ASP cc_start: 0.9284 (t0) cc_final: 0.8871 (t0) REVERT: q 72 ASN cc_start: 0.9255 (t0) cc_final: 0.9008 (t0) REVERT: q 76 ASP cc_start: 0.9087 (t0) cc_final: 0.8831 (t0) REVERT: s 51 ASP cc_start: 0.9183 (t0) cc_final: 0.8894 (t0) REVERT: A 10 ASN cc_start: 0.9242 (m-40) cc_final: 0.9001 (m110) REVERT: J 56 PHE cc_start: 0.9540 (t80) cc_final: 0.9275 (t80) REVERT: J 91 PHE cc_start: 0.7615 (m-10) cc_final: 0.7346 (m-10) REVERT: J 111 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6932 (pp20) REVERT: K 29 THR cc_start: 0.9509 (m) cc_final: 0.9280 (p) REVERT: L 579 ASN cc_start: 0.8041 (t0) cc_final: 0.7639 (t0) REVERT: M 108 MET cc_start: 0.9441 (mtp) cc_final: 0.9174 (mtp) REVERT: M 114 GLU cc_start: 0.8558 (tm-30) cc_final: 0.7988 (tm-30) REVERT: O 206 TYR cc_start: 0.8821 (OUTLIER) cc_final: 0.7898 (m-10) REVERT: O 272 TYR cc_start: 0.9045 (m-10) cc_final: 0.8639 (m-80) REVERT: Y 1 VAL cc_start: 0.7049 (m) cc_final: 0.6206 (m) REVERT: Y 5 PHE cc_start: 0.8059 (m-10) cc_final: 0.7831 (m-80) REVERT: Y 8 TYR cc_start: 0.9504 (t80) cc_final: 0.9000 (t80) REVERT: Y 82 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.9073 (pttp) REVERT: c 5 ARG cc_start: 0.8285 (ttp-110) cc_final: 0.7731 (ttm-80) REVERT: c 11 LYS cc_start: 0.9298 (mmmt) cc_final: 0.8966 (mmmt) REVERT: c 38 ASP cc_start: 0.9251 (m-30) cc_final: 0.8993 (m-30) REVERT: f 8 ARG cc_start: 0.7871 (mpt180) cc_final: 0.7151 (mpt180) REVERT: f 30 ASP cc_start: 0.9136 (m-30) cc_final: 0.8877 (m-30) REVERT: i 6 ASP cc_start: 0.8857 (m-30) cc_final: 0.8443 (m-30) REVERT: i 12 GLN cc_start: 0.9109 (tt0) cc_final: 0.8876 (tm-30) REVERT: k 19 MET cc_start: 0.8128 (tpp) cc_final: 0.7798 (tpp) REVERT: k 35 GLU cc_start: 0.9062 (tm-30) cc_final: 0.8793 (tm-30) REVERT: l 148 GLU cc_start: 0.9048 (tp30) cc_final: 0.8772 (tp30) REVERT: m 109 ASP cc_start: 0.9125 (m-30) cc_final: 0.8719 (m-30) REVERT: n 122 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8536 (mm-30) REVERT: o 43 GLN cc_start: 0.9128 (tp40) cc_final: 0.8708 (tp-100) REVERT: o 47 ASP cc_start: 0.9368 (m-30) cc_final: 0.9149 (m-30) outliers start: 133 outliers final: 103 residues processed: 1101 average time/residue: 0.6805 time to fit residues: 1285.0956 Evaluate side-chains 1112 residues out of total 7149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 1002 time to evaluate : 5.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 64 CYS Chi-restraints excluded: chain 6 residue 95 VAL Chi-restraints excluded: chain 6 residue 177 ILE Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain 2 residue 105 THR Chi-restraints excluded: chain 2 residue 171 GLU Chi-restraints excluded: chain 1 residue 105 CYS Chi-restraints excluded: chain 1 residue 269 GLU Chi-restraints excluded: chain 1 residue 327 THR Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 216 THR Chi-restraints excluded: chain 3 residue 267 THR Chi-restraints excluded: chain 3 residue 402 ASN Chi-restraints excluded: chain 3 residue 424 ASP Chi-restraints excluded: chain 3 residue 536 ASP Chi-restraints excluded: chain 3 residue 596 ASP Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain 9 residue 28 MET Chi-restraints excluded: chain 9 residue 85 CYS Chi-restraints excluded: chain 9 residue 124 CYS Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 185 TYR Chi-restraints excluded: chain P residue 305 VAL Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 110 VAL Chi-restraints excluded: chain 7 residue 79 THR Chi-restraints excluded: chain S residue 77 SER Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 85 GLU Chi-restraints excluded: chain S residue 95 SER Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain W residue 48 THR Chi-restraints excluded: chain q residue 12 GLN Chi-restraints excluded: chain r residue 24 GLN Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 71 SER Chi-restraints excluded: chain s residue 30 THR Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 97 ASN Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain J residue 16 CYS Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 111 GLU Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 109 HIS Chi-restraints excluded: chain L residue 338 MET Chi-restraints excluded: chain L residue 341 MET Chi-restraints excluded: chain L residue 404 THR Chi-restraints excluded: chain L residue 410 LEU Chi-restraints excluded: chain L residue 472 ILE Chi-restraints excluded: chain L residue 544 LEU Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 459 MET Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain O residue 250 LYS Chi-restraints excluded: chain U residue 29 LYS Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain X residue 63 ASN Chi-restraints excluded: chain Y residue 82 LYS Chi-restraints excluded: chain Y residue 128 LYS Chi-restraints excluded: chain Y residue 133 GLU Chi-restraints excluded: chain Z residue 95 ILE Chi-restraints excluded: chain Z residue 99 ASP Chi-restraints excluded: chain Z residue 134 ASN Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain b residue 21 SER Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain b residue 34 ILE Chi-restraints excluded: chain c residue 8 VAL Chi-restraints excluded: chain c residue 24 SER Chi-restraints excluded: chain c residue 44 ARG Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain e residue 41 GLU Chi-restraints excluded: chain g residue 41 ASP Chi-restraints excluded: chain h residue 18 ASP Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 59 MET Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 13 GLU Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 37 VAL Chi-restraints excluded: chain l residue 28 MET Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 70 MET Chi-restraints excluded: chain l residue 96 SER Chi-restraints excluded: chain n residue 74 GLN Chi-restraints excluded: chain n residue 122 GLU Chi-restraints excluded: chain n residue 130 GLU Chi-restraints excluded: chain n residue 131 SER Chi-restraints excluded: chain n residue 149 MET Chi-restraints excluded: chain o residue 37 VAL Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 60 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 257 optimal weight: 0.7980 chunk 690 optimal weight: 8.9990 chunk 151 optimal weight: 5.9990 chunk 450 optimal weight: 10.0000 chunk 189 optimal weight: 10.0000 chunk 767 optimal weight: 30.0000 chunk 636 optimal weight: 20.0000 chunk 355 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 chunk 253 optimal weight: 5.9990 chunk 402 optimal weight: 4.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 184 ASN ** P 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 47 ASN H 97 ASN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 170 GLN ** L 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 270 ASN L 506 ASN U 33 ASN ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 73 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.240 68780 Z= 0.563 Angle : 1.562 50.800 93023 Z= 1.013 Chirality : 0.310 6.435 10122 Planarity : 0.004 0.055 11607 Dihedral : 10.163 168.880 10191 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.49 % Favored : 96.50 % Rotamer: Outliers : 1.85 % Allowed : 12.23 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.22 (0.10), residues: 8031 helix: 1.64 (0.08), residues: 4442 sheet: -0.13 (0.25), residues: 400 loop : -0.17 (0.11), residues: 3189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP M 307 HIS 0.007 0.001 HIS P 250 PHE 0.029 0.001 PHE M 151 TYR 0.023 0.001 TYR A 104 ARG 0.009 0.000 ARG r 5 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1163 residues out of total 7149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 1031 time to evaluate : 6.051 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: 6 53 SER cc_start: 0.9236 (m) cc_final: 0.8983 (p) REVERT: 1 269 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8654 (tt0) REVERT: 3 447 LYS cc_start: 0.9217 (tppt) cc_final: 0.8954 (mmmt) REVERT: 3 651 LEU cc_start: 0.8653 (tp) cc_final: 0.8450 (tp) REVERT: 9 174 ASP cc_start: 0.9150 (t70) cc_final: 0.8881 (t70) REVERT: P 185 TYR cc_start: 0.7257 (OUTLIER) cc_final: 0.6474 (m-80) REVERT: P 248 MET cc_start: 0.8562 (mmm) cc_final: 0.8347 (mtp) REVERT: 7 30 ASP cc_start: 0.8874 (t0) cc_final: 0.8531 (t0) REVERT: S 38 GLN cc_start: 0.9118 (pp30) cc_final: 0.8460 (pp30) REVERT: S 42 GLU cc_start: 0.8792 (mp0) cc_final: 0.8537 (mp0) REVERT: S 81 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8403 (tp) REVERT: T 37 MET cc_start: 0.8929 (mpp) cc_final: 0.8265 (mpt) REVERT: T 47 GLN cc_start: 0.9083 (tm-30) cc_final: 0.8715 (tm-30) REVERT: T 52 MET cc_start: 0.7988 (ptm) cc_final: 0.7574 (mtm) REVERT: T 56 ASP cc_start: 0.7884 (p0) cc_final: 0.7385 (p0) REVERT: V 63 ASP cc_start: 0.8755 (t0) cc_final: 0.8327 (p0) REVERT: W 77 ASP cc_start: 0.9287 (t0) cc_final: 0.8877 (t0) REVERT: q 72 ASN cc_start: 0.9245 (t0) cc_final: 0.9004 (t0) REVERT: q 76 ASP cc_start: 0.9109 (t0) cc_final: 0.8864 (t0) REVERT: s 51 ASP cc_start: 0.9208 (t0) cc_final: 0.8939 (t0) REVERT: J 56 PHE cc_start: 0.9537 (t80) cc_final: 0.9285 (t80) REVERT: J 91 PHE cc_start: 0.7637 (m-10) cc_final: 0.7361 (m-10) REVERT: K 29 THR cc_start: 0.9518 (m) cc_final: 0.9279 (p) REVERT: L 579 ASN cc_start: 0.8090 (t0) cc_final: 0.7639 (t0) REVERT: M 108 MET cc_start: 0.9436 (mtp) cc_final: 0.9148 (mtp) REVERT: M 114 GLU cc_start: 0.8541 (tm-30) cc_final: 0.7985 (tm-30) REVERT: M 350 MET cc_start: 0.9306 (ttm) cc_final: 0.9094 (ttm) REVERT: O 206 TYR cc_start: 0.8901 (OUTLIER) cc_final: 0.7956 (m-10) REVERT: O 272 TYR cc_start: 0.9025 (m-10) cc_final: 0.8626 (m-80) REVERT: Y 1 VAL cc_start: 0.7151 (m) cc_final: 0.6281 (m) REVERT: Y 5 PHE cc_start: 0.8013 (m-10) cc_final: 0.7792 (m-80) REVERT: Y 8 TYR cc_start: 0.9509 (t80) cc_final: 0.8994 (t80) REVERT: Y 42 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9116 (mm) REVERT: a 4 GLU cc_start: 0.9292 (tp30) cc_final: 0.9067 (tp30) REVERT: c 5 ARG cc_start: 0.8281 (ttp-110) cc_final: 0.7734 (ttm-80) REVERT: c 11 LYS cc_start: 0.9303 (mmmt) cc_final: 0.9002 (mmmt) REVERT: c 13 ASN cc_start: 0.9215 (t0) cc_final: 0.8835 (t0) REVERT: c 38 ASP cc_start: 0.9240 (m-30) cc_final: 0.8979 (m-30) REVERT: f 8 ARG cc_start: 0.7899 (mpt180) cc_final: 0.7151 (mpt180) REVERT: f 30 ASP cc_start: 0.9132 (m-30) cc_final: 0.8871 (m-30) REVERT: i 6 ASP cc_start: 0.8841 (m-30) cc_final: 0.8412 (m-30) REVERT: i 12 GLN cc_start: 0.9083 (tt0) cc_final: 0.8848 (tm-30) REVERT: k 19 MET cc_start: 0.8131 (tpp) cc_final: 0.7811 (tpp) REVERT: k 35 GLU cc_start: 0.9080 (tm-30) cc_final: 0.8803 (tm-30) REVERT: l 148 GLU cc_start: 0.9028 (tp30) cc_final: 0.8758 (tp30) REVERT: n 56 MET cc_start: 0.7621 (OUTLIER) cc_final: 0.7351 (tpp) REVERT: n 122 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8541 (mm-30) REVERT: o 43 GLN cc_start: 0.9109 (tp40) cc_final: 0.8715 (tp-100) REVERT: o 47 ASP cc_start: 0.9350 (m-30) cc_final: 0.9148 (m-30) outliers start: 132 outliers final: 100 residues processed: 1108 average time/residue: 0.6450 time to fit residues: 1212.9677 Evaluate side-chains 1115 residues out of total 7149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 1008 time to evaluate : 5.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 64 CYS Chi-restraints excluded: chain 6 residue 95 VAL Chi-restraints excluded: chain 6 residue 177 ILE Chi-restraints excluded: chain 6 residue 181 GLN Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain 2 residue 105 THR Chi-restraints excluded: chain 2 residue 171 GLU Chi-restraints excluded: chain 1 residue 105 CYS Chi-restraints excluded: chain 1 residue 269 GLU Chi-restraints excluded: chain 1 residue 327 THR Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 216 THR Chi-restraints excluded: chain 3 residue 267 THR Chi-restraints excluded: chain 3 residue 402 ASN Chi-restraints excluded: chain 3 residue 424 ASP Chi-restraints excluded: chain 3 residue 536 ASP Chi-restraints excluded: chain 3 residue 596 ASP Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain 9 residue 28 MET Chi-restraints excluded: chain 9 residue 85 CYS Chi-restraints excluded: chain 9 residue 124 CYS Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 185 TYR Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 305 VAL Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain 7 residue 79 THR Chi-restraints excluded: chain S residue 18 ILE Chi-restraints excluded: chain S residue 77 SER Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 85 GLU Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain q residue 12 GLN Chi-restraints excluded: chain r residue 24 GLN Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 71 SER Chi-restraints excluded: chain s residue 30 THR Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain J residue 16 CYS Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 109 HIS Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 338 MET Chi-restraints excluded: chain L residue 341 MET Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 404 THR Chi-restraints excluded: chain L residue 410 LEU Chi-restraints excluded: chain L residue 472 ILE Chi-restraints excluded: chain L residue 544 LEU Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 459 MET Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain O residue 250 LYS Chi-restraints excluded: chain U residue 12 LYS Chi-restraints excluded: chain U residue 29 LYS Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain Y residue 128 LYS Chi-restraints excluded: chain Y residue 133 GLU Chi-restraints excluded: chain Z residue 95 ILE Chi-restraints excluded: chain Z residue 99 ASP Chi-restraints excluded: chain Z residue 134 ASN Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain b residue 21 SER Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain b residue 29 ILE Chi-restraints excluded: chain b residue 34 ILE Chi-restraints excluded: chain c residue 8 VAL Chi-restraints excluded: chain c residue 24 SER Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain e residue 41 GLU Chi-restraints excluded: chain g residue 41 ASP Chi-restraints excluded: chain h residue 18 ASP Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 13 GLU Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain l residue 28 MET Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 96 SER Chi-restraints excluded: chain n residue 56 MET Chi-restraints excluded: chain n residue 122 GLU Chi-restraints excluded: chain n residue 130 GLU Chi-restraints excluded: chain n residue 131 SER Chi-restraints excluded: chain n residue 149 MET Chi-restraints excluded: chain o residue 37 VAL Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 60 THR Chi-restraints excluded: chain p residue 83 CYS Chi-restraints excluded: chain p residue 107 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 739 optimal weight: 0.4980 chunk 86 optimal weight: 9.9990 chunk 437 optimal weight: 7.9990 chunk 560 optimal weight: 3.9990 chunk 434 optimal weight: 5.9990 chunk 645 optimal weight: 10.0000 chunk 428 optimal weight: 5.9990 chunk 764 optimal weight: 10.0000 chunk 478 optimal weight: 4.9990 chunk 465 optimal weight: 5.9990 chunk 352 optimal weight: 0.0070 overall best weight: 3.1004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 436 GLN ** P 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 47 ASN r 8 GLN ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN J 85 ASN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 270 ASN U 33 ASN X 63 ASN ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 78 ASN i 73 HIS n 74 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.243 68780 Z= 0.539 Angle : 1.554 50.783 93023 Z= 1.010 Chirality : 0.310 6.426 10122 Planarity : 0.004 0.055 11607 Dihedral : 9.995 169.352 10191 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.54 % Favored : 96.45 % Rotamer: Outliers : 1.80 % Allowed : 12.74 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.29 (0.10), residues: 8031 helix: 1.70 (0.08), residues: 4433 sheet: -0.18 (0.25), residues: 404 loop : -0.14 (0.11), residues: 3194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP M 307 HIS 0.005 0.001 HIS P 250 PHE 0.027 0.001 PHE M 151 TYR 0.022 0.001 TYR A 104 ARG 0.010 0.000 ARG S 88 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1161 residues out of total 7149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 1032 time to evaluate : 6.076 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: 6 53 SER cc_start: 0.9260 (m) cc_final: 0.8977 (p) REVERT: 1 269 GLU cc_start: 0.9081 (OUTLIER) cc_final: 0.8649 (tt0) REVERT: 1 436 GLN cc_start: 0.8709 (pt0) cc_final: 0.8302 (tm-30) REVERT: 3 447 LYS cc_start: 0.9239 (tppt) cc_final: 0.8968 (mmmt) REVERT: 9 174 ASP cc_start: 0.9130 (t70) cc_final: 0.8860 (t70) REVERT: P 185 TYR cc_start: 0.7417 (OUTLIER) cc_final: 0.6963 (m-80) REVERT: 7 30 ASP cc_start: 0.8863 (t0) cc_final: 0.8519 (t0) REVERT: 7 51 GLU cc_start: 0.8880 (tt0) cc_final: 0.8615 (tp30) REVERT: S 38 GLN cc_start: 0.9123 (pp30) cc_final: 0.8469 (pp30) REVERT: S 42 GLU cc_start: 0.8810 (mp0) cc_final: 0.8589 (mp0) REVERT: S 81 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8424 (tp) REVERT: T 37 MET cc_start: 0.8944 (mpp) cc_final: 0.8313 (mpt) REVERT: T 47 GLN cc_start: 0.9044 (tm-30) cc_final: 0.8699 (tm-30) REVERT: T 52 MET cc_start: 0.7882 (ptm) cc_final: 0.7507 (mtm) REVERT: T 56 ASP cc_start: 0.7867 (p0) cc_final: 0.7346 (p0) REVERT: V 63 ASP cc_start: 0.8745 (t0) cc_final: 0.8328 (p0) REVERT: W 17 THR cc_start: 0.8166 (p) cc_final: 0.7946 (t) REVERT: W 77 ASP cc_start: 0.9286 (t0) cc_final: 0.8878 (t0) REVERT: q 72 ASN cc_start: 0.9238 (t0) cc_final: 0.9018 (t0) REVERT: q 76 ASP cc_start: 0.9066 (t0) cc_final: 0.8833 (t0) REVERT: s 51 ASP cc_start: 0.9185 (t0) cc_final: 0.8945 (t0) REVERT: J 91 PHE cc_start: 0.7652 (m-10) cc_final: 0.7382 (m-10) REVERT: K 29 THR cc_start: 0.9514 (m) cc_final: 0.9282 (p) REVERT: L 579 ASN cc_start: 0.8070 (t0) cc_final: 0.7617 (t0) REVERT: M 108 MET cc_start: 0.9412 (mtp) cc_final: 0.9134 (mtp) REVERT: M 114 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8056 (tm-30) REVERT: M 139 GLN cc_start: 0.8747 (mp10) cc_final: 0.8428 (mt0) REVERT: N 225 MET cc_start: 0.8850 (mmt) cc_final: 0.8265 (mmp) REVERT: N 284 MET cc_start: 0.9050 (mmt) cc_final: 0.8821 (mmt) REVERT: O 206 TYR cc_start: 0.8904 (OUTLIER) cc_final: 0.7970 (m-10) REVERT: O 272 TYR cc_start: 0.8996 (m-10) cc_final: 0.8577 (m-80) REVERT: Y 1 VAL cc_start: 0.7243 (m) cc_final: 0.6414 (m) REVERT: Y 5 PHE cc_start: 0.8036 (m-10) cc_final: 0.7834 (m-80) REVERT: Y 8 TYR cc_start: 0.9494 (t80) cc_final: 0.8983 (t80) REVERT: Y 42 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9109 (mm) REVERT: a 4 GLU cc_start: 0.9291 (tp30) cc_final: 0.9075 (tp30) REVERT: a 59 ARG cc_start: 0.8858 (mmm-85) cc_final: 0.8632 (mmm-85) REVERT: c 5 ARG cc_start: 0.8281 (ttp-110) cc_final: 0.7732 (ttm-80) REVERT: c 13 ASN cc_start: 0.9195 (t0) cc_final: 0.8806 (t0) REVERT: c 38 ASP cc_start: 0.9237 (m-30) cc_final: 0.8971 (m-30) REVERT: f 8 ARG cc_start: 0.7951 (mpt180) cc_final: 0.7221 (mpt180) REVERT: f 30 ASP cc_start: 0.9104 (m-30) cc_final: 0.8866 (m-30) REVERT: h 68 LYS cc_start: 0.9289 (tmtt) cc_final: 0.9052 (tptp) REVERT: i 6 ASP cc_start: 0.8826 (m-30) cc_final: 0.8395 (m-30) REVERT: i 12 GLN cc_start: 0.9071 (tt0) cc_final: 0.8848 (tm-30) REVERT: k 19 MET cc_start: 0.8128 (tpp) cc_final: 0.7798 (tpp) REVERT: k 35 GLU cc_start: 0.9088 (tm-30) cc_final: 0.8865 (tm-30) REVERT: l 148 GLU cc_start: 0.9032 (tp30) cc_final: 0.8766 (tp30) REVERT: m 109 ASP cc_start: 0.9121 (m-30) cc_final: 0.8698 (m-30) REVERT: n 56 MET cc_start: 0.7485 (OUTLIER) cc_final: 0.7242 (tpp) REVERT: n 122 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8530 (mm-30) REVERT: o 43 GLN cc_start: 0.9101 (tp40) cc_final: 0.8700 (tp-100) REVERT: o 47 ASP cc_start: 0.9336 (m-30) cc_final: 0.9125 (m-30) outliers start: 129 outliers final: 98 residues processed: 1106 average time/residue: 0.6445 time to fit residues: 1211.6050 Evaluate side-chains 1118 residues out of total 7149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1013 time to evaluate : 5.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 64 CYS Chi-restraints excluded: chain 6 residue 95 VAL Chi-restraints excluded: chain 6 residue 177 ILE Chi-restraints excluded: chain 6 residue 181 GLN Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain 2 residue 171 GLU Chi-restraints excluded: chain 1 residue 105 CYS Chi-restraints excluded: chain 1 residue 269 GLU Chi-restraints excluded: chain 1 residue 327 THR Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 216 THR Chi-restraints excluded: chain 3 residue 267 THR Chi-restraints excluded: chain 3 residue 402 ASN Chi-restraints excluded: chain 3 residue 424 ASP Chi-restraints excluded: chain 3 residue 536 ASP Chi-restraints excluded: chain 3 residue 596 ASP Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain 9 residue 28 MET Chi-restraints excluded: chain 9 residue 85 CYS Chi-restraints excluded: chain 9 residue 124 CYS Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 185 TYR Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 305 VAL Chi-restraints excluded: chain P residue 338 LYS Chi-restraints excluded: chain Q residue 9 GLN Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain 7 residue 79 THR Chi-restraints excluded: chain S residue 18 ILE Chi-restraints excluded: chain S residue 77 SER Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 85 GLU Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain W residue 94 GLU Chi-restraints excluded: chain q residue 12 GLN Chi-restraints excluded: chain r residue 24 GLN Chi-restraints excluded: chain s residue 65 GLU Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 91 MET Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain J residue 16 CYS Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 109 HIS Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 338 MET Chi-restraints excluded: chain L residue 341 MET Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 404 THR Chi-restraints excluded: chain L residue 410 LEU Chi-restraints excluded: chain L residue 544 LEU Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain O residue 250 LYS Chi-restraints excluded: chain U residue 29 LYS Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain X residue 63 ASN Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain Y residue 128 LYS Chi-restraints excluded: chain Y residue 133 GLU Chi-restraints excluded: chain Z residue 95 ILE Chi-restraints excluded: chain Z residue 134 ASN Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain b residue 21 SER Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain b residue 29 ILE Chi-restraints excluded: chain c residue 8 VAL Chi-restraints excluded: chain c residue 24 SER Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain e residue 18 MET Chi-restraints excluded: chain e residue 41 GLU Chi-restraints excluded: chain h residue 18 ASP Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain j residue 13 GLU Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 70 MET Chi-restraints excluded: chain l residue 96 SER Chi-restraints excluded: chain n residue 56 MET Chi-restraints excluded: chain n residue 74 GLN Chi-restraints excluded: chain n residue 122 GLU Chi-restraints excluded: chain n residue 130 GLU Chi-restraints excluded: chain n residue 131 SER Chi-restraints excluded: chain n residue 149 MET Chi-restraints excluded: chain o residue 37 VAL Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 60 THR Chi-restraints excluded: chain p residue 83 CYS Chi-restraints excluded: chain p residue 107 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 472 optimal weight: 5.9990 chunk 305 optimal weight: 9.9990 chunk 456 optimal weight: 6.9990 chunk 230 optimal weight: 0.0370 chunk 150 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 485 optimal weight: 7.9990 chunk 520 optimal weight: 7.9990 chunk 377 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 600 optimal weight: 9.9990 overall best weight: 5.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 421 GLN ** P 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 72 GLN ** T 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 GLN H 97 ASN J 85 ASN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 270 ASN U 33 ASN X 63 ASN ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 73 HIS ** n 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.241 68780 Z= 0.562 Angle : 1.563 50.793 93023 Z= 1.013 Chirality : 0.310 6.432 10122 Planarity : 0.004 0.054 11607 Dihedral : 9.959 168.869 10191 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.52 % Favored : 96.46 % Rotamer: Outliers : 1.90 % Allowed : 12.97 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.27 (0.10), residues: 8031 helix: 1.67 (0.08), residues: 4441 sheet: -0.06 (0.25), residues: 390 loop : -0.15 (0.11), residues: 3200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP M 307 HIS 0.007 0.001 HIS n 75 PHE 0.028 0.001 PHE M 151 TYR 0.022 0.001 TYR A 104 ARG 0.010 0.000 ARG S 88 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1159 residues out of total 7149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1023 time to evaluate : 6.057 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: 6 53 SER cc_start: 0.9261 (m) cc_final: 0.8985 (p) REVERT: 1 269 GLU cc_start: 0.9093 (OUTLIER) cc_final: 0.8667 (tt0) REVERT: 1 436 GLN cc_start: 0.8735 (pt0) cc_final: 0.8320 (tm-30) REVERT: 3 35 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8279 (tmm) REVERT: 3 306 MET cc_start: 0.9161 (tpp) cc_final: 0.8631 (tpp) REVERT: 3 436 ARG cc_start: 0.8382 (ptp90) cc_final: 0.7813 (ptp90) REVERT: 3 447 LYS cc_start: 0.9250 (tppt) cc_final: 0.8981 (mmmt) REVERT: P 185 TYR cc_start: 0.7370 (OUTLIER) cc_final: 0.7007 (m-80) REVERT: 7 30 ASP cc_start: 0.8876 (t0) cc_final: 0.8505 (t0) REVERT: S 38 GLN cc_start: 0.9136 (pp30) cc_final: 0.8508 (pp30) REVERT: S 42 GLU cc_start: 0.8726 (mp0) cc_final: 0.8520 (mp0) REVERT: S 81 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8400 (tp) REVERT: T 37 MET cc_start: 0.8910 (mpp) cc_final: 0.8294 (mpt) REVERT: T 47 GLN cc_start: 0.9084 (tm-30) cc_final: 0.8739 (tm-30) REVERT: T 52 MET cc_start: 0.7903 (ptm) cc_final: 0.7535 (mtm) REVERT: T 56 ASP cc_start: 0.7881 (p0) cc_final: 0.7389 (p0) REVERT: V 63 ASP cc_start: 0.8759 (t0) cc_final: 0.8349 (p0) REVERT: W 17 THR cc_start: 0.8147 (p) cc_final: 0.7885 (t) REVERT: W 77 ASP cc_start: 0.9299 (t0) cc_final: 0.8901 (t0) REVERT: q 72 ASN cc_start: 0.9242 (t0) cc_final: 0.9001 (t0) REVERT: q 76 ASP cc_start: 0.9101 (t0) cc_final: 0.8866 (t0) REVERT: s 51 ASP cc_start: 0.9169 (t0) cc_final: 0.8888 (t0) REVERT: J 91 PHE cc_start: 0.7706 (m-10) cc_final: 0.7454 (m-10) REVERT: J 127 GLU cc_start: 0.9066 (tt0) cc_final: 0.8766 (tp30) REVERT: K 29 THR cc_start: 0.9525 (m) cc_final: 0.9285 (p) REVERT: L 579 ASN cc_start: 0.8077 (t0) cc_final: 0.7563 (t0) REVERT: M 108 MET cc_start: 0.9427 (mtp) cc_final: 0.9150 (mtp) REVERT: M 114 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8064 (tm-30) REVERT: M 139 GLN cc_start: 0.8767 (mp10) cc_final: 0.8429 (mp10) REVERT: N 284 MET cc_start: 0.9068 (mmt) cc_final: 0.8814 (mmt) REVERT: O 206 TYR cc_start: 0.8897 (OUTLIER) cc_final: 0.7943 (m-10) REVERT: O 272 TYR cc_start: 0.9013 (m-10) cc_final: 0.8598 (m-80) REVERT: O 298 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8582 (mp0) REVERT: Y 1 VAL cc_start: 0.7384 (m) cc_final: 0.6569 (m) REVERT: Y 5 PHE cc_start: 0.8050 (m-10) cc_final: 0.7787 (m-80) REVERT: Y 8 TYR cc_start: 0.9502 (t80) cc_final: 0.8972 (t80) REVERT: a 4 GLU cc_start: 0.9305 (tp30) cc_final: 0.9098 (tp30) REVERT: c 5 ARG cc_start: 0.8274 (ttp-110) cc_final: 0.7720 (ttm-80) REVERT: c 13 ASN cc_start: 0.9216 (t0) cc_final: 0.8829 (t0) REVERT: c 38 ASP cc_start: 0.9239 (m-30) cc_final: 0.8972 (m-30) REVERT: f 8 ARG cc_start: 0.7915 (mpt180) cc_final: 0.7199 (mpt180) REVERT: f 30 ASP cc_start: 0.9113 (m-30) cc_final: 0.8879 (m-30) REVERT: h 68 LYS cc_start: 0.9263 (tmtt) cc_final: 0.9057 (tptp) REVERT: i 6 ASP cc_start: 0.8836 (m-30) cc_final: 0.8405 (m-30) REVERT: i 12 GLN cc_start: 0.9083 (tt0) cc_final: 0.8847 (tm-30) REVERT: k 19 MET cc_start: 0.8142 (tpp) cc_final: 0.7812 (tpp) REVERT: k 35 GLU cc_start: 0.9156 (tm-30) cc_final: 0.8900 (tm-30) REVERT: l 148 GLU cc_start: 0.9046 (tp30) cc_final: 0.8775 (tp30) REVERT: m 86 SER cc_start: 0.9299 (m) cc_final: 0.9073 (m) REVERT: m 109 ASP cc_start: 0.9123 (m-30) cc_final: 0.8677 (m-30) REVERT: n 56 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.7212 (tpp) REVERT: n 122 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8550 (mm-30) REVERT: o 43 GLN cc_start: 0.9098 (tp40) cc_final: 0.8772 (tp-100) outliers start: 136 outliers final: 108 residues processed: 1098 average time/residue: 0.6721 time to fit residues: 1266.0935 Evaluate side-chains 1120 residues out of total 7149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 1004 time to evaluate : 5.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 64 CYS Chi-restraints excluded: chain 6 residue 95 VAL Chi-restraints excluded: chain 6 residue 177 ILE Chi-restraints excluded: chain 6 residue 181 GLN Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain 2 residue 105 THR Chi-restraints excluded: chain 2 residue 171 GLU Chi-restraints excluded: chain 1 residue 105 CYS Chi-restraints excluded: chain 1 residue 269 GLU Chi-restraints excluded: chain 1 residue 327 THR Chi-restraints excluded: chain 1 residue 362 CYS Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 35 MET Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 216 THR Chi-restraints excluded: chain 3 residue 267 THR Chi-restraints excluded: chain 3 residue 402 ASN Chi-restraints excluded: chain 3 residue 424 ASP Chi-restraints excluded: chain 3 residue 536 ASP Chi-restraints excluded: chain 3 residue 596 ASP Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain 9 residue 28 MET Chi-restraints excluded: chain 9 residue 85 CYS Chi-restraints excluded: chain 9 residue 124 CYS Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 185 TYR Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 305 VAL Chi-restraints excluded: chain P residue 338 LYS Chi-restraints excluded: chain Q residue 9 GLN Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 110 VAL Chi-restraints excluded: chain 7 residue 19 ASP Chi-restraints excluded: chain 7 residue 79 THR Chi-restraints excluded: chain S residue 18 ILE Chi-restraints excluded: chain S residue 77 SER Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 85 GLU Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain W residue 94 GLU Chi-restraints excluded: chain q residue 12 GLN Chi-restraints excluded: chain r residue 24 GLN Chi-restraints excluded: chain s residue 30 THR Chi-restraints excluded: chain s residue 65 GLU Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 91 MET Chi-restraints excluded: chain H residue 97 ASN Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain J residue 16 CYS Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 109 HIS Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 338 MET Chi-restraints excluded: chain L residue 341 MET Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 404 THR Chi-restraints excluded: chain L residue 410 LEU Chi-restraints excluded: chain L residue 544 LEU Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 375 LEU Chi-restraints excluded: chain M residue 433 GLU Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain O residue 250 LYS Chi-restraints excluded: chain O residue 298 GLU Chi-restraints excluded: chain U residue 12 LYS Chi-restraints excluded: chain U residue 29 LYS Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain X residue 63 ASN Chi-restraints excluded: chain Y residue 128 LYS Chi-restraints excluded: chain Y residue 133 GLU Chi-restraints excluded: chain Z residue 95 ILE Chi-restraints excluded: chain Z residue 99 ASP Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain b residue 21 SER Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain b residue 29 ILE Chi-restraints excluded: chain b residue 34 ILE Chi-restraints excluded: chain c residue 8 VAL Chi-restraints excluded: chain c residue 24 SER Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain e residue 18 MET Chi-restraints excluded: chain e residue 41 GLU Chi-restraints excluded: chain f residue 14 ILE Chi-restraints excluded: chain h residue 18 ASP Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain j residue 13 GLU Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 70 MET Chi-restraints excluded: chain l residue 96 SER Chi-restraints excluded: chain n residue 56 MET Chi-restraints excluded: chain n residue 122 GLU Chi-restraints excluded: chain n residue 130 GLU Chi-restraints excluded: chain n residue 131 SER Chi-restraints excluded: chain n residue 149 MET Chi-restraints excluded: chain o residue 23 SER Chi-restraints excluded: chain o residue 37 VAL Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 60 THR Chi-restraints excluded: chain p residue 83 CYS Chi-restraints excluded: chain p residue 107 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 695 optimal weight: 3.9990 chunk 732 optimal weight: 6.9990 chunk 668 optimal weight: 20.0000 chunk 712 optimal weight: 0.9990 chunk 428 optimal weight: 8.9990 chunk 310 optimal weight: 2.9990 chunk 559 optimal weight: 9.9990 chunk 218 optimal weight: 7.9990 chunk 643 optimal weight: 0.4980 chunk 673 optimal weight: 6.9990 chunk 709 optimal weight: 4.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 421 GLN ** P 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 10 ASN H 97 ASN J 85 ASN ** L 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 270 ASN L 580 GLN U 33 ASN X 63 ASN ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 73 HIS n 74 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.244 68780 Z= 0.537 Angle : 1.558 50.792 93023 Z= 1.011 Chirality : 0.310 6.423 10122 Planarity : 0.004 0.054 11607 Dihedral : 9.798 169.474 10191 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.42 % Favored : 96.56 % Rotamer: Outliers : 1.73 % Allowed : 13.37 % Favored : 84.89 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.33 (0.10), residues: 8031 helix: 1.73 (0.08), residues: 4420 sheet: -0.11 (0.25), residues: 402 loop : -0.10 (0.11), residues: 3209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP M 307 HIS 0.005 0.001 HIS P 250 PHE 0.029 0.001 PHE J 56 TYR 0.023 0.001 TYR L 422 ARG 0.010 0.000 ARG S 88 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1164 residues out of total 7149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 1040 time to evaluate : 6.149 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: 6 71 HIS cc_start: 0.9165 (OUTLIER) cc_final: 0.8437 (t-90) REVERT: C 49 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8297 (mt-10) REVERT: 1 269 GLU cc_start: 0.9076 (OUTLIER) cc_final: 0.8644 (tt0) REVERT: 1 436 GLN cc_start: 0.8712 (pt0) cc_final: 0.8274 (tm-30) REVERT: 3 35 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8306 (tmm) REVERT: 3 306 MET cc_start: 0.9151 (tpp) cc_final: 0.8696 (tpp) REVERT: 3 447 LYS cc_start: 0.9244 (tppt) cc_final: 0.8964 (mmmt) REVERT: 7 30 ASP cc_start: 0.8878 (t0) cc_final: 0.8519 (t0) REVERT: 7 51 GLU cc_start: 0.8881 (tt0) cc_final: 0.8628 (tp30) REVERT: S 38 GLN cc_start: 0.9124 (pp30) cc_final: 0.8464 (pp30) REVERT: S 42 GLU cc_start: 0.8809 (mp0) cc_final: 0.8597 (mp0) REVERT: S 81 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8428 (tp) REVERT: T 37 MET cc_start: 0.8906 (mpp) cc_final: 0.8302 (mpt) REVERT: T 47 GLN cc_start: 0.9078 (tm-30) cc_final: 0.8749 (tm-30) REVERT: T 52 MET cc_start: 0.7859 (ptm) cc_final: 0.7468 (mtm) REVERT: T 56 ASP cc_start: 0.7859 (p0) cc_final: 0.7364 (p0) REVERT: V 63 ASP cc_start: 0.8752 (t0) cc_final: 0.8354 (p0) REVERT: W 77 ASP cc_start: 0.9297 (t0) cc_final: 0.8894 (t0) REVERT: q 72 ASN cc_start: 0.9229 (t0) cc_final: 0.8996 (t0) REVERT: q 76 ASP cc_start: 0.9049 (t0) cc_final: 0.8783 (t0) REVERT: s 51 ASP cc_start: 0.9179 (t0) cc_final: 0.8937 (t0) REVERT: H 192 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7873 (mm-30) REVERT: J 91 PHE cc_start: 0.7783 (m-10) cc_final: 0.7480 (m-10) REVERT: J 127 GLU cc_start: 0.9035 (tt0) cc_final: 0.8741 (tp30) REVERT: K 29 THR cc_start: 0.9524 (m) cc_final: 0.9299 (p) REVERT: L 503 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8385 (mm-30) REVERT: L 579 ASN cc_start: 0.8058 (t0) cc_final: 0.7536 (t0) REVERT: M 108 MET cc_start: 0.9419 (mtp) cc_final: 0.9155 (mtp) REVERT: M 114 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8056 (tm-30) REVERT: M 123 GLU cc_start: 0.9097 (mp0) cc_final: 0.8853 (mp0) REVERT: M 139 GLN cc_start: 0.8741 (mp10) cc_final: 0.8342 (mt0) REVERT: M 310 MET cc_start: 0.9255 (tmm) cc_final: 0.8714 (ttp) REVERT: N 225 MET cc_start: 0.8822 (mmt) cc_final: 0.8263 (mmp) REVERT: N 284 MET cc_start: 0.8975 (mmt) cc_final: 0.8761 (mmt) REVERT: O 206 TYR cc_start: 0.8885 (OUTLIER) cc_final: 0.7929 (m-10) REVERT: O 272 TYR cc_start: 0.8988 (m-10) cc_final: 0.8576 (m-80) REVERT: O 298 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8560 (mp0) REVERT: Y 1 VAL cc_start: 0.7607 (m) cc_final: 0.6795 (m) REVERT: Y 5 PHE cc_start: 0.7990 (m-10) cc_final: 0.7738 (m-80) REVERT: Y 8 TYR cc_start: 0.9484 (t80) cc_final: 0.8964 (t80) REVERT: a 4 GLU cc_start: 0.9304 (tp30) cc_final: 0.9095 (tp30) REVERT: c 5 ARG cc_start: 0.8280 (ttp-110) cc_final: 0.7732 (ttm-80) REVERT: c 13 ASN cc_start: 0.9196 (t0) cc_final: 0.8833 (t0) REVERT: c 38 ASP cc_start: 0.9235 (m-30) cc_final: 0.8966 (m-30) REVERT: d 9 GLU cc_start: 0.8850 (pt0) cc_final: 0.8417 (pm20) REVERT: d 103 GLU cc_start: 0.9165 (mm-30) cc_final: 0.8382 (tm-30) REVERT: f 8 ARG cc_start: 0.7900 (mpt180) cc_final: 0.7220 (mpt180) REVERT: f 30 ASP cc_start: 0.9107 (m-30) cc_final: 0.8883 (m-30) REVERT: g 22 MET cc_start: 0.4333 (mmm) cc_final: 0.3610 (mmm) REVERT: h 68 LYS cc_start: 0.9252 (tmtt) cc_final: 0.8996 (tptp) REVERT: i 6 ASP cc_start: 0.8814 (m-30) cc_final: 0.8381 (m-30) REVERT: i 12 GLN cc_start: 0.9070 (tt0) cc_final: 0.8847 (tm-30) REVERT: k 35 GLU cc_start: 0.9162 (tm-30) cc_final: 0.8871 (tm-30) REVERT: l 148 GLU cc_start: 0.9016 (tp30) cc_final: 0.8731 (tp30) REVERT: m 86 SER cc_start: 0.9280 (m) cc_final: 0.9061 (m) REVERT: m 109 ASP cc_start: 0.9133 (m-30) cc_final: 0.8684 (m-30) REVERT: n 56 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.7250 (tpp) REVERT: n 122 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8531 (mm-30) REVERT: o 35 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8519 (mm-30) outliers start: 124 outliers final: 97 residues processed: 1113 average time/residue: 0.6456 time to fit residues: 1220.1371 Evaluate side-chains 1125 residues out of total 7149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1020 time to evaluate : 5.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 64 CYS Chi-restraints excluded: chain 6 residue 71 HIS Chi-restraints excluded: chain 6 residue 95 VAL Chi-restraints excluded: chain 6 residue 177 ILE Chi-restraints excluded: chain 6 residue 181 GLN Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain 2 residue 171 GLU Chi-restraints excluded: chain 1 residue 105 CYS Chi-restraints excluded: chain 1 residue 269 GLU Chi-restraints excluded: chain 1 residue 327 THR Chi-restraints excluded: chain 1 residue 362 CYS Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 35 MET Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 216 THR Chi-restraints excluded: chain 3 residue 267 THR Chi-restraints excluded: chain 3 residue 402 ASN Chi-restraints excluded: chain 3 residue 424 ASP Chi-restraints excluded: chain 3 residue 536 ASP Chi-restraints excluded: chain 3 residue 596 ASP Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain 9 residue 85 CYS Chi-restraints excluded: chain 9 residue 124 CYS Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 185 TYR Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 305 VAL Chi-restraints excluded: chain S residue 18 ILE Chi-restraints excluded: chain S residue 77 SER Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 85 GLU Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 17 ASP Chi-restraints excluded: chain W residue 94 GLU Chi-restraints excluded: chain q residue 12 GLN Chi-restraints excluded: chain r residue 24 GLN Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 91 MET Chi-restraints excluded: chain H residue 97 ASN Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain J residue 16 CYS Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 109 HIS Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 338 MET Chi-restraints excluded: chain L residue 341 MET Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 404 THR Chi-restraints excluded: chain L residue 410 LEU Chi-restraints excluded: chain L residue 544 LEU Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 375 LEU Chi-restraints excluded: chain M residue 433 GLU Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain O residue 250 LYS Chi-restraints excluded: chain O residue 298 GLU Chi-restraints excluded: chain U residue 29 LYS Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain X residue 63 ASN Chi-restraints excluded: chain Y residue 128 LYS Chi-restraints excluded: chain Y residue 133 GLU Chi-restraints excluded: chain Z residue 95 ILE Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain b residue 7 PHE Chi-restraints excluded: chain b residue 21 SER Chi-restraints excluded: chain b residue 29 ILE Chi-restraints excluded: chain c residue 8 VAL Chi-restraints excluded: chain c residue 24 SER Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain e residue 18 MET Chi-restraints excluded: chain e residue 41 GLU Chi-restraints excluded: chain h residue 18 ASP Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain j residue 13 GLU Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain l residue 48 MET Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 96 SER Chi-restraints excluded: chain n residue 56 MET Chi-restraints excluded: chain n residue 74 GLN Chi-restraints excluded: chain n residue 122 GLU Chi-restraints excluded: chain n residue 130 GLU Chi-restraints excluded: chain n residue 131 SER Chi-restraints excluded: chain n residue 149 MET Chi-restraints excluded: chain o residue 23 SER Chi-restraints excluded: chain o residue 37 VAL Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 83 CYS Chi-restraints excluded: chain p residue 107 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 467 optimal weight: 8.9990 chunk 753 optimal weight: 20.0000 chunk 459 optimal weight: 3.9990 chunk 357 optimal weight: 3.9990 chunk 523 optimal weight: 5.9990 chunk 790 optimal weight: 8.9990 chunk 727 optimal weight: 0.9990 chunk 629 optimal weight: 20.0000 chunk 65 optimal weight: 0.0470 chunk 485 optimal weight: 5.9990 chunk 385 optimal weight: 5.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN H 287 HIS J 85 ASN ** L 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 270 ASN U 33 ASN X 63 ASN ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 73 HIS n 74 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.244 68780 Z= 0.539 Angle : 1.559 50.782 93023 Z= 1.011 Chirality : 0.310 6.424 10122 Planarity : 0.004 0.055 11607 Dihedral : 9.705 169.663 10191 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.47 % Favored : 96.51 % Rotamer: Outliers : 1.58 % Allowed : 13.69 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.35 (0.10), residues: 8031 helix: 1.74 (0.08), residues: 4421 sheet: -0.07 (0.25), residues: 397 loop : -0.09 (0.11), residues: 3213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP O 316 HIS 0.005 0.001 HIS T 35 PHE 0.032 0.001 PHE J 56 TYR 0.022 0.001 TYR L 422 ARG 0.011 0.000 ARG S 88 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16062 Ramachandran restraints generated. 8031 Oldfield, 0 Emsley, 8031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1140 residues out of total 7149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1027 time to evaluate : 6.052 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: 6 71 HIS cc_start: 0.9169 (OUTLIER) cc_final: 0.8455 (t-90) REVERT: C 49 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8274 (mt-10) REVERT: 1 269 GLU cc_start: 0.9072 (OUTLIER) cc_final: 0.8648 (tt0) REVERT: 1 436 GLN cc_start: 0.8705 (pt0) cc_final: 0.8270 (tm-30) REVERT: 3 35 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8309 (tmm) REVERT: 3 436 ARG cc_start: 0.8419 (ptp90) cc_final: 0.7786 (ptp90) REVERT: 3 447 LYS cc_start: 0.9236 (tppt) cc_final: 0.8965 (mmmt) REVERT: Q 14 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7847 (t0) REVERT: 7 30 ASP cc_start: 0.8862 (t0) cc_final: 0.8499 (t0) REVERT: 7 51 GLU cc_start: 0.8877 (tt0) cc_final: 0.8644 (tp30) REVERT: S 38 GLN cc_start: 0.9112 (pp30) cc_final: 0.8447 (pp30) REVERT: S 42 GLU cc_start: 0.8807 (mp0) cc_final: 0.8596 (mp0) REVERT: S 81 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8443 (tp) REVERT: T 37 MET cc_start: 0.8907 (mpp) cc_final: 0.8297 (mpt) REVERT: T 47 GLN cc_start: 0.9091 (tm-30) cc_final: 0.8763 (tm-30) REVERT: T 52 MET cc_start: 0.7843 (ptm) cc_final: 0.7474 (mtm) REVERT: T 56 ASP cc_start: 0.7861 (p0) cc_final: 0.7367 (p0) REVERT: V 63 ASP cc_start: 0.8754 (t0) cc_final: 0.8356 (p0) REVERT: q 72 ASN cc_start: 0.9231 (t0) cc_final: 0.8994 (t0) REVERT: q 76 ASP cc_start: 0.9049 (t0) cc_final: 0.8723 (t0) REVERT: q 81 MET cc_start: 0.9449 (mtp) cc_final: 0.9248 (mtm) REVERT: s 51 ASP cc_start: 0.9154 (t0) cc_final: 0.8891 (t0) REVERT: J 91 PHE cc_start: 0.7793 (m-10) cc_final: 0.7493 (m-10) REVERT: J 127 GLU cc_start: 0.9037 (tt0) cc_final: 0.8742 (tp30) REVERT: K 29 THR cc_start: 0.9525 (m) cc_final: 0.9299 (p) REVERT: K 89 TYR cc_start: 0.9133 (m-80) cc_final: 0.8890 (m-80) REVERT: L 503 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8403 (mm-30) REVERT: L 579 ASN cc_start: 0.8072 (t0) cc_final: 0.7525 (t0) REVERT: M 108 MET cc_start: 0.9418 (mtp) cc_final: 0.9156 (mtp) REVERT: M 114 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8068 (tm-30) REVERT: M 139 GLN cc_start: 0.8723 (mp10) cc_final: 0.8317 (mt0) REVERT: N 225 MET cc_start: 0.8816 (mmt) cc_final: 0.8270 (mmp) REVERT: N 284 MET cc_start: 0.8952 (mmt) cc_final: 0.8737 (mmt) REVERT: O 206 TYR cc_start: 0.8881 (OUTLIER) cc_final: 0.7932 (m-10) REVERT: O 272 TYR cc_start: 0.8993 (m-10) cc_final: 0.8574 (m-80) REVERT: O 298 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8563 (mp0) REVERT: Y 1 VAL cc_start: 0.7870 (m) cc_final: 0.7070 (m) REVERT: Y 5 PHE cc_start: 0.7999 (m-10) cc_final: 0.7793 (m-80) REVERT: Y 8 TYR cc_start: 0.9487 (t80) cc_final: 0.8972 (t80) REVERT: c 5 ARG cc_start: 0.8282 (ttp-110) cc_final: 0.7732 (ttm-80) REVERT: c 13 ASN cc_start: 0.9180 (t0) cc_final: 0.8814 (t0) REVERT: c 38 ASP cc_start: 0.9236 (m-30) cc_final: 0.8971 (m-30) REVERT: d 9 GLU cc_start: 0.8836 (pt0) cc_final: 0.8410 (pm20) REVERT: d 103 GLU cc_start: 0.9170 (mm-30) cc_final: 0.8371 (tm-30) REVERT: f 30 ASP cc_start: 0.9105 (m-30) cc_final: 0.8880 (m-30) REVERT: h 68 LYS cc_start: 0.9251 (tmtt) cc_final: 0.9046 (tptp) REVERT: i 6 ASP cc_start: 0.8816 (m-30) cc_final: 0.8383 (m-30) REVERT: i 12 GLN cc_start: 0.9074 (tt0) cc_final: 0.8850 (tm-30) REVERT: i 59 MET cc_start: 0.0782 (mtp) cc_final: 0.0545 (mtp) REVERT: k 35 GLU cc_start: 0.9140 (tm-30) cc_final: 0.8856 (tm-30) REVERT: l 148 GLU cc_start: 0.9022 (tp30) cc_final: 0.8734 (tp30) REVERT: m 86 SER cc_start: 0.9261 (m) cc_final: 0.9046 (m) REVERT: m 109 ASP cc_start: 0.9149 (m-30) cc_final: 0.8692 (m-30) REVERT: n 122 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8530 (mm-30) REVERT: o 35 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8524 (mm-30) outliers start: 113 outliers final: 97 residues processed: 1095 average time/residue: 0.6513 time to fit residues: 1211.3682 Evaluate side-chains 1120 residues out of total 7149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1015 time to evaluate : 6.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 64 CYS Chi-restraints excluded: chain 6 residue 71 HIS Chi-restraints excluded: chain 6 residue 95 VAL Chi-restraints excluded: chain 6 residue 177 ILE Chi-restraints excluded: chain 6 residue 181 GLN Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain 2 residue 171 GLU Chi-restraints excluded: chain 1 residue 105 CYS Chi-restraints excluded: chain 1 residue 269 GLU Chi-restraints excluded: chain 1 residue 327 THR Chi-restraints excluded: chain 1 residue 362 CYS Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 35 MET Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 216 THR Chi-restraints excluded: chain 3 residue 267 THR Chi-restraints excluded: chain 3 residue 402 ASN Chi-restraints excluded: chain 3 residue 424 ASP Chi-restraints excluded: chain 3 residue 536 ASP Chi-restraints excluded: chain 3 residue 596 ASP Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain 9 residue 85 CYS Chi-restraints excluded: chain 9 residue 124 CYS Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 185 TYR Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 305 VAL Chi-restraints excluded: chain Q residue 9 GLN Chi-restraints excluded: chain Q residue 14 ASP Chi-restraints excluded: chain S residue 18 ILE Chi-restraints excluded: chain S residue 77 SER Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 85 GLU Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain W residue 94 GLU Chi-restraints excluded: chain q residue 12 GLN Chi-restraints excluded: chain r residue 24 GLN Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 91 MET Chi-restraints excluded: chain H residue 97 ASN Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain J residue 16 CYS Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 109 HIS Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 338 MET Chi-restraints excluded: chain L residue 341 MET Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 404 THR Chi-restraints excluded: chain L residue 410 LEU Chi-restraints excluded: chain L residue 544 LEU Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 375 LEU Chi-restraints excluded: chain M residue 433 GLU Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain O residue 250 LYS Chi-restraints excluded: chain O residue 298 GLU Chi-restraints excluded: chain U residue 29 LYS Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain X residue 63 ASN Chi-restraints excluded: chain Y residue 128 LYS Chi-restraints excluded: chain Y residue 133 GLU Chi-restraints excluded: chain Z residue 95 ILE Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain b residue 7 PHE Chi-restraints excluded: chain b residue 21 SER Chi-restraints excluded: chain b residue 29 ILE Chi-restraints excluded: chain c residue 8 VAL Chi-restraints excluded: chain c residue 24 SER Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain e residue 18 MET Chi-restraints excluded: chain e residue 41 GLU Chi-restraints excluded: chain h residue 18 ASP Chi-restraints excluded: chain j residue 13 GLU Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain l residue 48 MET Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 96 SER Chi-restraints excluded: chain n residue 74 GLN Chi-restraints excluded: chain n residue 122 GLU Chi-restraints excluded: chain n residue 130 GLU Chi-restraints excluded: chain n residue 131 SER Chi-restraints excluded: chain n residue 149 MET Chi-restraints excluded: chain o residue 23 SER Chi-restraints excluded: chain o residue 37 VAL Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 60 THR Chi-restraints excluded: chain p residue 83 CYS Chi-restraints excluded: chain p residue 107 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 499 optimal weight: 4.9990 chunk 670 optimal weight: 0.9980 chunk 192 optimal weight: 0.0870 chunk 580 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 chunk 174 optimal weight: 20.0000 chunk 630 optimal weight: 10.0000 chunk 263 optimal weight: 10.0000 chunk 647 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 116 optimal weight: 0.8980 overall best weight: 1.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN J 85 ASN ** L 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 33 ASN X 63 ASN ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 73 HIS n 74 GLN p 99 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.060675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.050452 restraints weight = 185368.080| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.20 r_work: 0.2731 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.246 68780 Z= 0.531 Angle : 1.555 50.774 93023 Z= 1.010 Chirality : 0.309 6.417 10122 Planarity : 0.004 0.062 11607 Dihedral : 9.543 170.311 10191 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.36 % Favored : 96.63 % Rotamer: Outliers : 1.44 % Allowed : 13.93 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.37 (0.10), residues: 8031 helix: 1.75 (0.08), residues: 4430 sheet: -0.04 (0.25), residues: 397 loop : -0.07 (0.12), residues: 3204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP O 316 HIS 0.005 0.001 HIS T 35 PHE 0.031 0.001 PHE J 56 TYR 0.024 0.001 TYR L 422 ARG 0.011 0.000 ARG S 88 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19322.39 seconds wall clock time: 337 minutes 13.88 seconds (20233.88 seconds total)