Starting phenix.real_space_refine on Fri Feb 16 01:39:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w35_32271/02_2024/7w35_32271_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w35_32271/02_2024/7w35_32271.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w35_32271/02_2024/7w35_32271_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w35_32271/02_2024/7w35_32271_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w35_32271/02_2024/7w35_32271_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w35_32271/02_2024/7w35_32271.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w35_32271/02_2024/7w35_32271.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w35_32271/02_2024/7w35_32271_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w35_32271/02_2024/7w35_32271_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 32 5.49 5 Mg 1 5.21 5 S 471 5.16 5 C 43031 2.51 5 N 11121 2.21 5 O 11947 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 121": "OE1" <-> "OE2" Residue "A GLU 129": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 448": "OE1" <-> "OE2" Residue "B GLU 80": "OE1" <-> "OE2" Residue "B GLU 160": "OE1" <-> "OE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "F GLU 43": "OE1" <-> "OE2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "H GLU 18": "OE1" <-> "OE2" Residue "H GLU 22": "OE1" <-> "OE2" Residue "H GLU 49": "OE1" <-> "OE2" Residue "H GLU 62": "OE1" <-> "OE2" Residue "H GLU 78": "OE1" <-> "OE2" Residue "H GLU 85": "OE1" <-> "OE2" Residue "H GLU 106": "OE1" <-> "OE2" Residue "I GLU 30": "OE1" <-> "OE2" Residue "I GLU 105": "OE1" <-> "OE2" Residue "J GLU 87": "OE1" <-> "OE2" Residue "J GLU 107": "OE1" <-> "OE2" Residue "J GLU 135": "OE1" <-> "OE2" Residue "J GLU 162": "OE1" <-> "OE2" Residue "K GLU 92": "OE1" <-> "OE2" Residue "L GLU 105": "OE1" <-> "OE2" Residue "L GLU 108": "OE1" <-> "OE2" Residue "M GLU 44": "OE1" <-> "OE2" Residue "M GLU 67": "OE1" <-> "OE2" Residue "M GLU 118": "OE1" <-> "OE2" Residue "M GLU 211": "OE1" <-> "OE2" Residue "M GLU 310": "OE1" <-> "OE2" Residue "M GLU 396": "OE1" <-> "OE2" Residue "M GLU 468": "OE1" <-> "OE2" Residue "M GLU 535": "OE1" <-> "OE2" Residue "O GLU 64": "OE1" <-> "OE2" Residue "O GLU 72": "OE1" <-> "OE2" Residue "O GLU 150": "OE1" <-> "OE2" Residue "O GLU 194": "OE1" <-> "OE2" Residue "P GLU 85": "OE1" <-> "OE2" Residue "P PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 209": "OE1" <-> "OE2" Residue "P GLU 222": "OE1" <-> "OE2" Residue "Q GLU 100": "OE1" <-> "OE2" Residue "Q GLU 260": "OE1" <-> "OE2" Residue "Q GLU 281": "OE1" <-> "OE2" Residue "S GLU 4": "OE1" <-> "OE2" Residue "S GLU 49": "OE1" <-> "OE2" Residue "T GLU 64": "OE1" <-> "OE2" Residue "T GLU 73": "OE1" <-> "OE2" Residue "T GLU 105": "OE1" <-> "OE2" Residue "V GLU 131": "OE1" <-> "OE2" Residue "W GLU 92": "OE1" <-> "OE2" Residue "W GLU 94": "OE1" <-> "OE2" Residue "W GLU 108": "OE1" <-> "OE2" Residue "W GLU 131": "OE1" <-> "OE2" Residue "W GLU 132": "OE1" <-> "OE2" Residue "X GLU 125": "OE1" <-> "OE2" Residue "X TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 41": "OE1" <-> "OE2" Residue "Z GLU 30": "OE1" <-> "OE2" Residue "Z GLU 34": "OE1" <-> "OE2" Residue "a GLU 103": "OE1" <-> "OE2" Residue "a GLU 134": "OE1" <-> "OE2" Residue "a GLU 143": "OE1" <-> "OE2" Residue "a GLU 145": "OE1" <-> "OE2" Residue "a GLU 155": "OE1" <-> "OE2" Residue "b GLU 8": "OE1" <-> "OE2" Residue "b GLU 27": "OE1" <-> "OE2" Residue "c GLU 63": "OE1" <-> "OE2" Residue "c GLU 85": "OE1" <-> "OE2" Residue "c GLU 103": "OE1" <-> "OE2" Residue "c GLU 177": "OE1" <-> "OE2" Residue "c GLU 179": "OE1" <-> "OE2" Residue "c GLU 185": "OE1" <-> "OE2" Residue "d GLU 117": "OE1" <-> "OE2" Residue "e GLU 64": "OE1" <-> "OE2" Residue "e GLU 68": "OE1" <-> "OE2" Residue "e GLU 151": "OE1" <-> "OE2" Residue "f GLU 64": "OE1" <-> "OE2" Residue "h GLU 24": "OE1" <-> "OE2" Residue "h GLU 37": "OE1" <-> "OE2" Residue "h GLU 42": "OE1" <-> "OE2" Residue "h GLU 59": "OE1" <-> "OE2" Residue "h GLU 65": "OE1" <-> "OE2" Residue "j GLU 112": "OE1" <-> "OE2" Residue "l GLU 207": "OE1" <-> "OE2" Residue "l GLU 268": "OE1" <-> "OE2" Residue "l GLU 353": "OE1" <-> "OE2" Residue "l TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 397": "OE1" <-> "OE2" Residue "o GLU 22": "OE1" <-> "OE2" Residue "o GLU 28": "OE1" <-> "OE2" Residue "o GLU 46": "OE1" <-> "OE2" Residue "o GLU 61": "OE1" <-> "OE2" Residue "o GLU 118": "OE1" <-> "OE2" Residue "p GLU 54": "OE1" <-> "OE2" Residue "p GLU 152": "OE1" <-> "OE2" Residue "p GLU 160": "OE1" <-> "OE2" Residue "r GLU 87": "OE1" <-> "OE2" Residue "r GLU 123": "OE1" <-> "OE2" Residue "r GLU 378": "OE1" <-> "OE2" Residue "u GLU 80": "OE1" <-> "OE2" Residue "v GLU 36": "OE1" <-> "OE2" Residue "v GLU 91": "OE1" <-> "OE2" Residue "v GLU 101": "OE1" <-> "OE2" Residue "v GLU 103": "OE1" <-> "OE2" Residue "w GLU 79": "OE1" <-> "OE2" Residue "w GLU 88": "OE1" <-> "OE2" Residue "w GLU 171": "OE1" <-> "OE2" Residue "w GLU 213": "OE1" <-> "OE2" Residue "w GLU 264": "OE1" <-> "OE2" Residue "w GLU 274": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 66632 Number of models: 1 Model: "" Number of chains: 64 Chain: "A" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3318 Classifications: {'peptide': 431} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 409} Chain: "B" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1412 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "C" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1248 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 971 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "F" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 691 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "G" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 693 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 910 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "I" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 11, 'TRANS': 85} Chain breaks: 1 Chain: "J" Number of atoms: 2615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2615 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 22, 'TRANS': 308} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "K" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 355 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 3, 'TRANS': 38} Chain: "L" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1016 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "M" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5296 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 32, 'TRANS': 657} Chain: "N" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1204 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} Chain: "O" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1668 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 195} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1738 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "Q" Number of atoms: 3377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3377 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 27, 'TRANS': 391} 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: "S" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 558 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 67} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "T" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 741 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "U" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 643 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 11, 'TRANS': 71} Chain: "V" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1018 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 133} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1167 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 133} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "X" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 695 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "Y" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 600 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 6, 'TRANS': 63} Chain: "Z" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 674 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain: "a" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1165 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 10, 'TRANS': 129} Chain: "b" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 879 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 11, 'TRANS': 91} Chain breaks: 1 Chain: "c" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1315 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 20, 'TRANS': 135} Chain: "d" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1461 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 10, 'TRANS': 164} Chain: "e" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 890 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 10, 'TRANS': 96} Chain: "f" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 342 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 40} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "g" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 999 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 109} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "h" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 867 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "i" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2710 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 328} Chain: "j" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 800 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 Chain: "k" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 748 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "l" Number of atoms: 4720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4720 Classifications: {'peptide': 603} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 28, 'TRANS': 574} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 28 Chain: "m" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 919 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 32 Chain: "n" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 479 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "o" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1062 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 11, 'TRANS': 116} Chain: "p" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1530 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 160} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "r" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3631 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Chain: "s" Number of atoms: 2394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2394 Classifications: {'peptide': 303} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 281} Chain breaks: 1 Chain: "u" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1398 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "v" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 998 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 51 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 45 Chain: "w" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2582 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'PEE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'PLX': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' MG': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 91 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "b" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "g" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 113 Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 38 Chain: "j" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'PEE': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "l" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 146 Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "m" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "r" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 354 Unusual residues: {'CDL': 2, 'PEE': 1, 'PLX': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {' UQ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {' UQ:plan-11': 1, ' UQ:plan-2': 1, ' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 35 Chain: "w" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2706 SG CYS A 382 49.700 49.574 173.941 1.00 23.05 S ATOM 3048 SG CYS A 425 48.812 46.107 179.601 1.00 20.41 S ATOM 2726 SG CYS A 385 46.400 45.264 173.936 1.00 27.49 S ATOM 2687 SG CYS A 379 44.455 50.435 177.833 1.00 21.24 S ATOM 3949 SG CYS B 113 40.317 66.333 139.215 1.00 15.46 S ATOM 3968 SG CYS B 116 45.167 63.465 143.021 1.00 9.73 S ATOM 3991 SG CYS B 119 46.539 66.135 137.541 1.00 0.00 S ATOM 4320 SG CYS B 162 43.487 60.597 138.174 1.00 0.00 S ATOM 4018 SG CYS B 123 52.783 68.509 133.254 1.00 1.02 S ATOM 4244 SG CYS B 152 50.953 66.889 127.258 1.00 2.41 S ATOM 4291 SG CYS B 158 48.775 63.423 132.116 1.00 11.20 S ATOM 4270 SG CYS B 155 54.883 63.032 130.609 1.00 7.56 S ATOM 5712 SG CYS C 166 57.428 66.406 123.159 1.00 0.00 S ATOM 4984 SG CYS C 72 58.474 67.754 117.034 1.00 9.30 S ATOM 4978 SG CYS C 71 63.267 65.966 119.724 1.00 0.00 S ATOM 5482 SG CYS C 136 60.196 70.705 121.909 1.00 3.85 S ATOM 14794 SG CYS M 131 44.211 63.545 155.050 1.00 19.15 S ATOM 14773 SG CYS M 128 47.538 58.682 151.937 1.00 6.29 S ATOM 14834 SG CYS M 137 49.750 61.999 157.174 1.00 0.00 S ATOM 15166 SG CYS M 179 48.026 62.293 168.248 1.00 4.24 S ATOM 15520 SG CYS M 226 45.224 65.185 164.049 1.00 3.87 S ATOM 15190 SG CYS M 182 42.781 65.318 169.962 1.00 14.37 S ATOM 15143 SG CYS M 176 42.162 59.774 166.565 1.00 9.24 S ATOM 14391 SG CYS M 78 59.038 56.610 172.131 1.00 12.85 S ATOM 14492 SG CYS M 92 57.412 58.795 174.441 1.00 12.25 S ATOM 14280 SG CYS M 64 52.974 59.162 172.000 1.00 19.57 S ATOM 14366 SG CYS M 75 54.068 57.173 169.071 1.00 3.72 S ATOM 21329 SG CYS O 135 32.399 33.295 181.615 1.00 34.37 S ATOM 21363 SG CYS O 140 32.105 29.984 182.744 1.00 58.92 S ATOM 21643 SG CYS O 176 36.875 34.507 184.488 1.00 57.39 S ATOM 21666 SG CYS O 180 37.135 31.270 185.586 1.00 58.16 S ATOM 28312 SG CYS T 86 31.989 53.492 146.926 1.00 26.25 S ATOM 28490 SG CYS T 111 33.296 56.876 147.632 1.00 9.21 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.62 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.62 Time building chain proxies: 26.15, per 1000 atoms: 0.39 Number of scatterers: 66632 At special positions: 0 Unit cell: (221.285, 219.137, 230.953, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 471 16.00 P 32 15.00 Mg 1 11.99 O 11947 8.00 N 11121 7.00 C 43031 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS F 24 " - pdb=" SG CYS F 58 " distance=2.03 Simple disulfide: pdb=" SG CYS V 95 " - pdb=" SG CYS V 115 " distance=2.04 Simple disulfide: pdb=" SG CYS d 113 " - pdb=" SG CYS d 125 " distance=2.03 Simple disulfide: pdb=" SG CYS h 33 " - pdb=" SG CYS h 66 " distance=2.03 Simple disulfide: pdb=" SG CYS h 43 " - pdb=" SG CYS h 56 " distance=2.03 Simple disulfide: pdb=" SG CYS u 88 " - pdb=" SG CYS u 100 " distance=2.03 Simple disulfide: pdb=" SG CYS v 69 " - pdb=" SG CYS v 80 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 22.25 Conformation dependent library (CDL) restraints added in 9.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 92 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 64 " pdb=" FES O 301 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 180 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 135 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 140 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb=" SF4 A 501 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb=" SF4 B 301 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 116 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " pdb=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " pdb=" SF4 C 301 " pdb="FE3 SF4 C 301 " - pdb=" NE2 HIS Q 223 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 71 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb=" SF4 M 801 " pdb="FE3 SF4 M 801 " - pdb=" NE2 HIS M 124 " pdb="FE4 SF4 M 801 " - pdb=" SG CYS M 137 " pdb="FE2 SF4 M 801 " - pdb=" SG CYS M 128 " pdb="FE1 SF4 M 801 " - pdb=" SG CYS M 131 " pdb=" SF4 M 802 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " pdb="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " pdb="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" NE2 HIS T 95 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 86 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 111 " 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 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: 341 helices and 29 sheets defined 53.1% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.72 Creating SS restraints... Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 73 through 82 Processing helix chain 'A' and resid 95 through 103 removed outlier: 3.557A pdb=" N ASN A 103 " --> pdb=" O TRP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 132 Processing helix chain 'A' and resid 135 through 149 Processing helix chain 'A' and resid 163 through 178 Processing helix chain 'A' and resid 204 through 207 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 245 through 257 Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 296 through 303 Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 329 through 334 removed outlier: 5.281A pdb=" N THR A 334 " --> pdb=" O SER A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 363 through 377 Processing helix chain 'A' and resid 383 through 401 removed outlier: 3.829A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 419 removed outlier: 3.922A pdb=" N ASP A 410 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 457 Proline residue: A 434 - end of helix Proline residue: A 444 - end of helix Processing helix chain 'B' and resid 50 through 62 Processing helix chain 'B' and resid 64 through 78 removed outlier: 3.583A pdb=" N PHE B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 187 through 211 removed outlier: 5.836A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LEU B 210 " --> pdb=" O GLN B 206 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N TYR B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 59 Processing helix chain 'C' and resid 71 through 79 Processing helix chain 'C' and resid 86 through 89 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 114 through 122 Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 141 through 143 No H-bonds generated for 'chain 'C' and resid 141 through 143' Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 190 through 195 Processing helix chain 'E' and resid 25 through 49 Proline residue: E 44 - end of helix Processing helix chain 'E' and resid 56 through 70 removed outlier: 4.101A pdb=" N ASN E 70 " --> pdb=" O MET E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 94 Processing helix chain 'E' and resid 100 through 106 removed outlier: 4.436A pdb=" N PHE E 106 " --> pdb=" O HIS E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 124 Processing helix chain 'F' and resid 28 through 47 removed outlier: 4.604A pdb=" N GLY F 32 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N TYR F 41 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VAL F 42 " --> pdb=" O LYS F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 72 No H-bonds generated for 'chain 'F' and resid 70 through 72' Processing helix chain 'F' and resid 84 through 96 Processing helix chain 'G' and resid 76 through 89 Processing helix chain 'G' and resid 112 through 126 Processing helix chain 'G' and resid 132 through 135 No H-bonds generated for 'chain 'G' and resid 132 through 135' Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'H' and resid 20 through 37 removed outlier: 3.958A pdb=" N GLN H 37 " --> pdb=" O ASP H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 60 Processing helix chain 'H' and resid 65 through 72 Processing helix chain 'H' and resid 77 through 97 Processing helix chain 'I' and resid 6 through 16 Processing helix chain 'I' and resid 54 through 56 No H-bonds generated for 'chain 'I' and resid 54 through 56' Processing helix chain 'I' and resid 60 through 62 No H-bonds generated for 'chain 'I' and resid 60 through 62' Processing helix chain 'J' and resid 38 through 40 No H-bonds generated for 'chain 'J' and resid 38 through 40' Processing helix chain 'J' and resid 64 through 76 removed outlier: 4.149A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N MET J 76 " --> pdb=" O HIS J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 97 removed outlier: 4.728A pdb=" N HIS J 93 " --> pdb=" O TYR J 89 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LEU J 94 " --> pdb=" O ASP J 90 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG J 95 " --> pdb=" O THR J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 113 through 119 Processing helix chain 'J' and resid 141 through 145 Processing helix chain 'J' and resid 147 through 159 Processing helix chain 'J' and resid 179 through 194 Processing helix chain 'J' and resid 213 through 223 removed outlier: 3.822A pdb=" N MET J 220 " --> pdb=" O TYR J 216 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG J 221 " --> pdb=" O PHE J 217 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N TRP J 222 " --> pdb=" O ALA J 218 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE J 223 " --> pdb=" O SER J 219 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 232 Processing helix chain 'J' and resid 242 through 254 Processing helix chain 'J' and resid 273 through 283 Processing helix chain 'J' and resid 295 through 307 removed outlier: 3.797A pdb=" N VAL J 307 " --> pdb=" O ARG J 303 " (cutoff:3.500A) Processing helix chain 'J' and resid 316 through 323 Processing helix chain 'J' and resid 336 through 338 No H-bonds generated for 'chain 'J' and resid 336 through 338' Processing helix chain 'J' and resid 345 through 356 removed outlier: 4.590A pdb=" N ILE J 350 " --> pdb=" O GLU J 346 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLU J 351 " --> pdb=" O LEU J 347 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ARG J 355 " --> pdb=" O GLU J 351 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N HIS J 356 " --> pdb=" O VAL J 352 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 80 Processing helix chain 'K' and resid 85 through 96 removed outlier: 4.386A pdb=" N LYS K 95 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N PHE K 96 " --> pdb=" O GLU K 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 71 No H-bonds generated for 'chain 'L' and resid 69 through 71' Processing helix chain 'L' and resid 131 through 140 Processing helix chain 'L' and resid 161 through 164 Processing helix chain 'M' and resid 49 through 56 removed outlier: 3.606A pdb=" N VAL M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 122 Processing helix chain 'M' and resid 138 through 146 Processing helix chain 'M' and resid 173 through 175 No H-bonds generated for 'chain 'M' and resid 173 through 175' Processing helix chain 'M' and resid 181 through 188 Processing helix chain 'M' and resid 201 through 203 No H-bonds generated for 'chain 'M' and resid 201 through 203' Processing helix chain 'M' and resid 219 through 225 removed outlier: 3.582A pdb=" N ILE M 222 " --> pdb=" O SER M 219 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE M 225 " --> pdb=" O ILE M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 298 removed outlier: 4.973A pdb=" N TYR M 294 " --> pdb=" O THR M 290 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASP M 295 " --> pdb=" O ARG M 291 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N GLY M 296 " --> pdb=" O PHE M 292 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU M 297 " --> pdb=" O ALA M 293 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LYS M 298 " --> pdb=" O TYR M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 319 through 332 removed outlier: 3.516A pdb=" N MET M 329 " --> pdb=" O ARG M 325 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 337 No H-bonds generated for 'chain 'M' and resid 335 through 337' Processing helix chain 'M' and resid 348 through 361 removed outlier: 3.633A pdb=" N VAL M 361 " --> pdb=" O LEU M 357 " (cutoff:3.500A) Processing helix chain 'M' and resid 382 through 385 Processing helix chain 'M' and resid 390 through 395 removed outlier: 3.660A pdb=" N VAL M 394 " --> pdb=" O THR M 390 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLU M 395 " --> pdb=" O ILE M 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 390 through 395' Processing helix chain 'M' and resid 407 through 410 No H-bonds generated for 'chain 'M' and resid 407 through 410' Processing helix chain 'M' and resid 412 through 424 Processing helix chain 'M' and resid 449 through 457 removed outlier: 3.821A pdb=" N SER M 457 " --> pdb=" O ASP M 454 " (cutoff:3.500A) Processing helix chain 'M' and resid 461 through 468 Processing helix chain 'M' and resid 478 through 482 Processing helix chain 'M' and resid 486 through 504 Processing helix chain 'M' and resid 521 through 527 Processing helix chain 'M' and resid 535 through 539 Processing helix chain 'M' and resid 619 through 630 Processing helix chain 'M' and resid 639 through 649 Processing helix chain 'M' and resid 651 through 653 No H-bonds generated for 'chain 'M' and resid 651 through 653' Processing helix chain 'M' and resid 665 through 672 Processing helix chain 'M' and resid 691 through 693 No H-bonds generated for 'chain 'M' and resid 691 through 693' Processing helix chain 'M' and resid 699 through 702 No H-bonds generated for 'chain 'M' and resid 699 through 702' Processing helix chain 'M' and resid 705 through 715 Processing helix chain 'N' and resid 3 through 17 removed outlier: 3.799A pdb=" N HIS N 17 " --> pdb=" O GLN N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 30 Processing helix chain 'N' and resid 79 through 81 No H-bonds generated for 'chain 'N' and resid 79 through 81' Processing helix chain 'N' and resid 84 through 90 Processing helix chain 'O' and resid 57 through 68 Processing helix chain 'O' and resid 76 through 90 removed outlier: 4.350A pdb=" N LEU O 80 " --> pdb=" O ALA O 77 " (cutoff:3.500A) Proline residue: O 81 - end of helix Processing helix chain 'O' and resid 95 through 105 Processing helix chain 'O' and resid 109 through 118 Processing helix chain 'O' and resid 138 through 142 Processing helix chain 'O' and resid 146 through 156 Processing helix chain 'O' and resid 180 through 182 No H-bonds generated for 'chain 'O' and resid 180 through 182' Processing helix chain 'O' and resid 198 through 210 Processing helix chain 'P' and resid 52 through 68 Processing helix chain 'P' and resid 90 through 102 removed outlier: 3.665A pdb=" N VAL P 93 " --> pdb=" O PRO P 90 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ILE P 94 " --> pdb=" O ASP P 91 " (cutoff:3.500A) Proline residue: P 95 - end of helix Processing helix chain 'P' and resid 161 through 173 removed outlier: 3.767A pdb=" N TRP P 165 " --> pdb=" O ALA P 162 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU P 167 " --> pdb=" O ASN P 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 243 through 245 No H-bonds generated for 'chain 'P' and resid 243 through 245' Processing helix chain 'Q' and resid 41 through 48 removed outlier: 3.830A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N PHE Q 47 " --> pdb=" O TRP Q 43 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY Q 48 " --> pdb=" O ALA Q 44 " (cutoff:3.500A) Processing helix chain 'Q' and resid 120 through 126 removed outlier: 3.726A pdb=" N GLU Q 125 " --> pdb=" O GLU Q 121 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYR Q 126 " --> pdb=" O LYS Q 122 " (cutoff:3.500A) Processing helix chain 'Q' and resid 129 through 139 Proline residue: Q 134 - end of helix removed outlier: 4.152A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG Q 138 " --> pdb=" O PRO Q 134 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 159 Processing helix chain 'Q' and resid 165 through 194 Processing helix chain 'Q' and resid 198 through 218 removed outlier: 4.241A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 240 through 248 Processing helix chain 'Q' and resid 251 through 262 Processing helix chain 'Q' and resid 266 through 272 Processing helix chain 'Q' and resid 280 through 285 Processing helix chain 'Q' and resid 290 through 296 removed outlier: 4.345A pdb=" N GLY Q 295 " --> pdb=" O MET Q 292 " (cutoff:3.500A) Processing helix chain 'Q' and resid 302 through 305 No H-bonds generated for 'chain 'Q' and resid 302 through 305' Processing helix chain 'Q' and resid 311 through 313 No H-bonds generated for 'chain 'Q' and resid 311 through 313' Processing helix chain 'Q' and resid 326 through 349 Processing helix chain 'Q' and resid 368 through 373 Processing helix chain 'Q' and resid 375 through 386 Processing helix chain 'Q' and resid 427 through 438 removed outlier: 4.403A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N LYS Q 437 " --> pdb=" O ALA Q 433 " (cutoff:3.500A) Processing helix chain 'Q' and resid 444 through 454 removed outlier: 3.704A pdb=" N VAL Q 448 " --> pdb=" O ALA Q 445 " (cutoff:3.500A) Processing helix chain 'Q' and resid 458 through 462 Processing helix chain 'S' and resid 2 through 30 Proline residue: S 7 - end of helix removed outlier: 3.794A pdb=" N ILE S 18 " --> pdb=" O CYS S 15 " (cutoff:3.500A) Proline residue: S 19 - end of helix removed outlier: 3.550A pdb=" N ALA S 22 " --> pdb=" O PRO S 19 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR S 23 " --> pdb=" O GLY S 20 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR S 30 " --> pdb=" O HIS S 27 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 55 Processing helix chain 'S' and resid 66 through 68 No H-bonds generated for 'chain 'S' and resid 66 through 68' Processing helix chain 'T' and resid 50 through 54 Processing helix chain 'T' and resid 67 through 72 Processing helix chain 'T' and resid 91 through 93 No H-bonds generated for 'chain 'T' and resid 91 through 93' Processing helix chain 'U' and resid 3 through 13 Processing helix chain 'U' and resid 17 through 35 Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 39 through 48 Processing helix chain 'U' and resid 79 through 83 Processing helix chain 'V' and resid 4 through 11 Processing helix chain 'V' and resid 18 through 43 Processing helix chain 'V' and resid 49 through 81 Processing helix chain 'V' and resid 87 through 105 Processing helix chain 'V' and resid 108 through 131 removed outlier: 3.548A pdb=" N THR V 121 " --> pdb=" O TYR V 117 " (cutoff:3.500A) Processing helix chain 'W' and resid 32 through 99 Proline residue: W 73 - end of helix removed outlier: 3.710A pdb=" N LYS W 99 " --> pdb=" O ALA W 95 " (cutoff:3.500A) Processing helix chain 'W' and resid 121 through 125 Processing helix chain 'W' and resid 130 through 142 removed outlier: 6.443A pdb=" N PHE W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ILE W 141 " --> pdb=" O THR W 137 " (cutoff:3.500A) Processing helix chain 'X' and resid 76 through 89 Processing helix chain 'X' and resid 112 through 126 Processing helix chain 'X' and resid 132 through 137 removed outlier: 4.426A pdb=" N LYS X 137 " --> pdb=" O ILE X 133 " (cutoff:3.500A) Processing helix chain 'X' and resid 141 through 152 Processing helix chain 'Y' and resid 52 through 75 Processing helix chain 'Y' and resid 78 through 81 No H-bonds generated for 'chain 'Y' and resid 78 through 81' Processing helix chain 'Y' and resid 89 through 91 No H-bonds generated for 'chain 'Y' and resid 89 through 91' Processing helix chain 'Z' and resid 19 through 21 No H-bonds generated for 'chain 'Z' and resid 19 through 21' Processing helix chain 'Z' and resid 28 through 37 Processing helix chain 'Z' and resid 47 through 53 removed outlier: 3.643A pdb=" N ALA Z 50 " --> pdb=" O ARG Z 47 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N TRP Z 51 " --> pdb=" O ASN Z 48 " (cutoff:3.500A) Processing helix chain 'Z' and resid 63 through 67 Processing helix chain 'Z' and resid 71 through 89 Processing helix chain 'a' and resid 62 through 92 Proline residue: a 81 - end of helix Processing helix chain 'a' and resid 109 through 112 removed outlier: 3.880A pdb=" N TYR a 112 " --> pdb=" O HIS a 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 109 through 112' Processing helix chain 'a' and resid 116 through 125 Processing helix chain 'a' and resid 129 through 163 Processing helix chain 'a' and resid 176 through 178 No H-bonds generated for 'chain 'a' and resid 176 through 178' Processing helix chain 'b' and resid 6 through 25 Processing helix chain 'b' and resid 65 through 73 removed outlier: 3.677A pdb=" N VAL b 72 " --> pdb=" O SER b 68 " (cutoff:3.500A) Processing helix chain 'b' and resid 76 through 88 Processing helix chain 'b' and resid 90 through 92 No H-bonds generated for 'chain 'b' and resid 90 through 92' Processing helix chain 'c' and resid 34 through 36 No H-bonds generated for 'chain 'c' and resid 34 through 36' Processing helix chain 'c' and resid 45 through 54 Processing helix chain 'c' and resid 109 through 111 No H-bonds generated for 'chain 'c' and resid 109 through 111' Processing helix chain 'c' and resid 126 through 149 Processing helix chain 'd' and resid 29 through 58 removed outlier: 4.870A pdb=" N ARG d 43 " --> pdb=" O LEU d 39 " (cutoff:3.500A) Proline residue: d 44 - end of helix Processing helix chain 'd' and resid 74 through 76 No H-bonds generated for 'chain 'd' and resid 74 through 76' Processing helix chain 'd' and resid 82 through 124 removed outlier: 3.703A pdb=" N GLY d 118 " --> pdb=" O GLN d 114 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLU d 119 " --> pdb=" O GLN d 115 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N SER d 120 " --> pdb=" O ARG d 116 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TYR d 121 " --> pdb=" O GLU d 117 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ARG d 122 " --> pdb=" O GLY d 118 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLN d 123 " --> pdb=" O GLU d 119 " (cutoff:3.500A) Processing helix chain 'd' and resid 126 through 143 Processing helix chain 'd' and resid 152 through 174 Processing helix chain 'e' and resid 80 through 94 Processing helix chain 'e' and resid 98 through 107 removed outlier: 3.847A pdb=" N SER e 103 " --> pdb=" O LEU e 99 " (cutoff:3.500A) Processing helix chain 'e' and resid 116 through 132 Processing helix chain 'e' and resid 144 through 146 No H-bonds generated for 'chain 'e' and resid 144 through 146' Processing helix chain 'f' and resid 41 through 73 Processing helix chain 'g' and resid 4 through 6 No H-bonds generated for 'chain 'g' and resid 4 through 6' Processing helix chain 'g' and resid 18 through 22 Processing helix chain 'g' and resid 31 through 50 Processing helix chain 'g' and resid 60 through 98 Processing helix chain 'g' and resid 100 through 102 No H-bonds generated for 'chain 'g' and resid 100 through 102' Processing helix chain 'g' and resid 111 through 113 No H-bonds generated for 'chain 'g' and resid 111 through 113' Processing helix chain 'h' and resid 6 through 10 Processing helix chain 'h' and resid 16 through 18 No H-bonds generated for 'chain 'h' and resid 16 through 18' Processing helix chain 'h' and resid 26 through 28 No H-bonds generated for 'chain 'h' and resid 26 through 28' Processing helix chain 'h' and resid 34 through 43 Processing helix chain 'h' and resid 49 through 55 Processing helix chain 'h' and resid 57 through 68 Processing helix chain 'h' and resid 70 through 89 Processing helix chain 'h' and resid 96 through 99 No H-bonds generated for 'chain 'h' and resid 96 through 99' Processing helix chain 'i' and resid 3 through 22 Processing helix chain 'i' and resid 26 through 44 removed outlier: 3.790A pdb=" N ILE i 41 " --> pdb=" O LEU i 37 " (cutoff:3.500A) Proline residue: i 42 - end of helix Processing helix chain 'i' and resid 50 through 80 Processing helix chain 'i' and resid 93 through 106 removed outlier: 3.551A pdb=" N MET i 97 " --> pdb=" O VAL i 93 " (cutoff:3.500A) Processing helix chain 'i' and resid 113 through 121 removed outlier: 4.148A pdb=" N GLU i 117 " --> pdb=" O PHE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 144 removed outlier: 3.796A pdb=" N GLN i 134 " --> pdb=" O LEU i 130 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LYS i 135 " --> pdb=" O LEU i 131 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU i 136 " --> pdb=" O THR i 132 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ALA i 137 " --> pdb=" O TRP i 133 " (cutoff:3.500A) Proline residue: i 138 - end of helix Processing helix chain 'i' and resid 146 through 148 No H-bonds generated for 'chain 'i' and resid 146 through 148' Processing helix chain 'i' and resid 151 through 171 removed outlier: 3.893A pdb=" N LEU i 170 " --> pdb=" O GLY i 166 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASN i 171 " --> pdb=" O TRP i 167 " (cutoff:3.500A) Processing helix chain 'i' and resid 175 through 191 Processing helix chain 'i' and resid 198 through 221 Processing helix chain 'i' and resid 227 through 235 removed outlier: 3.561A pdb=" N HIS i 232 " --> pdb=" O LEU i 228 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N THR i 233 " --> pdb=" O SER i 229 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TRP i 234 " --> pdb=" O LEU i 230 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ASN i 235 " --> pdb=" O SER i 231 " (cutoff:3.500A) Processing helix chain 'i' and resid 238 through 251 Processing helix chain 'i' and resid 258 through 272 Proline residue: i 262 - end of helix Processing helix chain 'i' and resid 277 through 300 removed outlier: 4.340A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) Processing helix chain 'i' and resid 309 through 316 Processing helix chain 'i' and resid 326 through 334 Processing helix chain 'i' and resid 337 through 345 Proline residue: i 341 - end of helix Processing helix chain 'j' and resid 2 through 27 Proline residue: j 25 - end of helix Processing helix chain 'j' and resid 53 through 78 Proline residue: j 74 - end of helix removed outlier: 5.791A pdb=" N TRP j 77 " --> pdb=" O LEU j 73 " (cutoff:3.500A) Processing helix chain 'j' and resid 84 through 107 Processing helix chain 'k' and resid 3 through 21 Processing helix chain 'k' and resid 26 through 50 Processing helix chain 'k' and resid 55 through 85 Proline residue: k 60 - end of helix 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 23 removed outlier: 4.276A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR l 16 " --> pdb=" O LEU l 12 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE l 17 " --> pdb=" O THR l 13 " (cutoff:3.500A) Proline residue: l 18 - end of helix removed outlier: 4.660A pdb=" N ASN l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) Processing helix chain 'l' and resid 26 through 28 No H-bonds generated for 'chain 'l' and resid 26 through 28' Processing helix chain 'l' and resid 32 through 57 removed outlier: 4.623A pdb=" N VAL l 49 " --> pdb=" O THR l 45 " (cutoff:3.500A) Proline residue: l 50 - end of helix Processing helix chain 'l' and resid 84 through 107 Proline residue: l 91 - end of helix removed outlier: 4.025A pdb=" N TRP l 106 " --> pdb=" O GLU l 102 " (cutoff:3.500A) Processing helix chain 'l' and resid 114 through 133 Processing helix chain 'l' and resid 137 through 155 Processing helix chain 'l' and resid 162 through 193 removed outlier: 3.968A pdb=" N GLY l 181 " --> pdb=" O ILE l 177 " (cutoff:3.500A) Processing helix chain 'l' and resid 198 through 204 Processing helix chain 'l' and resid 210 through 224 Processing helix chain 'l' and resid 227 through 229 No H-bonds generated for 'chain 'l' and resid 227 through 229' Processing helix chain 'l' and resid 231 through 238 removed outlier: 4.160A pdb=" N MET l 237 " --> pdb=" O LEU l 233 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N GLU l 238 " --> pdb=" O PRO l 234 " (cutoff:3.500A) Processing helix chain 'l' and resid 241 through 246 Processing helix chain 'l' and resid 255 through 262 Processing helix chain 'l' and resid 264 through 267 No H-bonds generated for 'chain 'l' and resid 264 through 267' Processing helix chain 'l' and resid 272 through 294 removed outlier: 4.476A pdb=" N THR l 294 " --> pdb=" O LEU l 290 " (cutoff:3.500A) Processing helix chain 'l' and resid 298 through 318 Processing helix chain 'l' and resid 322 through 349 removed outlier: 3.637A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) Processing helix chain 'l' and resid 356 through 358 No H-bonds generated for 'chain 'l' and resid 356 through 358' Processing helix chain 'l' and resid 367 through 381 Processing helix chain 'l' and resid 389 through 400 removed outlier: 4.635A pdb=" N LEU l 394 " --> 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 removed outlier: 3.595A pdb=" N LEU l 457 " --> pdb=" O SER l 453 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.253A 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 removed outlier: 3.656A pdb=" N THR l 507 " --> pdb=" O GLU l 503 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR l 508 " --> pdb=" O LEU l 504 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N TYR l 509 " --> pdb=" O ASN l 505 " (cutoff:3.500A) Processing helix chain 'l' and resid 518 through 524 Processing helix chain 'l' and resid 526 through 547 Proline residue: l 530 - end of helix removed outlier: 4.247A pdb=" N MET l 533 " --> pdb=" O PRO l 530 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N LEU l 536 " --> pdb=" O MET l 533 " (cutoff:3.500A) Proline residue: l 537 - end of helix removed outlier: 4.527A pdb=" N SER l 543 " --> pdb=" O HIS l 540 " (cutoff:3.500A) Processing helix chain 'l' and resid 557 through 561 Processing helix chain 'l' and resid 563 through 578 Processing helix chain 'l' and resid 584 through 601 Processing helix chain 'm' and resid 5 through 21 Processing helix chain 'm' and resid 26 through 47 Processing helix chain 'm' and resid 50 through 74 removed outlier: 3.875A pdb=" N LEU m 61 " --> pdb=" O PHE m 57 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU m 65 " --> pdb=" O LEU m 61 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL m 66 " --> pdb=" O GLY m 62 " (cutoff:3.500A) Processing helix chain 'm' and resid 138 through 146 removed outlier: 4.298A pdb=" N LEU m 146 " --> pdb=" O GLY m 142 " (cutoff:3.500A) Processing helix chain 'm' and resid 151 through 173 Processing helix chain 'n' and resid 8 through 34 removed outlier: 6.373A pdb=" N VAL n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N HIS n 14 " --> pdb=" O ASP n 10 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ILE n 15 " --> pdb=" O HIS n 11 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU n 16 " --> pdb=" O TRP n 12 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N VAL n 17 " --> pdb=" O VAL n 13 " (cutoff:3.500A) Proline residue: n 18 - end of helix removed outlier: 3.914A pdb=" N LYS n 34 " --> pdb=" O ARG n 30 " (cutoff:3.500A) Processing helix chain 'n' and resid 43 through 45 No H-bonds generated for 'chain 'n' and resid 43 through 45' Processing helix chain 'o' and resid 16 through 18 No H-bonds generated for 'chain 'o' and resid 16 through 18' Processing helix chain 'o' and resid 20 through 23 No H-bonds generated for 'chain 'o' and resid 20 through 23' Processing helix chain 'o' and resid 27 through 51 Processing helix chain 'o' and resid 63 through 73 Processing helix chain 'o' and resid 77 through 79 No H-bonds generated for 'chain 'o' and resid 77 through 79' Processing helix chain 'o' and resid 84 through 118 Proline residue: o 97 - end of helix Processing helix chain 'p' and resid 12 through 30 Processing helix chain 'p' and resid 34 through 51 removed outlier: 4.811A pdb=" N HIS p 51 " --> pdb=" O ARG p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 57 through 62 Processing helix chain 'p' and resid 65 through 73 Processing helix chain 'p' and resid 95 through 97 No H-bonds generated for 'chain 'p' and resid 95 through 97' Processing helix chain 'p' and resid 102 through 106 Processing helix chain 'p' and resid 109 through 113 Processing helix chain 'p' and resid 116 through 143 removed outlier: 4.183A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ARG p 135 " --> pdb=" O GLU p 131 " (cutoff:3.500A) Processing helix chain 'p' and resid 168 through 171 No H-bonds generated for 'chain 'p' and resid 168 through 171' Processing helix chain 'r' and resid 2 through 17 Proline residue: r 7 - end of helix removed outlier: 4.176A pdb=" N LEU r 12 " --> pdb=" O THR r 8 " (cutoff:3.500A) Proline residue: r 13 - end of helix Processing helix chain 'r' and resid 23 through 42 removed outlier: 4.229A pdb=" N SER r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU r 42 " --> pdb=" O SER r 38 " (cutoff:3.500A) Processing helix chain 'r' and resid 62 through 83 removed outlier: 3.856A pdb=" N LEU r 73 " --> pdb=" O THR r 69 " (cutoff:3.500A) Proline residue: r 74 - end of helix removed outlier: 4.382A pdb=" N SER r 82 " --> pdb=" O MET r 78 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N HIS r 83 " --> pdb=" O ALA r 79 " (cutoff:3.500A) Processing helix chain 'r' and resid 89 through 111 removed outlier: 3.682A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 115 through 135 removed outlier: 4.622A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL r 127 " --> pdb=" O GLU r 123 " (cutoff:3.500A) Proline residue: r 128 - end of helix Processing helix chain 'r' and resid 140 through 170 removed outlier: 4.099A pdb=" N LEU r 143 " --> pdb=" O THR r 140 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N TYR r 152 " --> pdb=" O PHE r 149 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N LEU r 158 " --> pdb=" O ALA r 155 " (cutoff:3.500A) Proline residue: r 159 - end of helix Processing helix chain 'r' and resid 176 through 181 Processing helix chain 'r' and resid 190 through 206 removed outlier: 4.331A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS r 206 " --> pdb=" O ALA r 202 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 222 removed outlier: 4.149A pdb=" N LYS r 218 " --> pdb=" O LEU r 214 " (cutoff:3.500A) Processing helix chain 'r' and resid 225 through 233 Processing helix chain 'r' and resid 235 through 246 removed outlier: 3.564A pdb=" N LEU r 238 " --> pdb=" O LEU r 235 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY r 239 " --> pdb=" O LEU r 236 " (cutoff:3.500A) Processing helix chain 'r' and resid 253 through 277 removed outlier: 4.648A pdb=" N TYR r 259 " --> pdb=" O ASN r 255 " (cutoff:3.500A) Proline residue: r 260 - end of helix removed outlier: 4.177A pdb=" N ILE r 270 " --> pdb=" O MET r 266 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU r 277 " --> pdb=" O SER r 273 " (cutoff:3.500A) Processing helix chain 'r' and resid 282 through 303 Processing helix chain 'r' and resid 306 through 337 removed outlier: 3.723A pdb=" N ARG r 336 " --> pdb=" O THR r 332 " (cutoff:3.500A) Processing helix chain 'r' and resid 348 through 351 No H-bonds generated for 'chain 'r' and resid 348 through 351' Processing helix chain 'r' and resid 353 through 366 Processing helix chain 'r' and resid 373 through 388 Processing helix chain 'r' and resid 390 through 415 removed outlier: 3.849A pdb=" N ILE r 393 " --> pdb=" O ASN r 390 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR r 413 " --> pdb=" O MET r 410 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR r 414 " --> pdb=" O LEU r 411 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN r 415 " --> pdb=" O ILE r 412 " (cutoff:3.500A) Processing helix chain 'r' and resid 431 through 449 Proline residue: r 443 - end of helix removed outlier: 4.280A pdb=" N LEU r 449 " --> pdb=" O LEU r 445 " (cutoff:3.500A) Processing helix chain 'r' and resid 451 through 454 Processing helix chain 's' and resid 2 through 32 Proline residue: s 12 - end of helix removed outlier: 3.892A pdb=" N LEU s 22 " --> pdb=" O ALA s 18 " (cutoff:3.500A) Processing helix chain 's' and resid 47 through 57 Processing helix chain 's' and resid 68 through 86 Proline residue: s 75 - end of helix removed outlier: 4.395A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 123 removed outlier: 4.449A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 156 removed outlier: 3.864A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 168 removed outlier: 3.556A pdb=" N THR s 168 " --> pdb=" O LEU s 165 " (cutoff:3.500A) Processing helix chain 's' and resid 174 through 177 No H-bonds generated for 'chain 's' and resid 174 through 177' Processing helix chain 's' and resid 179 through 192 Processing helix chain 's' and resid 218 through 242 Processing helix chain 's' and resid 252 through 276 Processing helix chain 's' and resid 282 through 311 removed outlier: 5.113A pdb=" N LEU s 294 " --> pdb=" O TRP s 290 " (cutoff:3.500A) Proline residue: s 295 - end of helix Proline residue: s 308 - end of helix Processing helix chain 'u' and resid 10 through 13 Processing helix chain 'u' and resid 22 through 35 removed outlier: 4.895A pdb=" N HIS u 30 " --> pdb=" O LYS u 26 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N HIS u 31 " --> pdb=" O ALA u 27 " (cutoff:3.500A) Processing helix chain 'u' and resid 37 through 50 Processing helix chain 'u' and resid 53 through 55 No H-bonds generated for 'chain 'u' and resid 53 through 55' Processing helix chain 'u' and resid 57 through 77 Processing helix chain 'u' and resid 79 through 91 Processing helix chain 'u' and resid 101 through 114 Processing helix chain 'v' and resid 3 through 10 Processing helix chain 'v' and resid 13 through 15 No H-bonds generated for 'chain 'v' and resid 13 through 15' Processing helix chain 'v' and resid 27 through 29 No H-bonds generated for 'chain 'v' and resid 27 through 29' Processing helix chain 'v' and resid 43 through 49 Processing helix chain 'v' and resid 60 through 72 Processing helix chain 'v' and resid 82 through 124 Processing helix chain 'w' and resid 40 through 45 Processing helix chain 'w' and resid 70 through 81 Processing helix chain 'w' and resid 94 through 96 No H-bonds generated for 'chain 'w' and resid 94 through 96' Processing helix chain 'w' and resid 114 through 119 Processing helix chain 'w' and resid 127 through 153 Processing helix chain 'w' and resid 166 through 175 removed outlier: 4.131A pdb=" N LEU w 170 " --> pdb=" O ASP w 166 " (cutoff:3.500A) Processing helix chain 'w' and resid 181 through 197 removed outlier: 5.561A pdb=" N GLU w 197 " --> pdb=" O VAL w 193 " (cutoff:3.500A) Processing helix chain 'w' and resid 211 through 221 Processing helix chain 'w' and resid 226 through 228 No H-bonds generated for 'chain 'w' and resid 226 through 228' Processing helix chain 'w' and resid 231 through 249 removed outlier: 3.542A pdb=" N THR w 244 " --> pdb=" O ALA w 240 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU w 246 " --> pdb=" O LYS w 242 " (cutoff:3.500A) Proline residue: w 247 - end of helix Processing helix chain 'w' and resid 266 through 275 Processing helix chain 'w' and resid 283 through 285 No H-bonds generated for 'chain 'w' and resid 283 through 285' Processing helix chain 'w' and resid 288 through 298 Processing helix chain 'w' and resid 301 through 304 No H-bonds generated for 'chain 'w' and resid 301 through 304' Processing helix chain 'w' and resid 306 through 309 removed outlier: 3.857A pdb=" N THR w 309 " --> pdb=" O ASN w 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 306 through 309' Processing helix chain 'w' and resid 321 through 332 Processing helix chain 'w' and resid 352 through 354 No H-bonds generated for 'chain 'w' and resid 352 through 354' Processing sheet with id= A, first strand: chain 'A' and resid 240 through 244 removed outlier: 7.279A pdb=" N TYR A 112 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N ALA A 243 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL A 114 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ALA A 153 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL A 115 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TYR A 155 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ALA A 117 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TYR A 157 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ASP A 194 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ILE A 156 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N PHE A 196 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ILE A 158 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL A 198 " --> pdb=" O ILE A 158 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 286 through 291 Processing sheet with id= C, first strand: chain 'B' and resid 101 through 103 Processing sheet with id= D, first strand: chain 'B' and resid 128 through 134 removed outlier: 6.089A pdb=" N GLU B 133 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N THR B 142 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 64 through 68 removed outlier: 6.523A pdb=" N VAL C 102 " --> pdb=" O MET C 65 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N PHE C 67 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ILE C 104 " --> pdb=" O PHE C 67 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TYR C 129 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N VAL C 105 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL C 131 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE C 161 " --> pdb=" O SER C 132 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'F' and resid 52 through 58 removed outlier: 3.514A pdb=" N GLU F 18 " --> pdb=" O ARG F 68 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 262 through 265 removed outlier: 6.652A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE J 167 " --> pdb=" O ASN J 128 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLN J 79 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N VAL J 58 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE J 81 " --> pdb=" O VAL J 58 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 226 through 229 Processing sheet with id= I, first strand: chain 'L' and resid 144 through 147 Processing sheet with id= J, first strand: chain 'L' and resid 106 through 108 Processing sheet with id= K, first strand: chain 'M' and resid 32 through 36 Processing sheet with id= L, first strand: chain 'M' and resid 79 through 81 Processing sheet with id= M, first strand: chain 'M' and resid 169 through 171 Processing sheet with id= N, first strand: chain 'M' and resid 196 through 198 Processing sheet with id= O, first strand: chain 'M' and resid 246 through 251 Processing sheet with id= P, first strand: chain 'M' and resid 306 through 308 Processing sheet with id= Q, first strand: chain 'M' and resid 366 through 368 removed outlier: 8.726A pdb=" N CYS M 367 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA M 340 " --> pdb=" O CYS M 367 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL M 544 " --> pdb=" O ALA M 339 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ILE M 341 " --> pdb=" O VAL M 544 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N PHE M 546 " --> pdb=" O ILE M 341 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHE M 565 " --> pdb=" O LEU M 545 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N LEU M 547 " --> pdb=" O PHE M 565 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE M 567 " --> pdb=" O LEU M 547 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL M 582 " --> pdb=" O TYR M 568 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N GLY M 570 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU M 584 " --> pdb=" O GLY M 570 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'M' and resid 513 through 516 removed outlier: 8.032A pdb=" N ASN M 514 " --> pdb=" O PRO M 472 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL M 399 " --> pdb=" O MET M 473 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LYS M 428 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N LEU M 402 " --> pdb=" O LYS M 428 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ALA M 430 " --> pdb=" O LEU M 402 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASP M 443 " --> pdb=" O LEU M 431 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'M' and resid 595 through 597 Processing sheet with id= T, first strand: chain 'N' and resid 60 through 63 removed outlier: 6.586A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N LEU N 38 " --> pdb=" O GLU N 50 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'O' and resid 169 through 174 removed outlier: 6.758A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL O 134 " --> pdb=" O VAL O 174 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'P' and resid 110 through 118 removed outlier: 6.804A pdb=" N ASN P 131 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU P 114 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL P 129 " --> pdb=" O LEU P 114 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA P 116 " --> pdb=" O GLU P 127 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLU P 127 " --> pdb=" O ALA P 116 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LEU P 84 " --> pdb=" O ARG P 140 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N TYR P 146 " --> pdb=" O ILE P 88 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'P' and resid 208 through 213 Processing sheet with id= X, first strand: chain 'Q' and resid 80 through 84 removed outlier: 3.772A pdb=" N ARG Q 96 " --> pdb=" O HIS Q 112 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL Q 106 " --> pdb=" O SER Q 102 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'Q' and resid 394 through 402 Processing sheet with id= Z, first strand: chain 'T' and resid 83 through 86 Processing sheet with id= AA, first strand: chain 'l' and resid 62 through 67 removed outlier: 6.462A pdb=" N LEU l 78 " --> pdb=" O ASN l 65 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'w' and resid 60 through 64 removed outlier: 6.504A pdb=" N VAL w 203 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ASP w 63 " --> pdb=" O VAL w 203 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL w 205 " --> pdb=" O ASP w 63 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLU w 254 " --> pdb=" O VAL w 204 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N TYR w 206 " --> pdb=" O GLU w 254 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEU w 256 " --> pdb=" O TYR w 206 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ASP w 208 " --> pdb=" O LEU w 256 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TYR w 258 " --> pdb=" O ASP w 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'w' and resid 84 through 86 2930 hydrogen bonds defined for protein. 8118 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: 22.89 Time building geometry restraints manager: 24.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 27344 1.40 - 1.62: 40040 1.62 - 1.84: 830 1.84 - 2.07: 0 2.07 - 2.29: 80 Bond restraints: 68294 Sorted by residual: bond pdb=" C3D NAI A 503 " pdb=" C4D NAI A 503 " ideal model delta sigma weight residual 1.524 1.266 0.258 2.00e-02 2.50e+03 1.67e+02 bond pdb=" C1D NAI A 503 " pdb=" C2D NAI A 503 " ideal model delta sigma weight residual 1.528 1.290 0.238 2.00e-02 2.50e+03 1.42e+02 bond pdb=" C1B NAI A 503 " pdb=" O4B NAI A 503 " ideal model delta sigma weight residual 1.397 1.632 -0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C1B NAI A 503 " pdb=" C2B NAI A 503 " ideal model delta sigma weight residual 1.528 1.301 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C3' ADP w 401 " pdb=" C4' ADP w 401 " ideal model delta sigma weight residual 1.524 1.298 0.226 2.00e-02 2.50e+03 1.28e+02 ... (remaining 68289 not shown) Histogram of bond angle deviations from ideal: 73.60 - 86.02: 76 86.02 - 98.43: 0 98.43 - 110.85: 24399 110.85 - 123.26: 65353 123.26 - 135.68: 2622 Bond angle restraints: 92450 Sorted by residual: angle pdb=" N HIS Q 233 " pdb=" CA HIS Q 233 " pdb=" C HIS Q 233 " ideal model delta sigma weight residual 111.07 120.91 -9.84 1.07e+00 8.73e-01 8.45e+01 angle pdb=" PA NDP J 401 " pdb=" O3 NDP J 401 " pdb=" PN NDP J 401 " ideal model delta sigma weight residual 107.74 124.03 -16.29 1.95e+00 2.62e-01 6.95e+01 angle pdb=" N GLN Q 234 " pdb=" CA GLN Q 234 " pdb=" C GLN Q 234 " ideal model delta sigma weight residual 111.71 122.63 -10.92 1.34e+00 5.57e-01 6.64e+01 angle pdb=" C5B NDP J 401 " pdb=" O5B NDP J 401 " pdb=" PA NDP J 401 " ideal model delta sigma weight residual 103.84 118.64 -14.80 1.91e+00 2.73e-01 5.98e+01 angle pdb=" C11 CDL a 201 " pdb=" CA5 CDL a 201 " pdb=" OA6 CDL a 201 " ideal model delta sigma weight residual 111.33 120.49 -9.16 1.32e+00 5.72e-01 4.80e+01 ... (remaining 92445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.33: 39615 35.33 - 70.67: 1660 70.67 - 106.00: 121 106.00 - 141.33: 20 141.33 - 176.66: 15 Dihedral angle restraints: 41431 sinusoidal: 17631 harmonic: 23800 Sorted by residual: dihedral pdb=" C10 FMN A 502 " pdb=" C1' FMN A 502 " pdb=" N10 FMN A 502 " pdb=" C2' FMN A 502 " ideal model delta sinusoidal sigma weight residual 257.59 81.36 176.23 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP w 401 " pdb=" O5' ADP w 401 " pdb=" PA ADP w 401 " pdb=" O2A ADP w 401 " ideal model delta sinusoidal sigma weight residual -60.00 96.90 -156.90 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" CB CYS u 88 " pdb=" SG CYS u 88 " pdb=" SG CYS u 100 " pdb=" CB CYS u 100 " ideal model delta sinusoidal sigma weight residual -86.00 -138.77 52.77 1 1.00e+01 1.00e-02 3.79e+01 ... (remaining 41428 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 9198 0.073 - 0.146: 817 0.146 - 0.219: 31 0.219 - 0.292: 7 0.292 - 0.365: 3 Chirality restraints: 10056 Sorted by residual: chirality pdb=" C3B NDP J 401 " pdb=" C2B NDP J 401 " pdb=" C4B NDP J 401 " pdb=" O3B NDP J 401 " both_signs ideal model delta sigma weight residual False -2.75 -2.38 -0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" CA GLN Q 234 " pdb=" N GLN Q 234 " pdb=" C GLN Q 234 " pdb=" CB GLN Q 234 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CA TYR M 695 " pdb=" N TYR M 695 " pdb=" C TYR M 695 " pdb=" CB TYR M 695 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 ... (remaining 10053 not shown) Planarity restraints: 11588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 UQ s 401 " 0.364 2.00e-02 2.50e+03 3.17e-01 1.26e+03 pdb=" C11 UQ s 401 " 0.003 2.00e-02 2.50e+03 pdb=" C7 UQ s 401 " 0.343 2.00e-02 2.50e+03 pdb=" C8 UQ s 401 " -0.329 2.00e-02 2.50e+03 pdb=" C9 UQ s 401 " -0.380 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP J 401 " 0.119 2.00e-02 2.50e+03 2.48e-01 7.68e+02 pdb=" C3N NDP J 401 " 0.416 2.00e-02 2.50e+03 pdb=" C4N NDP J 401 " -0.057 2.00e-02 2.50e+03 pdb=" C7N NDP J 401 " -0.280 2.00e-02 2.50e+03 pdb=" N1N NDP J 401 " -0.197 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ s 401 " 0.181 2.00e-02 2.50e+03 2.19e-01 5.97e+02 pdb=" C13 UQ s 401 " -0.115 2.00e-02 2.50e+03 pdb=" C14 UQ s 401 " -0.358 2.00e-02 2.50e+03 pdb=" C15 UQ s 401 " 0.042 2.00e-02 2.50e+03 pdb=" C16 UQ s 401 " 0.250 2.00e-02 2.50e+03 ... (remaining 11585 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 4776 2.74 - 3.28: 66918 3.28 - 3.82: 114505 3.82 - 4.36: 140281 4.36 - 4.90: 237719 Nonbonded interactions: 564199 Sorted by model distance: nonbonded pdb=" OG SER J 50 " pdb=" OE2 GLU P 225 " model vdw 2.197 2.440 nonbonded pdb=" NH2 ARG A 398 " pdb=" OE1 GLU A 408 " model vdw 2.202 2.520 nonbonded pdb=" OG SER J 204 " pdb=" O GLN J 238 " model vdw 2.205 2.440 nonbonded pdb=" OG1 THR Q 178 " pdb=" OH TYR Q 214 " model vdw 2.206 2.440 nonbonded pdb=" OD2 ASP S 51 " pdb=" OG SER u 22 " model vdw 2.208 2.440 ... (remaining 564194 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 'G' and (resid 69 through 93 or (resid 94 and (name N or name CA or name \ C or name O or name CB )) or resid 95 through 96 or (resid 97 through 99 and (na \ me N or name CA or name C or name O or name CB )) or resid 100 through 101 or (r \ esid 102 and (name N or name CA or name C or name O or name CB )) or resid 103 t \ hrough 156 or resid 201)) selection = (chain 'X' and (resid 69 through 149 or (resid 150 through 153 and (name N or na \ me CA or name C or name O or name CB )) or resid 154 through 156 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=0.62 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: 1.700 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: 0.090 Extract box with map and model: 8.760 Check model and map are aligned: 0.720 Set scattering table: 0.470 Process input model: 161.600 Find NCS groups from input model: 2.390 Set up NCS constraints: 0.290 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:13.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 189.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 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 0.313 68294 Z= 0.419 Angle : 0.746 17.394 92450 Z= 0.380 Chirality : 0.042 0.365 10056 Planarity : 0.007 0.317 11588 Dihedral : 18.385 176.664 26062 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.62 % Favored : 96.34 % Rotamer: Outliers : 1.70 % Allowed : 18.75 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.02 % 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 (0.09), residues: 8065 helix: 1.61 (0.08), residues: 4270 sheet: 0.29 (0.25), residues: 424 loop : -0.37 (0.11), residues: 3371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.012 0.001 HIS v 92 PHE 0.029 0.001 PHE i 292 TYR 0.031 0.001 TYR J 216 ARG 0.018 0.000 ARG n 30 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1179 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1059 time to evaluate : 5.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 76 TYR cc_start: 0.8526 (OUTLIER) cc_final: 0.7079 (t80) REVERT: C 126 GLU cc_start: 0.9103 (OUTLIER) cc_final: 0.8195 (mp0) REVERT: E 23 ARG cc_start: 0.6986 (mtp180) cc_final: 0.6712 (tpt90) REVERT: E 117 ASP cc_start: 0.8308 (p0) cc_final: 0.7966 (p0) REVERT: G 128 PHE cc_start: 0.7122 (p90) cc_final: 0.6571 (p90) REVERT: I 70 MET cc_start: 0.8182 (tmm) cc_final: 0.7974 (tmt) REVERT: M 629 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8271 (mp) REVERT: P 43 THR cc_start: 0.5963 (p) cc_final: 0.5706 (m) REVERT: Q 108 LYS cc_start: 0.8216 (tttm) cc_final: 0.7832 (ttmm) REVERT: Z 42 ARG cc_start: 0.6128 (ptm160) cc_final: 0.5861 (ptm160) REVERT: b 122 GLU cc_start: 0.7485 (tt0) cc_final: 0.7249 (tm-30) REVERT: e 127 LYS cc_start: 0.8466 (tptm) cc_final: 0.8246 (tttm) REVERT: l 482 MET cc_start: 0.6880 (tpt) cc_final: 0.6565 (mmt) REVERT: m 1 MET cc_start: 0.4525 (ttp) cc_final: 0.3197 (tpt) REVERT: m 169 MET cc_start: 0.8820 (mmm) cc_final: 0.8542 (mmm) REVERT: n 34 LYS cc_start: 0.8027 (mtpp) cc_final: 0.7435 (tptt) REVERT: r 269 MET cc_start: 0.9186 (ptm) cc_final: 0.8958 (ptp) REVERT: s 228 TYR cc_start: 0.8904 (m-80) cc_final: 0.8612 (m-80) REVERT: v 34 ARG cc_start: 0.5766 (tmt-80) cc_final: 0.5396 (tpm170) outliers start: 120 outliers final: 85 residues processed: 1161 average time/residue: 1.4248 time to fit residues: 2168.9553 Evaluate side-chains 1097 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1009 time to evaluate : 5.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain H residue 79 GLU Chi-restraints excluded: chain I residue 30 GLU Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 337 ASP Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 160 VAL Chi-restraints excluded: chain M residue 318 THR Chi-restraints excluded: chain M residue 365 SER Chi-restraints excluded: chain M residue 515 ILE Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 629 ILE Chi-restraints excluded: chain N residue 134 ILE Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain P residue 86 ILE Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 252 SER Chi-restraints excluded: chain Q residue 265 ASN Chi-restraints excluded: chain T residue 77 SER Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain V residue 95 CYS Chi-restraints excluded: chain V residue 124 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 66 GLU Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 114 THR Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain a residue 93 ILE Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 101 LYS Chi-restraints excluded: chain c residue 96 ASP Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 120 SER Chi-restraints excluded: chain d residue 136 SER Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain i residue 97 MET Chi-restraints excluded: chain i residue 300 SER Chi-restraints excluded: chain j residue 68 GLU Chi-restraints excluded: chain l residue 24 SER Chi-restraints excluded: chain l residue 79 SER Chi-restraints excluded: chain l residue 104 SER Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 185 SER Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 491 LEU Chi-restraints excluded: chain m residue 143 ILE Chi-restraints excluded: chain o residue 57 LEU Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 49 SER Chi-restraints excluded: chain r residue 90 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 218 LYS Chi-restraints excluded: chain r residue 248 THR Chi-restraints excluded: chain r residue 274 SER Chi-restraints excluded: chain r residue 337 VAL Chi-restraints excluded: chain r residue 350 THR Chi-restraints excluded: chain r residue 365 THR Chi-restraints excluded: chain r residue 452 LYS Chi-restraints excluded: chain s residue 113 VAL Chi-restraints excluded: chain s residue 115 SER Chi-restraints excluded: chain s residue 276 SER Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 55 ARG Chi-restraints excluded: chain u residue 109 GLU Chi-restraints excluded: chain u residue 115 LEU Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 24 THR Chi-restraints excluded: chain v residue 61 HIS Chi-restraints excluded: chain v residue 108 LEU Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 297 LEU Chi-restraints excluded: chain w residue 312 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 673 optimal weight: 5.9990 chunk 604 optimal weight: 2.9990 chunk 335 optimal weight: 3.9990 chunk 206 optimal weight: 0.4980 chunk 407 optimal weight: 10.0000 chunk 322 optimal weight: 4.9990 chunk 624 optimal weight: 6.9990 chunk 241 optimal weight: 20.0000 chunk 379 optimal weight: 6.9990 chunk 464 optimal weight: 10.0000 chunk 723 optimal weight: 0.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 GLN E 95 ASN ** G 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 ASN J 341 GLN K 90 ASN L 86 ASN ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 233 HIS ** Q 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 83 ASN ** V 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 129 GLN Y 57 GLN Z 21 GLN a 90 ASN ** a 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 56 ASN h 82 GLN i 91 ASN i 174 GLN i 322 GLN ** l 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 184 HIS s 47 GLN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 54 GLN w 111 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.0781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 68294 Z= 0.297 Angle : 0.596 11.067 92450 Z= 0.298 Chirality : 0.043 0.180 10056 Planarity : 0.005 0.070 11588 Dihedral : 14.040 178.746 10241 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.17 % Favored : 95.80 % Rotamer: Outliers : 3.75 % Allowed : 17.11 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.02 % Cis-general : 0.00 % Twisted Proline : 0.20 % 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: 0.86 (0.09), residues: 8065 helix: 1.45 (0.08), residues: 4278 sheet: 0.24 (0.26), residues: 387 loop : -0.48 (0.11), residues: 3400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP u 86 HIS 0.010 0.001 HIS v 92 PHE 0.034 0.002 PHE i 292 TYR 0.023 0.002 TYR J 216 ARG 0.007 0.000 ARG m 173 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1303 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 1039 time to evaluate : 6.315 Fit side-chains revert: symmetry clash REVERT: A 131 ILE cc_start: 0.8217 (mt) cc_final: 0.7973 (mt) REVERT: B 76 TYR cc_start: 0.8966 (OUTLIER) cc_final: 0.6862 (t80) REVERT: C 98 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8198 (tpt170) REVERT: C 126 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8122 (mp0) REVERT: E 23 ARG cc_start: 0.7079 (OUTLIER) cc_final: 0.6205 (mmt180) REVERT: E 99 GLN cc_start: 0.9178 (OUTLIER) cc_final: 0.7745 (mt0) REVERT: G 120 MET cc_start: 0.6680 (OUTLIER) cc_final: 0.6342 (ttm) REVERT: G 123 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6978 (mt-10) REVERT: H 70 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7608 (tm-30) REVERT: I 105 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7842 (mt-10) REVERT: J 179 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7482 (ptm160) REVERT: K 76 LEU cc_start: 0.7318 (mt) cc_final: 0.7112 (mp) REVERT: M 213 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7859 (mtt) REVERT: M 483 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7836 (ptm160) REVERT: M 628 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.7956 (tt0) REVERT: N 47 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8225 (mptm) REVERT: O 194 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7951 (mt-10) REVERT: Q 80 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8381 (pt) REVERT: Q 315 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7790 (mt-10) REVERT: T 81 SER cc_start: 0.8367 (m) cc_final: 0.8024 (p) REVERT: U 47 ARG cc_start: 0.8283 (mtt-85) cc_final: 0.8024 (mtp85) REVERT: V 140 LYS cc_start: 0.8854 (mptm) cc_final: 0.8605 (mptm) REVERT: W 52 LYS cc_start: 0.8622 (mtpt) cc_final: 0.8323 (mtpt) REVERT: W 66 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8565 (tp30) REVERT: X 84 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7187 (mt) REVERT: Z 34 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7359 (mt-10) REVERT: c 141 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8152 (mp) REVERT: d 15 ARG cc_start: 0.7958 (ptm-80) cc_final: 0.7601 (ptm-80) REVERT: d 78 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: g 29 THR cc_start: 0.9283 (p) cc_final: 0.8939 (t) REVERT: h 53 GLU cc_start: 0.8555 (tp30) cc_final: 0.8043 (tp30) REVERT: i 53 THR cc_start: 0.8663 (m) cc_final: 0.8389 (m) REVERT: i 95 MET cc_start: 0.8865 (tpt) cc_final: 0.8297 (tpt) REVERT: i 347 ASN cc_start: 0.6754 (OUTLIER) cc_final: 0.6524 (p0) REVERT: j 83 ASN cc_start: 0.8718 (t0) cc_final: 0.8443 (t0) REVERT: l 111 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7681 (t70) REVERT: l 355 ASP cc_start: 0.8801 (t0) cc_final: 0.8569 (t0) REVERT: l 495 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7929 (mm) REVERT: m 1 MET cc_start: 0.4715 (ttp) cc_final: 0.3337 (tpt) REVERT: n 29 ARG cc_start: 0.7266 (OUTLIER) cc_final: 0.6373 (mmt90) REVERT: n 30 ARG cc_start: 0.7421 (mmm-85) cc_final: 0.6734 (ttp-170) REVERT: o 110 ASP cc_start: 0.8390 (m-30) cc_final: 0.8185 (m-30) REVERT: p 48 PHE cc_start: 0.7360 (OUTLIER) cc_final: 0.5676 (t80) REVERT: p 65 ARG cc_start: 0.6587 (ttt90) cc_final: 0.6324 (ttt-90) REVERT: r 114 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8275 (tm-30) REVERT: r 401 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8704 (ttp) REVERT: u 17 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.6882 (mm-30) REVERT: v 34 ARG cc_start: 0.5648 (tmt-80) cc_final: 0.5302 (tpm170) REVERT: v 76 ASN cc_start: 0.8220 (t0) cc_final: 0.7978 (t0) REVERT: w 173 MET cc_start: 0.8021 (mtp) cc_final: 0.7533 (mtp) REVERT: w 227 MET cc_start: 0.6312 (OUTLIER) cc_final: 0.5428 (mpt) REVERT: w 314 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8517 (mp) REVERT: w 323 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8220 (tt0) outliers start: 264 outliers final: 101 residues processed: 1191 average time/residue: 1.4449 time to fit residues: 2252.9588 Evaluate side-chains 1128 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 995 time to evaluate : 5.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 23 ARG Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 50 ASP Chi-restraints excluded: chain G residue 120 MET Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain H residue 70 GLU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 179 ARG Chi-restraints excluded: chain J residue 336 GLU Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 108 GLU Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 74 ASN Chi-restraints excluded: chain M residue 160 VAL Chi-restraints excluded: chain M residue 213 MET Chi-restraints excluded: chain M residue 244 GLU Chi-restraints excluded: chain M residue 352 VAL Chi-restraints excluded: chain M residue 483 ARG Chi-restraints excluded: chain M residue 485 ASP Chi-restraints excluded: chain M residue 515 ILE Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 628 GLU Chi-restraints excluded: chain N residue 47 LYS Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain O residue 190 ASP Chi-restraints excluded: chain O residue 194 GLU Chi-restraints excluded: chain P residue 86 ILE Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 198 THR Chi-restraints excluded: chain Q residue 265 ASN Chi-restraints excluded: chain Q residue 315 GLU Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain V residue 124 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 66 GLU Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 84 LEU Chi-restraints excluded: chain X residue 139 MET Chi-restraints excluded: chain Z residue 34 GLU Chi-restraints excluded: chain a residue 78 THR Chi-restraints excluded: chain a residue 93 ILE Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 27 GLU Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain c residue 96 ASP Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 141 LEU Chi-restraints excluded: chain c residue 175 THR Chi-restraints excluded: chain c residue 182 VAL Chi-restraints excluded: chain d residue 46 THR Chi-restraints excluded: chain d residue 59 ASN Chi-restraints excluded: chain d residue 78 GLU Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain g residue 3 MET Chi-restraints excluded: chain i residue 37 LEU Chi-restraints excluded: chain i residue 97 MET Chi-restraints excluded: chain i residue 347 ASN Chi-restraints excluded: chain j residue 66 ASP Chi-restraints excluded: chain j residue 68 GLU Chi-restraints excluded: chain j residue 109 LYS Chi-restraints excluded: chain k residue 39 SER Chi-restraints excluded: chain k residue 81 VAL Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 386 LEU Chi-restraints excluded: chain l residue 392 LYS Chi-restraints excluded: chain l residue 491 LEU Chi-restraints excluded: chain l residue 495 ILE Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain m residue 143 ILE Chi-restraints excluded: chain n residue 15 ILE Chi-restraints excluded: chain n residue 29 ARG Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain p residue 48 PHE Chi-restraints excluded: chain r residue 81 GLN Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 248 THR Chi-restraints excluded: chain r residue 401 MET Chi-restraints excluded: chain s residue 57 THR Chi-restraints excluded: chain s residue 72 ILE Chi-restraints excluded: chain s residue 172 ILE Chi-restraints excluded: chain s residue 201 THR Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 9 THR Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 55 ARG Chi-restraints excluded: chain u residue 99 HIS Chi-restraints excluded: chain u residue 131 VAL Chi-restraints excluded: chain v residue 51 LEU Chi-restraints excluded: chain v residue 61 HIS Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 108 LEU Chi-restraints excluded: chain w residue 182 GLN Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 249 MET Chi-restraints excluded: chain w residue 297 LEU Chi-restraints excluded: chain w residue 312 VAL Chi-restraints excluded: chain w residue 314 LEU Chi-restraints excluded: chain w residue 323 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 402 optimal weight: 0.3980 chunk 224 optimal weight: 5.9990 chunk 602 optimal weight: 6.9990 chunk 492 optimal weight: 4.9990 chunk 199 optimal weight: 1.9990 chunk 725 optimal weight: 2.9990 chunk 783 optimal weight: 1.9990 chunk 645 optimal weight: 9.9990 chunk 719 optimal weight: 3.9990 chunk 247 optimal weight: 0.0670 chunk 581 optimal weight: 3.9990 overall best weight: 1.4924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 GLN E 95 ASN K 90 ASN L 86 ASN ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 83 ASN V 79 GLN V 129 GLN W 90 ASN Y 57 GLN Z 21 GLN a 90 ASN c 56 ASN i 322 GLN l 534 HIS r 184 HIS s 5 ASN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 111 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.0822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 68294 Z= 0.196 Angle : 0.539 10.703 92450 Z= 0.270 Chirality : 0.041 0.166 10056 Planarity : 0.005 0.068 11588 Dihedral : 13.039 177.984 10162 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.78 % Favored : 96.18 % Rotamer: Outliers : 3.42 % Allowed : 18.09 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.02 % 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: 0.96 (0.09), residues: 8065 helix: 1.54 (0.08), residues: 4285 sheet: 0.24 (0.26), residues: 387 loop : -0.44 (0.11), residues: 3393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP u 86 HIS 0.010 0.001 HIS v 92 PHE 0.031 0.001 PHE i 292 TYR 0.021 0.001 TYR l 422 ARG 0.006 0.000 ARG m 173 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1281 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 1040 time to evaluate : 5.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.9168 (OUTLIER) cc_final: 0.7302 (tmm) REVERT: B 76 TYR cc_start: 0.8964 (OUTLIER) cc_final: 0.7004 (t80) REVERT: C 126 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8023 (mp0) REVERT: E 23 ARG cc_start: 0.7077 (OUTLIER) cc_final: 0.6234 (mmt180) REVERT: E 99 GLN cc_start: 0.9184 (OUTLIER) cc_final: 0.7671 (mt0) REVERT: F 87 VAL cc_start: 0.7802 (m) cc_final: 0.7515 (t) REVERT: G 120 MET cc_start: 0.6564 (OUTLIER) cc_final: 0.6082 (ttm) REVERT: G 123 GLU cc_start: 0.7303 (mt-10) cc_final: 0.7068 (mt-10) REVERT: H 70 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7621 (tm-30) REVERT: I 105 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7789 (mt-10) REVERT: K 76 LEU cc_start: 0.7281 (mt) cc_final: 0.7074 (mp) REVERT: M 483 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7816 (ptm160) REVERT: M 629 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8409 (mp) REVERT: O 194 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7930 (mt-10) REVERT: Q 308 TYR cc_start: 0.8808 (OUTLIER) cc_final: 0.7638 (p90) REVERT: S 1 MET cc_start: 0.8450 (mmm) cc_final: 0.8244 (mmm) REVERT: S 64 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8697 (mmmt) REVERT: T 81 SER cc_start: 0.8321 (m) cc_final: 0.7999 (p) REVERT: U 47 ARG cc_start: 0.8251 (mtt-85) cc_final: 0.7893 (mtp85) REVERT: W 66 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8543 (tp30) REVERT: c 141 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8148 (mp) REVERT: c 154 GLN cc_start: 0.8161 (mm110) cc_final: 0.7957 (mp10) REVERT: c 182 VAL cc_start: 0.6908 (OUTLIER) cc_final: 0.6356 (m) REVERT: d 8 ASP cc_start: 0.8119 (m-30) cc_final: 0.7741 (m-30) REVERT: d 15 ARG cc_start: 0.7978 (ptm-80) cc_final: 0.7654 (ptm-80) REVERT: d 32 TYR cc_start: 0.7281 (t80) cc_final: 0.7010 (t80) REVERT: h 53 GLU cc_start: 0.8569 (tp30) cc_final: 0.8123 (tp30) REVERT: i 53 THR cc_start: 0.8642 (m) cc_final: 0.8375 (m) REVERT: i 80 TYR cc_start: 0.9071 (m-80) cc_final: 0.8693 (m-80) REVERT: i 347 ASN cc_start: 0.6537 (OUTLIER) cc_final: 0.6313 (p0) REVERT: l 111 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7683 (t70) REVERT: l 479 ASN cc_start: 0.7977 (m-40) cc_final: 0.7710 (m-40) REVERT: l 482 MET cc_start: 0.7090 (OUTLIER) cc_final: 0.6838 (mmt) REVERT: m 1 MET cc_start: 0.4494 (ttp) cc_final: 0.3132 (tpt) REVERT: n 30 ARG cc_start: 0.7403 (mmm-85) cc_final: 0.6761 (ttp-170) REVERT: n 41 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8408 (mptp) REVERT: p 48 PHE cc_start: 0.7281 (OUTLIER) cc_final: 0.5674 (t80) REVERT: p 65 ARG cc_start: 0.6591 (OUTLIER) cc_final: 0.6354 (ttt-90) REVERT: r 114 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8242 (tm-30) REVERT: r 126 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8858 (tp) REVERT: r 218 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8631 (mtpp) REVERT: r 269 MET cc_start: 0.9199 (OUTLIER) cc_final: 0.8971 (ptp) REVERT: u 17 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.6815 (mm-30) REVERT: v 21 ARG cc_start: 0.7241 (ptp-110) cc_final: 0.6664 (mtm-85) REVERT: v 76 ASN cc_start: 0.8237 (t0) cc_final: 0.7986 (t0) REVERT: w 173 MET cc_start: 0.8067 (mtp) cc_final: 0.7719 (mtp) REVERT: w 227 MET cc_start: 0.6305 (OUTLIER) cc_final: 0.5438 (mpt) REVERT: w 314 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8463 (mp) REVERT: w 323 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8191 (tt0) outliers start: 241 outliers final: 106 residues processed: 1183 average time/residue: 1.4601 time to fit residues: 2257.3657 Evaluate side-chains 1140 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1004 time to evaluate : 5.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 23 ARG Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 50 ASP Chi-restraints excluded: chain G residue 120 MET Chi-restraints excluded: chain H residue 70 GLU Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 30 GLU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 108 GLU Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 74 ASN Chi-restraints excluded: chain M residue 244 GLU Chi-restraints excluded: chain M residue 352 VAL Chi-restraints excluded: chain M residue 483 ARG Chi-restraints excluded: chain M residue 515 ILE Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 629 ILE Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain O residue 172 ILE Chi-restraints excluded: chain O residue 190 ASP Chi-restraints excluded: chain O residue 194 GLU Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 265 ASN Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 64 LYS Chi-restraints excluded: chain T residue 46 ASP Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 74 GLN Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain W residue 66 GLU Chi-restraints excluded: chain W residue 114 THR Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain Y residue 78 ASP Chi-restraints excluded: chain a residue 93 ILE Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 27 GLU Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain c residue 110 ASP Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 141 LEU Chi-restraints excluded: chain c residue 175 THR Chi-restraints excluded: chain c residue 182 VAL Chi-restraints excluded: chain d residue 59 ASN Chi-restraints excluded: chain d residue 78 GLU Chi-restraints excluded: chain d residue 79 GLU Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain g residue 5 SER Chi-restraints excluded: chain i residue 37 LEU Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain i residue 347 ASN Chi-restraints excluded: chain j residue 66 ASP Chi-restraints excluded: chain j residue 68 GLU Chi-restraints excluded: chain j residue 90 MET Chi-restraints excluded: chain j residue 109 LYS Chi-restraints excluded: chain k residue 39 SER Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 223 LYS Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 386 LEU Chi-restraints excluded: chain l residue 392 LYS Chi-restraints excluded: chain l residue 409 LEU Chi-restraints excluded: chain l residue 482 MET Chi-restraints excluded: chain n residue 15 ILE Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain o residue 57 LEU Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain p residue 48 PHE Chi-restraints excluded: chain p residue 65 ARG Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 50 LEU Chi-restraints excluded: chain r residue 81 GLN Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 126 LEU Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 218 LYS Chi-restraints excluded: chain r residue 269 MET Chi-restraints excluded: chain r residue 271 MET Chi-restraints excluded: chain r residue 337 VAL Chi-restraints excluded: chain s residue 57 THR Chi-restraints excluded: chain s residue 172 ILE Chi-restraints excluded: chain s residue 201 THR Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 9 THR Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 55 ARG Chi-restraints excluded: chain u residue 64 ASN Chi-restraints excluded: chain u residue 99 HIS Chi-restraints excluded: chain v residue 51 LEU Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain w residue 182 GLN Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 288 ASP Chi-restraints excluded: chain w residue 312 VAL Chi-restraints excluded: chain w residue 314 LEU Chi-restraints excluded: chain w residue 323 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 716 optimal weight: 0.9980 chunk 545 optimal weight: 0.9990 chunk 376 optimal weight: 0.0970 chunk 80 optimal weight: 0.0980 chunk 346 optimal weight: 8.9990 chunk 486 optimal weight: 2.9990 chunk 727 optimal weight: 3.9990 chunk 770 optimal weight: 4.9990 chunk 380 optimal weight: 4.9990 chunk 689 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 GLN E 95 ASN J 79 GLN K 90 ASN L 86 ASN ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 83 ASN V 79 GLN V 129 GLN W 90 ASN Z 21 GLN a 90 ASN c 56 ASN i 322 GLN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 54 GLN v 65 GLN w 111 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 68294 Z= 0.163 Angle : 0.517 10.569 92450 Z= 0.258 Chirality : 0.040 0.312 10056 Planarity : 0.004 0.064 11588 Dihedral : 12.198 178.146 10141 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.84 % Favored : 96.12 % Rotamer: Outliers : 3.42 % Allowed : 18.47 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.09 (0.09), residues: 8065 helix: 1.64 (0.08), residues: 4278 sheet: 0.29 (0.25), residues: 407 loop : -0.38 (0.11), residues: 3380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.010 0.001 HIS v 92 PHE 0.030 0.001 PHE i 292 TYR 0.022 0.001 TYR l 422 ARG 0.006 0.000 ARG b 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1286 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 1045 time to evaluate : 5.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.7327 (tmm) REVERT: B 50 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7515 (tpp) REVERT: B 76 TYR cc_start: 0.8996 (OUTLIER) cc_final: 0.6978 (t80) REVERT: C 42 ARG cc_start: 0.5751 (OUTLIER) cc_final: 0.5545 (tpt170) REVERT: C 126 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.7980 (mp0) REVERT: E 23 ARG cc_start: 0.7056 (OUTLIER) cc_final: 0.6238 (mmt180) REVERT: E 99 GLN cc_start: 0.9156 (OUTLIER) cc_final: 0.7565 (mt0) REVERT: F 87 VAL cc_start: 0.7754 (m) cc_final: 0.7475 (t) REVERT: G 120 MET cc_start: 0.6626 (ttm) cc_final: 0.6088 (ttm) REVERT: G 123 GLU cc_start: 0.7376 (mt-10) cc_final: 0.7075 (mt-10) REVERT: G 124 ASP cc_start: 0.6610 (OUTLIER) cc_final: 0.6366 (t70) REVERT: H 70 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7633 (tm-30) REVERT: J 179 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.7400 (ptm160) REVERT: J 341 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.6894 (mm110) REVERT: M 483 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7814 (ptm160) REVERT: M 688 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.7350 (mm-40) REVERT: Q 308 TYR cc_start: 0.8762 (OUTLIER) cc_final: 0.7644 (p90) REVERT: S 64 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8676 (mmmt) REVERT: T 81 SER cc_start: 0.8262 (m) cc_final: 0.7950 (p) REVERT: Z 49 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7672 (pm20) REVERT: b 122 GLU cc_start: 0.7529 (tt0) cc_final: 0.7305 (tm-30) REVERT: c 93 ASP cc_start: 0.8370 (m-30) cc_final: 0.8154 (m-30) REVERT: c 177 GLU cc_start: 0.7842 (mm-30) cc_final: 0.6742 (pp20) REVERT: d 8 ASP cc_start: 0.8130 (m-30) cc_final: 0.7752 (m-30) REVERT: d 15 ARG cc_start: 0.7920 (ptm-80) cc_final: 0.7466 (ptm-80) REVERT: d 32 TYR cc_start: 0.7235 (t80) cc_final: 0.7026 (t80) REVERT: h 53 GLU cc_start: 0.8556 (tp30) cc_final: 0.8174 (tp30) REVERT: h 81 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7639 (ptp90) REVERT: i 53 THR cc_start: 0.8616 (m) cc_final: 0.8379 (m) REVERT: i 80 TYR cc_start: 0.9005 (m-80) cc_final: 0.8674 (m-80) REVERT: i 97 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8324 (tpp) REVERT: i 157 MET cc_start: 0.9345 (mtm) cc_final: 0.9006 (mtm) REVERT: i 278 MET cc_start: 0.8359 (ttm) cc_final: 0.8104 (mmt) REVERT: i 334 THR cc_start: 0.9160 (m) cc_final: 0.8701 (p) REVERT: i 347 ASN cc_start: 0.6408 (OUTLIER) cc_final: 0.6187 (p0) REVERT: j 68 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.6588 (mp0) REVERT: l 111 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7649 (t70) REVERT: l 355 ASP cc_start: 0.8807 (t0) cc_final: 0.8528 (t0) REVERT: l 411 MET cc_start: 0.8465 (mmm) cc_final: 0.8108 (mmt) REVERT: l 479 ASN cc_start: 0.7976 (m-40) cc_final: 0.7692 (m-40) REVERT: l 482 MET cc_start: 0.7006 (OUTLIER) cc_final: 0.6712 (mmt) REVERT: m 1 MET cc_start: 0.4510 (ttp) cc_final: 0.3171 (tpt) REVERT: n 30 ARG cc_start: 0.7431 (mmm-85) cc_final: 0.6905 (ttp-170) REVERT: n 41 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8413 (mptp) REVERT: o 31 LYS cc_start: 0.8649 (tptt) cc_final: 0.8040 (ttpt) REVERT: o 85 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8069 (tttp) REVERT: p 43 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.7981 (mp) REVERT: p 48 PHE cc_start: 0.7340 (OUTLIER) cc_final: 0.5551 (t80) REVERT: p 69 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7931 (mt-10) REVERT: r 114 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8311 (tm-30) REVERT: r 126 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8831 (tp) REVERT: s 225 MET cc_start: 0.8571 (mtm) cc_final: 0.8316 (mtm) REVERT: u 17 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.6789 (mm-30) REVERT: v 21 ARG cc_start: 0.7321 (ptp-110) cc_final: 0.6837 (mtm-85) REVERT: v 76 ASN cc_start: 0.8192 (t0) cc_final: 0.7966 (t0) REVERT: w 173 MET cc_start: 0.8163 (mtp) cc_final: 0.7878 (mtp) REVERT: w 227 MET cc_start: 0.6286 (OUTLIER) cc_final: 0.5425 (mpt) REVERT: w 314 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8384 (mp) REVERT: w 323 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8161 (tt0) outliers start: 241 outliers final: 103 residues processed: 1197 average time/residue: 1.4860 time to fit residues: 2321.1818 Evaluate side-chains 1133 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 999 time to evaluate : 5.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 23 ARG Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 50 ASP Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 70 GLU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 179 ARG Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 341 GLN Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 74 ASN Chi-restraints excluded: chain M residue 244 GLU Chi-restraints excluded: chain M residue 352 VAL Chi-restraints excluded: chain M residue 483 ARG Chi-restraints excluded: chain M residue 535 GLU Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 688 GLN Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain O residue 172 ILE Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 198 THR Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 64 LYS Chi-restraints excluded: chain T residue 46 ASP Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 74 GLN Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain W residue 93 GLU Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 89 LEU Chi-restraints excluded: chain a residue 93 ILE Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain c residue 110 ASP Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 175 THR Chi-restraints excluded: chain c residue 182 VAL Chi-restraints excluded: chain d residue 59 ASN Chi-restraints excluded: chain d residue 78 GLU Chi-restraints excluded: chain d residue 79 GLU Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain g residue 3 MET Chi-restraints excluded: chain g residue 5 SER Chi-restraints excluded: chain h residue 81 ARG Chi-restraints excluded: chain i residue 37 LEU Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 97 MET Chi-restraints excluded: chain i residue 347 ASN Chi-restraints excluded: chain j residue 66 ASP Chi-restraints excluded: chain j residue 68 GLU Chi-restraints excluded: chain j residue 109 LYS Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 386 LEU Chi-restraints excluded: chain l residue 392 LYS Chi-restraints excluded: chain l residue 482 MET Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain o residue 57 LEU Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain o residue 85 LYS Chi-restraints excluded: chain p residue 43 LEU Chi-restraints excluded: chain p residue 48 PHE Chi-restraints excluded: chain p residue 132 SER Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 50 LEU Chi-restraints excluded: chain r residue 90 THR Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 126 LEU Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 218 LYS Chi-restraints excluded: chain r residue 248 THR Chi-restraints excluded: chain r residue 271 MET Chi-restraints excluded: chain r residue 337 VAL Chi-restraints excluded: chain s residue 57 THR Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 172 ILE Chi-restraints excluded: chain s residue 201 THR Chi-restraints excluded: chain u residue 9 THR Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 55 ARG Chi-restraints excluded: chain u residue 64 ASN Chi-restraints excluded: chain u residue 99 HIS Chi-restraints excluded: chain v residue 51 LEU Chi-restraints excluded: chain v residue 61 HIS Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 106 VAL Chi-restraints excluded: chain w residue 182 GLN Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 288 ASP Chi-restraints excluded: chain w residue 297 LEU Chi-restraints excluded: chain w residue 312 VAL Chi-restraints excluded: chain w residue 314 LEU Chi-restraints excluded: chain w residue 323 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 641 optimal weight: 0.6980 chunk 437 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 573 optimal weight: 0.9980 chunk 317 optimal weight: 0.9980 chunk 657 optimal weight: 10.0000 chunk 532 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 393 optimal weight: 3.9990 chunk 691 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 GLN E 95 ASN G 142 GLN K 90 ASN L 86 ASN ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 666 GLN M 667 GLN N 122 GLN U 83 ASN V 79 GLN V 129 GLN W 90 ASN Z 21 GLN a 90 ASN c 56 ASN i 322 GLN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 54 GLN ** v 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 111 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 68294 Z= 0.215 Angle : 0.544 10.764 92450 Z= 0.271 Chirality : 0.041 0.242 10056 Planarity : 0.005 0.065 11588 Dihedral : 11.846 178.292 10131 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.91 % Favored : 96.06 % Rotamer: Outliers : 3.60 % Allowed : 18.75 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.01 (0.09), residues: 8065 helix: 1.58 (0.08), residues: 4285 sheet: 0.25 (0.26), residues: 387 loop : -0.41 (0.11), residues: 3393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.009 0.001 HIS v 92 PHE 0.032 0.001 PHE i 292 TYR 0.027 0.001 TYR b 88 ARG 0.008 0.000 ARG m 173 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1276 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 1022 time to evaluate : 5.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.7434 (tmm) REVERT: B 50 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7478 (tpp) REVERT: B 76 TYR cc_start: 0.9025 (OUTLIER) cc_final: 0.7015 (t80) REVERT: C 126 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8014 (mp0) REVERT: E 23 ARG cc_start: 0.7066 (OUTLIER) cc_final: 0.6230 (mmt180) REVERT: E 99 GLN cc_start: 0.9178 (OUTLIER) cc_final: 0.7606 (mt0) REVERT: F 87 VAL cc_start: 0.7810 (m) cc_final: 0.7537 (t) REVERT: G 120 MET cc_start: 0.6721 (ttm) cc_final: 0.6297 (ttm) REVERT: G 123 GLU cc_start: 0.7393 (mt-10) cc_final: 0.7077 (mt-10) REVERT: G 124 ASP cc_start: 0.6709 (OUTLIER) cc_final: 0.6487 (t70) REVERT: J 179 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.7446 (ptm160) REVERT: J 341 GLN cc_start: 0.7589 (OUTLIER) cc_final: 0.6907 (mm110) REVERT: M 483 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7813 (ptm160) REVERT: M 629 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8275 (mp) REVERT: M 688 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.7372 (mm-40) REVERT: N 114 LYS cc_start: 0.8413 (mtmt) cc_final: 0.8201 (mtpt) REVERT: O 106 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8213 (mt0) REVERT: O 192 TYR cc_start: 0.8790 (OUTLIER) cc_final: 0.8348 (m-80) REVERT: O 194 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7628 (mp0) REVERT: Q 308 TYR cc_start: 0.8758 (OUTLIER) cc_final: 0.7608 (p90) REVERT: Q 315 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7696 (mt-10) REVERT: S 64 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8689 (mmmt) REVERT: T 81 SER cc_start: 0.8286 (m) cc_final: 0.7977 (p) REVERT: U 31 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8596 (mt) REVERT: Z 49 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7708 (pm20) REVERT: b 122 GLU cc_start: 0.7603 (tt0) cc_final: 0.7396 (tm-30) REVERT: c 141 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8193 (mp) REVERT: c 159 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8796 (tttm) REVERT: c 177 GLU cc_start: 0.7853 (mm-30) cc_final: 0.6746 (pp20) REVERT: d 8 ASP cc_start: 0.8125 (m-30) cc_final: 0.7727 (m-30) REVERT: d 15 ARG cc_start: 0.7914 (ptm-80) cc_final: 0.7438 (ptm-80) REVERT: d 172 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7335 (tt0) REVERT: h 53 GLU cc_start: 0.8602 (tp30) cc_final: 0.8289 (tp30) REVERT: h 73 MET cc_start: 0.8389 (mtp) cc_final: 0.8188 (mtp) REVERT: h 99 LEU cc_start: 0.8212 (mm) cc_final: 0.7964 (mm) REVERT: i 53 THR cc_start: 0.8657 (m) cc_final: 0.8398 (m) REVERT: i 80 TYR cc_start: 0.9094 (m-80) cc_final: 0.8817 (m-80) REVERT: i 157 MET cc_start: 0.9341 (mtm) cc_final: 0.8992 (mtm) REVERT: i 334 THR cc_start: 0.9174 (m) cc_final: 0.8818 (p) REVERT: i 347 ASN cc_start: 0.6473 (OUTLIER) cc_final: 0.6242 (p0) REVERT: j 68 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.6671 (mp0) REVERT: l 111 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7648 (t70) REVERT: l 355 ASP cc_start: 0.8840 (t0) cc_final: 0.8536 (t0) REVERT: l 411 MET cc_start: 0.8488 (mmm) cc_final: 0.8224 (mmt) REVERT: l 479 ASN cc_start: 0.8012 (m-40) cc_final: 0.7743 (m-40) REVERT: l 482 MET cc_start: 0.7181 (OUTLIER) cc_final: 0.6896 (mmt) REVERT: n 29 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.6351 (mmt90) REVERT: n 30 ARG cc_start: 0.7518 (mmm-85) cc_final: 0.7009 (ttp-170) REVERT: n 41 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8401 (mptp) REVERT: o 31 LYS cc_start: 0.8631 (tptt) cc_final: 0.8069 (ttpt) REVERT: o 85 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8079 (tttp) REVERT: p 43 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7973 (mp) REVERT: p 48 PHE cc_start: 0.7401 (OUTLIER) cc_final: 0.5422 (t80) REVERT: p 69 GLU cc_start: 0.8220 (mt-10) cc_final: 0.8008 (mt-10) REVERT: r 114 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8314 (tm-30) REVERT: r 126 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8854 (tp) REVERT: u 17 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.6810 (mm-30) REVERT: v 21 ARG cc_start: 0.7406 (ptp-110) cc_final: 0.6855 (mtm-85) REVERT: v 76 ASN cc_start: 0.8274 (t0) cc_final: 0.8047 (t0) REVERT: w 173 MET cc_start: 0.8194 (mtp) cc_final: 0.7928 (mtp) REVERT: w 227 MET cc_start: 0.6282 (OUTLIER) cc_final: 0.5416 (mpt) REVERT: w 314 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8427 (mp) REVERT: w 323 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8220 (tt0) outliers start: 254 outliers final: 134 residues processed: 1190 average time/residue: 1.4780 time to fit residues: 2298.4837 Evaluate side-chains 1163 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 992 time to evaluate : 5.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 23 ARG Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 30 GLU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 179 ARG Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 341 GLN Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 108 GLU Chi-restraints excluded: chain L residue 133 ASP Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 74 ASN Chi-restraints excluded: chain M residue 244 GLU Chi-restraints excluded: chain M residue 352 VAL Chi-restraints excluded: chain M residue 387 LEU Chi-restraints excluded: chain M residue 483 ARG Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 629 ILE Chi-restraints excluded: chain M residue 688 GLN Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 106 GLN Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain O residue 190 ASP Chi-restraints excluded: chain O residue 192 TYR Chi-restraints excluded: chain O residue 194 GLU Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 198 THR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 252 SER Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 315 GLU Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 64 LYS Chi-restraints excluded: chain T residue 46 ASP Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 74 GLN Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain V residue 124 LEU Chi-restraints excluded: chain V residue 140 LYS Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain W residue 93 GLU Chi-restraints excluded: chain W residue 114 THR Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Y residue 78 ASP Chi-restraints excluded: chain a residue 93 ILE Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain c residue 43 LYS Chi-restraints excluded: chain c residue 96 ASP Chi-restraints excluded: chain c residue 110 ASP Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 141 LEU Chi-restraints excluded: chain c residue 159 LYS Chi-restraints excluded: chain c residue 175 THR Chi-restraints excluded: chain d residue 59 ASN Chi-restraints excluded: chain d residue 78 GLU Chi-restraints excluded: chain d residue 79 GLU Chi-restraints excluded: chain d residue 172 GLU Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain g residue 3 MET Chi-restraints excluded: chain g residue 5 SER Chi-restraints excluded: chain g residue 92 MET Chi-restraints excluded: chain h residue 54 LYS Chi-restraints excluded: chain i residue 37 LEU Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 347 ASN Chi-restraints excluded: chain j residue 66 ASP Chi-restraints excluded: chain j residue 68 GLU Chi-restraints excluded: chain j residue 90 MET Chi-restraints excluded: chain j residue 109 LYS Chi-restraints excluded: chain k residue 39 SER Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 190 LEU Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 386 LEU Chi-restraints excluded: chain l residue 392 LYS Chi-restraints excluded: chain l residue 409 LEU Chi-restraints excluded: chain l residue 482 MET Chi-restraints excluded: chain l residue 499 MET Chi-restraints excluded: chain n residue 15 ILE Chi-restraints excluded: chain n residue 29 ARG Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain o residue 57 LEU Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain o residue 85 LYS Chi-restraints excluded: chain p residue 43 LEU Chi-restraints excluded: chain p residue 48 PHE Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 50 LEU Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 81 GLN Chi-restraints excluded: chain r residue 90 THR Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 126 LEU Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 218 LYS Chi-restraints excluded: chain r residue 248 THR Chi-restraints excluded: chain r residue 271 MET Chi-restraints excluded: chain r residue 337 VAL Chi-restraints excluded: chain r residue 350 THR Chi-restraints excluded: chain s residue 57 THR Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain s residue 172 ILE Chi-restraints excluded: chain s residue 201 THR Chi-restraints excluded: chain u residue 9 THR Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 55 ARG Chi-restraints excluded: chain u residue 64 ASN Chi-restraints excluded: chain u residue 99 HIS Chi-restraints excluded: chain v residue 51 LEU Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 106 VAL Chi-restraints excluded: chain w residue 114 LEU Chi-restraints excluded: chain w residue 182 GLN Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 288 ASP Chi-restraints excluded: chain w residue 297 LEU Chi-restraints excluded: chain w residue 312 VAL Chi-restraints excluded: chain w residue 314 LEU Chi-restraints excluded: chain w residue 323 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 259 optimal weight: 4.9990 chunk 693 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 452 optimal weight: 8.9990 chunk 190 optimal weight: 0.8980 chunk 771 optimal weight: 10.0000 chunk 640 optimal weight: 0.3980 chunk 357 optimal weight: 0.4980 chunk 64 optimal weight: 5.9990 chunk 255 optimal weight: 0.0570 chunk 404 optimal weight: 6.9990 overall best weight: 0.5700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN E 58 GLN E 95 ASN J 295 HIS K 90 ASN L 86 ASN ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 540 ASN M 667 GLN N 31 ASN N 122 GLN U 83 ASN V 79 GLN V 129 GLN W 90 ASN Z 21 GLN a 90 ASN a 181 HIS c 56 ASN i 322 GLN ** l 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 157 ASN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 54 GLN ** v 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 68294 Z= 0.137 Angle : 0.502 10.621 92450 Z= 0.250 Chirality : 0.039 0.222 10056 Planarity : 0.004 0.061 11588 Dihedral : 11.272 177.285 10131 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.63 % Favored : 96.33 % Rotamer: Outliers : 3.05 % Allowed : 19.96 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 8065 helix: 1.75 (0.08), residues: 4266 sheet: 0.30 (0.24), residues: 430 loop : -0.30 (0.11), residues: 3369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP l 144 HIS 0.007 0.001 HIS v 92 PHE 0.030 0.001 PHE i 292 TYR 0.030 0.001 TYR d 32 ARG 0.011 0.000 ARG M 538 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1264 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 1049 time to evaluate : 6.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.7370 (tmm) REVERT: B 50 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.6844 (tpp) REVERT: B 76 TYR cc_start: 0.8960 (OUTLIER) cc_final: 0.6991 (t80) REVERT: C 126 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8010 (mp0) REVERT: E 23 ARG cc_start: 0.7071 (mtp180) cc_final: 0.6199 (mmt180) REVERT: F 87 VAL cc_start: 0.7773 (m) cc_final: 0.7492 (t) REVERT: G 120 MET cc_start: 0.6701 (ttm) cc_final: 0.6290 (ttm) REVERT: G 123 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7047 (mt-10) REVERT: J 179 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7392 (ptm160) REVERT: J 341 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.6884 (mm110) REVERT: L 148 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7982 (mm-30) REVERT: M 387 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8415 (tt) REVERT: M 483 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7848 (ptm160) REVERT: M 629 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8242 (mp) REVERT: O 192 TYR cc_start: 0.8715 (OUTLIER) cc_final: 0.8302 (m-80) REVERT: Q 100 GLU cc_start: 0.8084 (tt0) cc_final: 0.7507 (tm-30) REVERT: Q 308 TYR cc_start: 0.8602 (OUTLIER) cc_final: 0.7473 (p90) REVERT: S 64 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8664 (mmmt) REVERT: T 81 SER cc_start: 0.8232 (m) cc_final: 0.7969 (p) REVERT: W 52 LYS cc_start: 0.8590 (mtpt) cc_final: 0.8251 (mtpt) REVERT: W 134 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7737 (tt) REVERT: Z 20 LYS cc_start: 0.8375 (mttm) cc_final: 0.8039 (mmtm) REVERT: Z 49 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7723 (pm20) REVERT: b 93 LYS cc_start: 0.8477 (mptt) cc_final: 0.7964 (mttt) REVERT: c 177 GLU cc_start: 0.7679 (mm-30) cc_final: 0.6632 (pp20) REVERT: d 15 ARG cc_start: 0.7886 (ptm-80) cc_final: 0.7445 (ptm-80) REVERT: g 4 MET cc_start: 0.8083 (mtm) cc_final: 0.7808 (mtm) REVERT: h 53 GLU cc_start: 0.8547 (tp30) cc_final: 0.8303 (tp30) REVERT: h 81 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7588 (ptp90) REVERT: h 99 LEU cc_start: 0.8355 (mm) cc_final: 0.8054 (mm) REVERT: i 80 TYR cc_start: 0.8960 (m-80) cc_final: 0.8628 (m-80) REVERT: i 157 MET cc_start: 0.9325 (mtm) cc_final: 0.8933 (mtm) REVERT: i 278 MET cc_start: 0.8284 (ttm) cc_final: 0.8075 (mmt) REVERT: i 339 MET cc_start: 0.9018 (mmp) cc_final: 0.8651 (mmp) REVERT: l 62 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8664 (mp) REVERT: l 111 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7674 (t70) REVERT: l 355 ASP cc_start: 0.8859 (t0) cc_final: 0.8540 (t0) REVERT: l 411 MET cc_start: 0.8371 (mmm) cc_final: 0.8163 (mmt) REVERT: l 479 ASN cc_start: 0.7974 (m-40) cc_final: 0.7684 (m-40) REVERT: l 482 MET cc_start: 0.6911 (OUTLIER) cc_final: 0.6646 (mmt) REVERT: m 1 MET cc_start: 0.4881 (ttp) cc_final: 0.3338 (tpt) REVERT: m 8 ILE cc_start: 0.6237 (OUTLIER) cc_final: 0.5986 (mp) REVERT: n 30 ARG cc_start: 0.7401 (mmm-85) cc_final: 0.7037 (ttp-170) REVERT: n 34 LYS cc_start: 0.8003 (mtpp) cc_final: 0.7416 (tptt) REVERT: n 41 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8298 (mptp) REVERT: o 31 LYS cc_start: 0.8628 (tptt) cc_final: 0.8064 (ttpt) REVERT: o 85 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7991 (tttp) REVERT: p 43 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.7991 (mp) REVERT: p 48 PHE cc_start: 0.7280 (OUTLIER) cc_final: 0.5357 (t80) REVERT: r 114 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8267 (tm-30) REVERT: r 126 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8798 (tp) REVERT: r 269 MET cc_start: 0.9185 (ptm) cc_final: 0.8950 (ptp) REVERT: v 16 GLU cc_start: 0.6831 (pm20) cc_final: 0.6581 (pm20) REVERT: v 33 GLU cc_start: 0.6600 (mp0) cc_final: 0.6353 (mp0) REVERT: v 34 ARG cc_start: 0.5668 (tpt170) cc_final: 0.5083 (tpm170) REVERT: v 52 MET cc_start: 0.6965 (ttp) cc_final: 0.6675 (mtt) REVERT: v 76 ASN cc_start: 0.8218 (t0) cc_final: 0.8015 (t0) REVERT: w 173 MET cc_start: 0.8156 (mtp) cc_final: 0.7892 (mtp) REVERT: w 288 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7694 (m-30) REVERT: w 314 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8346 (mp) REVERT: w 323 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8134 (tt0) outliers start: 215 outliers final: 86 residues processed: 1179 average time/residue: 1.4531 time to fit residues: 2243.8299 Evaluate side-chains 1118 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 1004 time to evaluate : 5.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 30 GLU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 64 MET Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 179 ARG Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 341 GLN Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 148 GLU Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 74 ASN Chi-restraints excluded: chain M residue 370 GLU Chi-restraints excluded: chain M residue 387 LEU Chi-restraints excluded: chain M residue 483 ARG Chi-restraints excluded: chain M residue 535 GLU Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 629 ILE Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain O residue 172 ILE Chi-restraints excluded: chain O residue 192 TYR Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 198 THR Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 435 LEU Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 64 LYS Chi-restraints excluded: chain T residue 46 ASP Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 74 GLN Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain W residue 66 GLU Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain a residue 93 ILE Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain c residue 96 ASP Chi-restraints excluded: chain c residue 110 ASP Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 175 THR Chi-restraints excluded: chain d residue 59 ASN Chi-restraints excluded: chain d residue 78 GLU Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain g residue 5 SER Chi-restraints excluded: chain h residue 81 ARG Chi-restraints excluded: chain i residue 37 LEU Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain j residue 66 ASP Chi-restraints excluded: chain k residue 39 SER Chi-restraints excluded: chain l residue 62 ILE Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 409 LEU Chi-restraints excluded: chain l residue 482 MET Chi-restraints excluded: chain m residue 8 ILE Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain o residue 85 LYS Chi-restraints excluded: chain p residue 43 LEU Chi-restraints excluded: chain p residue 48 PHE Chi-restraints excluded: chain p residue 64 LEU Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 50 LEU Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 126 LEU Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 440 HIS Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain u residue 9 THR Chi-restraints excluded: chain u residue 99 HIS Chi-restraints excluded: chain v residue 51 LEU Chi-restraints excluded: chain v residue 61 HIS Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 67 CYS Chi-restraints excluded: chain w residue 106 VAL Chi-restraints excluded: chain w residue 132 GLN Chi-restraints excluded: chain w residue 182 GLN Chi-restraints excluded: chain w residue 288 ASP Chi-restraints excluded: chain w residue 297 LEU Chi-restraints excluded: chain w residue 314 LEU Chi-restraints excluded: chain w residue 323 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 743 optimal weight: 0.0170 chunk 86 optimal weight: 9.9990 chunk 439 optimal weight: 0.9980 chunk 563 optimal weight: 5.9990 chunk 436 optimal weight: 5.9990 chunk 649 optimal weight: 1.9990 chunk 430 optimal weight: 3.9990 chunk 768 optimal weight: 1.9990 chunk 480 optimal weight: 8.9990 chunk 468 optimal weight: 3.9990 chunk 354 optimal weight: 7.9990 overall best weight: 1.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 GLN E 95 ASN K 90 ASN ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 666 GLN M 667 GLN N 31 ASN U 83 ASN V 79 GLN V 129 GLN W 90 ASN Z 21 GLN a 90 ASN c 56 ASN e 86 ASN i 322 GLN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 219 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 68294 Z= 0.221 Angle : 0.550 12.494 92450 Z= 0.273 Chirality : 0.041 0.209 10056 Planarity : 0.005 0.062 11588 Dihedral : 11.113 178.224 10119 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.09 % Favored : 95.87 % Rotamer: Outliers : 3.21 % Allowed : 20.05 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.02 % 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: 1.11 (0.09), residues: 8065 helix: 1.64 (0.08), residues: 4274 sheet: 0.35 (0.25), residues: 407 loop : -0.33 (0.11), residues: 3384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.007 0.001 HIS J 37 PHE 0.031 0.001 PHE i 292 TYR 0.024 0.001 TYR b 88 ARG 0.008 0.000 ARG b 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1253 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 1027 time to evaluate : 5.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.9203 (OUTLIER) cc_final: 0.7462 (tmm) REVERT: B 50 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.6855 (tpp) REVERT: B 65 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7892 (pm20) REVERT: B 76 TYR cc_start: 0.9029 (OUTLIER) cc_final: 0.7055 (t80) REVERT: C 126 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8090 (mp0) REVERT: E 23 ARG cc_start: 0.7035 (OUTLIER) cc_final: 0.6219 (mmt180) REVERT: E 99 GLN cc_start: 0.9150 (OUTLIER) cc_final: 0.7549 (mt0) REVERT: F 87 VAL cc_start: 0.7802 (m) cc_final: 0.7534 (t) REVERT: G 120 MET cc_start: 0.6763 (ttm) cc_final: 0.6385 (ttm) REVERT: G 123 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7056 (mt-10) REVERT: G 140 CYS cc_start: 0.6582 (OUTLIER) cc_final: 0.6111 (p) REVERT: I 21 GLN cc_start: 0.6637 (mm110) cc_final: 0.6199 (mm-40) REVERT: J 179 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7441 (ptm160) REVERT: J 341 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.6912 (mm110) REVERT: L 148 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8015 (mm-30) REVERT: M 333 PHE cc_start: 0.8065 (m-80) cc_final: 0.7712 (m-80) REVERT: M 387 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8497 (tt) REVERT: M 483 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7807 (ptm160) REVERT: M 629 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8279 (mp) REVERT: M 688 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.7374 (mm-40) REVERT: N 114 LYS cc_start: 0.8371 (mtmt) cc_final: 0.8158 (mtpt) REVERT: Q 100 GLU cc_start: 0.8093 (tt0) cc_final: 0.7519 (tm-30) REVERT: Q 308 TYR cc_start: 0.8742 (OUTLIER) cc_final: 0.7520 (p90) REVERT: S 64 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8710 (mmmt) REVERT: T 81 SER cc_start: 0.8290 (m) cc_final: 0.7986 (p) REVERT: Z 20 LYS cc_start: 0.8379 (mttm) cc_final: 0.8047 (mmtm) REVERT: Z 49 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7749 (pm20) REVERT: b 93 LYS cc_start: 0.8499 (mptt) cc_final: 0.8017 (mttt) REVERT: c 141 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8201 (mp) REVERT: c 177 GLU cc_start: 0.7699 (mm-30) cc_final: 0.6621 (pp20) REVERT: d 15 ARG cc_start: 0.7860 (ptm-80) cc_final: 0.7430 (ptm-80) REVERT: d 32 TYR cc_start: 0.7505 (t80) cc_final: 0.7274 (t80) REVERT: d 172 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7331 (tt0) REVERT: h 53 GLU cc_start: 0.8585 (tp30) cc_final: 0.8381 (tp30) REVERT: h 73 MET cc_start: 0.8404 (mtp) cc_final: 0.8195 (mtp) REVERT: h 81 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7622 (ptp90) REVERT: h 99 LEU cc_start: 0.8387 (mm) cc_final: 0.8123 (mm) REVERT: i 80 TYR cc_start: 0.9078 (m-80) cc_final: 0.8826 (m-80) REVERT: i 97 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8233 (ttp) REVERT: i 157 MET cc_start: 0.9340 (mtm) cc_final: 0.8890 (mtm) REVERT: i 334 THR cc_start: 0.9152 (m) cc_final: 0.8806 (p) REVERT: i 339 MET cc_start: 0.9118 (mmp) cc_final: 0.8782 (mmp) REVERT: i 347 ASN cc_start: 0.6374 (OUTLIER) cc_final: 0.6153 (p0) REVERT: j 13 LEU cc_start: 0.8641 (tt) cc_final: 0.8437 (tp) REVERT: j 19 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6806 (mp) REVERT: l 111 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7653 (t70) REVERT: l 355 ASP cc_start: 0.8875 (t0) cc_final: 0.8581 (t0) REVERT: l 479 ASN cc_start: 0.7841 (m-40) cc_final: 0.7548 (m-40) REVERT: l 482 MET cc_start: 0.7121 (OUTLIER) cc_final: 0.6883 (mmt) REVERT: l 500 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8020 (tt) REVERT: m 1 MET cc_start: 0.4906 (ttp) cc_final: 0.3455 (tpt) REVERT: n 30 ARG cc_start: 0.7430 (mmm-85) cc_final: 0.7042 (ttp-170) REVERT: n 41 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8354 (mptp) REVERT: o 31 LYS cc_start: 0.8643 (tptt) cc_final: 0.8083 (ttpt) REVERT: o 85 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8025 (tttp) REVERT: p 43 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.7991 (mp) REVERT: p 48 PHE cc_start: 0.7350 (OUTLIER) cc_final: 0.5310 (t80) REVERT: r 50 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8766 (mm) REVERT: r 114 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8330 (tm-30) REVERT: r 126 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8845 (tp) REVERT: v 16 GLU cc_start: 0.6834 (pm20) cc_final: 0.6587 (pm20) REVERT: v 21 ARG cc_start: 0.7497 (ptp-110) cc_final: 0.6983 (mtm-85) REVERT: v 33 GLU cc_start: 0.6737 (mp0) cc_final: 0.6515 (mp0) REVERT: v 34 ARG cc_start: 0.5765 (OUTLIER) cc_final: 0.5205 (tpm170) REVERT: v 52 MET cc_start: 0.7085 (ttp) cc_final: 0.6677 (mtt) REVERT: w 173 MET cc_start: 0.8207 (mtp) cc_final: 0.7967 (mtp) REVERT: w 262 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7681 (pt0) REVERT: w 275 TYR cc_start: 0.6774 (OUTLIER) cc_final: 0.6049 (m-10) REVERT: w 314 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8326 (mp) REVERT: w 323 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8212 (tt0) outliers start: 226 outliers final: 120 residues processed: 1173 average time/residue: 1.4564 time to fit residues: 2239.0401 Evaluate side-chains 1166 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1008 time to evaluate : 5.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 23 ARG Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain G residue 140 CYS Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 30 GLU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 179 ARG Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 341 GLN Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 108 GLU Chi-restraints excluded: chain L residue 133 ASP Chi-restraints excluded: chain L residue 148 GLU Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 74 ASN Chi-restraints excluded: chain M residue 370 GLU Chi-restraints excluded: chain M residue 387 LEU Chi-restraints excluded: chain M residue 421 SER Chi-restraints excluded: chain M residue 483 ARG Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 629 ILE Chi-restraints excluded: chain M residue 674 LEU Chi-restraints excluded: chain M residue 688 GLN Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain O residue 190 ASP Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 105 MET Chi-restraints excluded: chain Q residue 198 THR Chi-restraints excluded: chain Q residue 252 SER Chi-restraints excluded: chain Q residue 265 ASN Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 64 LYS Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 74 GLN Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain V residue 124 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain W residue 66 GLU Chi-restraints excluded: chain W residue 93 GLU Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain a residue 93 ILE Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 27 GLU Chi-restraints excluded: chain c residue 96 ASP Chi-restraints excluded: chain c residue 110 ASP Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 141 LEU Chi-restraints excluded: chain c residue 175 THR Chi-restraints excluded: chain d residue 59 ASN Chi-restraints excluded: chain d residue 78 GLU Chi-restraints excluded: chain d residue 172 GLU Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain g residue 5 SER Chi-restraints excluded: chain g residue 92 MET Chi-restraints excluded: chain h residue 47 ILE Chi-restraints excluded: chain h residue 54 LYS Chi-restraints excluded: chain h residue 81 ARG Chi-restraints excluded: chain i residue 37 LEU Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 97 MET Chi-restraints excluded: chain i residue 347 ASN Chi-restraints excluded: chain j residue 19 LEU Chi-restraints excluded: chain j residue 66 ASP Chi-restraints excluded: chain j residue 90 MET Chi-restraints excluded: chain j residue 109 LYS Chi-restraints excluded: chain k residue 39 SER Chi-restraints excluded: chain k residue 43 MET Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 79 SER Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 184 LEU Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 347 ILE Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 482 MET Chi-restraints excluded: chain l residue 491 LEU Chi-restraints excluded: chain l residue 500 LEU Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain o residue 5 LYS Chi-restraints excluded: chain o residue 57 LEU Chi-restraints excluded: chain o residue 85 LYS Chi-restraints excluded: chain p residue 43 LEU Chi-restraints excluded: chain p residue 48 PHE Chi-restraints excluded: chain p residue 64 LEU Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 50 LEU Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 126 LEU Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 248 THR Chi-restraints excluded: chain r residue 337 VAL Chi-restraints excluded: chain s residue 57 THR Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain s residue 172 ILE Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 9 THR Chi-restraints excluded: chain u residue 99 HIS Chi-restraints excluded: chain v residue 34 ARG Chi-restraints excluded: chain v residue 51 LEU Chi-restraints excluded: chain v residue 61 HIS Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 106 VAL Chi-restraints excluded: chain w residue 249 MET Chi-restraints excluded: chain w residue 262 GLU Chi-restraints excluded: chain w residue 275 TYR Chi-restraints excluded: chain w residue 288 ASP Chi-restraints excluded: chain w residue 297 LEU Chi-restraints excluded: chain w residue 314 LEU Chi-restraints excluded: chain w residue 323 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 475 optimal weight: 10.0000 chunk 306 optimal weight: 0.4980 chunk 458 optimal weight: 10.0000 chunk 231 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 chunk 488 optimal weight: 5.9990 chunk 523 optimal weight: 1.9990 chunk 379 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 603 optimal weight: 7.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN E 58 GLN E 95 ASN ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 GLN K 90 ASN L 86 ASN ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 122 GLN U 83 ASN V 79 GLN V 129 GLN W 90 ASN Y 57 GLN Z 21 GLN a 90 ASN c 56 ASN i 322 GLN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 68294 Z= 0.228 Angle : 0.559 11.978 92450 Z= 0.279 Chirality : 0.042 0.224 10056 Planarity : 0.005 0.065 11588 Dihedral : 11.028 178.391 10119 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.00 % Favored : 95.96 % Rotamer: Outliers : 3.16 % Allowed : 20.39 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.03 (0.09), residues: 8065 helix: 1.57 (0.08), residues: 4270 sheet: 0.30 (0.25), residues: 407 loop : -0.37 (0.11), residues: 3388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.007 0.001 HIS J 37 PHE 0.032 0.001 PHE i 292 TYR 0.025 0.001 TYR E 40 ARG 0.010 0.000 ARG m 173 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1247 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 1024 time to evaluate : 5.916 Fit side-chains revert: symmetry clash REVERT: A 102 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.7497 (tmm) REVERT: B 50 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.6844 (tpp) REVERT: B 65 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7933 (pm20) REVERT: B 76 TYR cc_start: 0.9060 (OUTLIER) cc_final: 0.7075 (t80) REVERT: C 126 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8093 (mp0) REVERT: E 23 ARG cc_start: 0.6999 (OUTLIER) cc_final: 0.6353 (mmt180) REVERT: E 99 GLN cc_start: 0.9164 (OUTLIER) cc_final: 0.7600 (mt0) REVERT: F 87 VAL cc_start: 0.7895 (m) cc_final: 0.7619 (t) REVERT: G 120 MET cc_start: 0.6841 (ttm) cc_final: 0.6470 (ttm) REVERT: G 123 GLU cc_start: 0.7420 (mt-10) cc_final: 0.7072 (mt-10) REVERT: I 21 GLN cc_start: 0.6693 (mm110) cc_final: 0.6265 (mm-40) REVERT: J 179 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7468 (ptm160) REVERT: L 148 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8022 (mm-30) REVERT: M 213 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7815 (mtt) REVERT: M 333 PHE cc_start: 0.8068 (m-80) cc_final: 0.7729 (m-80) REVERT: M 483 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7823 (ptm160) REVERT: M 629 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8274 (mp) REVERT: Q 100 GLU cc_start: 0.8119 (tt0) cc_final: 0.7530 (tm-30) REVERT: Q 308 TYR cc_start: 0.8785 (OUTLIER) cc_final: 0.7640 (p90) REVERT: S 64 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8701 (mmmt) REVERT: T 81 SER cc_start: 0.8317 (m) cc_final: 0.8018 (p) REVERT: U 31 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8652 (mt) REVERT: W 129 THR cc_start: 0.8182 (OUTLIER) cc_final: 0.7937 (t) REVERT: W 132 GLU cc_start: 0.7171 (pt0) cc_final: 0.6965 (pm20) REVERT: W 134 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7856 (tp) REVERT: Z 20 LYS cc_start: 0.8369 (mttm) cc_final: 0.8032 (mmtm) REVERT: Z 49 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7757 (pm20) REVERT: b 93 LYS cc_start: 0.8499 (mptt) cc_final: 0.8032 (mttt) REVERT: b 122 GLU cc_start: 0.7808 (tt0) cc_final: 0.7524 (tm-30) REVERT: c 141 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8265 (mp) REVERT: c 177 GLU cc_start: 0.7811 (mm-30) cc_final: 0.6641 (pp20) REVERT: d 8 ASP cc_start: 0.8132 (m-30) cc_final: 0.7627 (m-30) REVERT: d 15 ARG cc_start: 0.7862 (ptm-80) cc_final: 0.7427 (ptm-80) REVERT: d 172 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7392 (tt0) REVERT: h 81 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7608 (ptp90) REVERT: h 99 LEU cc_start: 0.8355 (mm) cc_final: 0.8075 (mm) REVERT: i 97 MET cc_start: 0.8513 (tpp) cc_final: 0.8261 (ttp) REVERT: i 334 THR cc_start: 0.9168 (m) cc_final: 0.8832 (p) REVERT: i 339 MET cc_start: 0.9151 (mmp) cc_final: 0.8834 (mmp) REVERT: i 347 ASN cc_start: 0.6437 (OUTLIER) cc_final: 0.6203 (p0) REVERT: j 16 LEU cc_start: 0.8303 (tt) cc_final: 0.8097 (tm) REVERT: j 19 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6848 (mp) REVERT: l 62 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8638 (mp) REVERT: l 111 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7612 (t70) REVERT: l 355 ASP cc_start: 0.8880 (t0) cc_final: 0.8585 (t0) REVERT: l 479 ASN cc_start: 0.7927 (m-40) cc_final: 0.7640 (m-40) REVERT: l 482 MET cc_start: 0.7375 (OUTLIER) cc_final: 0.7088 (mmt) REVERT: l 500 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8015 (tt) REVERT: m 8 ILE cc_start: 0.6282 (OUTLIER) cc_final: 0.6042 (mp) REVERT: n 30 ARG cc_start: 0.7537 (mmm-85) cc_final: 0.7210 (ttp-170) REVERT: n 41 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8388 (mptp) REVERT: o 31 LYS cc_start: 0.8653 (tptt) cc_final: 0.8090 (ttpt) REVERT: o 85 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8059 (tttp) REVERT: p 43 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.7967 (mp) REVERT: p 48 PHE cc_start: 0.7390 (OUTLIER) cc_final: 0.5338 (t80) REVERT: r 114 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8308 (tm-30) REVERT: r 126 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8853 (tp) REVERT: r 344 LEU cc_start: 0.8081 (tp) cc_final: 0.7596 (tt) REVERT: s 108 MET cc_start: 0.9136 (mmt) cc_final: 0.8707 (mmm) REVERT: v 16 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6719 (pm20) REVERT: v 21 ARG cc_start: 0.7386 (ptp-110) cc_final: 0.7026 (mtm-85) REVERT: v 33 GLU cc_start: 0.6767 (mp0) cc_final: 0.6500 (mp0) REVERT: v 34 ARG cc_start: 0.5734 (OUTLIER) cc_final: 0.5158 (tpm170) REVERT: v 46 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7689 (ttt) REVERT: w 173 MET cc_start: 0.8223 (mtp) cc_final: 0.7994 (mtp) REVERT: w 262 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7643 (pt0) REVERT: w 275 TYR cc_start: 0.6650 (OUTLIER) cc_final: 0.6032 (m-10) REVERT: w 314 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8305 (mp) REVERT: w 323 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8260 (tt0) outliers start: 223 outliers final: 125 residues processed: 1172 average time/residue: 1.4665 time to fit residues: 2251.7741 Evaluate side-chains 1166 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1001 time to evaluate : 5.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 23 ARG Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 50 ASP Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 30 GLU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 179 ARG Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 108 GLU Chi-restraints excluded: chain L residue 133 ASP Chi-restraints excluded: chain L residue 148 GLU Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 74 ASN Chi-restraints excluded: chain M residue 213 MET Chi-restraints excluded: chain M residue 318 THR Chi-restraints excluded: chain M residue 387 LEU Chi-restraints excluded: chain M residue 421 SER Chi-restraints excluded: chain M residue 483 ARG Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 629 ILE Chi-restraints excluded: chain N residue 122 GLN Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain O residue 190 ASP Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 105 MET Chi-restraints excluded: chain Q residue 198 THR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 252 SER Chi-restraints excluded: chain Q residue 265 ASN Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 435 LEU Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 64 LYS Chi-restraints excluded: chain T residue 46 ASP Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 74 GLN Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain V residue 124 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain W residue 66 GLU Chi-restraints excluded: chain W residue 93 GLU Chi-restraints excluded: chain W residue 114 THR Chi-restraints excluded: chain W residue 129 THR Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain a residue 93 ILE Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 27 GLU Chi-restraints excluded: chain c residue 43 LYS Chi-restraints excluded: chain c residue 96 ASP Chi-restraints excluded: chain c residue 110 ASP Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 141 LEU Chi-restraints excluded: chain c residue 175 THR Chi-restraints excluded: chain d residue 59 ASN Chi-restraints excluded: chain d residue 78 GLU Chi-restraints excluded: chain d residue 172 GLU Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain e residue 145 ASN Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 5 SER Chi-restraints excluded: chain h residue 73 MET Chi-restraints excluded: chain h residue 81 ARG Chi-restraints excluded: chain i residue 37 LEU Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 347 ASN Chi-restraints excluded: chain j residue 19 LEU Chi-restraints excluded: chain j residue 66 ASP Chi-restraints excluded: chain j residue 90 MET Chi-restraints excluded: chain j residue 109 LYS Chi-restraints excluded: chain k residue 39 SER Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 62 ILE Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 79 SER Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 184 LEU Chi-restraints excluded: chain l residue 190 LEU Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 480 THR Chi-restraints excluded: chain l residue 482 MET Chi-restraints excluded: chain l residue 500 LEU Chi-restraints excluded: chain m residue 8 ILE Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain o residue 5 LYS Chi-restraints excluded: chain o residue 57 LEU Chi-restraints excluded: chain o residue 85 LYS Chi-restraints excluded: chain p residue 43 LEU Chi-restraints excluded: chain p residue 48 PHE Chi-restraints excluded: chain p residue 64 LEU Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 50 LEU Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 90 THR Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 126 LEU Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 248 THR Chi-restraints excluded: chain s residue 57 THR Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 145 THR Chi-restraints excluded: chain s residue 172 ILE Chi-restraints excluded: chain s residue 201 THR Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 9 THR Chi-restraints excluded: chain u residue 99 HIS Chi-restraints excluded: chain v residue 16 GLU Chi-restraints excluded: chain v residue 34 ARG Chi-restraints excluded: chain v residue 46 MET Chi-restraints excluded: chain v residue 51 LEU Chi-restraints excluded: chain v residue 61 HIS Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 106 VAL Chi-restraints excluded: chain w residue 132 GLN Chi-restraints excluded: chain w residue 249 MET Chi-restraints excluded: chain w residue 262 GLU Chi-restraints excluded: chain w residue 275 TYR Chi-restraints excluded: chain w residue 288 ASP Chi-restraints excluded: chain w residue 297 LEU Chi-restraints excluded: chain w residue 314 LEU Chi-restraints excluded: chain w residue 323 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 698 optimal weight: 4.9990 chunk 735 optimal weight: 2.9990 chunk 671 optimal weight: 3.9990 chunk 715 optimal weight: 4.9990 chunk 430 optimal weight: 1.9990 chunk 311 optimal weight: 2.9990 chunk 562 optimal weight: 4.9990 chunk 219 optimal weight: 4.9990 chunk 646 optimal weight: 7.9990 chunk 677 optimal weight: 1.9990 chunk 713 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN E 58 GLN E 95 ASN ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 ASN ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN P 107 GLN P 124 ASN T 43 GLN U 83 ASN V 79 GLN V 129 GLN Y 57 GLN Z 21 GLN a 90 ASN c 56 ASN i 322 GLN l 328 HIS ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 4 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 68294 Z= 0.306 Angle : 0.609 13.360 92450 Z= 0.303 Chirality : 0.044 0.250 10056 Planarity : 0.005 0.066 11588 Dihedral : 11.158 178.822 10119 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.35 % Favored : 95.61 % Rotamer: Outliers : 3.02 % Allowed : 20.71 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.02 % 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: 0.85 (0.09), residues: 8065 helix: 1.42 (0.08), residues: 4270 sheet: 0.20 (0.25), residues: 407 loop : -0.44 (0.11), residues: 3388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.009 0.001 HIS J 37 PHE 0.033 0.002 PHE i 292 TYR 0.027 0.002 TYR d 32 ARG 0.010 0.000 ARG b 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1224 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 1011 time to evaluate : 5.917 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.9216 (OUTLIER) cc_final: 0.7497 (tmm) REVERT: B 50 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.7334 (tpp) REVERT: B 65 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7957 (pm20) REVERT: B 76 TYR cc_start: 0.9144 (OUTLIER) cc_final: 0.7165 (t80) REVERT: C 98 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8013 (tpt170) REVERT: C 126 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8026 (mp0) REVERT: E 23 ARG cc_start: 0.7019 (OUTLIER) cc_final: 0.6769 (mmt180) REVERT: E 99 GLN cc_start: 0.9199 (OUTLIER) cc_final: 0.7649 (mt0) REVERT: F 87 VAL cc_start: 0.7930 (m) cc_final: 0.7668 (t) REVERT: G 120 MET cc_start: 0.6952 (ttm) cc_final: 0.6526 (ttm) REVERT: G 122 MET cc_start: 0.7637 (mmt) cc_final: 0.7171 (mmp) REVERT: G 123 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7126 (mt-10) REVERT: I 21 GLN cc_start: 0.6717 (mm110) cc_final: 0.6208 (mm-40) REVERT: J 179 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7480 (ptm160) REVERT: K 98 MET cc_start: 0.8637 (mpm) cc_final: 0.8277 (mmm) REVERT: L 73 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7641 (mmtt) REVERT: L 148 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8035 (mm-30) REVERT: M 213 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7835 (mtt) REVERT: M 333 PHE cc_start: 0.8112 (m-80) cc_final: 0.7750 (m-80) REVERT: M 483 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7800 (ptm160) REVERT: M 629 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8261 (mp) REVERT: N 114 LYS cc_start: 0.8380 (mtmt) cc_final: 0.8154 (mtpt) REVERT: Q 100 GLU cc_start: 0.8119 (tt0) cc_final: 0.7523 (tm-30) REVERT: Q 308 TYR cc_start: 0.8936 (OUTLIER) cc_final: 0.7741 (p90) REVERT: Q 315 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7754 (mt-10) REVERT: S 64 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8110 (mmpt) REVERT: T 81 SER cc_start: 0.8384 (m) cc_final: 0.8057 (p) REVERT: U 31 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8672 (mt) REVERT: W 129 THR cc_start: 0.8116 (OUTLIER) cc_final: 0.7854 (t) REVERT: W 134 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8058 (tp) REVERT: Z 20 LYS cc_start: 0.8352 (mttm) cc_final: 0.8043 (mmtm) REVERT: Z 49 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7769 (pm20) REVERT: b 122 GLU cc_start: 0.7794 (tt0) cc_final: 0.7509 (tm-30) REVERT: c 141 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8258 (mp) REVERT: c 177 GLU cc_start: 0.7855 (mm-30) cc_final: 0.6676 (pp20) REVERT: d 15 ARG cc_start: 0.7866 (ptm-80) cc_final: 0.7415 (ptm-80) REVERT: d 16 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7820 (ptt180) REVERT: d 172 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7440 (tt0) REVERT: g 29 THR cc_start: 0.9287 (p) cc_final: 0.8981 (t) REVERT: h 81 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7570 (ptp90) REVERT: h 99 LEU cc_start: 0.8323 (mm) cc_final: 0.8110 (mm) REVERT: i 97 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8240 (ttp) REVERT: i 334 THR cc_start: 0.9210 (m) cc_final: 0.8908 (p) REVERT: i 347 ASN cc_start: 0.6584 (OUTLIER) cc_final: 0.6357 (p0) REVERT: j 16 LEU cc_start: 0.8377 (tt) cc_final: 0.8145 (tm) REVERT: j 19 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6909 (mp) REVERT: j 83 ASN cc_start: 0.8661 (t0) cc_final: 0.8297 (t0) REVERT: l 62 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8633 (mp) REVERT: l 111 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7631 (t70) REVERT: l 355 ASP cc_start: 0.8888 (t0) cc_final: 0.8594 (t0) REVERT: l 500 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.7991 (tt) REVERT: m 1 MET cc_start: 0.4978 (ttp) cc_final: 0.2943 (tpt) REVERT: n 29 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.6338 (mmt90) REVERT: n 30 ARG cc_start: 0.7583 (mmm-85) cc_final: 0.7361 (ttp-170) REVERT: n 41 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8447 (mptp) REVERT: o 31 LYS cc_start: 0.8675 (tptt) cc_final: 0.8099 (ttpt) REVERT: p 43 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.7956 (mp) REVERT: p 48 PHE cc_start: 0.7480 (OUTLIER) cc_final: 0.5304 (t80) REVERT: r 114 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8292 (tm-30) REVERT: r 126 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8937 (tp) REVERT: r 344 LEU cc_start: 0.8364 (tp) cc_final: 0.8139 (tt) REVERT: s 3 MET cc_start: 0.8610 (mmm) cc_final: 0.8367 (tpp) REVERT: s 61 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7456 (mt) REVERT: v 21 ARG cc_start: 0.7474 (ptp-110) cc_final: 0.7011 (mtm-85) REVERT: v 34 ARG cc_start: 0.5785 (OUTLIER) cc_final: 0.5175 (tpm170) REVERT: v 46 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7866 (ttt) REVERT: w 173 MET cc_start: 0.8268 (mtp) cc_final: 0.8051 (mtp) REVERT: w 262 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7618 (pt0) REVERT: w 275 TYR cc_start: 0.6735 (OUTLIER) cc_final: 0.6053 (m-10) REVERT: w 303 GLU cc_start: 0.8310 (tt0) cc_final: 0.8068 (tt0) REVERT: w 314 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8404 (mp) REVERT: w 323 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8329 (tt0) outliers start: 213 outliers final: 126 residues processed: 1152 average time/residue: 1.4895 time to fit residues: 2238.3110 Evaluate side-chains 1156 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 987 time to evaluate : 5.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 23 ARG Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 30 GLU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 179 ARG Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 305 PHE Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 108 GLU Chi-restraints excluded: chain L residue 133 ASP Chi-restraints excluded: chain L residue 148 GLU Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 74 ASN Chi-restraints excluded: chain M residue 160 VAL Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 213 MET Chi-restraints excluded: chain M residue 318 THR Chi-restraints excluded: chain M residue 352 VAL Chi-restraints excluded: chain M residue 387 LEU Chi-restraints excluded: chain M residue 421 SER Chi-restraints excluded: chain M residue 483 ARG Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 629 ILE Chi-restraints excluded: chain M residue 674 LEU Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain O residue 190 ASP Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 198 THR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 252 SER Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 315 GLU Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 12 MET Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 64 LYS Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 74 GLN Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain W residue 66 GLU Chi-restraints excluded: chain W residue 93 GLU Chi-restraints excluded: chain W residue 114 THR Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 129 THR Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain Y residue 78 ASP Chi-restraints excluded: chain a residue 93 ILE Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 27 GLU Chi-restraints excluded: chain c residue 43 LYS Chi-restraints excluded: chain c residue 96 ASP Chi-restraints excluded: chain c residue 110 ASP Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 141 LEU Chi-restraints excluded: chain c residue 154 GLN Chi-restraints excluded: chain c residue 175 THR Chi-restraints excluded: chain d residue 16 ARG Chi-restraints excluded: chain d residue 59 ASN Chi-restraints excluded: chain d residue 78 GLU Chi-restraints excluded: chain d residue 172 GLU Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain e residue 145 ASN Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 5 SER Chi-restraints excluded: chain g residue 92 MET Chi-restraints excluded: chain h residue 81 ARG Chi-restraints excluded: chain i residue 37 LEU Chi-restraints excluded: chain i residue 97 MET Chi-restraints excluded: chain i residue 347 ASN Chi-restraints excluded: chain j residue 19 LEU Chi-restraints excluded: chain j residue 66 ASP Chi-restraints excluded: chain j residue 75 LEU Chi-restraints excluded: chain j residue 90 MET Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain j residue 109 LYS Chi-restraints excluded: chain k residue 39 SER Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 62 ILE Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 79 SER Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 184 LEU Chi-restraints excluded: chain l residue 190 LEU Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 480 THR Chi-restraints excluded: chain l residue 500 LEU Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 29 ARG Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain o residue 5 LYS Chi-restraints excluded: chain o residue 57 LEU Chi-restraints excluded: chain p residue 43 LEU Chi-restraints excluded: chain p residue 48 PHE Chi-restraints excluded: chain p residue 64 LEU Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 50 LEU Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 90 THR Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 126 LEU Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 248 THR Chi-restraints excluded: chain r residue 453 MET Chi-restraints excluded: chain s residue 57 THR Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain s residue 145 THR Chi-restraints excluded: chain s residue 172 ILE Chi-restraints excluded: chain s residue 201 THR Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 9 THR Chi-restraints excluded: chain v residue 34 ARG Chi-restraints excluded: chain v residue 46 MET Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 106 VAL Chi-restraints excluded: chain w residue 132 GLN Chi-restraints excluded: chain w residue 249 MET Chi-restraints excluded: chain w residue 262 GLU Chi-restraints excluded: chain w residue 275 TYR Chi-restraints excluded: chain w residue 288 ASP Chi-restraints excluded: chain w residue 297 LEU Chi-restraints excluded: chain w residue 314 LEU Chi-restraints excluded: chain w residue 323 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 470 optimal weight: 5.9990 chunk 756 optimal weight: 20.0000 chunk 462 optimal weight: 7.9990 chunk 359 optimal weight: 8.9990 chunk 526 optimal weight: 1.9990 chunk 794 optimal weight: 0.9990 chunk 730 optimal weight: 3.9990 chunk 632 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 488 optimal weight: 6.9990 chunk 387 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 45 ASN E 58 GLN E 95 ASN ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 ASN ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** N 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 83 ASN V 79 GLN V 129 GLN Y 57 GLN Z 21 GLN a 90 ASN c 127 ASN i 322 GLN l 205 ASN l 580 GLN s 124 ASN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 151 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 68294 Z= 0.305 Angle : 0.613 14.598 92450 Z= 0.306 Chirality : 0.044 0.219 10056 Planarity : 0.005 0.068 11588 Dihedral : 11.170 178.871 10118 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.34 % Favored : 95.64 % Rotamer: Outliers : 2.74 % Allowed : 21.00 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.02 % 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: 0.75 (0.09), residues: 8065 helix: 1.35 (0.08), residues: 4272 sheet: 0.13 (0.25), residues: 407 loop : -0.50 (0.11), residues: 3386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.008 0.001 HIS J 37 PHE 0.033 0.002 PHE i 292 TYR 0.030 0.002 TYR d 32 ARG 0.010 0.000 ARG b 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1197 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 1004 time to evaluate : 5.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.7468 (tmm) REVERT: B 50 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7319 (tpp) REVERT: B 65 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7947 (pm20) REVERT: B 76 TYR cc_start: 0.9175 (OUTLIER) cc_final: 0.7279 (t80) REVERT: B 79 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8465 (ptp-170) REVERT: C 98 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8034 (tpt170) REVERT: C 126 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.7990 (mp0) REVERT: E 23 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.6347 (mmt180) REVERT: E 99 GLN cc_start: 0.9208 (OUTLIER) cc_final: 0.7664 (mt0) REVERT: F 87 VAL cc_start: 0.7941 (m) cc_final: 0.7711 (t) REVERT: G 123 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7139 (mt-10) REVERT: J 179 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7489 (ptm160) REVERT: K 98 MET cc_start: 0.8637 (mpm) cc_final: 0.8285 (mmm) REVERT: L 73 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7646 (mmtt) REVERT: L 148 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8048 (mm-30) REVERT: M 213 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7853 (mtt) REVERT: M 333 PHE cc_start: 0.8120 (m-80) cc_final: 0.7732 (m-80) REVERT: M 387 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8470 (tt) REVERT: M 483 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8241 (ptm160) REVERT: M 629 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8256 (mp) REVERT: Q 100 GLU cc_start: 0.8124 (tt0) cc_final: 0.7523 (tm-30) REVERT: Q 308 TYR cc_start: 0.8951 (OUTLIER) cc_final: 0.7770 (p90) REVERT: S 64 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8091 (mmpt) REVERT: T 81 SER cc_start: 0.8417 (m) cc_final: 0.8095 (p) REVERT: U 31 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8675 (mt) REVERT: U 79 GLU cc_start: 0.8246 (tp30) cc_final: 0.7825 (mm-30) REVERT: W 129 THR cc_start: 0.8154 (p) cc_final: 0.7845 (t) REVERT: W 132 GLU cc_start: 0.7177 (pt0) cc_final: 0.6849 (pm20) REVERT: W 134 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8188 (tp) REVERT: Y 88 ASP cc_start: 0.8120 (t0) cc_final: 0.7659 (t0) REVERT: Z 20 LYS cc_start: 0.8341 (mttm) cc_final: 0.8023 (mmtm) REVERT: Z 49 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7744 (pm20) REVERT: Z 73 TRP cc_start: 0.7192 (t60) cc_final: 0.6021 (m-10) REVERT: b 93 LYS cc_start: 0.8572 (mptt) cc_final: 0.8109 (mttt) REVERT: b 122 GLU cc_start: 0.7856 (tt0) cc_final: 0.7584 (tm-30) REVERT: c 141 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8267 (mp) REVERT: c 177 GLU cc_start: 0.7847 (mm-30) cc_final: 0.6711 (pp20) REVERT: d 15 ARG cc_start: 0.7879 (ptm-80) cc_final: 0.7406 (ptm-80) REVERT: d 16 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7803 (ptt180) REVERT: d 172 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7448 (tt0) REVERT: g 29 THR cc_start: 0.9281 (p) cc_final: 0.8983 (t) REVERT: h 81 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7552 (ptp90) REVERT: i 1 MET cc_start: 0.8777 (ptp) cc_final: 0.8541 (ptp) REVERT: i 311 MET cc_start: 0.9027 (tpp) cc_final: 0.8795 (tpp) REVERT: i 347 ASN cc_start: 0.6796 (OUTLIER) cc_final: 0.6565 (p0) REVERT: j 16 LEU cc_start: 0.8402 (tt) cc_final: 0.8157 (tm) REVERT: j 83 ASN cc_start: 0.8581 (t0) cc_final: 0.8199 (t0) REVERT: l 62 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8626 (mp) REVERT: l 111 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7667 (t70) REVERT: l 355 ASP cc_start: 0.8881 (t0) cc_final: 0.8582 (t0) REVERT: l 500 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7959 (tt) REVERT: n 29 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.6318 (mmt90) REVERT: n 30 ARG cc_start: 0.7584 (mmm-85) cc_final: 0.7365 (ttp-170) REVERT: n 41 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8381 (mptp) REVERT: o 31 LYS cc_start: 0.8655 (tptt) cc_final: 0.8074 (ttpt) REVERT: p 43 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8002 (mp) REVERT: p 48 PHE cc_start: 0.7491 (OUTLIER) cc_final: 0.5589 (t80) REVERT: r 114 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8306 (tm-30) REVERT: s 61 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7440 (mt) REVERT: v 21 ARG cc_start: 0.7550 (ptp-110) cc_final: 0.7124 (mtm-85) REVERT: v 46 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.8038 (ttt) REVERT: w 173 MET cc_start: 0.8311 (mtp) cc_final: 0.8108 (mtp) REVERT: w 262 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7655 (pt0) REVERT: w 275 TYR cc_start: 0.6647 (OUTLIER) cc_final: 0.6015 (m-10) REVERT: w 314 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8487 (mp) REVERT: w 323 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8342 (tt0) outliers start: 193 outliers final: 125 residues processed: 1132 average time/residue: 1.4924 time to fit residues: 2200.3424 Evaluate side-chains 1150 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 986 time to evaluate : 5.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 23 ARG Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 30 GLU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 179 ARG Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 305 PHE Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 108 GLU Chi-restraints excluded: chain L residue 133 ASP Chi-restraints excluded: chain L residue 148 GLU Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 74 ASN Chi-restraints excluded: chain M residue 160 VAL Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 213 MET Chi-restraints excluded: chain M residue 318 THR Chi-restraints excluded: chain M residue 352 VAL Chi-restraints excluded: chain M residue 387 LEU Chi-restraints excluded: chain M residue 421 SER Chi-restraints excluded: chain M residue 483 ARG Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 629 ILE Chi-restraints excluded: chain M residue 674 LEU Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain O residue 190 ASP Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 198 THR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 252 SER Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 435 LEU Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 12 MET Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 64 LYS Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 74 GLN Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain V residue 124 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain W residue 66 GLU Chi-restraints excluded: chain W residue 114 THR Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain Z residue 36 LEU Chi-restraints excluded: chain a residue 93 ILE Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 27 GLU Chi-restraints excluded: chain c residue 43 LYS Chi-restraints excluded: chain c residue 96 ASP Chi-restraints excluded: chain c residue 110 ASP Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 141 LEU Chi-restraints excluded: chain c residue 175 THR Chi-restraints excluded: chain c residue 186 ILE Chi-restraints excluded: chain d residue 16 ARG Chi-restraints excluded: chain d residue 59 ASN Chi-restraints excluded: chain d residue 78 GLU Chi-restraints excluded: chain d residue 172 GLU Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain e residue 145 ASN Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 5 SER Chi-restraints excluded: chain g residue 92 MET Chi-restraints excluded: chain h residue 81 ARG Chi-restraints excluded: chain i residue 37 LEU Chi-restraints excluded: chain i residue 347 ASN Chi-restraints excluded: chain j residue 66 ASP Chi-restraints excluded: chain j residue 75 LEU Chi-restraints excluded: chain j residue 90 MET Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain j residue 109 LYS Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 39 SER Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 62 ILE Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 79 SER Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 184 LEU Chi-restraints excluded: chain l residue 190 LEU Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 480 THR Chi-restraints excluded: chain l residue 500 LEU Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 29 ARG Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain o residue 5 LYS Chi-restraints excluded: chain o residue 57 LEU Chi-restraints excluded: chain p residue 43 LEU Chi-restraints excluded: chain p residue 48 PHE Chi-restraints excluded: chain p residue 64 LEU Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 50 LEU Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 90 THR Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 248 THR Chi-restraints excluded: chain r residue 350 THR Chi-restraints excluded: chain s residue 57 THR Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain s residue 145 THR Chi-restraints excluded: chain s residue 172 ILE Chi-restraints excluded: chain s residue 201 THR Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 9 THR Chi-restraints excluded: chain v residue 46 MET Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 106 VAL Chi-restraints excluded: chain w residue 132 GLN Chi-restraints excluded: chain w residue 249 MET Chi-restraints excluded: chain w residue 262 GLU Chi-restraints excluded: chain w residue 275 TYR Chi-restraints excluded: chain w residue 288 ASP Chi-restraints excluded: chain w residue 297 LEU Chi-restraints excluded: chain w residue 314 LEU Chi-restraints excluded: chain w residue 323 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 502 optimal weight: 0.0170 chunk 673 optimal weight: 2.9990 chunk 193 optimal weight: 0.0070 chunk 582 optimal weight: 6.9990 chunk 93 optimal weight: 0.0010 chunk 175 optimal weight: 0.9980 chunk 633 optimal weight: 5.9990 chunk 265 optimal weight: 5.9990 chunk 650 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 overall best weight: 0.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN E 58 GLN E 95 ASN ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 ASN L 86 ASN ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 667 GLN N 31 ASN N 122 GLN T 43 GLN U 83 ASN V 79 GLN V 129 GLN Y 57 GLN Z 21 GLN a 90 ASN c 127 ASN h 27 HIS i 322 GLN ** l 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 50 GLN s 124 ASN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.136568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.110170 restraints weight = 90532.965| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.87 r_work: 0.2994 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2839 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 68294 Z= 0.151 Angle : 0.543 15.025 92450 Z= 0.269 Chirality : 0.040 0.216 10056 Planarity : 0.004 0.070 11588 Dihedral : 10.671 177.558 10118 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.78 % Favored : 96.19 % Rotamer: Outliers : 2.14 % Allowed : 21.79 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.02 % 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: 1.04 (0.10), residues: 8065 helix: 1.58 (0.08), residues: 4277 sheet: 0.19 (0.25), residues: 416 loop : -0.35 (0.11), residues: 3372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP W 48 HIS 0.007 0.001 HIS v 92 PHE 0.030 0.001 PHE i 292 TYR 0.023 0.001 TYR l 422 ARG 0.011 0.000 ARG b 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29336.56 seconds wall clock time: 507 minutes 33.22 seconds (30453.22 seconds total)