Starting phenix.real_space_refine on Fri Feb 16 00:30:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2k_32263/02_2024/7w2k_32263_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2k_32263/02_2024/7w2k_32263.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2k_32263/02_2024/7w2k_32263_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2k_32263/02_2024/7w2k_32263_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2k_32263/02_2024/7w2k_32263_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2k_32263/02_2024/7w2k_32263.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2k_32263/02_2024/7w2k_32263.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2k_32263/02_2024/7w2k_32263_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2k_32263/02_2024/7w2k_32263_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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 36 5.49 5 Mg 1 5.21 5 S 472 5.16 5 C 42998 2.51 5 N 11059 2.21 5 O 11927 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 129": "OE1" <-> "OE2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B GLU 80": "OE1" <-> "OE2" Residue "B GLU 89": "OE1" <-> "OE2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "E GLU 34": "OE1" <-> "OE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E GLU 65": "OE1" <-> "OE2" Residue "E GLU 109": "OE1" <-> "OE2" Residue "E ASP 117": "OD1" <-> "OD2" Residue "H GLU 70": "OE1" <-> "OE2" Residue "H GLU 106": "OE1" <-> "OE2" Residue "I GLU 30": "OE1" <-> "OE2" Residue "J GLU 107": "OE1" <-> "OE2" Residue "J GLU 158": "OE1" <-> "OE2" Residue "J GLU 190": "OE1" <-> "OE2" Residue "J PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 320": "OE1" <-> "OE2" Residue "L GLU 108": "OE1" <-> "OE2" Residue "L GLU 132": "OE1" <-> "OE2" Residue "L GLU 139": "OE1" <-> "OE2" Residue "L GLU 148": "OE1" <-> "OE2" Residue "M GLU 44": "OE1" <-> "OE2" Residue "M GLU 67": "OE1" <-> "OE2" Residue "M GLU 211": "OE1" <-> "OE2" Residue "M GLU 269": "OE1" <-> "OE2" Residue "M GLU 310": "OE1" <-> "OE2" Residue "M GLU 369": "OE1" <-> "OE2" Residue "M TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 535": "OE1" <-> "OE2" Residue "M GLU 628": "OE1" <-> "OE2" Residue "N GLU 50": "OE1" <-> "OE2" Residue "N GLU 67": "OE1" <-> "OE2" Residue "N GLU 136": "OE1" <-> "OE2" Residue "O GLU 46": "OE1" <-> "OE2" Residue "O GLU 114": "OE1" <-> "OE2" Residue "O GLU 150": "OE1" <-> "OE2" Residue "O GLU 173": "OE1" <-> "OE2" Residue "P PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 83": "OE1" <-> "OE2" Residue "P GLU 85": "OE1" <-> "OE2" Residue "P GLU 169": "OE1" <-> "OE2" Residue "P GLU 222": "OE1" <-> "OE2" Residue "Q GLU 100": "OE1" <-> "OE2" Residue "Q PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 281": "OE1" <-> "OE2" Residue "S GLU 4": "OE1" <-> "OE2" Residue "S TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 105": "OE1" <-> "OE2" Residue "U GLU 16": "OE1" <-> "OE2" Residue "V GLU 17": "OE1" <-> "OE2" Residue "W GLU 123": "OE1" <-> "OE2" Residue "W GLU 131": "OE1" <-> "OE2" Residue "X GLU 77": "OE1" <-> "OE2" Residue "X GLU 117": "OE1" <-> "OE2" Residue "X GLU 129": "OE1" <-> "OE2" Residue "X GLU 143": "OE1" <-> "OE2" Residue "Y GLU 41": "OE1" <-> "OE2" Residue "Y GLU 95": "OE1" <-> "OE2" Residue "Z GLU 85": "OE1" <-> "OE2" Residue "a GLU 97": "OE1" <-> "OE2" Residue "a GLU 108": "OE1" <-> "OE2" Residue "a GLU 134": "OE1" <-> "OE2" Residue "a GLU 143": "OE1" <-> "OE2" Residue "a GLU 145": "OE1" <-> "OE2" Residue "a GLU 148": "OE1" <-> "OE2" Residue "b GLU 122": "OE1" <-> "OE2" Residue "c GLU 46": "OE1" <-> "OE2" Residue "c GLU 47": "OE1" <-> "OE2" Residue "c GLU 85": "OE1" <-> "OE2" Residue "c GLU 148": "OE1" <-> "OE2" Residue "c GLU 169": "OE1" <-> "OE2" Residue "d GLU 119": "OE1" <-> "OE2" Residue "d GLU 130": "OE1" <-> "OE2" Residue "e GLU 62": "OE1" <-> "OE2" Residue "e GLU 68": "OE1" <-> "OE2" Residue "e GLU 121": "OE1" <-> "OE2" Residue "e GLU 151": "OE1" <-> "OE2" Residue "g GLU 19": "OE1" <-> "OE2" Residue "g GLU 101": "OE1" <-> "OE2" Residue "g GLU 113": "OE1" <-> "OE2" Residue "g GLU 116": "OE1" <-> "OE2" Residue "h GLU 53": "OE1" <-> "OE2" Residue "h GLU 55": "OE1" <-> "OE2" Residue "i GLU 54": "OE1" <-> "OE2" Residue "i GLU 117": "OE1" <-> "OE2" Residue "i GLU 318": "OE1" <-> "OE2" Residue "k GLU 34": "OE1" <-> "OE2" Residue "l PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 60": "OE1" <-> "OE2" Residue "l GLU 75": "OE1" <-> "OE2" Residue "l GLU 353": "OE1" <-> "OE2" Residue "l GLU 445": "OE1" <-> "OE2" Residue "l GLU 503": "OE1" <-> "OE2" Residue "m TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 48": "OE1" <-> "OE2" Residue "n GLU 53": "OE1" <-> "OE2" Residue "n GLU 54": "OE1" <-> "OE2" Residue "o GLU 22": "OE1" <-> "OE2" Residue "o GLU 28": "OE1" <-> "OE2" Residue "o GLU 35": "OE1" <-> "OE2" Residue "o GLU 61": "OE1" <-> "OE2" Residue "o GLU 113": "OE1" <-> "OE2" Residue "p GLU 84": "OE1" <-> "OE2" Residue "p GLU 176": "OE1" <-> "OE2" Residue "r GLU 114": "OE1" <-> "OE2" Residue "r GLU 222": "OE1" <-> "OE2" Residue "s GLU 24": "OE1" <-> "OE2" Residue "s GLU 143": "OE1" <-> "OE2" Residue "s GLU 170": "OE1" <-> "OE2" Residue "s GLU 192": "OE1" <-> "OE2" Residue "u GLU 6": "OE1" <-> "OE2" Residue "u GLU 11": "OE1" <-> "OE2" Residue "u GLU 109": "OE1" <-> "OE2" Residue "v GLU 16": "OE1" <-> "OE2" Residue "v PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 103": "OE1" <-> "OE2" Residue "v GLU 105": "OE1" <-> "OE2" Residue "v GLU 116": "OE1" <-> "OE2" Residue "w GLU 76": "OE1" <-> "OE2" Residue "w GLU 79": "OE1" <-> "OE2" Residue "w GLU 115": "OE1" <-> "OE2" Residue "w GLU 148": "OE1" <-> "OE2" Residue "w GLU 171": "OE1" <-> "OE2" Residue "w GLU 185": "OE1" <-> "OE2" Residue "w GLU 251": "OE1" <-> "OE2" Residue "w GLU 271": "OE1" <-> "OE2" Residue "w GLU 303": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 66522 Number of models: 1 Model: "" Number of chains: 66 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: 1235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1235 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 965 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 108} 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: "F" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 688 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 81} 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: "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: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 762 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 85} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 2352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2352 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 280} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 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: 5293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5293 Classifications: {'peptide': 690} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 32, 'TRANS': 657} 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: "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: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1648 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 195} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 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: 3364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3364 Classifications: {'peptide': 419} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 27, 'TRANS': 391} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'2MR:plan-2': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "S" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 567 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} 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: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1021 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "W" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1161 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 133} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "X" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 696 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Y" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 583 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 63} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 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: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1152 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 129} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "b" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 875 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 91} Chain breaks: 1 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: "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: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1000 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 11, 'TRANS': 109} 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: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2706 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 328} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: 4782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4782 Classifications: {'peptide': 603} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 574} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "m" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 948 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "n" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 456 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 53} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "o" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1058 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 116} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "p" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1534 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 17, 'TRANS': 160} 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: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1020 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 28 Chain: "w" Number of atoms: 2574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2574 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 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: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'PEE': 1, 'PLX': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: "Q" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 143 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: "e" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} 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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 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: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 245 Unusual residues: {'CDL': 2, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "r" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 203 Unusual residues: {'CDL': 1, 'PEE': 1, 'PLX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "s" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 69 Unusual residues: {' UQ': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 38 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: "u" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 78 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 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 49.233 48.670 171.010 1.00 18.42 S ATOM 3048 SG CYS A 425 48.320 45.033 176.439 1.00 19.81 S ATOM 2726 SG CYS A 385 46.067 44.219 170.743 1.00 18.95 S ATOM 2687 SG CYS A 379 43.753 49.275 174.580 1.00 15.58 S ATOM 3949 SG CYS B 113 40.283 65.599 136.071 1.00 21.81 S ATOM 3968 SG CYS B 116 45.116 62.813 139.995 1.00 19.40 S ATOM 3991 SG CYS B 119 46.455 65.528 134.563 1.00 0.00 S ATOM 4320 SG CYS B 162 43.625 59.935 134.996 1.00 3.97 S ATOM 4018 SG CYS B 123 52.750 68.284 130.428 1.00 3.09 S ATOM 4244 SG CYS B 152 51.205 66.653 124.426 1.00 3.03 S ATOM 4291 SG CYS B 158 48.935 63.009 129.116 1.00 22.61 S ATOM 4270 SG CYS B 155 55.106 62.922 127.843 1.00 5.30 S ATOM 5699 SG CYS C 166 57.752 66.561 120.533 1.00 12.16 S ATOM 4984 SG CYS C 72 59.021 67.939 114.297 1.00 2.15 S ATOM 4978 SG CYS C 71 63.477 66.218 116.950 1.00 5.15 S ATOM 5469 SG CYS C 136 60.590 71.021 119.198 1.00 21.84 S ATOM 14491 SG CYS M 131 43.852 62.789 152.011 1.00 13.18 S ATOM 14470 SG CYS M 128 47.301 58.030 148.947 1.00 14.08 S ATOM 14531 SG CYS M 137 49.306 61.349 154.382 1.00 6.38 S ATOM 14863 SG CYS M 179 47.269 61.314 165.419 1.00 13.36 S ATOM 15217 SG CYS M 226 44.485 64.239 160.941 1.00 8.58 S ATOM 14887 SG CYS M 182 41.846 64.190 166.903 1.00 16.56 S ATOM 14840 SG CYS M 176 41.472 58.889 163.368 1.00 16.44 S ATOM 14088 SG CYS M 78 58.197 55.919 169.537 1.00 11.94 S ATOM 14189 SG CYS M 92 56.584 58.069 171.868 1.00 14.79 S ATOM 13977 SG CYS M 64 52.357 58.291 169.204 1.00 16.64 S ATOM 14063 SG CYS M 75 53.373 56.573 166.146 1.00 6.31 S ATOM 21023 SG CYS O 135 32.160 31.742 177.600 1.00 48.67 S ATOM 21057 SG CYS O 140 31.779 28.398 178.811 1.00 56.23 S ATOM 21337 SG CYS O 176 36.444 33.278 180.773 1.00 57.30 S ATOM 21360 SG CYS O 180 36.565 29.782 181.152 1.00 60.98 S ATOM 27982 SG CYS T 86 32.104 52.451 143.296 1.00 20.40 S ATOM 28160 SG CYS T 111 33.300 55.780 144.342 1.00 15.73 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.65 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.65 Time building chain proxies: 26.18, per 1000 atoms: 0.39 Number of scatterers: 66522 At special positions: 0 Unit cell: (221.285, 221.285, 226.656, 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 472 16.00 P 36 15.00 Mg 1 11.99 O 11927 8.00 N 11059 7.00 C 42998 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, 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=2.04 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 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: 20.91 Conformation dependent library (CDL) restraints added in 8.6 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="FE2 FES M 803 " - pdb=" SG CYS M 64 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 92 " 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="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb=" SF4 B 301 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " 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=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " 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="FE3 SF4 C 301 " - pdb=" SG CYS C 71 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " 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="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " pdb="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " pdb="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 86 " pdb="ZN ZN T 201 " - pdb=" NE2 HIS T 95 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 111 " 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15286 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 338 helices and 29 sheets defined 52.6% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.40 Creating SS restraints... Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 73 through 82 Processing helix chain 'A' and resid 95 through 103 removed outlier: 3.502A 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 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 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 302 Processing helix chain 'A' and resid 329 through 334 removed outlier: 4.405A 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 400 Processing helix chain 'A' and resid 406 through 419 removed outlier: 4.002A 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 77 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: 5.945A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N LEU B 210 " --> pdb=" O GLN B 206 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N TYR B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 60 removed outlier: 3.599A pdb=" N VAL C 47 " --> pdb=" O GLY C 43 " (cutoff:3.500A) 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 123 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 194 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: 4.136A 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: 4.343A 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 31 through 47 removed outlier: 3.511A pdb=" N TYR F 41 " --> pdb=" O ILE F 37 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N VAL F 42 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N GLU F 43 " --> 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: 4.026A 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 66 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: 4.213A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N MET J 76 " --> pdb=" O HIS J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 97 removed outlier: 4.925A pdb=" N HIS J 93 " --> pdb=" O ASP J 90 " (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 214 through 218 Processing helix chain 'J' and resid 242 through 254 Processing helix chain 'J' and resid 273 through 283 Processing helix chain 'J' and resid 317 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: 4.248A pdb=" N ILE J 350 " --> pdb=" O GLU J 346 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU J 351 " --> pdb=" O LEU J 347 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ARG J 355 " --> pdb=" O GLU J 351 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N HIS J 356 " --> pdb=" O VAL J 352 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 80 removed outlier: 3.826A pdb=" N GLU K 80 " --> pdb=" O GLN K 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 77 through 80' Processing helix chain 'K' and resid 85 through 96 removed outlier: 4.493A pdb=" N LYS K 95 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 4.750A 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 120 through 122 No H-bonds generated for 'chain 'L' and resid 120 through 122' 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: 3.654A 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: 3.954A pdb=" N ILE M 225 " --> pdb=" O ILE M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 292 Processing helix chain 'M' and resid 294 through 298 Processing helix chain 'M' and resid 319 through 332 removed outlier: 3.524A 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 360 Processing helix chain 'M' and resid 378 through 380 No H-bonds generated for 'chain 'M' and resid 378 through 380' Processing helix chain 'M' and resid 382 through 385 Processing helix chain 'M' and resid 392 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 425 Processing helix chain 'M' and resid 449 through 457 Processing helix chain 'M' and resid 461 through 467 Processing helix chain 'M' and resid 478 through 481 No H-bonds generated for 'chain 'M' and resid 478 through 481' Processing helix chain 'M' and resid 486 through 504 Processing helix chain 'M' and resid 522 through 527 Processing helix chain 'M' and resid 535 through 539 Processing helix chain 'M' and resid 619 through 629 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: 3.698A 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 69 Processing helix chain 'O' and resid 75 through 90 removed outlier: 4.369A 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 143 removed outlier: 4.049A pdb=" N ARG O 143 " --> pdb=" O PRO O 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 145 through 156 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: 3.590A pdb=" N VAL P 93 " --> pdb=" O PRO P 90 " (cutoff:3.500A) removed outlier: 5.011A 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 174 removed outlier: 4.032A pdb=" N TRP P 165 " --> pdb=" O ALA P 162 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE P 174 " --> pdb=" O TRP P 171 " (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: 4.034A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N PHE Q 47 " --> pdb=" O TRP Q 43 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY Q 48 " --> pdb=" O ALA Q 44 " (cutoff:3.500A) Processing helix chain 'Q' and resid 120 through 126 removed outlier: 3.732A pdb=" N GLU Q 125 " --> pdb=" O GLU Q 121 " (cutoff:3.500A) removed outlier: 3.978A 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: 4.020A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG Q 138 " --> pdb=" O PRO Q 134 " (cutoff:3.500A) Processing helix chain 'Q' and resid 141 through 159 removed outlier: 4.019A pdb=" N MET Q 144 " --> pdb=" O TYR Q 141 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N MET Q 145 " --> pdb=" O VAL Q 142 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N CYS Q 146 " --> pdb=" O SER Q 143 " (cutoff:3.500A) Processing helix chain 'Q' and resid 165 through 194 Processing helix chain 'Q' and resid 198 through 218 removed outlier: 4.163A 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: 4.407A 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: 4.533A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N LYS Q 437 " --> pdb=" O ALA Q 433 " (cutoff:3.500A) Processing helix chain 'Q' and resid 444 through 454 removed outlier: 4.318A pdb=" N VAL Q 448 " --> pdb=" O LEU Q 444 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA Q 449 " --> 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 29 Proline residue: S 7 - end of helix Proline residue: S 19 - end of helix Processing helix chain 'S' and resid 43 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 55 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 47 Processing helix chain 'U' and resid 79 through 83 Processing helix chain 'V' and resid 3 through 10 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: 3.640A pdb=" N THR V 121 " --> pdb=" O TYR V 117 " (cutoff:3.500A) Processing helix chain 'W' and resid 32 through 97 Proline residue: W 73 - end of helix Processing helix chain 'W' and resid 121 through 125 Processing helix chain 'W' and resid 130 through 142 removed outlier: 6.233A pdb=" N PHE W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ILE W 141 " --> pdb=" O THR W 137 " (cutoff:3.500A) Processing helix chain 'X' and resid 76 through 88 Processing helix chain 'X' and resid 112 through 126 Processing helix chain 'X' and resid 132 through 137 removed outlier: 4.385A 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 'Z' and resid 28 through 39 removed outlier: 3.804A pdb=" N ARG Z 39 " --> pdb=" O LYS Z 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 47 through 53 removed outlier: 4.990A 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: 3.876A 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 26 Processing helix chain 'b' and resid 65 through 74 Processing helix chain 'b' and resid 76 through 88 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 57 removed outlier: 4.783A 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: 3.755A pdb=" N GLY d 118 " --> pdb=" O GLN d 114 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLU d 119 " --> pdb=" O GLN d 115 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N SER d 120 " --> pdb=" O ARG d 116 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TYR d 121 " --> pdb=" O GLU d 117 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ARG d 122 " --> pdb=" O GLY d 118 " (cutoff:3.500A) removed outlier: 6.513A 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 66 through 69 No H-bonds generated for 'chain 'e' and resid 66 through 69' Processing helix chain 'e' and resid 80 through 95 Processing helix chain 'e' and resid 98 through 107 Processing helix chain 'e' and resid 115 through 131 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 19 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 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 44 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 'i' and resid 3 through 22 Processing helix chain 'i' and resid 26 through 45 Proline residue: i 42 - end of helix removed outlier: 3.730A pdb=" N MET i 45 " --> pdb=" O ILE i 41 " (cutoff:3.500A) Processing helix chain 'i' and resid 50 through 80 Processing helix chain 'i' and resid 92 through 106 Processing helix chain 'i' and resid 113 through 121 removed outlier: 4.357A pdb=" N GLU i 117 " --> pdb=" O PHE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 144 removed outlier: 3.817A pdb=" N GLN i 134 " --> pdb=" O LEU i 130 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N LYS i 135 " --> pdb=" O LEU i 131 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LEU i 136 " --> pdb=" O THR i 132 " (cutoff:3.500A) removed outlier: 4.905A 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: 3.843A pdb=" N LEU i 170 " --> pdb=" O GLY i 166 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASN i 171 " --> pdb=" O TRP i 167 " (cutoff:3.500A) Processing helix chain 'i' and resid 175 through 193 removed outlier: 4.115A pdb=" N VAL i 193 " --> pdb=" O TRP i 189 " (cutoff:3.500A) Processing helix chain 'i' and resid 198 through 221 Processing helix chain 'i' and resid 227 through 231 Processing helix chain 'i' and resid 233 through 235 No H-bonds generated for 'chain 'i' and resid 233 through 235' Processing helix chain 'i' and resid 238 through 251 Processing helix chain 'i' and resid 258 through 273 Proline residue: i 262 - end of helix Processing helix chain 'i' and resid 277 through 300 removed outlier: 4.296A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) Processing helix chain 'i' and resid 310 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 removed outlier: 3.574A pdb=" N SER i 344 " --> pdb=" O PRO i 341 " (cutoff:3.500A) Processing helix chain 'j' and resid 2 through 24 Processing helix chain 'j' and resid 53 through 78 Proline residue: j 74 - end of helix removed outlier: 5.783A 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 51 Processing helix chain 'k' and resid 54 through 85 removed outlier: 3.891A pdb=" N MET k 58 " --> pdb=" O LEU k 55 " (cutoff:3.500A) 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: 3.610A pdb=" N LEU l 9 " --> pdb=" O ALA l 5 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR l 16 " --> pdb=" O LEU l 12 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE l 17 " --> pdb=" O THR l 13 " (cutoff:3.500A) Proline residue: l 18 - end of helix removed outlier: 4.844A 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: 4.444A 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: 3.929A 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: 3.914A 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: 4.050A pdb=" N MET l 237 " --> pdb=" O LEU l 233 " (cutoff:3.500A) removed outlier: 5.191A 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: 4.337A 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 350 removed outlier: 3.617A 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 380 Processing helix chain 'l' and resid 389 through 400 removed outlier: 4.951A 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: 3.681A pdb=" N LEU l 457 " --> pdb=" O SER l 453 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.362A 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: 3.657A pdb=" N THR l 507 " --> pdb=" O GLU l 503 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N THR l 508 " --> pdb=" O LEU l 504 " (cutoff:3.500A) removed outlier: 4.552A 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: 4.239A pdb=" N MET l 533 " --> pdb=" O PRO l 530 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N LEU l 536 " --> pdb=" O MET l 533 " (cutoff:3.500A) Proline residue: l 537 - end of helix removed outlier: 3.510A pdb=" N SER l 543 " --> pdb=" O HIS l 540 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET l 544 " --> pdb=" O ASN l 541 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS l 547 " --> pdb=" O MET l 544 " (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 600 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: 3.813A pdb=" N LEU m 61 " --> pdb=" O PHE m 57 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU m 65 " --> pdb=" O LEU m 61 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL m 66 " --> pdb=" O GLY m 62 " (cutoff:3.500A) Processing helix chain 'm' and resid 138 through 146 removed outlier: 4.131A 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: 6.674A pdb=" N VAL n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N HIS n 14 " --> pdb=" O ASP n 10 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ILE n 15 " --> pdb=" O HIS n 11 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU n 16 " --> pdb=" O TRP n 12 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N VAL n 17 " --> pdb=" O VAL n 13 " (cutoff:3.500A) Proline residue: n 18 - end of helix removed outlier: 3.645A pdb=" N LYS n 34 " --> pdb=" O ARG n 30 " (cutoff:3.500A) 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 21 through 23 No H-bonds generated for 'chain 'o' and resid 21 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 47 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 101 through 106 Processing helix chain 'p' and resid 109 through 113 Processing helix chain 'p' and resid 116 through 143 removed outlier: 3.798A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS p 138 " --> pdb=" O GLU p 134 " (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: 4.168A 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: 3.558A pdb=" N LEU r 39 " --> pdb=" O SER r 35 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N SER r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU r 42 " --> pdb=" O SER r 38 " (cutoff:3.500A) Processing helix chain 'r' and resid 62 through 83 removed outlier: 3.906A pdb=" N LEU r 73 " --> pdb=" O THR r 69 " (cutoff:3.500A) Proline residue: r 74 - end of helix removed outlier: 4.493A pdb=" N SER r 82 " --> pdb=" O MET r 78 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N HIS r 83 " --> pdb=" O ALA r 79 " (cutoff:3.500A) Processing helix chain 'r' and resid 89 through 111 removed outlier: 3.801A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 115 through 135 removed outlier: 4.730A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.390A 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 171 removed outlier: 4.006A pdb=" N LEU r 143 " --> pdb=" O THR r 140 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N TYR r 152 " --> pdb=" O PHE r 149 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA r 155 " --> pdb=" O TYR r 152 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU r 158 " --> pdb=" O ALA r 155 " (cutoff:3.500A) Proline residue: r 159 - end of helix removed outlier: 3.796A pdb=" N THR r 171 " --> pdb=" O GLN r 168 " (cutoff:3.500A) Processing helix chain 'r' and resid 176 through 181 Processing helix chain 'r' and resid 190 through 204 removed outlier: 4.305A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 221 removed outlier: 4.246A 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 249 removed outlier: 4.778A pdb=" N GLY r 239 " --> pdb=" O LEU r 235 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLY r 240 " --> pdb=" O LEU r 236 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N THR r 248 " --> pdb=" O MET r 244 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ILE r 249 " --> pdb=" O ARG r 245 " (cutoff:3.500A) Processing helix chain 'r' and resid 253 through 257 removed outlier: 3.769A pdb=" N MET r 257 " --> pdb=" O THR r 254 " (cutoff:3.500A) Processing helix chain 'r' and resid 259 through 277 removed outlier: 3.976A pdb=" N ILE r 270 " --> pdb=" O MET r 266 " (cutoff:3.500A) removed outlier: 3.600A 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: 3.737A pdb=" N ARG r 336 " --> pdb=" O THR r 332 " (cutoff:3.500A) 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: 3.624A pdb=" N ILE r 393 " --> pdb=" O ASN r 390 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR r 413 " --> pdb=" O MET r 410 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR r 414 " --> pdb=" O LEU r 411 " (cutoff:3.500A) removed outlier: 3.783A 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: 4.327A 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: 3.844A pdb=" N THR s 21 " --> pdb=" O VAL s 17 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU s 22 " --> pdb=" O ALA s 18 " (cutoff:3.500A) Processing helix chain 's' and resid 45 through 57 Proline residue: s 48 - end of helix Processing helix chain 's' and resid 68 through 86 Proline residue: s 75 - end of helix removed outlier: 4.237A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 122 removed outlier: 4.358A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 156 removed outlier: 3.890A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 168 removed outlier: 3.905A pdb=" N THR s 167 " --> pdb=" O SER s 163 " (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: 5.165A 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 11 through 13 No H-bonds generated for 'chain 'u' and resid 11 through 13' Processing helix chain 'u' and resid 22 through 27 Processing helix chain 'u' and resid 29 through 35 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 removed outlier: 3.686A pdb=" N LEU u 62 " --> pdb=" O GLU u 58 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL u 63 " --> pdb=" O GLU u 59 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN u 64 " --> pdb=" O GLY u 60 " (cutoff:3.500A) Processing helix chain 'u' and resid 79 through 89 removed outlier: 3.576A pdb=" N CYS u 88 " --> pdb=" O GLU u 84 " (cutoff:3.500A) Processing helix chain 'u' and resid 101 through 112 Processing helix chain 'v' and resid 3 through 10 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 167 through 175 Processing helix chain 'w' and resid 181 through 197 removed outlier: 5.035A 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 243 Processing helix chain 'w' and resid 245 through 250 Processing helix chain 'w' and resid 261 through 263 No H-bonds generated for 'chain 'w' and resid 261 through 263' Processing helix chain 'w' and resid 266 through 275 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: 3.745A 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 341 through 343 No H-bonds generated for 'chain 'w' and resid 341 through 343' 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 239 through 244 removed outlier: 6.648A pdb=" N ALA A 153 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N VAL A 115 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N TYR A 155 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ALA A 117 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR A 157 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ASP A 194 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ILE A 156 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N PHE A 196 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE A 158 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL A 198 " --> pdb=" O ILE A 158 " (cutoff:3.500A) 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: 6.165A pdb=" N GLU B 133 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 5.300A 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: 6.436A pdb=" N VAL C 102 " --> pdb=" O MET C 65 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N PHE C 67 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE C 104 " --> pdb=" O PHE C 67 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TYR C 129 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL C 105 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL C 131 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.469A 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: 3.645A 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: 6.542A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE J 167 " --> pdb=" O ASN J 128 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLN J 79 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N VAL J 58 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE J 81 " --> pdb=" O VAL J 58 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'L' and resid 144 through 147 Processing sheet with id= I, first strand: chain 'L' and resid 106 through 108 Processing sheet with id= J, first strand: chain 'M' and resid 32 through 36 Processing sheet with id= K, first strand: chain 'M' and resid 79 through 81 Processing sheet with id= L, first strand: chain 'M' and resid 169 through 171 Processing sheet with id= M, first strand: chain 'M' and resid 196 through 198 Processing sheet with id= N, first strand: chain 'M' and resid 246 through 251 removed outlier: 6.306A pdb=" N ARG M 266 " --> pdb=" O VAL M 270 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N VAL M 270 " --> pdb=" O ARG M 266 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'M' and resid 306 through 308 Processing sheet with id= P, first strand: chain 'M' and resid 366 through 368 removed outlier: 8.478A pdb=" N CYS M 367 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ALA M 340 " --> pdb=" O CYS M 367 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL M 544 " --> pdb=" O ALA M 339 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N ILE M 341 " --> pdb=" O VAL M 544 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N PHE M 546 " --> pdb=" O ILE M 341 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE M 565 " --> pdb=" O LEU M 545 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N LEU M 547 " --> pdb=" O PHE M 565 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE M 567 " --> pdb=" O LEU M 547 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL M 582 " --> pdb=" O TYR M 568 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N GLY M 570 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU M 584 " --> pdb=" O GLY M 570 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'M' and resid 513 through 516 removed outlier: 8.027A pdb=" N ASN M 514 " --> pdb=" O PRO M 472 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL M 399 " --> pdb=" O MET M 473 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LYS M 428 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N LEU M 402 " --> pdb=" O LYS M 428 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA M 430 " --> pdb=" O LEU M 402 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASP M 443 " --> pdb=" O LEU M 431 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'M' and resid 595 through 597 Processing sheet with id= S, first strand: chain 'N' and resid 60 through 63 removed outlier: 6.367A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N LEU N 38 " --> pdb=" O GLU N 50 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'O' and resid 169 through 174 removed outlier: 6.527A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL O 134 " --> pdb=" O VAL O 174 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS O 135 " --> pdb=" O MET O 185 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N MET O 185 " --> pdb=" O CYS O 135 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'P' and resid 110 through 118 removed outlier: 6.835A pdb=" N ASN P 131 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU P 114 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL P 129 " --> pdb=" O LEU P 114 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ALA P 116 " --> pdb=" O GLU P 127 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLU P 127 " --> pdb=" O ALA P 116 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N LEU P 84 " --> pdb=" O ARG P 140 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N TYR P 146 " --> pdb=" O ILE P 88 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'P' and resid 208 through 213 Processing sheet with id= W, first strand: chain 'Q' and resid 80 through 84 removed outlier: 3.654A pdb=" N ARG Q 96 " --> pdb=" O HIS Q 112 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N VAL Q 106 " --> pdb=" O SER Q 102 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'Q' and resid 394 through 402 Processing sheet with id= Y, first strand: chain 'T' and resid 83 through 86 Processing sheet with id= Z, first strand: chain 'l' and resid 69 through 71 Processing sheet with id= AA, first strand: chain 'l' and resid 62 through 67 removed outlier: 6.563A 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: 6.600A pdb=" N VAL w 203 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ASP w 63 " --> pdb=" O VAL w 203 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL w 205 " --> pdb=" O ASP w 63 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLU w 254 " --> pdb=" O VAL w 204 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N TYR w 206 " --> pdb=" O GLU w 254 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU w 256 " --> pdb=" O TYR w 206 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ASP w 208 " --> pdb=" O LEU w 256 " (cutoff:3.500A) removed outlier: 6.703A 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 2909 hydrogen bonds defined for protein. 8055 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: 22.45 Time building geometry restraints manager: 23.03 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: 27249 1.40 - 1.63: 40000 1.63 - 1.85: 840 1.85 - 2.07: 1 2.07 - 2.29: 80 Bond restraints: 68170 Sorted by residual: bond pdb=" C3D NAI A 503 " pdb=" C4D NAI A 503 " ideal model delta sigma weight residual 1.524 1.264 0.260 2.00e-02 2.50e+03 1.69e+02 bond pdb=" C1D NAI A 503 " pdb=" C2D NAI A 503 " ideal model delta sigma weight residual 1.528 1.288 0.240 2.00e-02 2.50e+03 1.44e+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 1.299 0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C3' ADP w 401 " pdb=" C4' ADP w 401 " ideal model delta sigma weight residual 1.524 1.299 0.225 2.00e-02 2.50e+03 1.26e+02 ... (remaining 68165 not shown) Histogram of bond angle deviations from ideal: 73.52 - 85.92: 76 85.92 - 98.32: 0 98.32 - 110.72: 22544 110.72 - 123.12: 66410 123.12 - 135.52: 3218 Bond angle restraints: 92248 Sorted by residual: angle pdb=" N ILE c 105 " pdb=" CA ILE c 105 " pdb=" C ILE c 105 " ideal model delta sigma weight residual 110.62 122.43 -11.81 1.02e+00 9.61e-01 1.34e+02 angle pdb=" N LYS F 39 " pdb=" CA LYS F 39 " pdb=" C LYS F 39 " ideal model delta sigma weight residual 111.14 120.63 -9.49 1.08e+00 8.57e-01 7.72e+01 angle pdb=" C TYR c 75 " pdb=" N PRO c 76 " pdb=" CA PRO c 76 " ideal model delta sigma weight residual 119.85 128.71 -8.86 1.01e+00 9.80e-01 7.70e+01 angle pdb=" PA NDP J 401 " pdb=" O3 NDP J 401 " pdb=" PN NDP J 401 " ideal model delta sigma weight residual 107.74 123.93 -16.19 1.95e+00 2.62e-01 6.87e+01 angle pdb=" C5B NDP J 401 " pdb=" O5B NDP J 401 " pdb=" PA NDP J 401 " ideal model delta sigma weight residual 103.84 118.20 -14.36 1.91e+00 2.73e-01 5.62e+01 ... (remaining 92243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.62: 39612 35.62 - 71.24: 1624 71.24 - 106.86: 123 106.86 - 142.48: 26 142.48 - 178.10: 12 Dihedral angle restraints: 41397 sinusoidal: 17695 harmonic: 23702 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 79.49 178.10 1 2.00e+01 2.50e-03 4.80e+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 -60.00 109.21 -169.20 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" CB CYS F 24 " pdb=" SG CYS F 24 " pdb=" SG CYS F 58 " pdb=" CB CYS F 58 " ideal model delta sinusoidal sigma weight residual -86.00 -137.59 51.59 1 1.00e+01 1.00e-02 3.64e+01 ... (remaining 41394 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 9753 0.105 - 0.210: 257 0.210 - 0.315: 11 0.315 - 0.420: 7 0.420 - 0.525: 2 Chirality restraints: 10030 Sorted by residual: chirality pdb=" CA CYS O 225 " pdb=" N CYS O 225 " pdb=" C CYS O 225 " pdb=" CB CYS O 225 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.88e+00 chirality pdb=" CA ILE c 105 " pdb=" N ILE c 105 " pdb=" C ILE c 105 " pdb=" CB ILE c 105 " both_signs ideal model delta sigma weight residual False 2.43 1.97 0.46 2.00e-01 2.50e+01 5.31e+00 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 -2.35 -0.39 2.00e-01 2.50e+01 3.85e+00 ... (remaining 10027 not shown) Planarity restraints: 11533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 UQ s 402 " 0.153 2.00e-02 2.50e+03 4.72e-01 2.79e+03 pdb=" C11 UQ s 402 " 0.390 2.00e-02 2.50e+03 pdb=" C7 UQ s 402 " 0.554 2.00e-02 2.50e+03 pdb=" C8 UQ s 402 " -0.674 2.00e-02 2.50e+03 pdb=" C9 UQ s 402 " -0.422 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 UQ s 402 " -0.419 2.00e-02 2.50e+03 3.72e-01 1.73e+03 pdb=" C18 UQ s 402 " 0.436 2.00e-02 2.50e+03 pdb=" C19 UQ s 402 " 0.399 2.00e-02 2.50e+03 pdb=" C20 UQ s 402 " -0.009 2.00e-02 2.50e+03 pdb=" C21 UQ s 402 " -0.407 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP J 401 " 0.230 2.00e-02 2.50e+03 2.04e-01 5.19e+02 pdb=" C3N NDP J 401 " -0.351 2.00e-02 2.50e+03 pdb=" C4N NDP J 401 " 0.151 2.00e-02 2.50e+03 pdb=" C7N NDP J 401 " 0.051 2.00e-02 2.50e+03 pdb=" N1N NDP J 401 " -0.081 2.00e-02 2.50e+03 ... (remaining 11530 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 1244 2.68 - 3.24: 63450 3.24 - 3.79: 107913 3.79 - 4.35: 150578 4.35 - 4.90: 244096 Nonbonded interactions: 567281 Sorted by model distance: nonbonded pdb=" O ASN l 320 " pdb=" ND2 ASN l 320 " model vdw 2.125 2.520 nonbonded pdb=" O ALA l 245 " pdb=" OG SER l 249 " model vdw 2.205 2.440 nonbonded pdb=" O ASN w 65 " pdb=" OG SER w 68 " model vdw 2.206 2.440 nonbonded pdb=" OH TYR M 385 " pdb=" OD1 ASP M 527 " model vdw 2.208 2.440 nonbonded pdb=" OG SER M 650 " pdb=" OD1 ASN M 652 " model vdw 2.210 2.440 ... (remaining 567276 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 or (resid 96 through 97 and (name N or nam \ e CA or name C or name O or name CB )) or resid 98 through 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=0.65 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: 1.640 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: 8.610 Check model and map are aligned: 0.730 Set scattering table: 0.490 Process input model: 156.670 Find NCS groups from input model: 2.370 Set up NCS constraints: 0.300 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:14.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 185.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 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 : 0.007 0.312 68170 Z= 0.440 Angle : 0.775 17.064 92248 Z= 0.402 Chirality : 0.045 0.525 10030 Planarity : 0.008 0.472 11533 Dihedral : 18.563 178.101 26093 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.63 % Favored : 96.29 % Rotamer: Outliers : 1.51 % Allowed : 17.75 % Favored : 80.74 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.05 % 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: 1.00 (0.09), residues: 8027 helix: 1.62 (0.08), residues: 4235 sheet: 0.19 (0.25), residues: 411 loop : -0.47 (0.11), residues: 3381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP l 144 HIS 0.009 0.001 HIS Q 223 PHE 0.034 0.001 PHE J 213 TYR 0.031 0.001 TYR m 70 ARG 0.012 0.000 ARG A 359 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1248 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 1142 time to evaluate : 5.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 146 ASP cc_start: 0.8810 (m-30) cc_final: 0.8528 (m-30) REVERT: F 40 ARG cc_start: 0.7583 (ptp90) cc_final: 0.7284 (ptp-170) REVERT: J 269 ASN cc_start: 0.8069 (m-40) cc_final: 0.7817 (m110) REVERT: K 91 VAL cc_start: 0.8371 (p) cc_final: 0.7886 (t) REVERT: b 82 ILE cc_start: 0.9432 (OUTLIER) cc_final: 0.8880 (mt) REVERT: f 64 GLU cc_start: 0.8188 (mp0) cc_final: 0.7910 (mp0) REVERT: m 46 ASN cc_start: 0.8881 (t0) cc_final: 0.8647 (t0) REVERT: m 57 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.7967 (t80) REVERT: m 127 ILE cc_start: 0.6576 (pt) cc_final: 0.6132 (pp) REVERT: s 183 MET cc_start: 0.8758 (mtp) cc_final: 0.8556 (mtp) REVERT: v 76 ASN cc_start: 0.8162 (t0) cc_final: 0.7744 (p0) REVERT: v 116 GLU cc_start: 0.6242 (pt0) cc_final: 0.5954 (pt0) outliers start: 106 outliers final: 73 residues processed: 1227 average time/residue: 1.4907 time to fit residues: 2366.3838 Evaluate side-chains 1160 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 1085 time to evaluate : 5.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 48 LYS Chi-restraints excluded: chain J residue 132 ARG Chi-restraints excluded: chain J residue 156 SER Chi-restraints excluded: chain J residue 325 SER Chi-restraints excluded: chain J residue 350 ILE Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain M residue 330 LEU Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 403 VAL Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain S residue 67 GLU Chi-restraints excluded: chain U residue 22 SER Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 40 SER Chi-restraints excluded: chain V residue 72 LEU Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 82 ILE Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 120 SER Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 120 SER Chi-restraints excluded: chain d residue 136 SER Chi-restraints excluded: chain e residue 81 ILE Chi-restraints excluded: chain f residue 51 SER Chi-restraints excluded: chain h residue 77 SER Chi-restraints excluded: chain h residue 80 LYS Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain i residue 300 SER Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain l residue 320 ASN Chi-restraints excluded: chain l residue 364 LYS Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain m residue 27 ILE Chi-restraints excluded: chain m residue 57 PHE Chi-restraints excluded: chain m residue 65 LEU Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 9 SER Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain p residue 64 LEU Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 66 LEU Chi-restraints excluded: chain r residue 111 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 183 SER Chi-restraints excluded: chain s residue 54 LYS Chi-restraints excluded: chain s residue 57 THR Chi-restraints excluded: chain s residue 119 SER Chi-restraints excluded: chain u residue 56 CYS Chi-restraints excluded: chain u residue 87 THR Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 163 ILE Chi-restraints excluded: chain w residue 164 TYR Chi-restraints excluded: chain w residue 290 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 669 optimal weight: 3.9990 chunk 601 optimal weight: 0.9990 chunk 333 optimal weight: 5.9990 chunk 205 optimal weight: 4.9990 chunk 405 optimal weight: 9.9990 chunk 321 optimal weight: 5.9990 chunk 621 optimal weight: 0.2980 chunk 240 optimal weight: 0.8980 chunk 377 optimal weight: 1.9990 chunk 462 optimal weight: 4.9990 chunk 720 optimal weight: 4.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 62 GLN F 76 ASN H 71 GLN I 29 GLN M 460 HIS N 69 ASN O 187 GLN ** P 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 83 ASN ** Q 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 46 ASN U 40 ASN ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 26 GLN d 124 ASN e 145 ASN j 2 ASN ** j 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 2 ASN ** l 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 470 ASN ** p 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 65 GLN w 202 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.0474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 68170 Z= 0.216 Angle : 0.554 12.052 92248 Z= 0.278 Chirality : 0.041 0.191 10030 Planarity : 0.005 0.082 11533 Dihedral : 14.928 179.725 10335 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.64 % Favored : 96.30 % Rotamer: Outliers : 3.09 % Allowed : 16.50 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % 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: 0.99 (0.09), residues: 8027 helix: 1.58 (0.08), residues: 4229 sheet: 0.30 (0.26), residues: 393 loop : -0.44 (0.11), residues: 3405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP u 86 HIS 0.008 0.001 HIS Q 223 PHE 0.032 0.001 PHE i 292 TYR 0.024 0.001 TYR l 422 ARG 0.008 0.000 ARG h 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1345 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 1128 time to evaluate : 5.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7552 (mmm) REVERT: B 76 TYR cc_start: 0.9119 (OUTLIER) cc_final: 0.8695 (t80) REVERT: B 89 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8425 (mt-10) REVERT: B 146 ASP cc_start: 0.8848 (m-30) cc_final: 0.8541 (m-30) REVERT: C 126 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8391 (mt-10) REVERT: F 34 ARG cc_start: 0.7944 (mtm-85) cc_final: 0.7613 (ttm110) REVERT: F 40 ARG cc_start: 0.7560 (ptp90) cc_final: 0.7294 (ptp-170) REVERT: J 75 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.7879 (mtp180) REVERT: J 95 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8346 (mtt-85) REVERT: K 76 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7958 (mp) REVERT: K 91 VAL cc_start: 0.8480 (OUTLIER) cc_final: 0.7922 (t) REVERT: L 78 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.8077 (ttt90) REVERT: L 148 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7830 (mt-10) REVERT: M 360 ARG cc_start: 0.7674 (mtt90) cc_final: 0.7442 (mpt180) REVERT: M 470 LYS cc_start: 0.7852 (tppp) cc_final: 0.7482 (tptp) REVERT: O 201 ILE cc_start: 0.8683 (tp) cc_final: 0.8393 (tp) REVERT: P 161 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8071 (mtpp) REVERT: X 116 VAL cc_start: 0.8305 (OUTLIER) cc_final: 0.7920 (t) REVERT: e 116 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7952 (pm20) REVERT: e 152 ASP cc_start: 0.6347 (OUTLIER) cc_final: 0.5427 (p0) REVERT: f 64 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.8052 (mp0) REVERT: i 313 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8749 (ttp) REVERT: k 91 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7149 (pm20) REVERT: l 111 ASP cc_start: 0.8475 (OUTLIER) cc_final: 0.8221 (t70) REVERT: l 383 MET cc_start: 0.8989 (tpp) cc_final: 0.8696 (tpt) REVERT: l 586 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.6953 (mm) REVERT: m 127 ILE cc_start: 0.6604 (pt) cc_final: 0.6115 (pp) REVERT: p 44 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8285 (ttm) REVERT: r 114 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.7866 (tm-30) REVERT: s 111 LEU cc_start: 0.8855 (mp) cc_final: 0.8558 (mp) REVERT: v 94 ASP cc_start: 0.8799 (t0) cc_final: 0.8483 (t0) REVERT: w 102 LYS cc_start: 0.8241 (pptt) cc_final: 0.7876 (mmtt) outliers start: 217 outliers final: 85 residues processed: 1234 average time/residue: 1.5300 time to fit residues: 2442.0342 Evaluate side-chains 1195 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 1089 time to evaluate : 5.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain J residue 75 ARG Chi-restraints excluded: chain J residue 95 ARG Chi-restraints excluded: chain J residue 132 ARG Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 148 GLU Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 330 LEU Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 403 VAL Chi-restraints excluded: chain M residue 487 THR Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 654 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 190 ASP Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 161 LYS Chi-restraints excluded: chain Q residue 188 THR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 373 THR Chi-restraints excluded: chain S residue 12 MET Chi-restraints excluded: chain S residue 67 GLU Chi-restraints excluded: chain S residue 69 ILE Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain U residue 18 VAL Chi-restraints excluded: chain W residue 96 ILE Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain Z residue 47 ARG Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain c residue 35 ASP Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain e residue 81 ILE Chi-restraints excluded: chain e residue 116 GLU Chi-restraints excluded: chain e residue 124 ARG Chi-restraints excluded: chain e residue 137 MET Chi-restraints excluded: chain e residue 152 ASP Chi-restraints excluded: chain f residue 64 GLU Chi-restraints excluded: chain i residue 191 THR Chi-restraints excluded: chain i residue 313 MET Chi-restraints excluded: chain j residue 13 LEU Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain k residue 9 ILE Chi-restraints excluded: chain k residue 58 MET Chi-restraints excluded: chain k residue 87 THR Chi-restraints excluded: chain k residue 91 GLN Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 159 HIS Chi-restraints excluded: chain l residue 186 MET Chi-restraints excluded: chain l residue 271 LYS Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 488 MET Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 562 LEU Chi-restraints excluded: chain l residue 586 LEU Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 50 SER Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain p residue 44 MET Chi-restraints excluded: chain p residue 64 LEU Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 66 LEU Chi-restraints excluded: chain r residue 111 THR Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain s residue 57 THR Chi-restraints excluded: chain s residue 253 GLU Chi-restraints excluded: chain u residue 9 THR Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain u residue 87 THR Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 214 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 400 optimal weight: 6.9990 chunk 223 optimal weight: 7.9990 chunk 599 optimal weight: 2.9990 chunk 490 optimal weight: 0.6980 chunk 198 optimal weight: 1.9990 chunk 721 optimal weight: 2.9990 chunk 779 optimal weight: 4.9990 chunk 642 optimal weight: 0.7980 chunk 715 optimal weight: 0.9980 chunk 245 optimal weight: 0.9980 chunk 578 optimal weight: 0.0870 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 62 GLN F 76 ASN H 71 GLN I 29 GLN M 460 HIS M 540 ASN N 69 ASN O 187 GLN ** P 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 83 ASN ** Q 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 40 ASN ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 145 ASN j 2 ASN ** j 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 470 ASN v 65 GLN v 76 ASN w 107 GLN ** w 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.0667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 68170 Z= 0.150 Angle : 0.507 12.455 92248 Z= 0.255 Chirality : 0.039 0.179 10030 Planarity : 0.004 0.064 11533 Dihedral : 13.707 177.974 10265 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.39 % Favored : 96.56 % Rotamer: Outliers : 2.64 % Allowed : 17.86 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % 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: 1.13 (0.10), residues: 8027 helix: 1.69 (0.08), residues: 4235 sheet: 0.21 (0.25), residues: 426 loop : -0.34 (0.11), residues: 3366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP l 144 HIS 0.006 0.001 HIS l 109 PHE 0.031 0.001 PHE i 292 TYR 0.025 0.001 TYR l 422 ARG 0.010 0.000 ARG h 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1364 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1179 time to evaluate : 5.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 GLN cc_start: 0.7470 (OUTLIER) cc_final: 0.6957 (mt0) REVERT: B 43 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.7491 (mmm) REVERT: B 76 TYR cc_start: 0.9041 (OUTLIER) cc_final: 0.8414 (t80) REVERT: B 89 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8393 (mt-10) REVERT: B 146 ASP cc_start: 0.8788 (m-30) cc_final: 0.8475 (m-30) REVERT: F 34 ARG cc_start: 0.7907 (mtm-85) cc_final: 0.7509 (ttm110) REVERT: F 40 ARG cc_start: 0.7535 (ptp90) cc_final: 0.7234 (ptp-170) REVERT: G 98 LEU cc_start: 0.6608 (OUTLIER) cc_final: 0.6362 (pt) REVERT: J 269 ASN cc_start: 0.8080 (m-40) cc_final: 0.7802 (m110) REVERT: K 76 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7918 (mp) REVERT: K 91 VAL cc_start: 0.8447 (OUTLIER) cc_final: 0.7857 (t) REVERT: L 78 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7966 (ttt90) REVERT: L 148 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7821 (mt-10) REVERT: M 470 LYS cc_start: 0.7940 (tppp) cc_final: 0.7691 (tptp) REVERT: N 81 MET cc_start: 0.8776 (mtp) cc_final: 0.8377 (mtt) REVERT: P 161 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8027 (mtpp) REVERT: S 59 ARG cc_start: 0.8051 (mmt-90) cc_final: 0.7813 (mpt180) REVERT: V 73 THR cc_start: 0.8387 (m) cc_final: 0.8148 (p) REVERT: X 116 VAL cc_start: 0.8252 (OUTLIER) cc_final: 0.7888 (t) REVERT: Y 59 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7157 (mp0) REVERT: c 53 LYS cc_start: 0.8445 (tttt) cc_final: 0.8229 (tttp) REVERT: c 70 MET cc_start: 0.8240 (mmt) cc_final: 0.8002 (mmt) REVERT: c 131 LYS cc_start: 0.8752 (mtmm) cc_final: 0.8483 (mtpt) REVERT: d 8 ASP cc_start: 0.8071 (m-30) cc_final: 0.7773 (m-30) REVERT: e 83 ASP cc_start: 0.8830 (OUTLIER) cc_final: 0.8583 (t70) REVERT: e 116 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7922 (pm20) REVERT: e 151 GLU cc_start: 0.7453 (mp0) cc_final: 0.7159 (tp30) REVERT: f 64 GLU cc_start: 0.8275 (mp0) cc_final: 0.7990 (mp0) REVERT: k 91 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7032 (pm20) REVERT: l 338 MET cc_start: 0.9204 (OUTLIER) cc_final: 0.8921 (ttp) REVERT: l 383 MET cc_start: 0.8935 (tpp) cc_final: 0.8639 (tpt) REVERT: m 15 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8532 (mp) REVERT: m 57 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.8028 (t80) REVERT: m 127 ILE cc_start: 0.6404 (pt) cc_final: 0.5973 (pp) REVERT: s 24 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8492 (tt0) REVERT: v 34 ARG cc_start: 0.5347 (OUTLIER) cc_final: 0.4896 (tpp80) REVERT: v 76 ASN cc_start: 0.7940 (t0) cc_final: 0.7718 (p0) REVERT: v 94 ASP cc_start: 0.8615 (t0) cc_final: 0.8292 (t0) REVERT: v 116 GLU cc_start: 0.6371 (pt0) cc_final: 0.6043 (pt0) REVERT: w 102 LYS cc_start: 0.8229 (pptt) cc_final: 0.7940 (mmtm) outliers start: 185 outliers final: 71 residues processed: 1269 average time/residue: 1.5066 time to fit residues: 2495.9386 Evaluate side-chains 1180 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 1089 time to evaluate : 5.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain J residue 132 ARG Chi-restraints excluded: chain K residue 74 ARG Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain L residue 148 GLU Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain M residue 330 LEU Chi-restraints excluded: chain M residue 403 VAL Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 232 THR Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 161 LYS Chi-restraints excluded: chain Q residue 110 ASP Chi-restraints excluded: chain Q residue 188 THR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain S residue 67 GLU Chi-restraints excluded: chain V residue 40 SER Chi-restraints excluded: chain V residue 105 THR Chi-restraints excluded: chain W residue 96 ILE Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain Y residue 59 GLU Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain e residue 116 GLU Chi-restraints excluded: chain h residue 101 LYS Chi-restraints excluded: chain i residue 211 MET Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain j residue 13 LEU Chi-restraints excluded: chain k residue 58 MET Chi-restraints excluded: chain k residue 91 GLN Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 159 HIS Chi-restraints excluded: chain l residue 186 MET Chi-restraints excluded: chain l residue 338 MET Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 488 MET Chi-restraints excluded: chain l residue 496 MET Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 562 LEU Chi-restraints excluded: chain m residue 2 THR Chi-restraints excluded: chain m residue 15 ILE Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 57 PHE Chi-restraints excluded: chain p residue 64 LEU Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 57 THR Chi-restraints excluded: chain s residue 253 GLU Chi-restraints excluded: chain u residue 9 THR Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 34 ARG Chi-restraints excluded: chain w residue 56 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 712 optimal weight: 2.9990 chunk 542 optimal weight: 1.9990 chunk 374 optimal weight: 6.9990 chunk 79 optimal weight: 0.6980 chunk 344 optimal weight: 20.0000 chunk 484 optimal weight: 6.9990 chunk 724 optimal weight: 5.9990 chunk 766 optimal weight: 9.9990 chunk 378 optimal weight: 2.9990 chunk 686 optimal weight: 1.9990 chunk 206 optimal weight: 9.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 GLN F 62 GLN H 71 GLN I 29 GLN M 460 HIS ** M 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 69 ASN O 182 ASN O 187 GLN ** P 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 83 ASN ** Q 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 40 ASN ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 145 ASN j 2 ASN ** j 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 135 ASN l 170 GLN l 470 ASN l 541 ASN s 47 GLN s 194 ASN v 65 GLN w 107 GLN w 202 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 68170 Z= 0.258 Angle : 0.561 12.107 92248 Z= 0.282 Chirality : 0.042 0.195 10030 Planarity : 0.005 0.061 11533 Dihedral : 13.332 178.620 10252 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.63 % Favored : 96.31 % Rotamer: Outliers : 3.39 % Allowed : 18.01 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % 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: 0.99 (0.09), residues: 8027 helix: 1.55 (0.08), residues: 4238 sheet: 0.25 (0.26), residues: 405 loop : -0.40 (0.11), residues: 3384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP a 110 HIS 0.007 0.001 HIS J 37 PHE 0.030 0.002 PHE i 292 TYR 0.018 0.001 TYR l 422 ARG 0.009 0.000 ARG h 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1356 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 1118 time to evaluate : 5.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8956 (tp) REVERT: A 456 GLN cc_start: 0.7558 (OUTLIER) cc_final: 0.7056 (mt0) REVERT: B 43 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7537 (mmm) REVERT: B 76 TYR cc_start: 0.9163 (OUTLIER) cc_final: 0.8671 (t80) REVERT: B 146 ASP cc_start: 0.8863 (m-30) cc_final: 0.8546 (m-30) REVERT: F 34 ARG cc_start: 0.7933 (mtm-85) cc_final: 0.7539 (ttm110) REVERT: F 40 ARG cc_start: 0.7580 (ptp90) cc_final: 0.7327 (ptp-170) REVERT: F 94 VAL cc_start: 0.8592 (p) cc_final: 0.8321 (t) REVERT: G 98 LEU cc_start: 0.6698 (OUTLIER) cc_final: 0.6268 (pt) REVERT: J 75 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.7904 (mtp180) REVERT: J 95 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8412 (mtt90) REVERT: K 76 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.7993 (mp) REVERT: K 91 VAL cc_start: 0.8510 (OUTLIER) cc_final: 0.7916 (t) REVERT: L 78 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8039 (ttt90) REVERT: L 148 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7782 (mt-10) REVERT: M 470 LYS cc_start: 0.8076 (tppp) cc_final: 0.7814 (tptp) REVERT: M 680 LEU cc_start: 0.7894 (mt) cc_final: 0.7614 (tt) REVERT: N 21 ARG cc_start: 0.7151 (ttm110) cc_final: 0.6841 (ttt90) REVERT: O 72 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7890 (mp0) REVERT: O 201 ILE cc_start: 0.8707 (tp) cc_final: 0.8470 (tp) REVERT: P 161 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8140 (mtpp) REVERT: Q 107 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7949 (mmt180) REVERT: Q 145 MET cc_start: 0.9246 (ttm) cc_final: 0.9009 (mtt) REVERT: Q 185 MET cc_start: 0.9381 (OUTLIER) cc_final: 0.8416 (tpt) REVERT: S 59 ARG cc_start: 0.8097 (mmt-90) cc_final: 0.7875 (mpt180) REVERT: T 104 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7857 (mtmp) REVERT: V 73 THR cc_start: 0.8351 (m) cc_final: 0.8085 (p) REVERT: W 7 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8224 (tptp) REVERT: Y 59 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7152 (mp0) REVERT: Z 23 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.7912 (mmtt) REVERT: b 4 TYR cc_start: 0.8589 (m-80) cc_final: 0.8328 (m-10) REVERT: c 70 MET cc_start: 0.8343 (mmt) cc_final: 0.8128 (mmt) REVERT: c 131 LYS cc_start: 0.8762 (mtmm) cc_final: 0.8485 (mtpt) REVERT: e 116 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.8025 (pm20) REVERT: e 151 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7120 (tp30) REVERT: f 64 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8075 (mp0) REVERT: f 68 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8005 (tp30) REVERT: k 91 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7102 (pm20) REVERT: l 111 ASP cc_start: 0.8485 (OUTLIER) cc_final: 0.8225 (t70) REVERT: l 338 MET cc_start: 0.9216 (OUTLIER) cc_final: 0.8958 (ttp) REVERT: l 383 MET cc_start: 0.8963 (tpp) cc_final: 0.8726 (tpt) REVERT: m 15 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8477 (mp) REVERT: m 57 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.8167 (t80) REVERT: m 127 ILE cc_start: 0.6490 (pt) cc_final: 0.6004 (pp) REVERT: o 111 LYS cc_start: 0.8795 (mttm) cc_final: 0.8578 (mtmm) REVERT: r 114 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.7858 (tm-30) REVERT: s 24 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8483 (tt0) REVERT: v 38 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7706 (tt0) REVERT: v 94 ASP cc_start: 0.8559 (t0) cc_final: 0.8242 (t0) outliers start: 238 outliers final: 111 residues processed: 1244 average time/residue: 1.5337 time to fit residues: 2461.5767 Evaluate side-chains 1219 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1078 time to evaluate : 5.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 73 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 E residue 87 LYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain J residue 75 ARG Chi-restraints excluded: chain J residue 95 ARG Chi-restraints excluded: chain J residue 132 ARG Chi-restraints excluded: chain K residue 74 ARG Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain L residue 148 GLU Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 315 THR Chi-restraints excluded: chain M residue 330 LEU Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 403 VAL Chi-restraints excluded: chain M residue 487 THR Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 654 VAL Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 190 ASP Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 161 LYS Chi-restraints excluded: chain Q residue 107 ARG Chi-restraints excluded: chain Q residue 110 ASP Chi-restraints excluded: chain Q residue 185 MET Chi-restraints excluded: chain Q residue 188 THR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain S residue 67 GLU Chi-restraints excluded: chain T residue 104 LYS Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain U residue 18 VAL Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 40 SER Chi-restraints excluded: chain V residue 105 THR Chi-restraints excluded: chain W residue 7 LYS Chi-restraints excluded: chain W residue 96 ILE Chi-restraints excluded: chain X residue 88 LYS Chi-restraints excluded: chain X residue 154 VAL Chi-restraints excluded: chain Y residue 59 GLU Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain Z residue 23 LYS Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 82 ILE Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 136 SER Chi-restraints excluded: chain e residue 81 ILE Chi-restraints excluded: chain e residue 116 GLU Chi-restraints excluded: chain e residue 124 ARG Chi-restraints excluded: chain e residue 137 MET Chi-restraints excluded: chain e residue 146 LYS Chi-restraints excluded: chain e residue 151 GLU Chi-restraints excluded: chain f residue 56 ILE Chi-restraints excluded: chain f residue 64 GLU Chi-restraints excluded: chain i residue 191 THR Chi-restraints excluded: chain i residue 211 MET Chi-restraints excluded: chain k residue 9 ILE Chi-restraints excluded: chain k residue 87 THR Chi-restraints excluded: chain k residue 91 GLN 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 136 ASN Chi-restraints excluded: chain l residue 159 HIS Chi-restraints excluded: chain l residue 186 MET Chi-restraints excluded: chain l residue 252 MET Chi-restraints excluded: chain l residue 314 MET Chi-restraints excluded: chain l residue 338 MET Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 499 MET Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 562 LEU Chi-restraints excluded: chain m residue 2 THR Chi-restraints excluded: chain m residue 15 ILE Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 50 SER Chi-restraints excluded: chain m residue 57 PHE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain p residue 64 LEU Chi-restraints excluded: chain p residue 171 VAL Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 66 LEU Chi-restraints excluded: chain r residue 111 THR Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain s residue 9 LEU Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 57 THR Chi-restraints excluded: chain s residue 164 THR Chi-restraints excluded: chain s residue 253 GLU Chi-restraints excluded: chain u residue 9 THR Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain u residue 87 THR Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 21 ARG Chi-restraints excluded: chain v residue 38 GLU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 163 ILE Chi-restraints excluded: chain w residue 164 TYR Chi-restraints excluded: chain w residue 214 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 638 optimal weight: 6.9990 chunk 435 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 570 optimal weight: 5.9990 chunk 316 optimal weight: 3.9990 chunk 654 optimal weight: 9.9990 chunk 529 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 391 optimal weight: 7.9990 chunk 688 optimal weight: 4.9990 chunk 193 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN F 62 GLN H 71 GLN I 29 GLN J 341 GLN M 460 HIS ** M 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 558 GLN N 31 ASN N 69 ASN O 187 GLN ** P 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 83 ASN ** Q 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 40 ASN ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 145 ASN j 2 ASN ** j 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 274 GLN l 447 ASN l 470 ASN l 541 ASN p 141 GLN s 47 GLN v 65 GLN v 76 ASN ** w 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 68170 Z= 0.361 Angle : 0.621 12.320 92248 Z= 0.313 Chirality : 0.045 0.420 10030 Planarity : 0.005 0.070 11533 Dihedral : 13.286 179.387 10252 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.06 % Favored : 95.88 % Rotamer: Outliers : 3.95 % Allowed : 18.06 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % 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: 0.70 (0.09), residues: 8027 helix: 1.30 (0.08), residues: 4249 sheet: 0.20 (0.26), residues: 405 loop : -0.53 (0.11), residues: 3373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP a 110 HIS 0.009 0.001 HIS p 76 PHE 0.031 0.002 PHE i 292 TYR 0.019 0.002 TYR Y 44 ARG 0.009 0.001 ARG v 114 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1389 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 277 poor density : 1112 time to evaluate : 5.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9049 (tp) REVERT: A 456 GLN cc_start: 0.7495 (OUTLIER) cc_final: 0.7010 (mt0) REVERT: B 43 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7558 (mmm) REVERT: B 146 ASP cc_start: 0.8891 (m-30) cc_final: 0.8575 (m-30) REVERT: C 187 GLU cc_start: 0.8491 (pt0) cc_final: 0.8289 (pt0) REVERT: F 34 ARG cc_start: 0.7981 (mtm-85) cc_final: 0.7667 (ttm110) REVERT: F 40 ARG cc_start: 0.7561 (ptp90) cc_final: 0.7272 (ptp-170) REVERT: F 94 VAL cc_start: 0.8647 (p) cc_final: 0.8428 (t) REVERT: G 111 ASP cc_start: 0.6530 (t70) cc_final: 0.6210 (t0) REVERT: G 114 ASP cc_start: 0.6952 (OUTLIER) cc_final: 0.6369 (m-30) REVERT: H 70 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7569 (mm-30) REVERT: I 30 GLU cc_start: 0.8283 (pm20) cc_final: 0.7989 (pm20) REVERT: J 75 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.7988 (mtp180) REVERT: J 319 VAL cc_start: 0.7859 (OUTLIER) cc_final: 0.7649 (t) REVERT: L 78 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8108 (ttt90) REVERT: L 108 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8172 (tt0) REVERT: L 148 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7783 (mt-10) REVERT: M 470 LYS cc_start: 0.8143 (tppp) cc_final: 0.7827 (tptt) REVERT: Q 107 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7840 (mmt180) REVERT: Q 185 MET cc_start: 0.9400 (OUTLIER) cc_final: 0.8418 (tpt) REVERT: S 59 ARG cc_start: 0.8169 (mmt-90) cc_final: 0.7901 (mpt180) REVERT: T 104 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7945 (mtmp) REVERT: U 9 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8113 (tm) REVERT: V 41 ILE cc_start: 0.8035 (OUTLIER) cc_final: 0.7771 (mm) REVERT: V 73 THR cc_start: 0.8335 (m) cc_final: 0.8048 (p) REVERT: W 7 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8232 (tptp) REVERT: Y 59 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7094 (mp0) REVERT: Z 23 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.7932 (mmtt) REVERT: b 4 TYR cc_start: 0.8715 (m-80) cc_final: 0.8486 (m-10) REVERT: c 170 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7321 (mtm-85) REVERT: e 116 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7972 (pm20) REVERT: f 68 GLU cc_start: 0.8361 (mm-30) cc_final: 0.7956 (tp30) REVERT: k 91 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7133 (pm20) REVERT: k 97 GLN cc_start: 0.7354 (OUTLIER) cc_final: 0.6995 (pm20) REVERT: l 52 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.9034 (mt) REVERT: l 111 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.8249 (t70) REVERT: l 140 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9066 (tt) REVERT: l 338 MET cc_start: 0.9232 (OUTLIER) cc_final: 0.9002 (ttp) REVERT: l 383 MET cc_start: 0.8993 (tpp) cc_final: 0.8723 (tpt) REVERT: l 518 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.7942 (mt0) REVERT: l 586 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7183 (mt) REVERT: m 15 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8577 (mp) REVERT: m 57 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.8161 (t80) REVERT: m 127 ILE cc_start: 0.6662 (pt) cc_final: 0.6184 (pp) REVERT: o 95 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8625 (mm) REVERT: o 111 LYS cc_start: 0.8728 (mttm) cc_final: 0.8523 (mtmm) REVERT: r 114 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.7869 (tm-30) REVERT: s 111 LEU cc_start: 0.8969 (mp) cc_final: 0.8457 (mp) REVERT: v 38 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7868 (tt0) REVERT: v 94 ASP cc_start: 0.8631 (t0) cc_final: 0.8303 (t0) outliers start: 277 outliers final: 139 residues processed: 1268 average time/residue: 1.5011 time to fit residues: 2465.5529 Evaluate side-chains 1246 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 1075 time to evaluate : 5.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 73 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 E residue 65 GLU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain J residue 75 ARG Chi-restraints excluded: chain J residue 132 ARG Chi-restraints excluded: chain J residue 269 ASN Chi-restraints excluded: chain J residue 319 VAL Chi-restraints excluded: chain K residue 74 ARG Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 108 GLU Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 148 GLU Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 74 ASN Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain M residue 151 SER Chi-restraints excluded: chain M residue 295 ASP Chi-restraints excluded: chain M residue 315 THR Chi-restraints excluded: chain M residue 330 LEU Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 403 VAL Chi-restraints excluded: chain M residue 487 THR Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 654 VAL Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain M residue 701 SER Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 190 ASP Chi-restraints excluded: chain O residue 232 THR Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 159 VAL Chi-restraints excluded: chain Q residue 107 ARG Chi-restraints excluded: chain Q residue 110 ASP Chi-restraints excluded: chain Q residue 185 MET Chi-restraints excluded: chain Q residue 188 THR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 437 LYS Chi-restraints excluded: chain S residue 67 GLU Chi-restraints excluded: chain T residue 36 GLU Chi-restraints excluded: chain T residue 104 LYS Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 18 VAL Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 40 SER Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain V residue 72 LEU Chi-restraints excluded: chain V residue 95 CYS Chi-restraints excluded: chain V residue 105 THR Chi-restraints excluded: chain W residue 7 LYS Chi-restraints excluded: chain W residue 96 ILE Chi-restraints excluded: chain X residue 70 ASP Chi-restraints excluded: chain X residue 88 LYS Chi-restraints excluded: chain X residue 154 VAL Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 59 GLU Chi-restraints excluded: chain Y residue 76 ASP Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain Z residue 23 LYS Chi-restraints excluded: chain b residue 2 SER Chi-restraints excluded: chain b residue 82 ILE Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain c residue 35 ASP Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 170 ARG Chi-restraints excluded: chain c residue 186 ILE Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain d residue 136 SER Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain e residue 81 ILE Chi-restraints excluded: chain e residue 116 GLU Chi-restraints excluded: chain e residue 137 MET Chi-restraints excluded: chain e residue 146 LYS Chi-restraints excluded: chain f residue 56 ILE Chi-restraints excluded: chain i residue 191 THR Chi-restraints excluded: chain i residue 211 MET Chi-restraints excluded: chain i residue 324 LYS Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 9 ILE Chi-restraints excluded: chain k residue 58 MET Chi-restraints excluded: chain k residue 87 THR Chi-restraints excluded: chain k residue 91 GLN Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 52 LEU Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 136 ASN Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 159 HIS Chi-restraints excluded: chain l residue 186 MET Chi-restraints excluded: chain l residue 314 MET Chi-restraints excluded: chain l residue 338 MET Chi-restraints excluded: chain l residue 350 LEU Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 488 MET Chi-restraints excluded: chain l residue 499 MET Chi-restraints excluded: chain l residue 518 GLN Chi-restraints excluded: chain l residue 562 LEU Chi-restraints excluded: chain l residue 586 LEU Chi-restraints excluded: chain m residue 2 THR Chi-restraints excluded: chain m residue 15 ILE Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 50 SER Chi-restraints excluded: chain m residue 57 PHE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 31 LYS Chi-restraints excluded: chain o residue 95 ILE Chi-restraints excluded: chain p residue 48 PHE Chi-restraints excluded: chain p residue 64 LEU Chi-restraints excluded: chain p residue 171 VAL Chi-restraints excluded: chain r residue 111 THR Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 355 MET Chi-restraints excluded: chain s residue 57 THR Chi-restraints excluded: chain s residue 59 GLU Chi-restraints excluded: chain s residue 253 GLU Chi-restraints excluded: chain u residue 9 THR Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain u residue 87 THR Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain v residue 21 ARG Chi-restraints excluded: chain v residue 38 GLU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 68 SER Chi-restraints excluded: chain w residue 163 ILE Chi-restraints excluded: chain w residue 164 TYR Chi-restraints excluded: chain w residue 194 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 257 optimal weight: 0.3980 chunk 690 optimal weight: 4.9990 chunk 151 optimal weight: 8.9990 chunk 450 optimal weight: 5.9990 chunk 189 optimal weight: 3.9990 chunk 767 optimal weight: 7.9990 chunk 636 optimal weight: 1.9990 chunk 355 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 253 optimal weight: 3.9990 chunk 402 optimal weight: 2.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 ASN F 62 GLN H 71 GLN I 29 GLN ** M 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 GLN N 31 ASN O 187 GLN ** P 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 83 ASN Q 182 ASN U 40 ASN ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 145 ASN ** j 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 470 ASN l 541 ASN r 103 GLN s 157 ASN v 65 GLN v 76 ASN ** w 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 68170 Z= 0.245 Angle : 0.563 11.705 92248 Z= 0.284 Chirality : 0.042 0.383 10030 Planarity : 0.005 0.069 11533 Dihedral : 12.876 178.902 10251 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.79 % Favored : 96.15 % Rotamer: Outliers : 3.35 % Allowed : 19.12 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % 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: 0.79 (0.09), residues: 8027 helix: 1.39 (0.08), residues: 4252 sheet: 0.26 (0.26), residues: 411 loop : -0.51 (0.11), residues: 3364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP u 86 HIS 0.008 0.001 HIS l 109 PHE 0.031 0.002 PHE i 292 TYR 0.021 0.001 TYR l 422 ARG 0.009 0.000 ARG h 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1351 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 1116 time to evaluate : 5.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.6996 (mt0) REVERT: B 43 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.7513 (mmm) REVERT: B 146 ASP cc_start: 0.8859 (m-30) cc_final: 0.8538 (m-30) REVERT: F 34 ARG cc_start: 0.7943 (mtm-85) cc_final: 0.7634 (ttm110) REVERT: F 40 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.7277 (ptp-170) REVERT: F 94 VAL cc_start: 0.8623 (p) cc_final: 0.8403 (t) REVERT: G 111 ASP cc_start: 0.6514 (t70) cc_final: 0.6200 (t0) REVERT: G 114 ASP cc_start: 0.6907 (OUTLIER) cc_final: 0.6315 (m-30) REVERT: H 71 GLN cc_start: 0.7952 (mt0) cc_final: 0.7552 (mp10) REVERT: I 30 GLU cc_start: 0.8283 (pm20) cc_final: 0.7955 (pm20) REVERT: J 75 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.7906 (mtp180) REVERT: J 95 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8350 (mtt90) REVERT: J 319 VAL cc_start: 0.7769 (OUTLIER) cc_final: 0.7556 (t) REVERT: K 76 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8077 (mp) REVERT: K 91 VAL cc_start: 0.8405 (p) cc_final: 0.7836 (t) REVERT: K 92 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6894 (mt-10) REVERT: L 78 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8141 (ttt90) REVERT: L 148 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7884 (mt-10) REVERT: M 470 LYS cc_start: 0.8121 (tppp) cc_final: 0.7832 (tptp) REVERT: N 132 LYS cc_start: 0.8826 (ttpp) cc_final: 0.8560 (ttpt) REVERT: P 154 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7182 (tm-30) REVERT: P 161 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8133 (mtpp) REVERT: Q 107 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7857 (mmt180) REVERT: Q 185 MET cc_start: 0.9345 (OUTLIER) cc_final: 0.8441 (tpt) REVERT: S 1 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8187 (mmm) REVERT: S 59 ARG cc_start: 0.8122 (mmt-90) cc_final: 0.7885 (mpt180) REVERT: T 104 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7875 (mtmp) REVERT: V 73 THR cc_start: 0.8324 (OUTLIER) cc_final: 0.8041 (p) REVERT: W 7 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8235 (tptp) REVERT: X 155 TYR cc_start: 0.8862 (p90) cc_final: 0.8532 (p90) REVERT: Y 59 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7020 (mp0) REVERT: Z 23 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.7935 (mmtt) REVERT: b 4 TYR cc_start: 0.8688 (m-80) cc_final: 0.8407 (m-10) REVERT: b 9 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8163 (mtpp) REVERT: c 35 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7892 (p0) REVERT: f 63 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8437 (mtpp) REVERT: f 64 GLU cc_start: 0.8265 (mp0) cc_final: 0.8041 (mp0) REVERT: f 68 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8010 (tp30) REVERT: k 91 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7070 (pm20) REVERT: k 97 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.7130 (pm20) REVERT: l 52 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.9002 (mt) REVERT: l 111 ASP cc_start: 0.8565 (OUTLIER) cc_final: 0.8311 (t70) REVERT: l 140 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9028 (tt) REVERT: l 338 MET cc_start: 0.9196 (OUTLIER) cc_final: 0.8925 (ttp) REVERT: l 383 MET cc_start: 0.8989 (tpp) cc_final: 0.8784 (tpt) REVERT: l 518 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.7957 (mt0) REVERT: l 586 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.6976 (mt) REVERT: m 57 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.8098 (t80) REVERT: m 127 ILE cc_start: 0.6601 (pt) cc_final: 0.6143 (pp) REVERT: r 1 MET cc_start: 0.8482 (tpt) cc_final: 0.8014 (tpt) REVERT: r 114 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7798 (tm-30) REVERT: v 94 ASP cc_start: 0.8613 (t0) cc_final: 0.8280 (t0) REVERT: v 116 GLU cc_start: 0.6384 (pt0) cc_final: 0.6097 (pt0) outliers start: 235 outliers final: 122 residues processed: 1245 average time/residue: 1.5438 time to fit residues: 2483.1561 Evaluate side-chains 1243 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1088 time to evaluate : 5.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 108 LYS Chi-restraints excluded: chain J residue 75 ARG Chi-restraints excluded: chain J residue 95 ARG Chi-restraints excluded: chain J residue 181 LEU Chi-restraints excluded: chain J residue 319 VAL Chi-restraints excluded: chain K residue 74 ARG Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain L residue 148 GLU Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 295 ASP Chi-restraints excluded: chain M residue 330 LEU Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 387 LEU Chi-restraints excluded: chain M residue 403 VAL Chi-restraints excluded: chain M residue 487 THR Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 654 VAL Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 190 ASP Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 161 LYS Chi-restraints excluded: chain Q residue 40 ASP Chi-restraints excluded: chain Q residue 70 ASP Chi-restraints excluded: chain Q residue 107 ARG Chi-restraints excluded: chain Q residue 185 MET Chi-restraints excluded: chain Q residue 188 THR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 437 LYS Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 67 GLU Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain T residue 104 LYS Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain U residue 18 VAL Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain V residue 40 SER Chi-restraints excluded: chain V residue 72 LEU Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 95 CYS Chi-restraints excluded: chain W residue 7 LYS Chi-restraints excluded: chain W residue 96 ILE Chi-restraints excluded: chain X residue 88 LYS Chi-restraints excluded: chain X residue 154 VAL Chi-restraints excluded: chain Y residue 59 GLU Chi-restraints excluded: chain Z residue 23 LYS Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 82 ILE Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain c residue 35 ASP Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain e residue 137 MET Chi-restraints excluded: chain f residue 63 LYS Chi-restraints excluded: chain i residue 68 MET Chi-restraints excluded: chain i residue 191 THR Chi-restraints excluded: chain j residue 13 LEU Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain j residue 105 GLU Chi-restraints excluded: chain k residue 9 ILE Chi-restraints excluded: chain k residue 87 THR Chi-restraints excluded: chain k residue 91 GLN Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 52 LEU Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 136 ASN Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 159 HIS Chi-restraints excluded: chain l residue 186 MET Chi-restraints excluded: chain l residue 252 MET Chi-restraints excluded: chain l residue 314 MET Chi-restraints excluded: chain l residue 338 MET Chi-restraints excluded: chain l residue 364 LYS Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 488 MET Chi-restraints excluded: chain l residue 518 GLN Chi-restraints excluded: chain l residue 562 LEU Chi-restraints excluded: chain l residue 586 LEU Chi-restraints excluded: chain m residue 2 THR Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 50 SER Chi-restraints excluded: chain m residue 57 PHE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 31 LYS Chi-restraints excluded: chain p residue 48 PHE Chi-restraints excluded: chain p residue 64 LEU Chi-restraints excluded: chain r residue 38 SER Chi-restraints excluded: chain r residue 66 LEU Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 122 PHE Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain s residue 57 THR Chi-restraints excluded: chain s residue 59 GLU Chi-restraints excluded: chain s residue 161 THR Chi-restraints excluded: chain s residue 253 GLU Chi-restraints excluded: chain u residue 9 THR Chi-restraints excluded: chain u residue 16 GLN Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 21 ARG Chi-restraints excluded: chain w residue 44 VAL Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 163 ILE Chi-restraints excluded: chain w residue 164 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 739 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 437 optimal weight: 0.8980 chunk 560 optimal weight: 0.9990 chunk 434 optimal weight: 0.2980 chunk 645 optimal weight: 4.9990 chunk 428 optimal weight: 4.9990 chunk 764 optimal weight: 10.0000 chunk 478 optimal weight: 0.3980 chunk 465 optimal weight: 4.9990 chunk 352 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN I 29 GLN ** M 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 GLN N 31 ASN O 187 GLN Q 83 ASN ** Q 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 40 ASN ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 145 ASN j 2 ASN ** j 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 541 ASN p 141 GLN r 103 GLN s 171 HIS v 65 GLN v 76 ASN ** w 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 202 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 68170 Z= 0.176 Angle : 0.532 11.640 92248 Z= 0.268 Chirality : 0.041 0.381 10030 Planarity : 0.004 0.065 11533 Dihedral : 12.262 177.881 10247 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.69 % Favored : 96.26 % Rotamer: Outliers : 3.02 % Allowed : 19.53 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % 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: 0.95 (0.09), residues: 8027 helix: 1.52 (0.08), residues: 4256 sheet: 0.32 (0.26), residues: 411 loop : -0.44 (0.11), residues: 3360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP a 110 HIS 0.006 0.001 HIS J 37 PHE 0.032 0.001 PHE i 292 TYR 0.022 0.001 TYR l 422 ARG 0.010 0.000 ARG h 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1357 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1145 time to evaluate : 6.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7790 (tm-30) REVERT: A 456 GLN cc_start: 0.7465 (OUTLIER) cc_final: 0.6971 (mt0) REVERT: B 43 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.7450 (mmm) REVERT: B 76 TYR cc_start: 0.9117 (OUTLIER) cc_final: 0.8706 (t80) REVERT: B 146 ASP cc_start: 0.8803 (m-30) cc_final: 0.8467 (m-30) REVERT: F 34 ARG cc_start: 0.7837 (mtm-85) cc_final: 0.7520 (ttm110) REVERT: F 94 VAL cc_start: 0.8559 (p) cc_final: 0.8318 (t) REVERT: G 111 ASP cc_start: 0.6469 (t70) cc_final: 0.6168 (t0) REVERT: G 114 ASP cc_start: 0.6845 (OUTLIER) cc_final: 0.6225 (m-30) REVERT: I 30 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7962 (pm20) REVERT: J 95 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8388 (mtt90) REVERT: J 319 VAL cc_start: 0.7853 (OUTLIER) cc_final: 0.7615 (t) REVERT: K 91 VAL cc_start: 0.8476 (p) cc_final: 0.7892 (t) REVERT: L 108 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8184 (tt0) REVERT: M 470 LYS cc_start: 0.8103 (tppp) cc_final: 0.7815 (tptp) REVERT: M 696 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.7653 (mmt) REVERT: N 81 MET cc_start: 0.8679 (mtp) cc_final: 0.8268 (mtt) REVERT: P 154 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7545 (tm-30) REVERT: P 161 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8074 (mtpp) REVERT: Q 185 MET cc_start: 0.9315 (OUTLIER) cc_final: 0.8481 (tpt) REVERT: S 59 ARG cc_start: 0.8094 (mmt-90) cc_final: 0.7874 (mpt180) REVERT: T 104 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7813 (mtmp) REVERT: U 9 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8128 (tm) REVERT: V 73 THR cc_start: 0.8315 (m) cc_final: 0.8038 (p) REVERT: X 155 TYR cc_start: 0.8824 (p90) cc_final: 0.8468 (p90) REVERT: Y 59 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7056 (mp0) REVERT: b 4 TYR cc_start: 0.8617 (m-80) cc_final: 0.8349 (m-10) REVERT: b 9 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8121 (mtpp) REVERT: b 93 LYS cc_start: 0.8667 (mtmt) cc_final: 0.8449 (mtmt) REVERT: c 35 ASP cc_start: 0.8202 (m-30) cc_final: 0.7910 (p0) REVERT: c 53 LYS cc_start: 0.8409 (tttt) cc_final: 0.8194 (tttp) REVERT: c 74 ASP cc_start: 0.8050 (t0) cc_final: 0.7822 (t0) REVERT: d 8 ASP cc_start: 0.8142 (m-30) cc_final: 0.7841 (m-30) REVERT: f 64 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7990 (mp0) REVERT: f 68 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7938 (tp30) REVERT: k 91 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7066 (pm20) REVERT: k 97 GLN cc_start: 0.7355 (OUTLIER) cc_final: 0.7090 (pm20) REVERT: l 111 ASP cc_start: 0.8551 (OUTLIER) cc_final: 0.8309 (t70) REVERT: l 140 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.8970 (tt) REVERT: l 338 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8908 (ttp) REVERT: l 383 MET cc_start: 0.8953 (tpp) cc_final: 0.8732 (tpt) REVERT: l 482 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.7934 (ttm) REVERT: l 518 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.7961 (mt0) REVERT: l 586 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.6976 (mm) REVERT: m 57 PHE cc_start: 0.8310 (OUTLIER) cc_final: 0.8062 (t80) REVERT: m 127 ILE cc_start: 0.6531 (pt) cc_final: 0.6079 (pp) REVERT: p 62 GLN cc_start: 0.7300 (tp-100) cc_final: 0.6960 (mp10) REVERT: r 114 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.7875 (tm-30) REVERT: v 34 ARG cc_start: 0.5442 (tmt90) cc_final: 0.5063 (tpp80) REVERT: v 94 ASP cc_start: 0.8563 (t0) cc_final: 0.8310 (t0) REVERT: v 116 GLU cc_start: 0.6498 (pt0) cc_final: 0.6208 (pt0) outliers start: 212 outliers final: 110 residues processed: 1265 average time/residue: 1.5582 time to fit residues: 2562.0668 Evaluate side-chains 1229 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1091 time to evaluate : 6.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 30 GLU Chi-restraints excluded: chain J residue 95 ARG Chi-restraints excluded: chain J residue 132 ARG Chi-restraints excluded: chain J residue 181 LEU Chi-restraints excluded: chain J residue 319 VAL Chi-restraints excluded: chain K residue 74 ARG Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 108 GLU Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 330 LEU Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 387 LEU Chi-restraints excluded: chain M residue 403 VAL Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 159 VAL Chi-restraints excluded: chain P residue 161 LYS Chi-restraints excluded: chain Q residue 185 MET Chi-restraints excluded: chain Q residue 188 THR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain S residue 67 GLU Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain T residue 104 LYS Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain V residue 40 SER Chi-restraints excluded: chain V residue 53 VAL Chi-restraints excluded: chain V residue 95 CYS Chi-restraints excluded: chain V residue 105 THR Chi-restraints excluded: chain W residue 96 ILE Chi-restraints excluded: chain X residue 88 LYS Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 154 VAL Chi-restraints excluded: chain Y residue 59 GLU Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain b residue 82 ILE Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain e residue 81 ILE Chi-restraints excluded: chain e residue 137 MET Chi-restraints excluded: chain f residue 64 GLU Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain j residue 13 LEU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 58 MET Chi-restraints excluded: chain k residue 91 GLN Chi-restraints excluded: chain k residue 97 GLN 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 136 ASN Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 159 HIS Chi-restraints excluded: chain l residue 186 MET Chi-restraints excluded: chain l residue 252 MET Chi-restraints excluded: chain l residue 314 MET Chi-restraints excluded: chain l residue 338 MET Chi-restraints excluded: chain l residue 364 LYS Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 482 MET Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 488 MET Chi-restraints excluded: chain l residue 518 GLN Chi-restraints excluded: chain l residue 562 LEU Chi-restraints excluded: chain l residue 586 LEU Chi-restraints excluded: chain m residue 2 THR Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 57 PHE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 31 LYS Chi-restraints excluded: chain p residue 48 PHE Chi-restraints excluded: chain r residue 66 LEU Chi-restraints excluded: chain r residue 111 THR Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 122 PHE Chi-restraints excluded: chain r residue 130 LEU Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 374 ASN Chi-restraints excluded: chain s residue 57 THR Chi-restraints excluded: chain s residue 253 GLU Chi-restraints excluded: chain u residue 9 THR Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 21 ARG Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 68 SER Chi-restraints excluded: chain w residue 163 ILE Chi-restraints excluded: chain w residue 164 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 472 optimal weight: 0.7980 chunk 305 optimal weight: 1.9990 chunk 456 optimal weight: 0.9990 chunk 230 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 148 optimal weight: 10.0000 chunk 485 optimal weight: 6.9990 chunk 520 optimal weight: 2.9990 chunk 377 optimal weight: 0.2980 chunk 71 optimal weight: 4.9990 chunk 600 optimal weight: 7.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 GLN F 62 GLN H 71 GLN I 29 GLN M 498 GLN M 558 GLN N 12 GLN N 31 ASN O 187 GLN Q 83 ASN ** Q 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 40 ASN Y 57 GLN ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 145 ASN j 2 ASN ** j 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 541 ASN r 103 GLN s 47 GLN v 65 GLN ** w 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 202 HIS w 239 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 68170 Z= 0.201 Angle : 0.547 11.312 92248 Z= 0.275 Chirality : 0.041 0.379 10030 Planarity : 0.004 0.063 11533 Dihedral : 12.025 178.212 10245 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.75 % Favored : 96.20 % Rotamer: Outliers : 3.15 % Allowed : 19.70 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % 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: 8027 helix: 1.52 (0.08), residues: 4253 sheet: 0.32 (0.26), residues: 411 loop : -0.42 (0.11), residues: 3363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP a 110 HIS 0.007 0.001 HIS l 109 PHE 0.031 0.001 PHE i 292 TYR 0.021 0.001 TYR T 50 ARG 0.010 0.000 ARG h 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1327 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1106 time to evaluate : 5.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.6981 (mt0) REVERT: B 43 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7546 (mmm) REVERT: B 76 TYR cc_start: 0.9123 (OUTLIER) cc_final: 0.8707 (t80) REVERT: B 146 ASP cc_start: 0.8816 (m-30) cc_final: 0.8477 (m-30) REVERT: F 34 ARG cc_start: 0.7851 (mtm-85) cc_final: 0.7516 (ttm110) REVERT: F 40 ARG cc_start: 0.7490 (ptp-170) cc_final: 0.7169 (ptp-170) REVERT: G 111 ASP cc_start: 0.6452 (t70) cc_final: 0.6134 (t0) REVERT: G 114 ASP cc_start: 0.6876 (OUTLIER) cc_final: 0.6232 (m-30) REVERT: I 30 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7965 (pm20) REVERT: I 108 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7772 (ptmm) REVERT: J 95 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8387 (mtt90) REVERT: J 319 VAL cc_start: 0.7846 (OUTLIER) cc_final: 0.7485 (t) REVERT: K 76 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8078 (mp) REVERT: K 82 SER cc_start: 0.8496 (t) cc_final: 0.8230 (p) REVERT: K 91 VAL cc_start: 0.8479 (p) cc_final: 0.7869 (t) REVERT: L 108 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8163 (tt0) REVERT: M 470 LYS cc_start: 0.8114 (tppp) cc_final: 0.7824 (tptp) REVERT: M 696 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.7777 (mmt) REVERT: N 132 LYS cc_start: 0.8843 (ttpp) cc_final: 0.8447 (ttpt) REVERT: P 154 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7604 (tm-30) REVERT: P 161 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8091 (mtpp) REVERT: Q 185 MET cc_start: 0.9321 (OUTLIER) cc_final: 0.8466 (tpt) REVERT: S 59 ARG cc_start: 0.8103 (mmt-90) cc_final: 0.7884 (mpt180) REVERT: T 104 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7842 (mtmp) REVERT: U 9 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8130 (tm) REVERT: V 73 THR cc_start: 0.8310 (m) cc_final: 0.8031 (p) REVERT: W 7 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8157 (tptp) REVERT: Y 59 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7025 (mp0) REVERT: Z 23 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.7905 (mmtt) REVERT: b 4 TYR cc_start: 0.8605 (m-80) cc_final: 0.8326 (m-10) REVERT: b 9 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8135 (mtpp) REVERT: c 35 ASP cc_start: 0.8219 (m-30) cc_final: 0.7943 (p0) REVERT: e 116 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7849 (pm20) REVERT: f 64 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7992 (mp0) REVERT: f 68 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7936 (tp30) REVERT: k 34 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7885 (mm-30) REVERT: k 91 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7071 (pm20) REVERT: k 97 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.7086 (pm20) REVERT: l 46 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8896 (tp) REVERT: l 111 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.8307 (t70) REVERT: l 140 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.8967 (tt) REVERT: l 338 MET cc_start: 0.9164 (OUTLIER) cc_final: 0.8919 (ttp) REVERT: l 383 MET cc_start: 0.8952 (tpp) cc_final: 0.8746 (tpt) REVERT: l 482 MET cc_start: 0.8406 (ttp) cc_final: 0.7943 (ttm) REVERT: l 518 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.7963 (mt0) REVERT: l 586 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.6998 (mm) REVERT: m 57 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.8053 (t80) REVERT: m 127 ILE cc_start: 0.6553 (pt) cc_final: 0.6087 (pp) REVERT: p 47 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7596 (ttt90) REVERT: r 114 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.7873 (tm-30) REVERT: v 94 ASP cc_start: 0.8526 (t0) cc_final: 0.8206 (t0) REVERT: v 116 GLU cc_start: 0.6418 (pt0) cc_final: 0.6133 (pt0) REVERT: w 258 TYR cc_start: 0.7146 (m-10) cc_final: 0.6884 (m-10) outliers start: 221 outliers final: 125 residues processed: 1229 average time/residue: 1.5492 time to fit residues: 2473.6401 Evaluate side-chains 1244 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1086 time to evaluate : 5.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 30 GLU Chi-restraints excluded: chain I residue 108 LYS Chi-restraints excluded: chain J residue 95 ARG Chi-restraints excluded: chain J residue 132 ARG Chi-restraints excluded: chain J residue 181 LEU Chi-restraints excluded: chain J residue 319 VAL Chi-restraints excluded: chain K residue 74 ARG Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 108 GLU Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain M residue 151 SER Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 330 LEU Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 387 LEU Chi-restraints excluded: chain M residue 403 VAL Chi-restraints excluded: chain M residue 487 THR Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 654 VAL Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 190 ASP Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 159 VAL Chi-restraints excluded: chain P residue 161 LYS Chi-restraints excluded: chain Q residue 185 MET Chi-restraints excluded: chain Q residue 188 THR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain S residue 67 GLU Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain T residue 104 LYS Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 18 VAL Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain V residue 40 SER Chi-restraints excluded: chain V residue 53 VAL Chi-restraints excluded: chain V residue 72 LEU Chi-restraints excluded: chain V residue 95 CYS Chi-restraints excluded: chain V residue 105 THR Chi-restraints excluded: chain W residue 7 LYS Chi-restraints excluded: chain X residue 88 LYS Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 154 VAL Chi-restraints excluded: chain Y residue 59 GLU Chi-restraints excluded: chain Z residue 23 LYS Chi-restraints excluded: chain Z residue 42 ARG Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain b residue 82 ILE Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain e residue 81 ILE Chi-restraints excluded: chain e residue 116 GLU Chi-restraints excluded: chain e residue 137 MET Chi-restraints excluded: chain f residue 64 GLU Chi-restraints excluded: chain i residue 191 THR Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain j residue 13 LEU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain j residue 105 GLU Chi-restraints excluded: chain k residue 58 MET Chi-restraints excluded: chain k residue 87 THR Chi-restraints excluded: chain k residue 91 GLN Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 46 LEU 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 136 ASN Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 159 HIS Chi-restraints excluded: chain l residue 186 MET Chi-restraints excluded: chain l residue 252 MET Chi-restraints excluded: chain l residue 314 MET Chi-restraints excluded: chain l residue 338 MET Chi-restraints excluded: chain l residue 364 LYS Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 488 MET Chi-restraints excluded: chain l residue 518 GLN Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 562 LEU Chi-restraints excluded: chain l residue 586 LEU Chi-restraints excluded: chain m residue 2 THR Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 50 SER Chi-restraints excluded: chain m residue 57 PHE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain p residue 47 ARG Chi-restraints excluded: chain p residue 48 PHE Chi-restraints excluded: chain p residue 171 VAL Chi-restraints excluded: chain r residue 66 LEU Chi-restraints excluded: chain r residue 111 THR Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 122 PHE Chi-restraints excluded: chain r residue 130 LEU Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain s residue 57 THR Chi-restraints excluded: chain s residue 59 GLU Chi-restraints excluded: chain s residue 253 GLU Chi-restraints excluded: chain u residue 9 THR Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain u residue 87 THR Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 21 ARG Chi-restraints excluded: chain w residue 44 VAL Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 68 SER Chi-restraints excluded: chain w residue 163 ILE Chi-restraints excluded: chain w residue 164 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 695 optimal weight: 4.9990 chunk 732 optimal weight: 6.9990 chunk 668 optimal weight: 6.9990 chunk 712 optimal weight: 0.8980 chunk 428 optimal weight: 4.9990 chunk 310 optimal weight: 5.9990 chunk 559 optimal weight: 5.9990 chunk 218 optimal weight: 7.9990 chunk 643 optimal weight: 3.9990 chunk 673 optimal weight: 2.9990 chunk 709 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN A 451 GLN F 62 GLN H 71 GLN I 29 GLN ** M 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 558 GLN N 12 GLN N 31 ASN O 187 GLN ** P 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 40 ASN Y 57 GLN ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 145 ASN j 2 ASN ** j 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 447 ASN l 470 ASN l 541 ASN p 141 GLN s 47 GLN v 65 GLN w 202 HIS w 239 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 68170 Z= 0.386 Angle : 0.641 11.784 92248 Z= 0.323 Chirality : 0.046 0.433 10030 Planarity : 0.005 0.067 11533 Dihedral : 12.309 179.304 10244 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.05 % Favored : 95.89 % Rotamer: Outliers : 3.22 % Allowed : 19.60 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % 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: 0.68 (0.09), residues: 8027 helix: 1.29 (0.08), residues: 4245 sheet: 0.22 (0.26), residues: 403 loop : -0.56 (0.11), residues: 3379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP a 110 HIS 0.008 0.001 HIS l 109 PHE 0.078 0.002 PHE C 67 TYR 0.023 0.002 TYR d 32 ARG 0.010 0.001 ARG v 114 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1305 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 1079 time to evaluate : 7.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9032 (tp) REVERT: A 456 GLN cc_start: 0.7542 (OUTLIER) cc_final: 0.7042 (mt0) REVERT: B 43 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.7545 (mmm) REVERT: B 146 ASP cc_start: 0.8914 (m-30) cc_final: 0.8587 (m-30) REVERT: F 34 ARG cc_start: 0.7861 (mtm-85) cc_final: 0.7533 (ttm110) REVERT: F 40 ARG cc_start: 0.7647 (ptp-170) cc_final: 0.7368 (ptp-170) REVERT: G 114 ASP cc_start: 0.6972 (OUTLIER) cc_final: 0.6357 (m-30) REVERT: I 30 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8058 (pm20) REVERT: J 75 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.7940 (mtp180) REVERT: L 148 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.8023 (mt-10) REVERT: M 470 LYS cc_start: 0.8150 (tppp) cc_final: 0.7856 (tptp) REVERT: N 132 LYS cc_start: 0.8843 (ttpp) cc_final: 0.8614 (ttpt) REVERT: P 154 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7588 (tm-30) REVERT: Q 185 MET cc_start: 0.9380 (OUTLIER) cc_final: 0.8397 (tpt) REVERT: S 1 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.8177 (mmm) REVERT: S 59 ARG cc_start: 0.8149 (mmt-90) cc_final: 0.7907 (mpt180) REVERT: T 104 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7917 (mtmp) REVERT: U 9 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8154 (tm) REVERT: V 73 THR cc_start: 0.8326 (OUTLIER) cc_final: 0.8035 (p) REVERT: W 7 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8220 (tptp) REVERT: Y 59 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7097 (mp0) REVERT: Z 23 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.7874 (mmtt) REVERT: b 4 TYR cc_start: 0.8687 (m-80) cc_final: 0.8433 (m-10) REVERT: b 9 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8201 (mtpp) REVERT: c 35 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7920 (p0) REVERT: c 74 ASP cc_start: 0.8147 (t0) cc_final: 0.7771 (t0) REVERT: e 116 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7950 (pm20) REVERT: f 64 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.8075 (mp0) REVERT: f 68 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8003 (tp30) REVERT: k 91 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7094 (pm20) REVERT: k 97 GLN cc_start: 0.7476 (OUTLIER) cc_final: 0.7150 (pm20) REVERT: l 46 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8931 (tp) REVERT: l 111 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.8320 (t70) REVERT: l 140 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9045 (tt) REVERT: l 383 MET cc_start: 0.8984 (tpp) cc_final: 0.8775 (tpt) REVERT: l 518 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.7981 (mt0) REVERT: l 586 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7072 (mt) REVERT: m 57 PHE cc_start: 0.8483 (OUTLIER) cc_final: 0.8194 (t80) REVERT: m 127 ILE cc_start: 0.6666 (pt) cc_final: 0.6162 (pp) REVERT: o 111 LYS cc_start: 0.8825 (mttm) cc_final: 0.8577 (mtmm) REVERT: p 47 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7531 (ttt90) REVERT: p 62 GLN cc_start: 0.7433 (tp-100) cc_final: 0.7049 (mp10) REVERT: r 114 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.7864 (tm-30) REVERT: v 94 ASP cc_start: 0.8530 (t0) cc_final: 0.8225 (t0) outliers start: 226 outliers final: 138 residues processed: 1209 average time/residue: 1.5253 time to fit residues: 2392.4867 Evaluate side-chains 1234 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1066 time to evaluate : 5.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 30 GLU Chi-restraints excluded: chain I residue 108 LYS Chi-restraints excluded: chain J residue 75 ARG Chi-restraints excluded: chain K residue 74 ARG Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 148 GLU Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 74 ASN Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain M residue 151 SER Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 330 LEU Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 387 LEU Chi-restraints excluded: chain M residue 403 VAL Chi-restraints excluded: chain M residue 487 THR 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 654 VAL Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain M residue 701 SER Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 159 VAL Chi-restraints excluded: chain Q residue 40 ASP Chi-restraints excluded: chain Q residue 185 MET Chi-restraints excluded: chain Q residue 188 THR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 437 LYS Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 67 GLU Chi-restraints excluded: chain T residue 36 GLU Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain T residue 104 LYS Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 18 VAL Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain V residue 40 SER Chi-restraints excluded: chain V residue 53 VAL Chi-restraints excluded: chain V residue 72 LEU Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 95 CYS Chi-restraints excluded: chain V residue 105 THR Chi-restraints excluded: chain W residue 7 LYS Chi-restraints excluded: chain X residue 70 ASP Chi-restraints excluded: chain X residue 88 LYS Chi-restraints excluded: chain X residue 154 VAL Chi-restraints excluded: chain Y residue 59 GLU Chi-restraints excluded: chain Z residue 23 LYS Chi-restraints excluded: chain Z residue 42 ARG Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 82 ILE Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain c residue 35 ASP Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain e residue 81 ILE Chi-restraints excluded: chain e residue 116 GLU Chi-restraints excluded: chain e residue 137 MET Chi-restraints excluded: chain f residue 56 ILE Chi-restraints excluded: chain f residue 64 GLU Chi-restraints excluded: chain i residue 191 THR Chi-restraints excluded: chain i residue 261 MET Chi-restraints excluded: chain j residue 13 LEU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 9 ILE Chi-restraints excluded: chain k residue 58 MET Chi-restraints excluded: chain k residue 87 THR Chi-restraints excluded: chain k residue 91 GLN Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 46 LEU Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 136 ASN Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 159 HIS Chi-restraints excluded: chain l residue 186 MET Chi-restraints excluded: chain l residue 252 MET Chi-restraints excluded: chain l residue 314 MET Chi-restraints excluded: chain l residue 350 LEU Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 488 MET Chi-restraints excluded: chain l residue 518 GLN Chi-restraints excluded: chain l residue 562 LEU Chi-restraints excluded: chain l residue 586 LEU Chi-restraints excluded: chain m residue 2 THR Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 50 SER Chi-restraints excluded: chain m residue 57 PHE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain p residue 47 ARG Chi-restraints excluded: chain p residue 48 PHE Chi-restraints excluded: chain p residue 171 VAL Chi-restraints excluded: chain r residue 38 SER Chi-restraints excluded: chain r residue 66 LEU Chi-restraints excluded: chain r residue 111 THR Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 122 PHE Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain s residue 57 THR Chi-restraints excluded: chain s residue 59 GLU Chi-restraints excluded: chain s residue 253 GLU Chi-restraints excluded: chain s residue 257 ILE Chi-restraints excluded: chain u residue 9 THR Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain u residue 87 THR Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain u residue 114 LYS Chi-restraints excluded: chain v residue 21 ARG Chi-restraints excluded: chain v residue 76 ASN Chi-restraints excluded: chain w residue 44 VAL Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 68 SER Chi-restraints excluded: chain w residue 163 ILE Chi-restraints excluded: chain w residue 164 TYR Chi-restraints excluded: chain w residue 194 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 467 optimal weight: 0.6980 chunk 753 optimal weight: 9.9990 chunk 459 optimal weight: 4.9990 chunk 357 optimal weight: 1.9990 chunk 523 optimal weight: 0.9990 chunk 790 optimal weight: 4.9990 chunk 727 optimal weight: 1.9990 chunk 629 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 485 optimal weight: 4.9990 chunk 385 optimal weight: 8.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 GLN F 62 GLN H 71 GLN I 29 GLN ** M 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 558 GLN N 12 GLN N 31 ASN O 187 GLN ** Q 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 40 ASN Y 57 GLN ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 145 ASN ** j 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 470 ASN l 541 ASN o 123 GLN s 47 GLN v 65 GLN w 202 HIS w 239 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 68170 Z= 0.245 Angle : 0.578 11.994 92248 Z= 0.291 Chirality : 0.042 0.430 10030 Planarity : 0.005 0.069 11533 Dihedral : 12.050 178.687 10244 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.80 % Favored : 96.14 % Rotamer: Outliers : 2.74 % Allowed : 20.16 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % 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: 0.78 (0.09), residues: 8027 helix: 1.38 (0.08), residues: 4245 sheet: 0.20 (0.26), residues: 407 loop : -0.51 (0.11), residues: 3375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP a 110 HIS 0.008 0.001 HIS b 127 PHE 0.030 0.001 PHE i 292 TYR 0.026 0.001 TYR d 32 ARG 0.010 0.000 ARG h 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1291 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1099 time to evaluate : 5.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 GLN cc_start: 0.7466 (OUTLIER) cc_final: 0.6961 (mt0) REVERT: B 43 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.7470 (mmm) REVERT: B 146 ASP cc_start: 0.8854 (m-30) cc_final: 0.8541 (m-30) REVERT: F 34 ARG cc_start: 0.7901 (mtm-85) cc_final: 0.7562 (ttm110) REVERT: F 40 ARG cc_start: 0.7590 (ptp-170) cc_final: 0.7236 (ptp-170) REVERT: G 114 ASP cc_start: 0.6870 (OUTLIER) cc_final: 0.6244 (m-30) REVERT: I 30 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8113 (pm20) REVERT: L 148 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.8006 (mt-10) REVERT: M 470 LYS cc_start: 0.8133 (tppp) cc_final: 0.7834 (tptp) REVERT: N 132 LYS cc_start: 0.8832 (ttpp) cc_final: 0.8571 (ttpt) REVERT: P 154 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7536 (tm-30) REVERT: Q 185 MET cc_start: 0.9332 (OUTLIER) cc_final: 0.8445 (tpt) REVERT: S 1 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8043 (mmm) REVERT: S 59 ARG cc_start: 0.8110 (mmt-90) cc_final: 0.7882 (mpt180) REVERT: T 104 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7870 (mtmp) REVERT: U 9 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8144 (tm) REVERT: V 73 THR cc_start: 0.8315 (OUTLIER) cc_final: 0.8026 (p) REVERT: W 7 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8194 (tptp) REVERT: Y 59 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7061 (mp0) REVERT: Z 23 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.7869 (mmtt) REVERT: b 4 TYR cc_start: 0.8655 (m-80) cc_final: 0.8411 (m-10) REVERT: b 9 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8154 (mtpp) REVERT: b 93 LYS cc_start: 0.8652 (mtmt) cc_final: 0.8435 (mtmt) REVERT: c 35 ASP cc_start: 0.8162 (m-30) cc_final: 0.7906 (p0) REVERT: e 116 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7897 (pm20) REVERT: f 64 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.8048 (mp0) REVERT: f 68 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8031 (tp30) REVERT: k 91 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7079 (pm20) REVERT: k 97 GLN cc_start: 0.7388 (OUTLIER) cc_final: 0.7091 (pm20) REVERT: l 46 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8903 (tp) REVERT: l 111 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8306 (t70) REVERT: l 140 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9022 (tt) REVERT: l 383 MET cc_start: 0.8976 (tpp) cc_final: 0.8768 (tpt) REVERT: l 482 MET cc_start: 0.8247 (ttm) cc_final: 0.7906 (ttm) REVERT: l 518 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.7968 (mt0) REVERT: l 586 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.6893 (mt) REVERT: m 57 PHE cc_start: 0.8370 (OUTLIER) cc_final: 0.8091 (t80) REVERT: m 127 ILE cc_start: 0.6585 (pt) cc_final: 0.6109 (pp) REVERT: p 47 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7442 (ttt90) REVERT: p 62 GLN cc_start: 0.7447 (tp-100) cc_final: 0.7061 (mp10) REVERT: r 114 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.7804 (tm-30) REVERT: v 94 ASP cc_start: 0.8510 (t0) cc_final: 0.8200 (t0) REVERT: v 116 GLU cc_start: 0.6246 (pt0) cc_final: 0.5979 (pt0) outliers start: 192 outliers final: 134 residues processed: 1209 average time/residue: 1.5327 time to fit residues: 2403.4008 Evaluate side-chains 1238 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 1077 time to evaluate : 5.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 30 GLU Chi-restraints excluded: chain I residue 108 LYS Chi-restraints excluded: chain J residue 132 ARG Chi-restraints excluded: chain K residue 74 ARG Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 148 GLU Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 74 ASN Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain M residue 151 SER Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 330 LEU Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 387 LEU Chi-restraints excluded: chain M residue 403 VAL Chi-restraints excluded: chain M residue 487 THR 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 654 VAL Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain M residue 701 SER Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 159 VAL Chi-restraints excluded: chain Q residue 185 MET Chi-restraints excluded: chain Q residue 188 THR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 67 GLU Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain T residue 104 LYS Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 18 VAL Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain V residue 40 SER Chi-restraints excluded: chain V residue 53 VAL Chi-restraints excluded: chain V residue 72 LEU Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 95 CYS Chi-restraints excluded: chain V residue 105 THR Chi-restraints excluded: chain W residue 7 LYS Chi-restraints excluded: chain X residue 88 LYS Chi-restraints excluded: chain X residue 154 VAL Chi-restraints excluded: chain Y residue 59 GLU Chi-restraints excluded: chain Z residue 23 LYS Chi-restraints excluded: chain Z residue 42 ARG Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain b residue 82 ILE Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain e residue 81 ILE Chi-restraints excluded: chain e residue 116 GLU Chi-restraints excluded: chain e residue 137 MET Chi-restraints excluded: chain f residue 64 GLU Chi-restraints excluded: chain i residue 191 THR Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain j residue 13 LEU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 9 ILE Chi-restraints excluded: chain k residue 58 MET Chi-restraints excluded: chain k residue 87 THR Chi-restraints excluded: chain k residue 91 GLN Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 46 LEU Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 136 ASN Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 159 HIS Chi-restraints excluded: chain l residue 186 MET Chi-restraints excluded: chain l residue 252 MET Chi-restraints excluded: chain l residue 314 MET Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 488 MET Chi-restraints excluded: chain l residue 518 GLN Chi-restraints excluded: chain l residue 562 LEU Chi-restraints excluded: chain l residue 586 LEU Chi-restraints excluded: chain m residue 2 THR Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 50 SER Chi-restraints excluded: chain m residue 57 PHE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain p residue 47 ARG Chi-restraints excluded: chain p residue 48 PHE Chi-restraints excluded: chain p residue 171 VAL Chi-restraints excluded: chain r residue 38 SER Chi-restraints excluded: chain r residue 66 LEU Chi-restraints excluded: chain r residue 111 THR Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 122 PHE Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain s residue 57 THR Chi-restraints excluded: chain s residue 59 GLU Chi-restraints excluded: chain s residue 161 THR Chi-restraints excluded: chain s residue 253 GLU Chi-restraints excluded: chain u residue 9 THR Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain u residue 87 THR Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain u residue 114 LYS Chi-restraints excluded: chain v residue 21 ARG Chi-restraints excluded: chain v residue 76 ASN Chi-restraints excluded: chain w residue 44 VAL Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 68 SER Chi-restraints excluded: chain w residue 163 ILE Chi-restraints excluded: chain w residue 164 TYR Chi-restraints excluded: chain w residue 171 GLU Chi-restraints excluded: chain w residue 194 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 499 optimal weight: 5.9990 chunk 670 optimal weight: 6.9990 chunk 192 optimal weight: 2.9990 chunk 580 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 174 optimal weight: 0.9990 chunk 630 optimal weight: 9.9990 chunk 263 optimal weight: 0.0020 chunk 647 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 GLN F 62 GLN H 71 GLN I 29 GLN ** M 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 558 GLN N 12 GLN N 31 ASN O 187 GLN ** Q 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 40 ASN Y 57 GLN ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 145 ASN ** j 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 470 ASN l 541 ASN p 141 GLN r 103 GLN s 47 GLN v 65 GLN ** w 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 202 HIS w 239 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.123110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.099172 restraints weight = 94274.314| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.37 r_work: 0.2949 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2845 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2845 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 68170 Z= 0.219 Angle : 0.566 11.619 92248 Z= 0.285 Chirality : 0.042 0.415 10030 Planarity : 0.005 0.065 11533 Dihedral : 11.795 178.249 10244 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.86 % Favored : 96.08 % Rotamer: Outliers : 2.64 % Allowed : 20.30 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % 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: 8027 helix: 1.44 (0.08), residues: 4247 sheet: 0.28 (0.26), residues: 403 loop : -0.48 (0.11), residues: 3377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP a 110 HIS 0.009 0.001 HIS b 127 PHE 0.031 0.001 PHE i 292 TYR 0.026 0.001 TYR d 32 ARG 0.010 0.000 ARG h 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31619.54 seconds wall clock time: 546 minutes 17.47 seconds (32777.47 seconds total)