Starting phenix.real_space_refine on Fri Feb 16 00:57:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4q_32312/02_2024/7w4q_32312_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4q_32312/02_2024/7w4q_32312.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4q_32312/02_2024/7w4q_32312_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4q_32312/02_2024/7w4q_32312_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4q_32312/02_2024/7w4q_32312_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4q_32312/02_2024/7w4q_32312.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4q_32312/02_2024/7w4q_32312.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4q_32312/02_2024/7w4q_32312_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4q_32312/02_2024/7w4q_32312_updated.pdb" } resolution = 3.3 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 36 5.49 5 Mg 1 5.21 5 S 474 5.16 5 C 43022 2.51 5 N 11090 2.21 5 O 11929 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 38": "OE1" <-> "OE2" Residue "A GLU 129": "OE1" <-> "OE2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A GLU 448": "OE1" <-> "OE2" Residue "B GLU 89": "OE1" <-> "OE2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B GLU 174": "OE1" <-> "OE2" Residue "B GLU 178": "OE1" <-> "OE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "E GLU 34": "OE1" <-> "OE2" Residue "E GLU 65": "OE1" <-> "OE2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 91": "OE1" <-> "OE2" Residue "E GLU 109": "OE1" <-> "OE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "G GLU 129": "OE1" <-> "OE2" Residue "G GLU 143": "OE1" <-> "OE2" Residue "H GLU 18": "OE1" <-> "OE2" Residue "H GLU 54": "OE1" <-> "OE2" Residue "H GLU 62": "OE1" <-> "OE2" Residue "H GLU 70": "OE1" <-> "OE2" Residue "H GLU 78": "OE1" <-> "OE2" Residue "H GLU 85": "OE1" <-> "OE2" Residue "H GLU 105": "OE1" <-> "OE2" Residue "H GLU 106": "OE1" <-> "OE2" Residue "I GLU 62": "OE1" <-> "OE2" Residue "J GLU 107": "OE1" <-> "OE2" Residue "J GLU 121": "OE1" <-> "OE2" Residue "J GLU 162": "OE1" <-> "OE2" Residue "J GLU 197": "OE1" <-> "OE2" Residue "J GLU 210": "OE1" <-> "OE2" Residue "J GLU 320": "OE1" <-> "OE2" Residue "L GLU 105": "OE1" <-> "OE2" Residue "L GLU 108": "OE1" <-> "OE2" Residue "L GLU 132": "OE1" <-> "OE2" Residue "L GLU 148": "OE1" <-> "OE2" Residue "M GLU 67": "OE1" <-> "OE2" Residue "M GLU 81": "OE1" <-> "OE2" Residue "M GLU 118": "OE1" <-> "OE2" Residue "M GLU 155": "OE1" <-> "OE2" Residue "M GLU 217": "OE1" <-> "OE2" Residue "M GLU 249": "OE1" <-> "OE2" Residue "M GLU 269": "OE1" <-> "OE2" Residue "M GLU 283": "OE1" <-> "OE2" Residue "M GLU 310": "OE1" <-> "OE2" Residue "M GLU 395": "OE1" <-> "OE2" Residue "M GLU 535": "OE1" <-> "OE2" Residue "M GLU 628": "OE1" <-> "OE2" Residue "N GLU 67": "OE1" <-> "OE2" Residue "O GLU 46": "OE1" <-> "OE2" Residue "O GLU 64": "OE1" <-> "OE2" Residue "O GLU 150": "OE1" <-> "OE2" Residue "O GLU 194": "OE1" <-> "OE2" Residue "P TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 85": "OE1" <-> "OE2" Residue "P GLU 194": "OE1" <-> "OE2" Residue "P GLU 215": "OE1" <-> "OE2" Residue "Q GLU 42": "OE1" <-> "OE2" Residue "Q GLU 100": "OE1" <-> "OE2" Residue "Q TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 205": "OE1" <-> "OE2" Residue "Q GLU 212": "OE1" <-> "OE2" Residue "Q GLU 246": "OE1" <-> "OE2" Residue "Q GLU 260": "OE1" <-> "OE2" Residue "Q GLU 335": "OE1" <-> "OE2" Residue "Q GLU 370": "OE1" <-> "OE2" Residue "S GLU 35": "OE1" <-> "OE2" Residue "T GLU 36": "OE1" <-> "OE2" Residue "T GLU 73": "OE1" <-> "OE2" Residue "V GLU 82": "OE1" <-> "OE2" Residue "V PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 93": "OE1" <-> "OE2" Residue "W GLU 131": "OE1" <-> "OE2" Residue "W GLU 132": "OE1" <-> "OE2" Residue "X GLU 123": "OE1" <-> "OE2" Residue "X GLU 129": "OE1" <-> "OE2" Residue "X GLU 136": "OE1" <-> "OE2" Residue "Y GLU 95": "OE1" <-> "OE2" Residue "Z GLU 34": "OE1" <-> "OE2" Residue "a GLU 103": "OE1" <-> "OE2" Residue "a GLU 108": "OE1" <-> "OE2" Residue "b GLU 8": "OE1" <-> "OE2" Residue "b GLU 115": "OE1" <-> "OE2" Residue "c GLU 85": "OE1" <-> "OE2" Residue "c GLU 103": "OE1" <-> "OE2" Residue "c GLU 148": "OE1" <-> "OE2" Residue "c GLU 169": "OE1" <-> "OE2" Residue "c GLU 185": "OE1" <-> "OE2" Residue "d GLU 12": "OE1" <-> "OE2" Residue "d GLU 78": "OE1" <-> "OE2" Residue "d GLU 117": "OE1" <-> "OE2" Residue "d GLU 130": "OE1" <-> "OE2" Residue "d GLU 166": "OE1" <-> "OE2" Residue "d GLU 172": "OE1" <-> "OE2" Residue "e GLU 62": "OE1" <-> "OE2" Residue "f GLU 64": "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 "g GLU 117": "OE1" <-> "OE2" Residue "h GLU 24": "OE1" <-> "OE2" Residue "h GLU 53": "OE1" <-> "OE2" Residue "h GLU 65": "OE1" <-> "OE2" Residue "h GLU 89": "OE1" <-> "OE2" Residue "i GLU 318": "OE1" <-> "OE2" Residue "l PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 353": "OE1" <-> "OE2" Residue "l GLU 397": "OE1" <-> "OE2" Residue "n GLU 33": "OE1" <-> "OE2" Residue "n GLU 48": "OE1" <-> "OE2" Residue "o GLU 28": "OE1" <-> "OE2" Residue "p GLU 28": "OE1" <-> "OE2" Residue "p GLU 54": "OE1" <-> "OE2" Residue "p GLU 95": "OE1" <-> "OE2" Residue "p GLU 101": "OE1" <-> "OE2" Residue "p GLU 134": "OE1" <-> "OE2" Residue "p GLU 142": "OE1" <-> "OE2" Residue "p GLU 160": "OE1" <-> "OE2" Residue "p GLU 176": "OE1" <-> "OE2" Residue "r GLU 47": "OE1" <-> "OE2" Residue "r GLU 87": "OE1" <-> "OE2" Residue "r GLU 222": "OE1" <-> "OE2" Residue "r GLU 335": "OE1" <-> "OE2" Residue "r TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 170": "OE1" <-> "OE2" Residue "u GLU 49": "OE1" <-> "OE2" Residue "u GLU 59": "OE1" <-> "OE2" Residue "u TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 139": "OE1" <-> "OE2" Residue "v GLU 16": "OE1" <-> "OE2" Residue "v GLU 33": "OE1" <-> "OE2" Residue "v GLU 36": "OE1" <-> "OE2" Residue "v GLU 83": "OE1" <-> "OE2" Residue "v PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 105": "OE1" <-> "OE2" Residue "w GLU 76": "OE1" <-> "OE2" Residue "w GLU 88": "OE1" <-> "OE2" Residue "w GLU 160": "OE1" <-> "OE2" Residue "w GLU 171": "OE1" <-> "OE2" Residue "w GLU 185": "OE1" <-> "OE2" Residue "w GLU 345": "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: 66581 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: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1248 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "E" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 961 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 108} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 691 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "G" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 693 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 910 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "I" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 11, 'TRANS': 85} Chain breaks: 1 Chain: "J" Number of atoms: 2348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2348 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 280} Chain breaks: 3 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "K" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 355 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 3, 'TRANS': 38} Chain: "L" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1016 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "M" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5296 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 32, 'TRANS': 657} Chain: "N" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1204 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} Chain: "O" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1664 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 195} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1734 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 192} 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: "Q" Number of atoms: 3377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3377 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 27, 'TRANS': 391} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 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: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1011 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 133} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "W" Number of atoms: 1173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1173 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 8, 'TRANS': 133} 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: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 597 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 63} 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: "Z" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 674 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain: "a" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1165 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 10, 'TRANS': 129} Chain: "b" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 879 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 11, 'TRANS': 91} Chain breaks: 1 Chain: "c" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1315 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 20, 'TRANS': 135} Chain: "d" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1461 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 10, 'TRANS': 164} Chain: "e" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 890 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 10, 'TRANS': 96} Chain: "f" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 342 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 40} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "g" Number of atoms: 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: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 847 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 97} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "i" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2710 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 328} Chain: "j" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 800 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 Chain: "k" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 748 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "l" Number of atoms: 4781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4781 Classifications: {'peptide': 603} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 574} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 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: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 479 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "o" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1062 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 11, 'TRANS': 116} Chain: "p" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1520 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 160} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "r" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3630 Classifications: {'peptide': 459} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 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: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1386 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 158} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "v" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1028 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "w" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2582 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'PEE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'PEE': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: "I" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 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: "N" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} 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: "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: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 291 Unusual residues: {'CDL': 2, 'PEE': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "m" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "r" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 255 Unusual residues: {'CDL': 1, 'PEE': 1, 'PLX': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "s" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {' UQ': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {' UQ:plan-11': 1, ' UQ:plan-2': 1, ' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 35 Chain: "w" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2706 SG CYS A 382 48.008 50.254 171.353 1.00 31.31 S ATOM 3048 SG CYS A 425 47.277 46.247 176.540 1.00 48.35 S ATOM 2726 SG CYS A 385 44.803 45.505 170.884 1.00 31.31 S ATOM 2687 SG CYS A 379 42.543 50.323 174.998 1.00 33.90 S ATOM 3949 SG CYS B 113 37.118 67.974 137.440 1.00 24.93 S ATOM 3968 SG CYS B 116 42.259 65.250 141.149 1.00 26.64 S ATOM 3991 SG CYS B 119 43.213 68.218 135.767 1.00 18.47 S ATOM 4320 SG CYS B 162 40.431 62.464 136.204 1.00 39.03 S ATOM 4018 SG CYS B 123 49.389 71.295 131.447 1.00 32.19 S ATOM 4244 SG CYS B 152 47.556 69.752 125.498 1.00 30.29 S ATOM 4291 SG CYS B 158 45.467 65.905 129.966 1.00 3.37 S ATOM 4270 SG CYS B 155 51.649 66.129 128.600 1.00 26.97 S ATOM 5712 SG CYS C 166 53.811 69.827 121.254 1.00 13.67 S ATOM 4984 SG CYS C 72 55.051 71.662 115.007 1.00 0.00 S ATOM 4978 SG CYS C 71 59.201 70.121 117.400 1.00 24.15 S ATOM 5482 SG CYS C 136 56.521 74.555 119.921 1.00 32.58 S ATOM 14517 SG CYS M 131 41.555 64.804 153.193 1.00 27.73 S ATOM 14496 SG CYS M 128 44.972 60.314 149.808 1.00 12.54 S ATOM 14557 SG CYS M 137 47.115 63.460 155.170 1.00 15.12 S ATOM 14889 SG CYS M 179 45.377 62.965 166.248 1.00 24.10 S ATOM 15243 SG CYS M 226 42.411 65.817 162.065 1.00 31.22 S ATOM 14913 SG CYS M 182 39.947 65.695 168.148 1.00 19.88 S ATOM 14866 SG CYS M 176 39.749 60.294 164.422 1.00 26.92 S ATOM 14114 SG CYS M 78 57.000 57.851 169.853 1.00 41.34 S ATOM 14215 SG CYS M 92 55.186 59.724 172.246 1.00 25.30 S ATOM 14003 SG CYS M 64 50.907 59.866 169.767 1.00 36.50 S ATOM 14089 SG CYS M 75 51.849 58.303 166.642 1.00 17.34 S ATOM 21052 SG CYS O 135 31.443 32.495 178.655 1.00 82.49 S ATOM 21086 SG CYS O 140 31.139 28.951 179.183 1.00 88.87 S ATOM 21359 SG CYS O 176 35.869 33.980 181.294 1.00 76.93 S ATOM 21382 SG CYS O 180 35.694 30.335 180.903 1.00 93.07 S ATOM 28036 SG CYS T 86 29.511 54.425 144.608 1.00 19.65 S ATOM 28214 SG CYS T 111 30.509 57.568 145.760 1.00 25.75 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: 26.08, per 1000 atoms: 0.39 Number of scatterers: 66581 At special positions: 0 Unit cell: (214.09, 229.461, 226.167, 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 474 16.00 P 36 15.00 Mg 1 11.99 O 11929 8.00 N 11090 7.00 C 43022 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 d 113 " - pdb=" SG CYS d 125 " distance=2.03 Simple disulfide: pdb=" SG CYS h 33 " - pdb=" SG CYS h 66 " distance=2.03 Simple disulfide: pdb=" SG CYS h 43 " - pdb=" SG CYS h 56 " distance=2.03 Simple disulfide: pdb=" SG CYS u 88 " - pdb=" SG CYS u 100 " distance=1.98 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 19.88 Conformation dependent library (CDL) restraints added in 8.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 92 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 64 " pdb=" FES O 301 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 180 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 140 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 135 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb=" SF4 A 501 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb=" SF4 B 301 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 116 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " 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="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " pdb="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " pdb="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " Number of angles added : 83 Zn2+ tetrahedral coordination pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 111 " pdb="ZN ZN T 201 " - pdb=" NE2 HIS T 95 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 86 " 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 28 sheets defined 52.9% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.61 Creating SS restraints... Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 73 through 82 Processing helix chain 'A' and resid 95 through 103 removed outlier: 3.614A 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 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 329 through 334 removed outlier: 5.056A pdb=" N THR A 334 " --> pdb=" O SER A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 363 through 377 Processing helix chain 'A' and resid 383 through 401 removed outlier: 3.809A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 419 removed outlier: 4.075A pdb=" N ASP A 410 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 457 Proline residue: A 434 - end of helix Proline residue: A 444 - end of helix Processing helix chain 'B' and resid 50 through 62 Processing helix chain 'B' and resid 64 through 78 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: 5.745A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N LEU B 210 " --> pdb=" O GLN B 206 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N TYR B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 59 removed outlier: 3.671A 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 111 through 123 Proline residue: C 115 - end of helix 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 69 Processing helix chain 'E' and resid 76 through 94 Processing helix chain 'E' and resid 100 through 106 removed outlier: 4.469A pdb=" N PHE E 106 " --> pdb=" O HIS E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 124 Processing helix chain 'F' and resid 28 through 47 removed outlier: 4.785A pdb=" N GLY F 32 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N TYR F 41 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL F 42 " --> pdb=" O LYS F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 72 No H-bonds generated for 'chain 'F' and resid 70 through 72' Processing helix chain 'F' and resid 84 through 96 Processing helix chain 'G' and resid 76 through 89 Processing helix chain 'G' and resid 104 through 107 No H-bonds generated for 'chain 'G' and resid 104 through 107' 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: 4.041A 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 74 removed outlier: 4.141A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 97 Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 113 through 119 Processing helix chain 'J' and resid 141 through 145 Processing helix chain 'J' and resid 147 through 159 Processing helix chain 'J' and resid 179 through 194 Processing helix chain 'J' and resid 213 through 219 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 335 through 338 No H-bonds generated for 'chain 'J' and resid 335 through 338' Processing helix chain 'J' and resid 345 through 356 removed outlier: 4.746A pdb=" N ILE J 350 " --> pdb=" O GLU J 346 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLU J 351 " --> pdb=" O LEU J 347 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ARG J 355 " --> pdb=" O GLU J 351 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N HIS J 356 " --> pdb=" O VAL J 352 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 80 removed outlier: 3.847A 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: 4.377A pdb=" N LYS K 95 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N PHE K 96 " --> pdb=" O GLU K 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 71 No H-bonds generated for 'chain 'L' and resid 69 through 71' Processing helix chain 'L' and resid 131 through 140 Processing helix chain 'L' and resid 160 through 164 removed outlier: 3.512A pdb=" N ASN L 163 " --> pdb=" O TYR L 160 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 56 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: 3.621A pdb=" N ILE M 222 " --> pdb=" O SER M 219 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE M 225 " --> pdb=" O ILE M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 298 removed outlier: 4.986A pdb=" N TYR M 294 " --> pdb=" O THR M 290 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ASP M 295 " --> pdb=" O ARG M 291 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N GLY M 296 " --> pdb=" O PHE M 292 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU M 297 " --> pdb=" O ALA M 293 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYS M 298 " --> pdb=" O TYR M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 319 through 332 removed outlier: 3.795A 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 382 through 385 Processing helix chain 'M' and resid 390 through 395 removed outlier: 3.802A pdb=" N VAL M 394 " --> pdb=" O THR M 390 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLU M 395 " --> pdb=" O ILE M 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 390 through 395' Processing helix chain 'M' and resid 407 through 410 No H-bonds generated for 'chain 'M' and resid 407 through 410' Processing helix chain 'M' and resid 412 through 424 Processing helix chain 'M' and resid 449 through 457 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 528 Processing helix chain 'M' and resid 535 through 539 Processing helix chain 'M' and resid 557 through 559 No H-bonds generated for 'chain 'M' and resid 557 through 559' Processing helix chain 'M' and resid 619 through 629 Processing helix chain 'M' and resid 639 through 649 Processing helix chain 'M' and resid 665 through 671 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: 3.804A pdb=" N HIS N 17 " --> pdb=" O GLN N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 30 Processing helix chain 'N' and resid 79 through 81 No H-bonds generated for 'chain 'N' and resid 79 through 81' Processing helix chain 'N' and resid 84 through 90 Processing helix chain 'O' and resid 57 through 68 Processing helix chain 'O' and resid 75 through 90 removed outlier: 4.362A pdb=" N LEU O 80 " --> pdb=" O ALA O 77 " (cutoff:3.500A) Proline residue: O 81 - end of helix Processing helix chain 'O' and resid 95 through 105 Processing helix chain 'O' and resid 109 through 118 Processing helix chain 'O' and resid 138 through 142 Processing helix chain 'O' and resid 146 through 156 Processing helix chain 'O' and resid 180 through 182 No H-bonds generated for 'chain 'O' and resid 180 through 182' Processing helix chain 'O' and resid 198 through 210 Processing helix chain 'P' and resid 52 through 68 Processing helix chain 'P' and resid 90 through 102 removed outlier: 3.667A pdb=" N VAL P 93 " --> pdb=" O PRO P 90 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ILE P 94 " --> pdb=" O ASP P 91 " (cutoff:3.500A) Proline residue: P 95 - end of helix Processing helix chain 'P' and resid 161 through 173 removed outlier: 3.613A pdb=" N ASN P 164 " --> pdb=" O LYS P 161 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TRP P 165 " --> pdb=" O ALA P 162 " (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 47 removed outlier: 4.332A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N PHE Q 47 " --> pdb=" O TRP Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 120 through 126 removed outlier: 3.775A pdb=" N GLU Q 125 " --> pdb=" O GLU Q 121 " (cutoff:3.500A) removed outlier: 4.132A 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: 4.065A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG Q 138 " --> pdb=" O PRO Q 134 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 159 Processing helix chain 'Q' and resid 165 through 194 Processing helix chain 'Q' and resid 198 through 218 removed outlier: 4.160A 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: 4.243A 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: 4.348A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N LYS Q 437 " --> pdb=" O ALA Q 433 " (cutoff:3.500A) Processing helix chain 'Q' and resid 444 through 454 removed outlier: 3.843A pdb=" N VAL Q 448 " --> pdb=" O ALA Q 445 " (cutoff:3.500A) Processing helix chain 'Q' and resid 458 through 462 Processing helix chain 'S' and resid 2 through 30 Proline residue: S 7 - end of helix Proline residue: S 19 - end of helix removed outlier: 4.125A pdb=" N THR S 30 " --> pdb=" O HIS S 27 " (cutoff:3.500A) 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 4 through 11 Processing helix chain 'V' and resid 18 through 43 Processing helix chain 'V' and resid 49 through 81 Processing helix chain 'V' and resid 87 through 105 Processing helix chain 'V' and resid 108 through 131 removed outlier: 3.630A pdb=" N ALA V 116 " --> pdb=" O ALA V 112 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR V 117 " --> pdb=" O ALA V 113 " (cutoff:3.500A) removed outlier: 3.819A 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 124 No H-bonds generated for 'chain 'W' and resid 121 through 124' Processing helix chain 'W' and resid 130 through 142 removed outlier: 6.335A pdb=" N PHE W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ILE W 141 " --> pdb=" O THR W 137 " (cutoff:3.500A) Processing helix chain 'X' and resid 76 through 89 Processing helix chain 'X' and resid 112 through 126 Processing helix chain 'X' and resid 132 through 135 No H-bonds generated for 'chain 'X' and resid 132 through 135' Processing helix chain 'X' and resid 141 through 152 Processing helix chain 'Y' and resid 52 through 75 Processing helix chain 'Y' and resid 78 through 81 No H-bonds generated for 'chain 'Y' and resid 78 through 81' Processing helix chain 'Y' and resid 89 through 91 No H-bonds generated for 'chain 'Y' and resid 89 through 91' Processing helix chain 'Z' and resid 19 through 21 No H-bonds generated for 'chain 'Z' and resid 19 through 21' Processing helix chain 'Z' and resid 28 through 39 removed outlier: 3.599A pdb=" N ARG Z 39 " --> pdb=" O LYS Z 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 46 through 53 removed outlier: 3.610A pdb=" N GLU Z 49 " --> pdb=" O GLY Z 46 " (cutoff:3.500A) removed outlier: 4.307A 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: 3.833A 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 'c' and resid 174 through 176 No H-bonds generated for 'chain 'c' and resid 174 through 176' Processing helix chain 'd' and resid 29 through 58 removed outlier: 4.584A 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: 4.108A pdb=" N GLY d 118 " --> pdb=" O GLN d 114 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLU d 119 " --> pdb=" O GLN d 115 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N SER d 120 " --> pdb=" O ARG d 116 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N TYR d 121 " --> pdb=" O GLU d 117 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ARG d 122 " --> pdb=" O GLY d 118 " (cutoff:3.500A) removed outlier: 6.511A 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 94 Processing helix chain 'e' and resid 98 through 107 removed outlier: 4.017A pdb=" N SER e 103 " --> pdb=" O LEU e 99 " (cutoff:3.500A) 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 18 through 22 Processing helix chain 'g' and resid 31 through 50 Processing helix chain 'g' and resid 60 through 98 Processing helix chain 'g' and resid 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 'h' and resid 96 through 99 No H-bonds generated for 'chain 'h' and resid 96 through 99' Processing helix chain 'i' and resid 3 through 22 Processing helix chain 'i' and resid 26 through 44 removed outlier: 3.610A pdb=" N ILE i 41 " --> pdb=" O LEU i 37 " (cutoff:3.500A) Proline residue: i 42 - end of helix Processing helix chain 'i' and resid 50 through 80 Processing helix chain 'i' and resid 92 through 106 Processing helix chain 'i' and resid 113 through 121 removed outlier: 4.363A 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: 5.467A pdb=" N LYS i 135 " --> pdb=" O LEU i 131 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LEU i 136 " --> pdb=" O THR i 132 " (cutoff:3.500A) removed outlier: 4.880A 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 151 through 171 removed outlier: 4.016A pdb=" N LEU i 170 " --> pdb=" O GLY i 166 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASN i 171 " --> pdb=" O TRP i 167 " (cutoff:3.500A) Processing helix chain 'i' and resid 175 through 193 removed outlier: 4.028A 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 235 removed outlier: 3.737A pdb=" N HIS i 232 " --> pdb=" O LEU i 228 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N THR i 233 " --> pdb=" O SER i 229 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N TRP i 234 " --> pdb=" O LEU i 230 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ASN i 235 " --> pdb=" O SER i 231 " (cutoff:3.500A) Processing helix chain 'i' and resid 238 through 251 Processing helix chain 'i' and resid 258 through 273 Proline residue: i 262 - end of helix Processing helix chain 'i' and resid 277 through 300 removed outlier: 4.279A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) Processing helix chain 'i' and resid 309 through 316 removed outlier: 3.563A pdb=" N MET i 313 " --> pdb=" O ASN i 310 " (cutoff:3.500A) Processing helix chain 'i' and resid 326 through 334 Processing helix chain 'i' and resid 337 through 345 Proline residue: i 341 - end of helix Processing helix chain 'j' and resid 2 through 26 Proline residue: j 25 - end of helix Processing helix chain 'j' and resid 53 through 78 Proline residue: j 74 - end of helix removed outlier: 5.965A pdb=" N TRP j 77 " --> pdb=" O LEU j 73 " (cutoff:3.500A) Processing helix chain 'j' and resid 84 through 107 Processing helix chain 'k' and resid 3 through 21 Processing helix chain 'k' and resid 26 through 50 Processing helix chain 'k' and resid 55 through 85 removed outlier: 3.845A 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: 3.810A pdb=" N LEU l 9 " --> pdb=" O ALA l 5 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR l 16 " --> pdb=" O LEU l 12 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE l 17 " --> pdb=" O THR l 13 " (cutoff:3.500A) Proline residue: l 18 - end of helix removed outlier: 4.848A 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 56 removed outlier: 4.379A 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: 3.813A 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: 3.906A 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 231 through 238 removed outlier: 4.125A pdb=" N MET l 237 " --> pdb=" O LEU l 233 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N GLU l 238 " --> pdb=" O PRO l 234 " (cutoff:3.500A) Processing helix chain 'l' and resid 241 through 250 removed outlier: 3.595A pdb=" N HIS l 248 " --> pdb=" O SER l 244 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER l 249 " --> pdb=" O ALA l 245 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER l 250 " --> pdb=" O LEU l 246 " (cutoff:3.500A) Processing helix chain 'l' and resid 253 through 262 removed outlier: 4.269A pdb=" N GLY l 256 " --> pdb=" O VAL l 253 " (cutoff:3.500A) Processing helix chain 'l' and resid 264 through 269 removed outlier: 4.204A pdb=" N THR l 269 " --> pdb=" O PRO l 265 " (cutoff:3.500A) Processing helix chain 'l' and resid 271 through 294 removed outlier: 4.440A pdb=" N THR l 294 " --> pdb=" O LEU l 290 " (cutoff:3.500A) Processing helix chain 'l' and resid 298 through 319 Processing helix chain 'l' and resid 322 through 349 removed outlier: 3.652A 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: 4.494A 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: 3.665A pdb=" N LEU l 457 " --> pdb=" O SER l 453 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.317A 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: 3.596A pdb=" N THR l 507 " --> pdb=" O GLU l 503 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N THR l 508 " --> pdb=" O LEU l 504 " (cutoff:3.500A) removed outlier: 4.712A 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: 4.256A pdb=" N MET l 533 " --> pdb=" O PRO l 530 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LEU l 536 " --> pdb=" O MET l 533 " (cutoff:3.500A) Proline residue: l 537 - end of helix removed outlier: 4.923A pdb=" N SER l 543 " --> pdb=" O HIS l 540 " (cutoff:3.500A) Processing helix chain 'l' and resid 557 through 561 Processing helix chain 'l' and resid 563 through 578 Processing helix chain 'l' and resid 584 through 601 Processing helix chain 'm' and resid 5 through 21 Processing helix chain 'm' and resid 26 through 47 Processing helix chain 'm' and resid 50 through 74 removed outlier: 3.887A pdb=" N LEU m 61 " --> pdb=" O PHE m 57 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU m 65 " --> pdb=" O LEU m 61 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL m 66 " --> pdb=" O GLY m 62 " (cutoff:3.500A) Processing helix chain 'm' and resid 138 through 146 removed outlier: 4.200A 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: 6.559A pdb=" N VAL n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N HIS n 14 " --> pdb=" O ASP n 10 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE n 15 " --> pdb=" O HIS n 11 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU n 16 " --> pdb=" O TRP n 12 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL n 17 " --> pdb=" O VAL n 13 " (cutoff:3.500A) Proline residue: n 18 - end of helix removed outlier: 4.044A 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 20 through 23 No H-bonds generated for 'chain 'o' and resid 20 through 23' Processing helix chain 'o' and resid 27 through 51 Processing helix chain 'o' and resid 63 through 73 Processing helix chain 'o' and resid 84 through 118 Proline residue: o 97 - end of helix Processing helix chain 'p' and resid 12 through 30 Processing helix chain 'p' and resid 34 through 51 removed outlier: 3.685A pdb=" N GLU p 50 " --> pdb=" O ALA p 46 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N HIS p 51 " --> pdb=" O ARG p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 57 through 62 Processing helix chain 'p' and resid 66 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: 3.745A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 4.097A 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 16 Proline residue: r 7 - end of helix removed outlier: 4.203A pdb=" N LEU r 12 " --> pdb=" O THR r 8 " (cutoff:3.500A) Proline residue: r 13 - end of helix Processing helix chain 'r' and resid 23 through 42 removed outlier: 4.177A pdb=" N SER r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LEU r 42 " --> pdb=" O SER r 38 " (cutoff:3.500A) Processing helix chain 'r' and resid 62 through 83 removed outlier: 3.873A pdb=" N LEU r 73 " --> pdb=" O THR r 69 " (cutoff:3.500A) Proline residue: r 74 - end of helix removed outlier: 4.543A pdb=" N SER r 82 " --> pdb=" O MET r 78 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N HIS r 83 " --> pdb=" O ALA r 79 " (cutoff:3.500A) Processing helix chain 'r' and resid 89 through 111 removed outlier: 3.618A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 115 through 135 removed outlier: 4.657A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.400A 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: 4.112A pdb=" N LEU r 143 " --> pdb=" O THR r 140 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA r 145 " --> pdb=" O ARG r 142 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TYR r 152 " --> pdb=" O PHE r 149 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA r 155 " --> pdb=" O TYR r 152 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU r 158 " --> pdb=" O ALA r 155 " (cutoff:3.500A) Proline residue: r 159 - end of helix removed outlier: 4.024A 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 206 removed outlier: 4.190A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS r 206 " --> pdb=" O ALA r 202 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 222 removed outlier: 4.005A 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 237 through 246 Processing helix chain 'r' and resid 253 through 257 removed outlier: 3.982A pdb=" N MET r 257 " --> pdb=" O THR r 254 " (cutoff:3.500A) Processing helix chain 'r' and resid 259 through 277 removed outlier: 4.159A pdb=" N ILE r 270 " --> pdb=" O MET r 266 " (cutoff:3.500A) removed outlier: 3.543A 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: 3.729A pdb=" N ARG r 336 " --> pdb=" O THR r 332 " (cutoff:3.500A) Processing helix chain 'r' and resid 348 through 351 No H-bonds generated for 'chain 'r' and resid 348 through 351' Processing helix chain 'r' and resid 353 through 366 Processing helix chain 'r' and resid 373 through 388 Processing helix chain 'r' and resid 392 through 415 removed outlier: 3.962A pdb=" N THR r 414 " --> pdb=" O MET r 410 " (cutoff:3.500A) Processing helix chain 'r' and resid 431 through 449 Proline residue: r 443 - end of helix removed outlier: 4.236A 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: 3.838A pdb=" N THR s 21 " --> pdb=" O VAL s 17 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU s 22 " --> pdb=" O ALA s 18 " (cutoff:3.500A) Processing helix chain 's' and resid 47 through 57 Processing helix chain 's' and resid 68 through 86 Proline residue: s 75 - end of helix removed outlier: 4.225A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 123 removed outlier: 4.246A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 156 removed outlier: 3.966A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 168 removed outlier: 3.561A pdb=" N THR s 168 " --> pdb=" O LEU s 165 " (cutoff:3.500A) Processing helix chain 's' and resid 174 through 177 No H-bonds generated for 'chain 's' and resid 174 through 177' Processing helix chain 's' and resid 179 through 192 Processing helix chain 's' and resid 218 through 242 Processing helix chain 's' and resid 252 through 276 Processing helix chain 's' and resid 282 through 311 removed outlier: 5.134A 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 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 Processing helix chain 'u' and resid 79 through 91 Processing helix chain 'u' and resid 98 through 114 removed outlier: 3.989A pdb=" N ARG u 101 " --> pdb=" O ARG u 98 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LYS u 102 " --> pdb=" O HIS u 99 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN u 103 " --> pdb=" O CYS u 100 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP u 108 " --> pdb=" O ALA u 105 " (cutoff:3.500A) Processing helix chain 'v' and resid 3 through 9 Processing helix chain 'v' and resid 13 through 15 No H-bonds generated for 'chain 'v' and resid 13 through 15' Processing helix chain 'v' and resid 27 through 29 No H-bonds generated for 'chain 'v' and resid 27 through 29' Processing helix chain 'v' and resid 43 through 49 Processing helix chain 'v' and resid 60 through 72 Processing helix chain 'v' and resid 82 through 124 Processing helix chain 'w' and resid 40 through 45 Processing helix chain 'w' and resid 49 through 51 No H-bonds generated for 'chain 'w' and resid 49 through 51' Processing helix chain 'w' and resid 70 through 81 Processing helix chain 'w' and resid 94 through 97 No H-bonds generated for 'chain 'w' and resid 94 through 97' 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: 5.055A 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 250 removed outlier: 4.681A pdb=" N LEU w 246 " --> pdb=" O LYS w 242 " (cutoff:3.500A) Proline residue: w 247 - end of helix Processing helix chain 'w' and resid 266 through 275 Processing helix chain 'w' and resid 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: 3.895A pdb=" N THR w 309 " --> pdb=" O ASN w 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 306 through 309' Processing helix chain 'w' and resid 321 through 332 Processing helix chain 'w' and resid 352 through 354 No H-bonds generated for 'chain 'w' and resid 352 through 354' Processing sheet with id= A, first strand: chain 'A' and resid 240 through 244 removed outlier: 7.576A pdb=" N TYR A 112 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N ALA A 243 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL A 114 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ALA A 153 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL A 115 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TYR A 155 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ALA A 117 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TYR A 157 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ASP A 194 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ILE A 156 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N PHE A 196 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ILE A 158 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL A 198 " --> pdb=" O ILE A 158 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 286 through 291 Processing sheet with id= C, first strand: chain 'B' and resid 101 through 103 Processing sheet with id= D, first strand: chain 'B' and resid 128 through 134 removed outlier: 6.085A pdb=" N GLU B 133 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 5.388A 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: 6.522A pdb=" N VAL C 102 " --> pdb=" O MET C 65 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N PHE C 67 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE C 104 " --> pdb=" O PHE C 67 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N TYR C 129 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N VAL C 105 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL C 131 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.348A 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: 3.855A 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: 6.589A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE J 167 " --> pdb=" O ASN J 128 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLN J 79 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N VAL J 58 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.762A 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 169 through 171 Processing sheet with id= L, first strand: chain 'M' and resid 196 through 198 Processing sheet with id= M, first strand: chain 'M' and resid 246 through 251 Processing sheet with id= N, first strand: chain 'M' and resid 306 through 308 Processing sheet with id= O, first strand: chain 'M' and resid 366 through 368 removed outlier: 8.630A pdb=" N CYS M 367 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ALA M 340 " --> pdb=" O CYS M 367 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL M 544 " --> pdb=" O ALA M 339 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ILE M 341 " --> pdb=" O VAL M 544 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N PHE M 546 " --> pdb=" O ILE M 341 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N PHE M 565 " --> pdb=" O LEU M 545 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N LEU M 547 " --> pdb=" O PHE M 565 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE M 567 " --> pdb=" O LEU M 547 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL M 582 " --> pdb=" O TYR M 568 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N GLY M 570 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LEU M 584 " --> pdb=" O GLY M 570 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'M' and resid 513 through 516 removed outlier: 8.189A pdb=" N ASN M 514 " --> pdb=" O PRO M 472 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL M 399 " --> pdb=" O MET M 473 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS M 428 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N LEU M 402 " --> pdb=" O LYS M 428 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA M 430 " --> pdb=" O LEU M 402 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP M 443 " --> pdb=" O LEU M 431 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'M' and resid 595 through 597 Processing sheet with id= R, first strand: chain 'N' and resid 60 through 63 removed outlier: 6.229A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU N 38 " --> pdb=" O GLU N 50 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'O' and resid 169 through 174 removed outlier: 6.672A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N VAL O 134 " --> pdb=" O VAL O 174 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N CYS O 135 " --> pdb=" O MET O 185 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N MET O 185 " --> pdb=" O CYS O 135 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'P' and resid 110 through 118 removed outlier: 6.733A pdb=" N ASN P 131 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU P 114 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL P 129 " --> pdb=" O LEU P 114 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA P 116 " --> pdb=" O GLU P 127 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLU P 127 " --> pdb=" O ALA P 116 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU P 84 " --> pdb=" O ARG P 142 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N LYS P 144 " --> pdb=" O LEU P 84 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE P 86 " --> pdb=" O LYS P 144 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N TYR P 146 " --> pdb=" O ILE P 86 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N ILE P 88 " --> pdb=" O TYR P 146 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'P' and resid 208 through 213 Processing sheet with id= V, first strand: chain 'Q' and resid 80 through 84 removed outlier: 3.752A pdb=" N ARG Q 96 " --> pdb=" O HIS Q 112 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N VAL Q 106 " --> pdb=" O SER Q 102 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'Q' and resid 394 through 402 Processing sheet with id= X, first strand: chain 'T' and resid 83 through 86 Processing sheet with id= Y, first strand: chain 'l' and resid 69 through 71 Processing sheet with id= Z, first strand: chain 'l' and resid 62 through 67 removed outlier: 6.540A pdb=" N LEU l 78 " --> pdb=" O ASN l 65 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'w' and resid 60 through 64 removed outlier: 6.802A pdb=" N VAL w 203 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ASP w 63 " --> pdb=" O VAL w 203 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL w 205 " --> pdb=" O ASP w 63 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLU w 254 " --> pdb=" O VAL w 204 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N TYR w 206 " --> pdb=" O GLU w 254 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU w 256 " --> pdb=" O TYR w 206 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASP w 208 " --> pdb=" O LEU w 256 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TYR w 258 " --> pdb=" O ASP w 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'w' and resid 84 through 86 2910 hydrogen bonds defined for protein. 8079 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: 21.34 Time building geometry restraints manager: 22.00 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: 27259 1.40 - 1.62: 40051 1.62 - 1.85: 840 1.85 - 2.07: 0 2.07 - 2.29: 80 Bond restraints: 68230 Sorted by residual: bond pdb=" C3D NAI A 503 " pdb=" C4D NAI A 503 " ideal model delta sigma weight residual 1.524 1.263 0.261 2.00e-02 2.50e+03 1.70e+02 bond pdb=" C1D NAI A 503 " pdb=" C2D NAI A 503 " ideal model delta sigma weight residual 1.528 1.292 0.236 2.00e-02 2.50e+03 1.39e+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 1.39e+02 bond pdb=" C1B NAI A 503 " pdb=" C2B NAI A 503 " ideal model delta sigma weight residual 1.528 1.300 0.228 2.00e-02 2.50e+03 1.30e+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 68225 not shown) Histogram of bond angle deviations from ideal: 73.61 - 86.02: 76 86.02 - 98.43: 0 98.43 - 110.84: 24201 110.84 - 123.25: 65369 123.25 - 135.66: 2673 Bond angle restraints: 92319 Sorted by residual: angle pdb=" N HIS u 77 " pdb=" CA HIS u 77 " pdb=" C HIS u 77 " ideal model delta sigma weight residual 111.14 122.22 -11.08 1.08e+00 8.57e-01 1.05e+02 angle pdb=" N HIS Q 233 " pdb=" CA HIS Q 233 " pdb=" C HIS Q 233 " ideal model delta sigma weight residual 111.28 122.44 -11.16 1.09e+00 8.42e-01 1.05e+02 angle pdb=" C ASP h 103 " pdb=" N PRO h 104 " pdb=" CA PRO h 104 " ideal model delta sigma weight residual 120.31 128.81 -8.50 9.80e-01 1.04e+00 7.52e+01 angle pdb=" PA NDP J 401 " pdb=" O3 NDP J 401 " pdb=" PN NDP J 401 " ideal model delta sigma weight residual 107.74 123.67 -15.93 1.95e+00 2.62e-01 6.64e+01 angle pdb=" C5B NDP J 401 " pdb=" O5B NDP J 401 " pdb=" PA NDP J 401 " ideal model delta sigma weight residual 103.84 119.23 -15.39 1.91e+00 2.73e-01 6.46e+01 ... (remaining 92314 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 39832 35.78 - 71.56: 1462 71.56 - 107.35: 110 107.35 - 143.13: 29 143.13 - 178.91: 11 Dihedral angle restraints: 41444 sinusoidal: 17743 harmonic: 23701 Sorted by residual: dihedral pdb=" CB CYS u 88 " pdb=" SG CYS u 88 " pdb=" SG CYS u 100 " pdb=" CB CYS u 100 " ideal model delta sinusoidal sigma weight residual 93.00 15.50 77.50 1 1.00e+01 1.00e-02 7.52e+01 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 79.03 178.57 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 98.08 -158.07 1 2.00e+01 2.50e-03 4.63e+01 ... (remaining 41441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 9619 0.095 - 0.191: 386 0.191 - 0.286: 21 0.286 - 0.381: 4 0.381 - 0.476: 2 Chirality restraints: 10032 Sorted by residual: chirality pdb=" CA GLN Q 234 " pdb=" N GLN Q 234 " pdb=" C GLN Q 234 " pdb=" CB GLN Q 234 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.67e+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 -2.36 -0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CA HIS u 77 " pdb=" N HIS u 77 " pdb=" C HIS u 77 " pdb=" CB HIS u 77 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.46e+00 ... (remaining 10029 not shown) Planarity restraints: 11542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 UQ s 402 " 0.215 2.00e-02 2.50e+03 4.83e-01 2.92e+03 pdb=" C11 UQ s 402 " 0.346 2.00e-02 2.50e+03 pdb=" C7 UQ s 402 " 0.568 2.00e-02 2.50e+03 pdb=" C8 UQ s 402 " -0.707 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 " -0.445 2.00e-02 2.50e+03 3.94e-01 1.95e+03 pdb=" C18 UQ s 402 " 0.482 2.00e-02 2.50e+03 pdb=" C19 UQ s 402 " 0.411 2.00e-02 2.50e+03 pdb=" C20 UQ s 402 " -0.024 2.00e-02 2.50e+03 pdb=" C21 UQ s 402 " -0.423 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP J 401 " 0.151 2.00e-02 2.50e+03 2.63e-01 8.61e+02 pdb=" C3N NDP J 401 " 0.423 2.00e-02 2.50e+03 pdb=" C4N NDP J 401 " -0.050 2.00e-02 2.50e+03 pdb=" C7N NDP J 401 " -0.301 2.00e-02 2.50e+03 pdb=" N1N NDP J 401 " -0.223 2.00e-02 2.50e+03 ... (remaining 11539 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 1064 2.67 - 3.23: 63241 3.23 - 3.79: 105235 3.79 - 4.34: 145665 4.34 - 4.90: 239919 Nonbonded interactions: 555124 Sorted by model distance: nonbonded pdb=" OG1 THR r 414 " pdb=" OE1 GLN r 415 " model vdw 2.115 2.440 nonbonded pdb=" N ASP O 166 " pdb=" OD1 ASP O 166 " model vdw 2.132 2.520 nonbonded pdb=" OH TYR w 118 " pdb=" O2' ADP w 401 " model vdw 2.197 2.440 nonbonded pdb=" O ILE b 69 " pdb=" OG1 THR b 73 " model vdw 2.202 2.440 nonbonded pdb=" OE2 GLU S 35 " pdb=" OH TYR s 93 " model vdw 2.202 2.440 ... (remaining 555119 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: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 8.300 Check model and map are aligned: 0.740 Set scattering table: 0.470 Process input model: 154.000 Find NCS groups from input model: 2.170 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 170.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.314 68230 Z= 0.433 Angle : 0.781 17.007 92319 Z= 0.410 Chirality : 0.043 0.476 10032 Planarity : 0.009 0.483 11542 Dihedral : 18.227 178.909 26140 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.96 % Favored : 96.01 % Rotamer: Outliers : 0.36 % Allowed : 15.76 % Favored : 83.88 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 2.85 % Cis-general : 0.00 % Twisted Proline : 0.20 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.09), residues: 8027 helix: 1.56 (0.08), residues: 4240 sheet: 0.24 (0.26), residues: 405 loop : -0.51 (0.11), residues: 3382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 75 HIS 0.009 0.001 HIS J 37 PHE 0.029 0.001 PHE i 292 TYR 0.030 0.001 TYR l 422 ARG 0.023 0.000 ARG n 30 *********************** 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 1245 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 1220 time to evaluate : 5.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 THR cc_start: 0.7323 (m) cc_final: 0.6816 (p) REVERT: B 44 ARG cc_start: 0.8530 (mmm-85) cc_final: 0.8267 (mmm160) REVERT: C 79 MET cc_start: 0.9064 (ttp) cc_final: 0.8778 (ttt) REVERT: H 96 ARG cc_start: 0.7093 (mmm160) cc_final: 0.6840 (mtp-110) REVERT: N 44 TYR cc_start: 0.8749 (m-80) cc_final: 0.8540 (m-80) REVERT: P 183 ASP cc_start: 0.7682 (p0) cc_final: 0.7150 (t70) REVERT: Q 46 GLN cc_start: 0.7303 (pt0) cc_final: 0.6955 (pt0) REVERT: Q 144 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8403 (mpp) REVERT: V 118 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8353 (mtt) REVERT: W 135 SER cc_start: 0.8544 (t) cc_final: 0.8105 (m) REVERT: Y 41 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7179 (mm-30) REVERT: a 78 THR cc_start: 0.8225 (m) cc_final: 0.8015 (m) REVERT: b 8 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7572 (mt-10) REVERT: c 185 GLU cc_start: 0.7072 (tm-30) cc_final: 0.6748 (tm-30) REVERT: d 151 SER cc_start: 0.9053 (p) cc_final: 0.8795 (t) REVERT: h 88 LYS cc_start: 0.7614 (mptt) cc_final: 0.7340 (mptt) REVERT: i 117 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8597 (mt-10) REVERT: i 339 MET cc_start: 0.8789 (mmm) cc_final: 0.8552 (mmm) REVERT: j 8 LEU cc_start: 0.8243 (tt) cc_final: 0.7995 (tp) REVERT: l 314 MET cc_start: 0.9013 (mmm) cc_final: 0.8786 (mmm) REVERT: l 393 ASP cc_start: 0.8172 (m-30) cc_final: 0.7857 (m-30) REVERT: n 30 ARG cc_start: 0.6855 (mmm-85) cc_final: 0.5589 (ttp-170) REVERT: o 110 ASP cc_start: 0.7975 (m-30) cc_final: 0.7757 (m-30) REVERT: s 174 MET cc_start: 0.8170 (mtp) cc_final: 0.7947 (mtp) REVERT: w 80 LYS cc_start: 0.6337 (mmtp) cc_final: 0.6102 (mmtm) outliers start: 25 outliers final: 13 residues processed: 1232 average time/residue: 0.6494 time to fit residues: 1368.5279 Evaluate side-chains 1155 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1140 time to evaluate : 5.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 650 SER Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain Q residue 141 TYR Chi-restraints excluded: chain Q residue 142 VAL Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain V residue 118 MET Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain e residue 137 MET Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain i residue 154 MET Chi-restraints excluded: chain r residue 256 TYR Chi-restraints excluded: chain u residue 78 CYS Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 103 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 669 optimal weight: 4.9990 chunk 601 optimal weight: 2.9990 chunk 333 optimal weight: 6.9990 chunk 205 optimal weight: 7.9990 chunk 405 optimal weight: 9.9990 chunk 321 optimal weight: 9.9990 chunk 621 optimal weight: 2.9990 chunk 240 optimal weight: 0.9990 chunk 377 optimal weight: 1.9990 chunk 462 optimal weight: 8.9990 chunk 720 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 456 GLN A 457 HIS C 123 GLN F 62 GLN F 93 ASN J 154 GLN J 323 HIS K 79 HIS M 334 GLN ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 GLN ** P 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 138 ASN Q 233 HIS Q 234 GLN T 123 HIS U 11 ASN V 89 ASN W 130 ASN b 13 GLN ** g 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 82 ASN ** o 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 220 HIS ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 110 GLN w 239 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.0696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 68230 Z= 0.267 Angle : 0.575 11.776 92319 Z= 0.286 Chirality : 0.042 0.178 10032 Planarity : 0.005 0.070 11542 Dihedral : 14.270 179.213 10228 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.20 % Favored : 95.78 % Rotamer: Outliers : 2.83 % Allowed : 15.35 % Favored : 81.82 % 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: 0.84 (0.09), residues: 8027 helix: 1.48 (0.08), residues: 4273 sheet: 0.25 (0.26), residues: 401 loop : -0.58 (0.11), residues: 3353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP l 144 HIS 0.008 0.001 HIS J 37 PHE 0.029 0.001 PHE i 292 TYR 0.028 0.001 TYR r 406 ARG 0.005 0.000 ARG P 125 *********************** 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 1382 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 1183 time to evaluate : 5.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8310 (tp) REVERT: A 127 ASP cc_start: 0.7856 (m-30) cc_final: 0.7557 (m-30) REVERT: A 287 THR cc_start: 0.7267 (m) cc_final: 0.6849 (p) REVERT: B 48 MET cc_start: 0.7339 (mmm) cc_final: 0.6638 (mmm) REVERT: C 99 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8019 (pm20) REVERT: G 120 MET cc_start: 0.7012 (OUTLIER) cc_final: 0.6387 (mtp) REVERT: J 175 LYS cc_start: 0.6740 (mmtm) cc_final: 0.5926 (mmmt) REVERT: J 324 MET cc_start: 0.7667 (ptm) cc_final: 0.7146 (ptp) REVERT: K 75 ASN cc_start: 0.6601 (t0) cc_final: 0.6322 (t0) REVERT: L 149 GLU cc_start: 0.8087 (pt0) cc_final: 0.7758 (pt0) REVERT: M 54 GLU cc_start: 0.7392 (tp30) cc_final: 0.7128 (mm-30) REVERT: M 77 MET cc_start: 0.9365 (tpt) cc_final: 0.8678 (tpt) REVERT: M 249 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7990 (mm-30) REVERT: Q 282 ASP cc_start: 0.7744 (OUTLIER) cc_final: 0.7539 (t0) REVERT: Q 414 ASP cc_start: 0.9219 (p0) cc_final: 0.8898 (p0) REVERT: Q 437 LYS cc_start: 0.8511 (tttp) cc_final: 0.8307 (tttp) REVERT: T 107 LYS cc_start: 0.7641 (tmtt) cc_final: 0.7141 (ptmt) REVERT: V 118 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8202 (mtt) REVERT: W 135 SER cc_start: 0.8573 (t) cc_final: 0.8130 (m) REVERT: X 89 LEU cc_start: 0.8971 (mt) cc_final: 0.8709 (mt) REVERT: X 122 MET cc_start: 0.8613 (mmm) cc_final: 0.8349 (mmm) REVERT: Z 20 LYS cc_start: 0.8701 (ptpp) cc_final: 0.8434 (mtmm) REVERT: b 112 GLU cc_start: 0.7651 (mp0) cc_final: 0.7211 (mp0) REVERT: g 108 LYS cc_start: 0.8091 (ptpt) cc_final: 0.7456 (pttp) REVERT: i 62 THR cc_start: 0.9381 (m) cc_final: 0.9088 (m) REVERT: i 117 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8622 (mt-10) REVERT: l 393 ASP cc_start: 0.8234 (m-30) cc_final: 0.8011 (m-30) REVERT: m 135 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.8629 (t80) REVERT: n 30 ARG cc_start: 0.7202 (mmm-85) cc_final: 0.6047 (ttp-170) REVERT: u 77 HIS cc_start: 0.7997 (m-70) cc_final: 0.7640 (m-70) REVERT: u 106 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8364 (mtmm) REVERT: v 16 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7088 (mt-10) REVERT: v 35 LYS cc_start: 0.6997 (tmtt) cc_final: 0.6796 (tmtt) REVERT: v 54 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7216 (pp30) REVERT: w 241 TYR cc_start: 0.7990 (OUTLIER) cc_final: 0.7634 (t80) outliers start: 199 outliers final: 124 residues processed: 1295 average time/residue: 0.6128 time to fit residues: 1360.7777 Evaluate side-chains 1268 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1134 time to evaluate : 5.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 78 SER Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 120 MET Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 75 ARG Chi-restraints excluded: chain J residue 114 ASP Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain L residue 133 ASP Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 249 GLU Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 362 ASP Chi-restraints excluded: chain M residue 380 ASP Chi-restraints excluded: chain M residue 437 ASP Chi-restraints excluded: chain M residue 559 ASP Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 134 ILE Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 138 ASN Chi-restraints excluded: chain Q residue 141 TYR Chi-restraints excluded: chain Q residue 281 GLU Chi-restraints excluded: chain Q residue 282 ASP Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain U residue 65 ASP 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 V residue 118 MET Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain V residue 125 VAL Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 111 ASP Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 71 MET Chi-restraints excluded: chain a residue 188 ASP Chi-restraints excluded: chain b residue 7 ASP Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 64 THR Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain b residue 91 THR Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain d residue 38 ASP Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain d residue 85 MET Chi-restraints excluded: chain d residue 120 SER Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain f residue 60 LYS Chi-restraints excluded: chain g residue 33 LEU Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain h residue 72 THR Chi-restraints excluded: chain h residue 87 ILE Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain i residue 45 MET Chi-restraints excluded: chain i residue 49 ASN Chi-restraints excluded: chain i residue 161 SER Chi-restraints excluded: chain i residue 237 MET Chi-restraints excluded: chain j residue 9 THR Chi-restraints excluded: chain j residue 19 LEU Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain k residue 22 TYR Chi-restraints excluded: chain l residue 127 THR Chi-restraints excluded: chain l residue 308 SER Chi-restraints excluded: chain l residue 401 MET Chi-restraints excluded: chain l residue 410 LEU Chi-restraints excluded: chain l residue 445 GLU Chi-restraints excluded: chain m residue 10 SER Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain m residue 148 SER Chi-restraints excluded: chain o residue 9 SER Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain o residue 128 SER Chi-restraints excluded: chain p residue 24 LEU Chi-restraints excluded: chain p residue 42 CYS Chi-restraints excluded: chain p residue 57 MET Chi-restraints excluded: chain r residue 50 LEU Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 256 TYR Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 105 MET Chi-restraints excluded: chain s residue 172 ILE Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain u residue 106 LYS Chi-restraints excluded: chain u residue 133 THR Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 110 GLN Chi-restraints excluded: chain w residue 65 ASN Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 204 VAL Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 312 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 400 optimal weight: 0.0270 chunk 223 optimal weight: 4.9990 chunk 599 optimal weight: 30.0000 chunk 490 optimal weight: 7.9990 chunk 198 optimal weight: 5.9990 chunk 721 optimal weight: 2.9990 chunk 779 optimal weight: 5.9990 chunk 642 optimal weight: 10.0000 chunk 715 optimal weight: 0.9990 chunk 245 optimal weight: 0.9980 chunk 578 optimal weight: 3.9990 overall best weight: 1.8044 ------------------------------------------------------------------------------- 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 456 GLN A 457 HIS C 123 GLN F 62 GLN F 93 ASN J 323 HIS ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 GLN ** P 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 138 ASN T 122 HIS U 11 ASN W 130 ASN a 189 ASN ** g 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 82 ASN ** o 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 220 HIS r 304 GLN s 169 GLN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 110 GLN w 239 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 68230 Z= 0.217 Angle : 0.537 10.739 92319 Z= 0.269 Chirality : 0.041 0.247 10032 Planarity : 0.004 0.061 11542 Dihedral : 13.429 179.349 10211 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.17 % Favored : 95.80 % Rotamer: Outliers : 2.93 % Allowed : 16.19 % Favored : 80.88 % 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: 0.89 (0.09), residues: 8027 helix: 1.53 (0.08), residues: 4274 sheet: 0.29 (0.26), residues: 401 loop : -0.57 (0.11), residues: 3352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP l 144 HIS 0.009 0.001 HIS T 122 PHE 0.028 0.001 PHE i 292 TYR 0.024 0.001 TYR r 406 ARG 0.006 0.000 ARG H 96 *********************** 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 1377 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 1171 time to evaluate : 5.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 THR cc_start: 0.7335 (m) cc_final: 0.6846 (p) REVERT: B 48 MET cc_start: 0.7345 (mmm) cc_final: 0.6657 (mmm) REVERT: B 76 TYR cc_start: 0.8835 (OUTLIER) cc_final: 0.8512 (m-80) REVERT: C 99 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8011 (pm20) REVERT: G 120 MET cc_start: 0.6868 (OUTLIER) cc_final: 0.6537 (mtp) REVERT: H 54 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6919 (mp0) REVERT: H 66 LYS cc_start: 0.6703 (mtpp) cc_final: 0.6046 (tttt) REVERT: J 175 LYS cc_start: 0.6750 (mmtm) cc_final: 0.5959 (mmmt) REVERT: J 324 MET cc_start: 0.7789 (ptm) cc_final: 0.7331 (ptp) REVERT: K 75 ASN cc_start: 0.6943 (t0) cc_final: 0.6678 (t0) REVERT: L 149 GLU cc_start: 0.8204 (pt0) cc_final: 0.7860 (pt0) REVERT: M 54 GLU cc_start: 0.7418 (tp30) cc_final: 0.7158 (mm-30) REVERT: M 249 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7971 (mm-30) REVERT: M 360 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.6938 (ttm110) REVERT: Q 282 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7517 (t0) REVERT: V 118 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8141 (mtt) REVERT: W 135 SER cc_start: 0.8565 (t) cc_final: 0.8129 (m) REVERT: X 89 LEU cc_start: 0.8952 (mt) cc_final: 0.8705 (mt) REVERT: b 112 GLU cc_start: 0.7693 (mp0) cc_final: 0.7215 (mp0) REVERT: c 185 GLU cc_start: 0.7187 (tm-30) cc_final: 0.6767 (tm-30) REVERT: d 151 SER cc_start: 0.9122 (p) cc_final: 0.8891 (t) REVERT: g 108 LYS cc_start: 0.8076 (ptpt) cc_final: 0.7453 (pttp) REVERT: i 62 THR cc_start: 0.9381 (m) cc_final: 0.9039 (m) REVERT: i 117 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8558 (mt-10) REVERT: l 15 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8533 (mt) REVERT: l 314 MET cc_start: 0.9048 (mmm) cc_final: 0.8763 (mmm) REVERT: m 135 PHE cc_start: 0.9147 (OUTLIER) cc_final: 0.8619 (t80) REVERT: r 231 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9024 (mt) REVERT: u 106 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8373 (mtmm) REVERT: v 54 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7108 (pp30) REVERT: w 241 TYR cc_start: 0.8031 (OUTLIER) cc_final: 0.7481 (t80) outliers start: 206 outliers final: 139 residues processed: 1291 average time/residue: 0.6743 time to fit residues: 1506.7013 Evaluate side-chains 1275 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 1122 time to evaluate : 5.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 120 MET Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 75 ARG Chi-restraints excluded: chain J residue 114 ASP Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain J residue 319 VAL Chi-restraints excluded: chain J residue 320 GLU Chi-restraints excluded: chain L residue 133 ASP Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 249 GLU Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 360 ARG Chi-restraints excluded: chain M residue 380 ASP Chi-restraints excluded: chain M residue 437 ASP Chi-restraints excluded: chain M residue 537 ILE Chi-restraints excluded: chain M residue 559 ASP Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 59 HIS Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain O residue 149 LEU Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain Q residue 141 TYR Chi-restraints excluded: chain Q residue 222 MET Chi-restraints excluded: chain Q residue 281 GLU Chi-restraints excluded: chain Q residue 282 ASP Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain U residue 65 ASP Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 105 THR Chi-restraints excluded: chain V residue 118 MET Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain a residue 71 MET Chi-restraints excluded: chain a residue 100 ASP Chi-restraints excluded: chain a residue 188 ASP Chi-restraints excluded: chain b residue 7 ASP Chi-restraints excluded: chain b residue 64 THR Chi-restraints excluded: chain b residue 91 THR Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain d residue 38 ASP Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain d residue 120 SER Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain f residue 60 LYS Chi-restraints excluded: chain g residue 33 LEU Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain h residue 72 THR Chi-restraints excluded: chain h residue 87 ILE Chi-restraints excluded: chain h residue 88 LYS Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain i residue 45 MET Chi-restraints excluded: chain i residue 49 ASN Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 161 SER Chi-restraints excluded: chain i residue 237 MET Chi-restraints excluded: chain j residue 9 THR Chi-restraints excluded: chain j residue 19 LEU Chi-restraints excluded: chain j residue 28 ASN Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain k residue 22 TYR Chi-restraints excluded: chain l residue 6 SER Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 15 LEU Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 127 THR Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 401 MET Chi-restraints excluded: chain l residue 410 LEU Chi-restraints excluded: chain l residue 418 LEU Chi-restraints excluded: chain l residue 445 GLU Chi-restraints excluded: chain m residue 10 SER Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 7 ILE Chi-restraints excluded: chain o residue 9 SER Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain o residue 57 LEU Chi-restraints excluded: chain o residue 128 SER Chi-restraints excluded: chain p residue 42 CYS Chi-restraints excluded: chain r residue 23 ILE Chi-restraints excluded: chain r residue 50 LEU Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 231 LEU Chi-restraints excluded: chain r residue 256 TYR Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 100 LEU Chi-restraints excluded: chain s residue 105 MET Chi-restraints excluded: chain s residue 145 THR Chi-restraints excluded: chain s residue 172 ILE Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain u residue 106 LYS Chi-restraints excluded: chain u residue 131 VAL Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 204 VAL Chi-restraints excluded: chain w residue 207 VAL Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 312 VAL 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: 8.9990 chunk 374 optimal weight: 8.9990 chunk 79 optimal weight: 0.9980 chunk 344 optimal weight: 0.8980 chunk 484 optimal weight: 6.9990 chunk 724 optimal weight: 5.9990 chunk 766 optimal weight: 5.9990 chunk 378 optimal weight: 7.9990 chunk 686 optimal weight: 1.9990 chunk 206 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 F 93 ASN J 323 HIS N 31 ASN O 153 GLN ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 GLN ** P 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 130 ASN g 48 ASN g 63 GLN j 82 ASN ** o 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 220 HIS s 124 ASN ** v 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 110 GLN w 65 ASN w 239 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 68230 Z= 0.282 Angle : 0.569 11.013 92319 Z= 0.284 Chirality : 0.042 0.249 10032 Planarity : 0.005 0.057 11542 Dihedral : 12.822 178.806 10211 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.50 % Favored : 95.48 % Rotamer: Outliers : 3.88 % Allowed : 16.36 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.09), residues: 8027 helix: 1.44 (0.08), residues: 4283 sheet: 0.21 (0.26), residues: 399 loop : -0.63 (0.11), residues: 3345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP u 86 HIS 0.009 0.001 HIS J 37 PHE 0.027 0.002 PHE i 292 TYR 0.025 0.001 TYR r 406 ARG 0.008 0.000 ARG r 336 *********************** 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 1415 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 1142 time to evaluate : 5.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8429 (tp) REVERT: A 287 THR cc_start: 0.7375 (m) cc_final: 0.6871 (p) REVERT: A 337 MET cc_start: 0.7675 (mmm) cc_final: 0.7473 (mmm) REVERT: B 48 MET cc_start: 0.7364 (mmm) cc_final: 0.6657 (mmm) REVERT: B 76 TYR cc_start: 0.8837 (OUTLIER) cc_final: 0.8574 (m-80) REVERT: B 169 GLU cc_start: 0.9069 (mt-10) cc_final: 0.8833 (mt-10) REVERT: C 67 PHE cc_start: 0.8823 (OUTLIER) cc_final: 0.8606 (m-80) REVERT: C 99 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.7996 (pm20) REVERT: C 188 LYS cc_start: 0.7788 (ptpt) cc_final: 0.7556 (ptpp) REVERT: F 46 LYS cc_start: 0.7661 (mtmm) cc_final: 0.7284 (mtmm) REVERT: G 120 MET cc_start: 0.6923 (mtp) cc_final: 0.6575 (mtp) REVERT: H 54 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6945 (mp0) REVERT: H 66 LYS cc_start: 0.6870 (mtpp) cc_final: 0.6096 (tttt) REVERT: J 175 LYS cc_start: 0.6615 (mmtm) cc_final: 0.5850 (mmmt) REVERT: J 324 MET cc_start: 0.7802 (ptm) cc_final: 0.7373 (ptp) REVERT: L 149 GLU cc_start: 0.8197 (pt0) cc_final: 0.7931 (pt0) REVERT: M 54 GLU cc_start: 0.7473 (tp30) cc_final: 0.7227 (mm-30) REVERT: M 77 MET cc_start: 0.9511 (tpt) cc_final: 0.9090 (tpt) REVERT: M 215 MET cc_start: 0.7205 (mmt) cc_final: 0.6598 (mmt) REVERT: M 249 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7984 (mm-30) REVERT: M 360 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.7067 (ttm110) REVERT: M 696 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.6568 (mmt) REVERT: N 78 ASP cc_start: 0.8836 (OUTLIER) cc_final: 0.8503 (p0) REVERT: O 169 PHE cc_start: 0.8413 (m-10) cc_final: 0.8118 (m-10) REVERT: Q 414 ASP cc_start: 0.9196 (p0) cc_final: 0.8875 (p0) REVERT: T 107 LYS cc_start: 0.7743 (tmtt) cc_final: 0.7164 (ptpt) REVERT: U 68 SER cc_start: 0.8709 (m) cc_final: 0.8472 (m) REVERT: V 118 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8255 (mtt) REVERT: W 135 SER cc_start: 0.8597 (t) cc_final: 0.8161 (m) REVERT: X 89 LEU cc_start: 0.9022 (mt) cc_final: 0.8817 (mt) REVERT: X 101 ASN cc_start: 0.8627 (OUTLIER) cc_final: 0.8368 (m-40) REVERT: a 180 ASP cc_start: 0.8296 (t0) cc_final: 0.7900 (t0) REVERT: b 115 GLU cc_start: 0.7949 (pp20) cc_final: 0.7288 (pp20) REVERT: c 46 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.6993 (mt-10) REVERT: d 61 TYR cc_start: 0.8641 (OUTLIER) cc_final: 0.8255 (p90) REVERT: g 108 LYS cc_start: 0.8108 (ptpt) cc_final: 0.7866 (mmtp) REVERT: h 24 GLU cc_start: 0.7707 (tp30) cc_final: 0.7415 (tp30) REVERT: i 62 THR cc_start: 0.9423 (m) cc_final: 0.9113 (m) REVERT: i 117 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8551 (mt-10) REVERT: i 293 TYR cc_start: 0.9033 (m-80) cc_final: 0.8785 (m-80) REVERT: j 57 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8292 (mm) REVERT: l 108 MET cc_start: 0.9027 (mmm) cc_final: 0.8716 (mmt) REVERT: l 393 ASP cc_start: 0.8251 (m-30) cc_final: 0.8049 (m-30) REVERT: l 409 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8165 (tt) REVERT: m 1 MET cc_start: 0.3895 (ttm) cc_final: 0.3455 (mtp) REVERT: m 135 PHE cc_start: 0.9162 (OUTLIER) cc_final: 0.8577 (t80) REVERT: n 30 ARG cc_start: 0.7479 (mmm-85) cc_final: 0.7258 (mmm160) REVERT: r 114 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8014 (tm-30) REVERT: r 231 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9009 (mt) REVERT: u 106 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8377 (mtmm) REVERT: v 54 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7220 (pp30) REVERT: w 241 TYR cc_start: 0.8076 (OUTLIER) cc_final: 0.7170 (t80) outliers start: 273 outliers final: 192 residues processed: 1310 average time/residue: 0.6470 time to fit residues: 1463.9507 Evaluate side-chains 1318 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 1105 time to evaluate : 5.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 58 GLN Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 78 SER Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 71 GLN Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 75 ARG Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 114 ASP Chi-restraints excluded: chain J residue 148 ILE Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain J residue 319 VAL Chi-restraints excluded: chain J residue 340 ILE Chi-restraints excluded: chain L residue 133 ASP Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 249 GLU Chi-restraints excluded: chain M residue 255 ASP Chi-restraints excluded: chain M residue 315 THR Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 360 ARG Chi-restraints excluded: chain M residue 380 ASP Chi-restraints excluded: chain M residue 437 ASP Chi-restraints excluded: chain M residue 537 ILE Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 59 HIS Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 78 ASP Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain O residue 149 LEU Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 222 ARG Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain P residue 153 ILE Chi-restraints excluded: chain P residue 240 GLU Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 141 TYR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 222 MET Chi-restraints excluded: chain Q residue 281 GLU Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain T residue 68 ILE Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain U residue 65 ASP Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain V residue 40 SER Chi-restraints excluded: chain V residue 53 VAL Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 105 THR Chi-restraints excluded: chain V residue 118 MET Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 101 ASN Chi-restraints excluded: chain X residue 102 SER Chi-restraints excluded: chain X residue 111 ASP Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 71 MET Chi-restraints excluded: chain a residue 78 THR Chi-restraints excluded: chain a residue 100 ASP Chi-restraints excluded: chain a residue 188 ASP Chi-restraints excluded: chain b residue 7 ASP Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 64 THR Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain b residue 91 THR Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 46 GLU Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 182 VAL Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 38 ASP Chi-restraints excluded: chain d residue 61 TYR Chi-restraints excluded: chain d residue 85 MET Chi-restraints excluded: chain d residue 120 SER Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain f residue 60 LYS Chi-restraints excluded: chain g residue 33 LEU Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain h residue 72 THR Chi-restraints excluded: chain h residue 87 ILE Chi-restraints excluded: chain h residue 88 LYS Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain i residue 45 MET Chi-restraints excluded: chain i residue 49 ASN Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 95 MET Chi-restraints excluded: chain i residue 161 SER Chi-restraints excluded: chain i residue 237 MET Chi-restraints excluded: chain j residue 9 THR Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 19 LEU Chi-restraints excluded: chain j residue 28 ASN Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 22 TYR Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain l residue 6 SER Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 15 LEU Chi-restraints excluded: chain l residue 52 LEU Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 127 THR Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 401 MET Chi-restraints excluded: chain l residue 409 LEU Chi-restraints excluded: chain l residue 410 LEU Chi-restraints excluded: chain l residue 418 LEU Chi-restraints excluded: chain l residue 445 GLU Chi-restraints excluded: chain l residue 503 GLU Chi-restraints excluded: chain l residue 577 VAL Chi-restraints excluded: chain l residue 584 ILE Chi-restraints excluded: chain m residue 10 SER Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain m residue 148 SER Chi-restraints excluded: chain n residue 7 ILE Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain o residue 9 SER Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain o residue 128 SER Chi-restraints excluded: chain p residue 24 LEU Chi-restraints excluded: chain p residue 42 CYS Chi-restraints excluded: chain r residue 23 ILE Chi-restraints excluded: chain r residue 55 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 186 LEU Chi-restraints excluded: chain r residue 231 LEU Chi-restraints excluded: chain r residue 256 TYR Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 105 MET Chi-restraints excluded: chain s residue 145 THR Chi-restraints excluded: chain s residue 172 ILE Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain u residue 89 ILE Chi-restraints excluded: chain u residue 106 LYS Chi-restraints excluded: chain u residue 131 VAL Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 110 GLN Chi-restraints excluded: chain w residue 65 ASN Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 204 VAL Chi-restraints excluded: chain w residue 207 VAL Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 312 VAL 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: 2.9990 chunk 11 optimal weight: 7.9990 chunk 570 optimal weight: 4.9990 chunk 316 optimal weight: 0.0980 chunk 654 optimal weight: 8.9990 chunk 529 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 391 optimal weight: 1.9990 chunk 688 optimal weight: 8.9990 chunk 193 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 93 ASN I 25 GLN J 323 HIS O 153 GLN ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 GLN ** P 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 270 ASN U 11 ASN W 130 ASN k 7 ASN ** o 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 220 HIS s 169 GLN u 64 ASN ** v 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 142 GLN w 149 HIS w 239 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 68230 Z= 0.245 Angle : 0.549 10.902 92319 Z= 0.275 Chirality : 0.041 0.211 10032 Planarity : 0.005 0.055 11542 Dihedral : 12.489 178.641 10211 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.47 % Favored : 95.50 % Rotamer: Outliers : 3.52 % Allowed : 17.19 % Favored : 79.29 % 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: 0.80 (0.09), residues: 8027 helix: 1.48 (0.08), residues: 4279 sheet: 0.22 (0.26), residues: 407 loop : -0.63 (0.11), residues: 3341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 311 HIS 0.009 0.001 HIS J 37 PHE 0.027 0.001 PHE i 292 TYR 0.024 0.001 TYR r 406 ARG 0.010 0.000 ARG H 96 *********************** 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 1394 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 1146 time to evaluate : 5.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8425 (tp) REVERT: A 287 THR cc_start: 0.7405 (m) cc_final: 0.6907 (p) REVERT: A 292 MET cc_start: 0.7211 (mtp) cc_final: 0.6833 (mtp) REVERT: B 48 MET cc_start: 0.7373 (mmm) cc_final: 0.6676 (mmm) REVERT: B 76 TYR cc_start: 0.8897 (OUTLIER) cc_final: 0.8676 (m-80) REVERT: C 67 PHE cc_start: 0.8811 (OUTLIER) cc_final: 0.8595 (m-80) REVERT: C 99 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.7997 (pm20) REVERT: C 188 LYS cc_start: 0.7841 (ptpt) cc_final: 0.7627 (ptpp) REVERT: E 96 VAL cc_start: 0.8967 (OUTLIER) cc_final: 0.8736 (p) REVERT: F 85 ASP cc_start: 0.6793 (m-30) cc_final: 0.6411 (m-30) REVERT: G 120 MET cc_start: 0.6969 (OUTLIER) cc_final: 0.6286 (mtp) REVERT: H 54 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.7016 (mp0) REVERT: H 66 LYS cc_start: 0.6856 (mtpp) cc_final: 0.6082 (tttt) REVERT: J 175 LYS cc_start: 0.6631 (mmtm) cc_final: 0.5854 (mmmt) REVERT: J 324 MET cc_start: 0.7839 (ptm) cc_final: 0.7413 (ptp) REVERT: L 149 GLU cc_start: 0.8223 (pt0) cc_final: 0.7929 (pt0) REVERT: M 54 GLU cc_start: 0.7469 (tp30) cc_final: 0.7224 (mm-30) REVERT: M 77 MET cc_start: 0.9531 (tpt) cc_final: 0.9075 (tpt) REVERT: M 100 TRP cc_start: 0.9031 (OUTLIER) cc_final: 0.8729 (m-10) REVERT: M 215 MET cc_start: 0.7162 (mmt) cc_final: 0.6591 (mmt) REVERT: M 249 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8001 (mm-30) REVERT: M 360 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.7036 (ttm110) REVERT: N 68 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.7004 (ttt) REVERT: N 78 ASP cc_start: 0.8816 (OUTLIER) cc_final: 0.8449 (p0) REVERT: T 107 LYS cc_start: 0.7703 (tmtt) cc_final: 0.7134 (ptpt) REVERT: U 68 SER cc_start: 0.8633 (m) cc_final: 0.8417 (m) REVERT: V 118 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8301 (mtt) REVERT: W 64 ASP cc_start: 0.8203 (m-30) cc_final: 0.7878 (m-30) REVERT: W 135 SER cc_start: 0.8580 (t) cc_final: 0.8156 (m) REVERT: a 180 ASP cc_start: 0.8269 (t0) cc_final: 0.7860 (t0) REVERT: b 115 GLU cc_start: 0.7924 (pp20) cc_final: 0.7217 (pp20) REVERT: c 46 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.6979 (mt-10) REVERT: d 61 TYR cc_start: 0.8639 (OUTLIER) cc_final: 0.8254 (p90) REVERT: d 151 SER cc_start: 0.9101 (p) cc_final: 0.8821 (t) REVERT: g 108 LYS cc_start: 0.8075 (ptpt) cc_final: 0.7526 (pttp) REVERT: h 24 GLU cc_start: 0.7677 (tp30) cc_final: 0.7460 (tp30) REVERT: i 62 THR cc_start: 0.9416 (m) cc_final: 0.9090 (m) REVERT: i 117 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8477 (mt-10) REVERT: i 293 TYR cc_start: 0.9015 (m-80) cc_final: 0.8762 (m-80) REVERT: j 57 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8287 (mm) REVERT: l 286 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8712 (tp) REVERT: m 1 MET cc_start: 0.3786 (ttm) cc_final: 0.3394 (mtp) REVERT: m 135 PHE cc_start: 0.9161 (OUTLIER) cc_final: 0.8577 (t80) REVERT: n 30 ARG cc_start: 0.7461 (mmm-85) cc_final: 0.7234 (mmm160) REVERT: p 170 ILE cc_start: 0.9449 (OUTLIER) cc_final: 0.9130 (mp) REVERT: r 231 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.9000 (mt) REVERT: v 36 GLU cc_start: 0.6841 (tp30) cc_final: 0.6552 (tp30) REVERT: v 54 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7206 (pp30) REVERT: v 81 LYS cc_start: 0.8035 (ttmm) cc_final: 0.7749 (ttmm) REVERT: v 101 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8189 (mm-30) REVERT: w 241 TYR cc_start: 0.7988 (OUTLIER) cc_final: 0.7080 (t80) outliers start: 248 outliers final: 187 residues processed: 1292 average time/residue: 0.6319 time to fit residues: 1402.5208 Evaluate side-chains 1316 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 1107 time to evaluate : 5.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 78 SER Chi-restraints excluded: chain F residue 81 ASN Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 120 MET Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 71 GLN Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 75 ARG Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 114 ASP Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain J residue 320 GLU Chi-restraints excluded: chain J residue 340 ILE Chi-restraints excluded: chain L residue 133 ASP Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 100 TRP Chi-restraints excluded: chain M residue 249 GLU Chi-restraints excluded: chain M residue 255 ASP Chi-restraints excluded: chain M residue 315 THR Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 360 ARG Chi-restraints excluded: chain M residue 380 ASP Chi-restraints excluded: chain M residue 437 ASP Chi-restraints excluded: chain M residue 537 ILE Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 59 HIS Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 68 MET Chi-restraints excluded: chain N residue 78 ASP Chi-restraints excluded: chain N residue 134 ILE Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain O residue 149 LEU Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 222 ARG Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 128 ILE Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain P residue 153 ILE Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 141 TYR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 222 MET Chi-restraints excluded: chain Q residue 281 GLU Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain U residue 65 ASP Chi-restraints excluded: chain V residue 28 ILE Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain V residue 40 SER Chi-restraints excluded: chain V residue 53 VAL Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 105 THR Chi-restraints excluded: chain V residue 118 MET Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 102 SER Chi-restraints excluded: chain X residue 111 ASP Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 71 MET Chi-restraints excluded: chain a residue 78 THR Chi-restraints excluded: chain a residue 100 ASP Chi-restraints excluded: chain a residue 188 ASP Chi-restraints excluded: chain b residue 7 ASP Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 64 THR Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain b residue 91 THR Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 46 GLU Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain d residue 38 ASP Chi-restraints excluded: chain d residue 61 TYR Chi-restraints excluded: chain d residue 85 MET Chi-restraints excluded: chain d residue 120 SER Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain f residue 60 LYS Chi-restraints excluded: chain g residue 33 LEU Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain h residue 72 THR Chi-restraints excluded: chain h residue 87 ILE Chi-restraints excluded: chain h residue 88 LYS Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain i residue 45 MET Chi-restraints excluded: chain i residue 49 ASN Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 161 SER Chi-restraints excluded: chain i residue 182 SER Chi-restraints excluded: chain i residue 237 MET Chi-restraints excluded: chain j residue 9 THR Chi-restraints excluded: chain j residue 19 LEU Chi-restraints excluded: chain j residue 28 ASN Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 22 TYR Chi-restraints excluded: chain k residue 64 LEU Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain l residue 6 SER Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 15 LEU Chi-restraints excluded: chain l residue 52 LEU Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 127 THR Chi-restraints excluded: chain l residue 149 ILE Chi-restraints excluded: chain l residue 286 LEU Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 401 MET Chi-restraints excluded: chain l residue 410 LEU Chi-restraints excluded: chain l residue 418 LEU Chi-restraints excluded: chain l residue 445 GLU Chi-restraints excluded: chain l residue 503 GLU Chi-restraints excluded: chain l residue 584 ILE Chi-restraints excluded: chain m residue 10 SER Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain m residue 148 SER Chi-restraints excluded: chain n residue 7 ILE Chi-restraints excluded: chain o residue 9 SER Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain o residue 57 LEU Chi-restraints excluded: chain o residue 114 LYS Chi-restraints excluded: chain o residue 128 SER Chi-restraints excluded: chain p residue 42 CYS Chi-restraints excluded: chain p residue 170 ILE Chi-restraints excluded: chain r residue 23 ILE Chi-restraints excluded: chain r residue 50 LEU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 231 LEU Chi-restraints excluded: chain r residue 256 TYR Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 100 LEU Chi-restraints excluded: chain s residue 105 MET Chi-restraints excluded: chain s residue 145 THR Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain u residue 37 ASP Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 89 ILE Chi-restraints excluded: chain u residue 131 VAL Chi-restraints excluded: chain v residue 51 LEU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 204 VAL Chi-restraints excluded: chain w residue 207 VAL Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 312 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 257 optimal weight: 0.0370 chunk 690 optimal weight: 5.9990 chunk 151 optimal weight: 30.0000 chunk 450 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 chunk 767 optimal weight: 6.9990 chunk 636 optimal weight: 6.9990 chunk 355 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 253 optimal weight: 0.0050 chunk 402 optimal weight: 5.9990 overall best weight: 1.6076 ------------------------------------------------------------------------------- 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 136 HIS F 93 ASN J 323 HIS ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 GLN ** P 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 270 ASN W 130 ASN b 127 HIS k 92 ASN r 220 HIS ** v 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 239 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 68230 Z= 0.201 Angle : 0.529 10.782 92319 Z= 0.265 Chirality : 0.040 0.233 10032 Planarity : 0.004 0.054 11542 Dihedral : 12.091 179.328 10211 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.34 % Favored : 95.64 % Rotamer: Outliers : 3.54 % Allowed : 17.68 % Favored : 78.78 % 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: 0.88 (0.09), residues: 8027 helix: 1.53 (0.08), residues: 4291 sheet: 0.24 (0.26), residues: 407 loop : -0.59 (0.11), residues: 3329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 75 HIS 0.007 0.001 HIS J 37 PHE 0.027 0.001 PHE i 292 TYR 0.024 0.001 TYR r 406 ARG 0.007 0.000 ARG F 34 *********************** 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 1419 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 1170 time to evaluate : 6.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8401 (tp) REVERT: A 287 THR cc_start: 0.7383 (m) cc_final: 0.6885 (p) REVERT: A 292 MET cc_start: 0.7091 (mtp) cc_final: 0.6806 (mtp) REVERT: B 48 MET cc_start: 0.7429 (mmm) cc_final: 0.6756 (mmm) REVERT: B 76 TYR cc_start: 0.8884 (OUTLIER) cc_final: 0.8601 (m-80) REVERT: B 169 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8762 (mt-10) REVERT: C 99 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.7980 (pm20) REVERT: G 120 MET cc_start: 0.6830 (OUTLIER) cc_final: 0.6464 (mtp) REVERT: G 136 GLU cc_start: 0.6531 (pp20) cc_final: 0.5739 (tm-30) REVERT: H 66 LYS cc_start: 0.6858 (mtpp) cc_final: 0.6054 (tttt) REVERT: J 175 LYS cc_start: 0.6669 (mmtm) cc_final: 0.5904 (mmmt) REVERT: J 324 MET cc_start: 0.7888 (ptm) cc_final: 0.7484 (ptp) REVERT: K 75 ASN cc_start: 0.6794 (t0) cc_final: 0.6576 (t0) REVERT: L 149 GLU cc_start: 0.8220 (pt0) cc_final: 0.7913 (pt0) REVERT: M 54 GLU cc_start: 0.7451 (tp30) cc_final: 0.7201 (mm-30) REVERT: M 100 TRP cc_start: 0.9036 (OUTLIER) cc_final: 0.8745 (m-10) REVERT: M 215 MET cc_start: 0.7165 (mmt) cc_final: 0.6566 (mmt) REVERT: M 249 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7987 (mm-30) REVERT: M 360 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.7005 (ttm110) REVERT: M 696 MET cc_start: 0.7695 (OUTLIER) cc_final: 0.6542 (mmt) REVERT: N 68 MET cc_start: 0.7580 (OUTLIER) cc_final: 0.7064 (ttt) REVERT: N 78 ASP cc_start: 0.8821 (OUTLIER) cc_final: 0.8450 (p0) REVERT: O 169 PHE cc_start: 0.8454 (m-10) cc_final: 0.8173 (m-10) REVERT: O 222 ARG cc_start: 0.6767 (OUTLIER) cc_final: 0.4931 (mmm160) REVERT: Q 414 ASP cc_start: 0.9189 (p0) cc_final: 0.8860 (p0) REVERT: S 35 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8369 (mt-10) REVERT: T 61 GLU cc_start: 0.8397 (tp30) cc_final: 0.8008 (tt0) REVERT: U 68 SER cc_start: 0.8700 (m) cc_final: 0.8485 (m) REVERT: V 118 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8148 (mtp) REVERT: W 135 SER cc_start: 0.8612 (t) cc_final: 0.8198 (m) REVERT: X 101 ASN cc_start: 0.8573 (OUTLIER) cc_final: 0.8301 (m-40) REVERT: a 180 ASP cc_start: 0.8255 (t0) cc_final: 0.7833 (t0) REVERT: b 115 GLU cc_start: 0.7852 (pp20) cc_final: 0.7169 (pp20) REVERT: d 61 TYR cc_start: 0.8625 (OUTLIER) cc_final: 0.8147 (p90) REVERT: d 151 SER cc_start: 0.9159 (p) cc_final: 0.8907 (t) REVERT: e 128 TYR cc_start: 0.8108 (t80) cc_final: 0.7838 (t80) REVERT: g 108 LYS cc_start: 0.8060 (ptpt) cc_final: 0.7836 (mmtp) REVERT: h 24 GLU cc_start: 0.7621 (tp30) cc_final: 0.7395 (tp30) REVERT: i 62 THR cc_start: 0.9416 (m) cc_final: 0.9110 (m) REVERT: i 117 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8456 (mt-10) REVERT: l 286 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8737 (tp) REVERT: l 393 ASP cc_start: 0.8201 (m-30) cc_final: 0.7912 (m-30) REVERT: l 409 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7992 (tp) REVERT: m 1 MET cc_start: 0.3953 (ttm) cc_final: 0.3632 (mtp) REVERT: m 135 PHE cc_start: 0.9151 (OUTLIER) cc_final: 0.8556 (t80) REVERT: n 30 ARG cc_start: 0.7457 (mmm-85) cc_final: 0.7236 (mmm160) REVERT: p 170 ILE cc_start: 0.9453 (OUTLIER) cc_final: 0.9132 (mp) REVERT: r 114 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.7953 (tm-30) REVERT: r 231 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9016 (mt) REVERT: v 54 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7186 (pp30) REVERT: v 81 LYS cc_start: 0.7962 (ttmm) cc_final: 0.7693 (ttmm) REVERT: w 241 TYR cc_start: 0.7921 (OUTLIER) cc_final: 0.6764 (t80) outliers start: 249 outliers final: 182 residues processed: 1320 average time/residue: 0.6379 time to fit residues: 1452.8695 Evaluate side-chains 1328 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1124 time to evaluate : 5.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 78 SER Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 120 MET Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 71 GLN Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 75 ARG Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 114 ASP Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 154 GLN Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain J residue 320 GLU Chi-restraints excluded: chain J residue 340 ILE Chi-restraints excluded: chain L residue 133 ASP Chi-restraints excluded: chain L residue 151 LYS Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 100 TRP Chi-restraints excluded: chain M residue 249 GLU Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 360 ARG Chi-restraints excluded: chain M residue 380 ASP Chi-restraints excluded: chain M residue 437 ASP Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 68 MET Chi-restraints excluded: chain N residue 78 ASP Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 222 ARG Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 128 ILE Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 98 VAL Chi-restraints excluded: chain Q residue 141 TYR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 222 MET Chi-restraints excluded: chain Q residue 281 GLU Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain T residue 68 ILE Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain U residue 65 ASP Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain V residue 40 SER Chi-restraints excluded: chain V residue 53 VAL Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 105 THR Chi-restraints excluded: chain V residue 118 MET Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 101 ASN Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 71 MET Chi-restraints excluded: chain a residue 78 THR Chi-restraints excluded: chain a residue 188 ASP Chi-restraints excluded: chain b residue 7 ASP Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 64 THR Chi-restraints excluded: chain b residue 91 THR Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain d residue 38 ASP Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain d residue 61 TYR Chi-restraints excluded: chain d residue 85 MET Chi-restraints excluded: chain d residue 120 SER Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain f residue 60 LYS Chi-restraints excluded: chain g residue 33 LEU Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain h residue 72 THR Chi-restraints excluded: chain h residue 87 ILE Chi-restraints excluded: chain h residue 88 LYS Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain i residue 45 MET Chi-restraints excluded: chain i residue 49 ASN Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 161 SER Chi-restraints excluded: chain i residue 237 MET Chi-restraints excluded: chain j residue 9 THR Chi-restraints excluded: chain j residue 19 LEU Chi-restraints excluded: chain j residue 28 ASN Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 22 TYR Chi-restraints excluded: chain k residue 64 LEU Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain l residue 6 SER Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 15 LEU Chi-restraints excluded: chain l residue 52 LEU Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 127 THR Chi-restraints excluded: chain l residue 286 LEU Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 401 MET Chi-restraints excluded: chain l residue 409 LEU Chi-restraints excluded: chain l residue 418 LEU Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 445 GLU Chi-restraints excluded: chain l residue 503 GLU Chi-restraints excluded: chain m residue 10 SER Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 66 VAL Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain m residue 148 SER Chi-restraints excluded: chain n residue 7 ILE Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain o residue 9 SER Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain o residue 114 LYS Chi-restraints excluded: chain o residue 128 SER Chi-restraints excluded: chain p residue 24 LEU Chi-restraints excluded: chain p residue 42 CYS Chi-restraints excluded: chain p residue 170 ILE Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 23 ILE Chi-restraints excluded: chain r residue 50 LEU Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 122 PHE Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 184 HIS Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 231 LEU Chi-restraints excluded: chain r residue 256 TYR Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 100 LEU Chi-restraints excluded: chain s residue 145 THR Chi-restraints excluded: chain s residue 161 THR Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 267 THR Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 131 VAL Chi-restraints excluded: chain v residue 51 LEU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 204 VAL Chi-restraints excluded: chain w residue 207 VAL Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 312 VAL 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: 9.9990 chunk 437 optimal weight: 2.9990 chunk 560 optimal weight: 0.6980 chunk 434 optimal weight: 5.9990 chunk 645 optimal weight: 0.9990 chunk 428 optimal weight: 0.9990 chunk 764 optimal weight: 10.0000 chunk 478 optimal weight: 0.9990 chunk 465 optimal weight: 0.7980 chunk 352 optimal weight: 6.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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 136 HIS F 93 ASN J 323 HIS ** O 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 74 GLN ** P 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 GLN ** P 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 11 ASN W 130 ASN b 13 GLN r 220 HIS s 169 GLN ** v 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 110 GLN w 239 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 68230 Z= 0.153 Angle : 0.510 10.527 92319 Z= 0.254 Chirality : 0.039 0.207 10032 Planarity : 0.004 0.052 11542 Dihedral : 11.597 179.202 10211 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.12 % Favored : 95.85 % Rotamer: Outliers : 2.95 % Allowed : 18.52 % Favored : 78.53 % 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: 1.04 (0.10), residues: 8027 helix: 1.66 (0.08), residues: 4290 sheet: 0.29 (0.26), residues: 414 loop : -0.51 (0.11), residues: 3323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 75 HIS 0.006 0.001 HIS J 37 PHE 0.027 0.001 PHE l 335 TYR 0.024 0.001 TYR l 422 ARG 0.013 0.000 ARG H 96 *********************** 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 1412 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 1204 time to evaluate : 5.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8009 (m-30) cc_final: 0.7700 (m-30) REVERT: A 287 THR cc_start: 0.7363 (m) cc_final: 0.6863 (p) REVERT: A 337 MET cc_start: 0.7559 (mmm) cc_final: 0.7209 (mmt) REVERT: B 48 MET cc_start: 0.7373 (mmm) cc_final: 0.6753 (mmm) REVERT: B 76 TYR cc_start: 0.8869 (OUTLIER) cc_final: 0.8535 (m-80) REVERT: C 99 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.7959 (pm20) REVERT: E 96 VAL cc_start: 0.8851 (OUTLIER) cc_final: 0.8622 (p) REVERT: F 85 ASP cc_start: 0.6710 (m-30) cc_final: 0.6312 (m-30) REVERT: G 136 GLU cc_start: 0.6594 (pp20) cc_final: 0.5832 (tm-30) REVERT: H 38 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7464 (mp) REVERT: H 54 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6916 (mp0) REVERT: H 66 LYS cc_start: 0.6960 (mtpp) cc_final: 0.6143 (tttt) REVERT: J 175 LYS cc_start: 0.6636 (mmtm) cc_final: 0.5935 (mmmt) REVERT: J 324 MET cc_start: 0.7932 (ptm) cc_final: 0.7509 (ptp) REVERT: K 75 ASN cc_start: 0.6824 (t0) cc_final: 0.6602 (t0) REVERT: M 54 GLU cc_start: 0.7440 (tp30) cc_final: 0.7224 (mm-30) REVERT: M 77 MET cc_start: 0.9527 (tpt) cc_final: 0.9095 (tpt) REVERT: M 249 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7964 (mm-30) REVERT: M 360 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.6993 (ttm110) REVERT: N 78 ASP cc_start: 0.8851 (OUTLIER) cc_final: 0.8478 (p0) REVERT: O 222 ARG cc_start: 0.6700 (OUTLIER) cc_final: 0.6139 (mtp180) REVERT: V 118 MET cc_start: 0.8698 (mtt) cc_final: 0.8300 (mtp) REVERT: W 135 SER cc_start: 0.8580 (t) cc_final: 0.8169 (m) REVERT: a 180 ASP cc_start: 0.8237 (t0) cc_final: 0.7793 (t0) REVERT: b 115 GLU cc_start: 0.7823 (pp20) cc_final: 0.7118 (pp20) REVERT: d 6 ASP cc_start: 0.7767 (t0) cc_final: 0.7436 (t0) REVERT: e 128 TYR cc_start: 0.8062 (t80) cc_final: 0.7821 (t80) REVERT: h 24 GLU cc_start: 0.7461 (tp30) cc_final: 0.7235 (tp30) REVERT: i 117 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8581 (mt-10) REVERT: i 339 MET cc_start: 0.8691 (mmm) cc_final: 0.8344 (mmm) REVERT: j 57 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8187 (mm) REVERT: k 34 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8092 (mm-30) REVERT: k 89 TYR cc_start: 0.6299 (m-80) cc_final: 0.6006 (m-80) REVERT: l 15 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8472 (mt) REVERT: l 108 MET cc_start: 0.8962 (mmm) cc_final: 0.8529 (mmt) REVERT: l 286 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8718 (tp) REVERT: l 393 ASP cc_start: 0.8187 (m-30) cc_final: 0.7900 (m-30) REVERT: l 395 ILE cc_start: 0.8976 (mm) cc_final: 0.8672 (mt) REVERT: m 64 MET cc_start: 0.8252 (ttp) cc_final: 0.7871 (ttm) REVERT: m 66 VAL cc_start: 0.9486 (OUTLIER) cc_final: 0.9236 (p) REVERT: o 44 LYS cc_start: 0.8928 (tppp) cc_final: 0.8685 (tppt) REVERT: p 170 ILE cc_start: 0.9418 (OUTLIER) cc_final: 0.9070 (mp) REVERT: r 114 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.7925 (tm-30) REVERT: r 378 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7884 (tt0) REVERT: s 121 TRP cc_start: 0.7275 (t60) cc_final: 0.6660 (t60) REVERT: w 241 TYR cc_start: 0.7854 (OUTLIER) cc_final: 0.6633 (t80) outliers start: 208 outliers final: 140 residues processed: 1323 average time/residue: 0.6157 time to fit residues: 1402.3112 Evaluate side-chains 1303 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1146 time to evaluate : 5.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 78 SER Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 71 GLN Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain J residue 75 ARG Chi-restraints excluded: chain J residue 154 GLN Chi-restraints excluded: chain J residue 320 GLU Chi-restraints excluded: chain J residue 340 ILE Chi-restraints excluded: chain L residue 133 ASP Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 249 GLU Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 360 ARG Chi-restraints excluded: chain M residue 380 ASP Chi-restraints excluded: chain M residue 437 ASP Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 78 ASP Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 222 ARG Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 98 VAL Chi-restraints excluded: chain Q residue 141 TYR Chi-restraints excluded: chain Q residue 222 MET Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain U residue 65 ASP Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain V residue 40 SER Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 105 THR Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 71 MET Chi-restraints excluded: chain a residue 78 THR Chi-restraints excluded: chain a residue 188 ASP Chi-restraints excluded: chain b residue 7 ASP Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 64 THR Chi-restraints excluded: chain b residue 91 THR Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain d residue 38 ASP Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain f residue 60 LYS Chi-restraints excluded: chain g residue 89 ASP Chi-restraints excluded: chain h residue 72 THR Chi-restraints excluded: chain h residue 87 ILE Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain i residue 45 MET Chi-restraints excluded: chain i residue 49 ASN Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 161 SER Chi-restraints excluded: chain i residue 182 SER Chi-restraints excluded: chain i residue 237 MET Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 6 SER Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 15 LEU Chi-restraints excluded: chain l residue 52 LEU Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 127 THR Chi-restraints excluded: chain l residue 149 ILE Chi-restraints excluded: chain l residue 286 LEU Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 418 LEU Chi-restraints excluded: chain l residue 445 GLU Chi-restraints excluded: chain l residue 503 GLU Chi-restraints excluded: chain m residue 10 SER Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 66 VAL Chi-restraints excluded: chain m residue 148 SER Chi-restraints excluded: chain n residue 7 ILE Chi-restraints excluded: chain o residue 9 SER Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain o residue 114 LYS Chi-restraints excluded: chain p residue 24 LEU Chi-restraints excluded: chain p residue 42 CYS Chi-restraints excluded: chain p residue 170 ILE Chi-restraints excluded: chain r residue 23 ILE Chi-restraints excluded: chain r residue 50 LEU Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 256 TYR Chi-restraints excluded: chain r residue 378 GLU Chi-restraints excluded: chain r residue 448 THR Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 100 LEU Chi-restraints excluded: chain s residue 145 THR Chi-restraints excluded: chain s residue 161 THR Chi-restraints excluded: chain s residue 267 THR Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 89 ILE Chi-restraints excluded: chain v residue 51 LEU Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 110 GLN Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 163 ILE Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 204 VAL Chi-restraints excluded: chain w residue 207 VAL Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 312 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 472 optimal weight: 9.9990 chunk 305 optimal weight: 3.9990 chunk 456 optimal weight: 4.9990 chunk 230 optimal weight: 10.0000 chunk 150 optimal weight: 0.8980 chunk 148 optimal weight: 6.9990 chunk 485 optimal weight: 6.9990 chunk 520 optimal weight: 0.6980 chunk 377 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 600 optimal weight: 3.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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 136 HIS ** J 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 GLN ** P 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 454 GLN W 130 ASN b 127 HIS ** e 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 7 GLN ** l 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 220 HIS s 235 ASN ** v 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 68230 Z= 0.308 Angle : 0.593 14.252 92319 Z= 0.295 Chirality : 0.043 0.252 10032 Planarity : 0.005 0.056 11542 Dihedral : 11.748 178.502 10208 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.77 % Favored : 95.22 % Rotamer: Outliers : 3.42 % Allowed : 18.32 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.09), residues: 8027 helix: 1.44 (0.08), residues: 4292 sheet: 0.22 (0.26), residues: 409 loop : -0.64 (0.11), residues: 3326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 75 HIS 0.007 0.001 HIS J 37 PHE 0.026 0.002 PHE i 292 TYR 0.023 0.002 TYR r 406 ARG 0.010 0.000 ARG F 34 *********************** 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 1388 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 1147 time to evaluate : 5.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 THR cc_start: 0.7449 (m) cc_final: 0.7022 (p) REVERT: B 48 MET cc_start: 0.7403 (mmm) cc_final: 0.6744 (mmm) REVERT: B 169 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8837 (mt-10) REVERT: C 99 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.7996 (pm20) REVERT: E 96 VAL cc_start: 0.8986 (OUTLIER) cc_final: 0.8760 (p) REVERT: F 92 GLU cc_start: 0.6337 (tp30) cc_final: 0.6045 (tp30) REVERT: G 136 GLU cc_start: 0.6542 (pp20) cc_final: 0.5890 (tm-30) REVERT: H 38 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7443 (mp) REVERT: H 54 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.7027 (mp0) REVERT: J 175 LYS cc_start: 0.6587 (mmtm) cc_final: 0.5864 (mmmt) REVERT: J 323 HIS cc_start: 0.6097 (m-70) cc_final: 0.5852 (m-70) REVERT: J 324 MET cc_start: 0.7941 (ptm) cc_final: 0.7521 (ptp) REVERT: M 54 GLU cc_start: 0.7519 (tp30) cc_final: 0.7286 (mm-30) REVERT: M 217 GLU cc_start: 0.7820 (pm20) cc_final: 0.7503 (pm20) REVERT: M 249 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7965 (mm-30) REVERT: M 360 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.6985 (ttm110) REVERT: M 696 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.6526 (mmt) REVERT: N 67 GLU cc_start: 0.7468 (tm-30) cc_final: 0.7079 (tm-30) REVERT: N 78 ASP cc_start: 0.8802 (OUTLIER) cc_final: 0.8315 (p0) REVERT: Q 414 ASP cc_start: 0.9205 (p0) cc_final: 0.8891 (p0) REVERT: T 61 GLU cc_start: 0.8426 (tp30) cc_final: 0.8058 (tt0) REVERT: T 107 LYS cc_start: 0.7684 (tmtt) cc_final: 0.7097 (ptpt) REVERT: U 71 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.6395 (mm-40) REVERT: W 135 SER cc_start: 0.8578 (t) cc_final: 0.8216 (m) REVERT: a 180 ASP cc_start: 0.8251 (t0) cc_final: 0.7825 (t0) REVERT: c 46 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.6976 (mt-10) REVERT: d 61 TYR cc_start: 0.8648 (OUTLIER) cc_final: 0.8146 (p90) REVERT: e 128 TYR cc_start: 0.8118 (t80) cc_final: 0.7892 (t80) REVERT: g 108 LYS cc_start: 0.8034 (mmtp) cc_final: 0.7769 (ptmm) REVERT: i 62 THR cc_start: 0.9438 (m) cc_final: 0.9155 (m) REVERT: i 117 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8447 (mt-10) REVERT: j 57 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8323 (mm) REVERT: k 34 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8077 (mm-30) REVERT: k 89 TYR cc_start: 0.6387 (m-80) cc_final: 0.6049 (m-80) REVERT: l 286 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8735 (tp) REVERT: l 393 ASP cc_start: 0.8215 (m-30) cc_final: 0.7961 (m-30) REVERT: l 395 ILE cc_start: 0.8996 (mm) cc_final: 0.8739 (mt) REVERT: l 409 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8103 (tt) REVERT: m 135 PHE cc_start: 0.9168 (OUTLIER) cc_final: 0.8563 (t80) REVERT: n 30 ARG cc_start: 0.7587 (mmm-85) cc_final: 0.7357 (mmm160) REVERT: p 170 ILE cc_start: 0.9456 (OUTLIER) cc_final: 0.9152 (mp) REVERT: r 114 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8022 (tm-30) REVERT: r 231 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9054 (mt) REVERT: v 54 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7171 (pp30) REVERT: w 241 TYR cc_start: 0.7979 (OUTLIER) cc_final: 0.6814 (t80) outliers start: 241 outliers final: 181 residues processed: 1294 average time/residue: 0.6138 time to fit residues: 1368.6654 Evaluate side-chains 1319 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1118 time to evaluate : 5.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 78 SER Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 71 GLN Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 114 ASP Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 148 ILE Chi-restraints excluded: chain J residue 154 GLN Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain J residue 320 GLU Chi-restraints excluded: chain J residue 340 ILE Chi-restraints excluded: chain L residue 133 ASP Chi-restraints excluded: chain L residue 151 LYS Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 249 GLU Chi-restraints excluded: chain M residue 315 THR Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 360 ARG Chi-restraints excluded: chain M residue 380 ASP Chi-restraints excluded: chain M residue 437 ASP Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 59 HIS Chi-restraints excluded: chain N residue 78 ASP Chi-restraints excluded: chain N residue 134 ILE Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 222 ARG Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 128 ILE Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain P residue 240 GLU Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 98 VAL Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 281 GLU Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain T residue 68 ILE Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain U residue 65 ASP Chi-restraints excluded: chain U residue 71 GLN Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain V residue 40 SER Chi-restraints excluded: chain V residue 53 VAL Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 105 THR Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 71 MET Chi-restraints excluded: chain a residue 78 THR Chi-restraints excluded: chain a residue 111 GLU Chi-restraints excluded: chain a residue 188 ASP Chi-restraints excluded: chain b residue 7 ASP Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 64 THR Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain b residue 91 THR Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 46 GLU Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain d residue 38 ASP Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 61 TYR Chi-restraints excluded: chain d residue 85 MET Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain f residue 60 LYS Chi-restraints excluded: chain h residue 19 THR Chi-restraints excluded: chain h residue 47 ILE Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain h residue 72 THR Chi-restraints excluded: chain h residue 87 ILE Chi-restraints excluded: chain h residue 88 LYS Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain i residue 45 MET Chi-restraints excluded: chain i residue 49 ASN Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 95 MET Chi-restraints excluded: chain i residue 161 SER Chi-restraints excluded: chain i residue 182 SER Chi-restraints excluded: chain i residue 237 MET Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain j residue 19 LEU Chi-restraints excluded: chain j residue 28 ASN Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain k residue 22 TYR Chi-restraints excluded: chain k residue 64 LEU Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain l residue 6 SER Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 15 LEU Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 127 THR Chi-restraints excluded: chain l residue 149 ILE Chi-restraints excluded: chain l residue 286 LEU Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 409 LEU Chi-restraints excluded: chain l residue 410 LEU Chi-restraints excluded: chain l residue 418 LEU Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 503 GLU Chi-restraints excluded: chain l residue 577 VAL Chi-restraints excluded: chain m residue 10 SER Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 66 VAL Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain m residue 148 SER Chi-restraints excluded: chain n residue 7 ILE Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain o residue 9 SER Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain o residue 114 LYS Chi-restraints excluded: chain p residue 11 THR Chi-restraints excluded: chain p residue 24 LEU Chi-restraints excluded: chain p residue 42 CYS Chi-restraints excluded: chain p residue 170 ILE Chi-restraints excluded: chain r residue 23 ILE Chi-restraints excluded: chain r residue 50 LEU Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 231 LEU Chi-restraints excluded: chain r residue 256 TYR Chi-restraints excluded: chain r residue 448 THR Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 105 MET Chi-restraints excluded: chain s residue 145 THR Chi-restraints excluded: chain s residue 161 THR Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 267 THR Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 89 ILE Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 204 VAL Chi-restraints excluded: chain w residue 207 VAL Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 312 VAL 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: 3.9990 chunk 668 optimal weight: 0.8980 chunk 712 optimal weight: 3.9990 chunk 428 optimal weight: 2.9990 chunk 310 optimal weight: 3.9990 chunk 559 optimal weight: 4.9990 chunk 218 optimal weight: 0.9980 chunk 643 optimal weight: 3.9990 chunk 673 optimal weight: 0.9980 chunk 709 optimal weight: 3.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- 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 136 HIS F 93 ASN ** J 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 GLN ** P 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 130 ASN ** e 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 23 ASN r 220 HIS s 235 ASN ** v 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 110 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 68230 Z= 0.231 Angle : 0.556 15.401 92319 Z= 0.277 Chirality : 0.041 0.238 10032 Planarity : 0.004 0.054 11542 Dihedral : 11.630 178.864 10206 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.32 % Favored : 95.66 % Rotamer: Outliers : 2.91 % Allowed : 18.99 % Favored : 78.10 % 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: 0.81 (0.09), residues: 8027 helix: 1.46 (0.08), residues: 4299 sheet: 0.26 (0.26), residues: 408 loop : -0.62 (0.11), residues: 3320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 75 HIS 0.007 0.001 HIS J 37 PHE 0.026 0.001 PHE i 292 TYR 0.027 0.001 TYR A 63 ARG 0.010 0.000 ARG F 34 *********************** 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 1340 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 1135 time to evaluate : 5.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 THR cc_start: 0.7408 (m) cc_final: 0.6910 (p) REVERT: A 337 MET cc_start: 0.7492 (mmm) cc_final: 0.7148 (mmt) REVERT: B 48 MET cc_start: 0.7395 (mmm) cc_final: 0.6748 (mmm) REVERT: C 99 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.7969 (pm20) REVERT: E 96 VAL cc_start: 0.8984 (OUTLIER) cc_final: 0.8764 (p) REVERT: G 136 GLU cc_start: 0.6532 (pp20) cc_final: 0.5881 (tm-30) REVERT: H 38 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.7494 (mp) REVERT: H 54 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.7055 (mp0) REVERT: J 175 LYS cc_start: 0.6584 (mmtm) cc_final: 0.5850 (mmmt) REVERT: J 323 HIS cc_start: 0.6075 (m-70) cc_final: 0.5831 (m-70) REVERT: J 324 MET cc_start: 0.7913 (ptm) cc_final: 0.7380 (ptp) REVERT: K 75 ASN cc_start: 0.6979 (t0) cc_final: 0.6756 (t0) REVERT: L 174 THR cc_start: 0.9017 (p) cc_final: 0.8777 (t) REVERT: M 54 GLU cc_start: 0.7492 (tp30) cc_final: 0.7246 (mm-30) REVERT: M 249 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7986 (mm-30) REVERT: M 360 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.6908 (ttm110) REVERT: M 696 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.6508 (mmt) REVERT: N 67 GLU cc_start: 0.7482 (tm-30) cc_final: 0.7097 (tm-30) REVERT: N 78 ASP cc_start: 0.8814 (OUTLIER) cc_final: 0.8328 (p0) REVERT: Q 414 ASP cc_start: 0.9200 (p0) cc_final: 0.8878 (p0) REVERT: T 61 GLU cc_start: 0.8419 (tp30) cc_final: 0.8039 (tt0) REVERT: T 107 LYS cc_start: 0.7684 (tmtt) cc_final: 0.7104 (ptpt) REVERT: U 71 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.6374 (mm-40) REVERT: V 118 MET cc_start: 0.8500 (mtt) cc_final: 0.8192 (mtp) REVERT: W 135 SER cc_start: 0.8555 (t) cc_final: 0.8197 (m) REVERT: d 61 TYR cc_start: 0.8637 (OUTLIER) cc_final: 0.8149 (p90) REVERT: e 128 TYR cc_start: 0.8080 (t80) cc_final: 0.7876 (t80) REVERT: g 108 LYS cc_start: 0.8020 (mmtp) cc_final: 0.7728 (mmtm) REVERT: i 62 THR cc_start: 0.9433 (m) cc_final: 0.9135 (m) REVERT: i 117 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8448 (mt-10) REVERT: j 57 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8300 (mm) REVERT: k 34 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8054 (mm-30) REVERT: k 89 TYR cc_start: 0.6336 (m-80) cc_final: 0.5883 (m-80) REVERT: l 286 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8739 (tp) REVERT: l 393 ASP cc_start: 0.8215 (m-30) cc_final: 0.7963 (m-30) REVERT: l 395 ILE cc_start: 0.8977 (mm) cc_final: 0.8685 (mt) REVERT: l 409 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8070 (tt) REVERT: m 135 PHE cc_start: 0.9149 (OUTLIER) cc_final: 0.8518 (t80) REVERT: n 30 ARG cc_start: 0.7621 (mmm-85) cc_final: 0.7398 (mmm160) REVERT: p 170 ILE cc_start: 0.9438 (OUTLIER) cc_final: 0.9130 (mp) REVERT: r 114 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.7994 (tm-30) REVERT: v 54 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7191 (pp30) REVERT: w 241 TYR cc_start: 0.7935 (OUTLIER) cc_final: 0.6712 (t80) outliers start: 205 outliers final: 173 residues processed: 1256 average time/residue: 0.6575 time to fit residues: 1428.5184 Evaluate side-chains 1311 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 1120 time to evaluate : 5.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 78 SER Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 71 GLN Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 114 ASP Chi-restraints excluded: chain J residue 154 GLN Chi-restraints excluded: chain J residue 320 GLU Chi-restraints excluded: chain J residue 340 ILE Chi-restraints excluded: chain L residue 133 ASP Chi-restraints excluded: chain L residue 151 LYS Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 249 GLU Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 360 ARG Chi-restraints excluded: chain M residue 380 ASP Chi-restraints excluded: chain M residue 437 ASP Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 59 HIS Chi-restraints excluded: chain N residue 78 ASP Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 222 ARG Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 128 ILE Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain P residue 153 ILE Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 98 VAL Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 281 GLU Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain U residue 65 ASP Chi-restraints excluded: chain U residue 71 GLN Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain V residue 40 SER Chi-restraints excluded: chain V residue 53 VAL Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 105 THR Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 71 MET Chi-restraints excluded: chain a residue 78 THR Chi-restraints excluded: chain a residue 111 GLU Chi-restraints excluded: chain a residue 188 ASP Chi-restraints excluded: chain b residue 7 ASP Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 64 THR Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain b residue 91 THR Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain d residue 38 ASP Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 61 TYR Chi-restraints excluded: chain d residue 120 SER Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain f residue 60 LYS Chi-restraints excluded: chain h residue 19 THR Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain h residue 72 THR Chi-restraints excluded: chain h residue 87 ILE Chi-restraints excluded: chain h residue 88 LYS Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain i residue 45 MET Chi-restraints excluded: chain i residue 49 ASN Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 95 MET Chi-restraints excluded: chain i residue 154 MET Chi-restraints excluded: chain i residue 161 SER Chi-restraints excluded: chain i residue 182 SER Chi-restraints excluded: chain i residue 237 MET Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain j residue 9 THR Chi-restraints excluded: chain j residue 28 ASN Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain k residue 22 TYR Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain l residue 6 SER Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 15 LEU Chi-restraints excluded: chain l residue 23 ASN Chi-restraints excluded: chain l residue 52 LEU Chi-restraints excluded: chain l residue 127 THR Chi-restraints excluded: chain l residue 149 ILE Chi-restraints excluded: chain l residue 286 LEU Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 409 LEU Chi-restraints excluded: chain l residue 418 LEU Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 577 VAL Chi-restraints excluded: chain m residue 10 SER Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 66 VAL Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain m residue 148 SER Chi-restraints excluded: chain n residue 7 ILE Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain o residue 9 SER Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain o residue 114 LYS Chi-restraints excluded: chain p residue 24 LEU Chi-restraints excluded: chain p residue 42 CYS Chi-restraints excluded: chain p residue 170 ILE Chi-restraints excluded: chain r residue 23 ILE Chi-restraints excluded: chain r residue 50 LEU Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 256 TYR Chi-restraints excluded: chain r residue 448 THR Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 100 LEU Chi-restraints excluded: chain s residue 105 MET Chi-restraints excluded: chain s residue 145 THR Chi-restraints excluded: chain s residue 161 THR Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 267 THR Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 89 ILE Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 163 ILE Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 204 VAL Chi-restraints excluded: chain w residue 207 VAL Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 312 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 467 optimal weight: 1.9990 chunk 753 optimal weight: 7.9990 chunk 459 optimal weight: 0.8980 chunk 357 optimal weight: 9.9990 chunk 523 optimal weight: 6.9990 chunk 790 optimal weight: 8.9990 chunk 727 optimal weight: 3.9990 chunk 629 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 485 optimal weight: 7.9990 chunk 385 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 136 HIS ** J 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 GLN ** P 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 130 ASN Z 11 HIS ** e 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 23 ASN p 12 HIS r 220 HIS ** v 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 110 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 68230 Z= 0.230 Angle : 0.559 15.685 92319 Z= 0.278 Chirality : 0.041 0.235 10032 Planarity : 0.004 0.052 11542 Dihedral : 11.529 178.970 10206 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.47 % Favored : 95.52 % Rotamer: Outliers : 2.90 % Allowed : 19.12 % 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: 0.82 (0.09), residues: 8027 helix: 1.47 (0.08), residues: 4300 sheet: 0.25 (0.26), residues: 406 loop : -0.62 (0.11), residues: 3321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 75 HIS 0.005 0.001 HIS J 37 PHE 0.026 0.001 PHE i 292 TYR 0.031 0.001 TYR A 63 ARG 0.012 0.000 ARG F 34 ********************** 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 1343 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1139 time to evaluate : 5.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 THR cc_start: 0.7397 (m) cc_final: 0.6912 (p) REVERT: B 48 MET cc_start: 0.7393 (mmm) cc_final: 0.6747 (mmm) REVERT: C 99 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.7982 (pm20) REVERT: E 96 VAL cc_start: 0.8954 (OUTLIER) cc_final: 0.8734 (p) REVERT: G 136 GLU cc_start: 0.6531 (pp20) cc_final: 0.5888 (tm-30) REVERT: H 38 ILE cc_start: 0.7921 (OUTLIER) cc_final: 0.7488 (mp) REVERT: H 54 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6911 (mp0) REVERT: J 175 LYS cc_start: 0.6608 (mmtm) cc_final: 0.5858 (mmmt) REVERT: J 323 HIS cc_start: 0.6075 (m-70) cc_final: 0.5830 (m-70) REVERT: J 324 MET cc_start: 0.7935 (ptm) cc_final: 0.7392 (ptp) REVERT: K 75 ASN cc_start: 0.6980 (t0) cc_final: 0.6755 (t0) REVERT: L 174 THR cc_start: 0.8959 (p) cc_final: 0.8734 (t) REVERT: M 54 GLU cc_start: 0.7491 (tp30) cc_final: 0.7250 (mm-30) REVERT: M 217 GLU cc_start: 0.7793 (pm20) cc_final: 0.7409 (pm20) REVERT: M 249 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7984 (mm-30) REVERT: M 360 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.6905 (ttm110) REVERT: M 696 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.6560 (mmt) REVERT: N 67 GLU cc_start: 0.7469 (tm-30) cc_final: 0.7077 (tm-30) REVERT: N 78 ASP cc_start: 0.8815 (OUTLIER) cc_final: 0.8323 (p0) REVERT: Q 414 ASP cc_start: 0.9198 (p0) cc_final: 0.8875 (p0) REVERT: T 61 GLU cc_start: 0.8425 (tp30) cc_final: 0.8040 (tt0) REVERT: T 107 LYS cc_start: 0.7729 (tmtt) cc_final: 0.7145 (ptpt) REVERT: U 71 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.6359 (mm-40) REVERT: V 118 MET cc_start: 0.8556 (mtt) cc_final: 0.8258 (mtp) REVERT: W 135 SER cc_start: 0.8587 (t) cc_final: 0.8207 (m) REVERT: X 129 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8509 (pp20) REVERT: d 61 TYR cc_start: 0.8631 (OUTLIER) cc_final: 0.8054 (p90) REVERT: d 117 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7952 (mm-30) REVERT: e 128 TYR cc_start: 0.8056 (t80) cc_final: 0.7851 (t80) REVERT: f 65 ASP cc_start: 0.8712 (m-30) cc_final: 0.8128 (m-30) REVERT: g 36 MET cc_start: 0.8976 (mmm) cc_final: 0.8426 (mmm) REVERT: g 108 LYS cc_start: 0.8036 (mmtp) cc_final: 0.7757 (mmtm) REVERT: i 62 THR cc_start: 0.9429 (m) cc_final: 0.9117 (m) REVERT: i 117 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8446 (mt-10) REVERT: i 339 MET cc_start: 0.8630 (mmm) cc_final: 0.8303 (mmm) REVERT: j 57 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8287 (mm) REVERT: k 34 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8052 (mm-30) REVERT: k 89 TYR cc_start: 0.6292 (m-80) cc_final: 0.5847 (m-80) REVERT: l 286 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8737 (tp) REVERT: l 393 ASP cc_start: 0.8219 (m-30) cc_final: 0.7967 (m-30) REVERT: l 395 ILE cc_start: 0.8975 (mm) cc_final: 0.8686 (mt) REVERT: l 409 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8053 (tt) REVERT: m 135 PHE cc_start: 0.9147 (OUTLIER) cc_final: 0.8516 (t80) REVERT: n 30 ARG cc_start: 0.7620 (mmm-85) cc_final: 0.7391 (mmm160) REVERT: p 170 ILE cc_start: 0.9442 (OUTLIER) cc_final: 0.9134 (mp) REVERT: r 114 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.7992 (tm-30) REVERT: v 54 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7189 (pp30) REVERT: w 241 TYR cc_start: 0.7932 (OUTLIER) cc_final: 0.6719 (t80) outliers start: 204 outliers final: 176 residues processed: 1261 average time/residue: 0.6104 time to fit residues: 1327.8063 Evaluate side-chains 1315 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 1120 time to evaluate : 5.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 78 SER Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 71 GLN Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 114 ASP Chi-restraints excluded: chain J residue 154 GLN Chi-restraints excluded: chain J residue 320 GLU Chi-restraints excluded: chain J residue 340 ILE Chi-restraints excluded: chain L residue 133 ASP Chi-restraints excluded: chain L residue 151 LYS Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 249 GLU Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 360 ARG Chi-restraints excluded: chain M residue 380 ASP Chi-restraints excluded: chain M residue 437 ASP Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 59 HIS Chi-restraints excluded: chain N residue 78 ASP Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 222 ARG Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 128 ILE Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain P residue 153 ILE Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 98 VAL Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 281 GLU Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain U residue 65 ASP Chi-restraints excluded: chain U residue 71 GLN Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain V residue 40 SER Chi-restraints excluded: chain V residue 53 VAL Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 105 THR Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 71 MET Chi-restraints excluded: chain a residue 78 THR Chi-restraints excluded: chain a residue 111 GLU Chi-restraints excluded: chain a residue 188 ASP Chi-restraints excluded: chain b residue 7 ASP Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 64 THR Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain b residue 91 THR Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain d residue 38 ASP Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 61 TYR Chi-restraints excluded: chain d residue 85 MET Chi-restraints excluded: chain d residue 120 SER Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain f residue 60 LYS Chi-restraints excluded: chain h residue 19 THR Chi-restraints excluded: chain h residue 47 ILE Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain h residue 72 THR Chi-restraints excluded: chain h residue 87 ILE Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain i residue 45 MET Chi-restraints excluded: chain i residue 49 ASN Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 95 MET Chi-restraints excluded: chain i residue 154 MET Chi-restraints excluded: chain i residue 161 SER Chi-restraints excluded: chain i residue 182 SER Chi-restraints excluded: chain i residue 237 MET Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain j residue 9 THR Chi-restraints excluded: chain j residue 28 ASN Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain k residue 22 TYR Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain l residue 6 SER Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 15 LEU Chi-restraints excluded: chain l residue 127 THR Chi-restraints excluded: chain l residue 149 ILE Chi-restraints excluded: chain l residue 286 LEU Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 409 LEU Chi-restraints excluded: chain l residue 410 LEU Chi-restraints excluded: chain l residue 418 LEU Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 577 VAL Chi-restraints excluded: chain m residue 10 SER Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 66 VAL Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain m residue 148 SER Chi-restraints excluded: chain n residue 7 ILE Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain o residue 9 SER Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain o residue 114 LYS Chi-restraints excluded: chain p residue 11 THR Chi-restraints excluded: chain p residue 24 LEU Chi-restraints excluded: chain p residue 42 CYS Chi-restraints excluded: chain p residue 170 ILE Chi-restraints excluded: chain r residue 23 ILE Chi-restraints excluded: chain r residue 50 LEU Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 256 TYR Chi-restraints excluded: chain r residue 448 THR Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 105 MET Chi-restraints excluded: chain s residue 145 THR Chi-restraints excluded: chain s residue 161 THR Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 267 THR Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 89 ILE Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 110 GLN Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 163 ILE Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 204 VAL Chi-restraints excluded: chain w residue 207 VAL Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 312 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 499 optimal weight: 3.9990 chunk 670 optimal weight: 7.9990 chunk 192 optimal weight: 0.7980 chunk 580 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 174 optimal weight: 10.0000 chunk 630 optimal weight: 0.6980 chunk 263 optimal weight: 10.0000 chunk 647 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 116 optimal weight: 0.0970 overall best weight: 1.5182 ------------------------------------------------------------------------------- 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 136 HIS F 93 ASN ** J 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 GLN ** P 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 130 ASN ** e 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 23 ASN r 220 HIS ** v 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.124858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.101410 restraints weight = 104743.491| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.48 r_work: 0.2960 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.161 68230 Z= 0.232 Angle : 0.606 59.166 92319 Z= 0.316 Chirality : 0.041 0.695 10032 Planarity : 0.004 0.052 11542 Dihedral : 11.530 178.983 10206 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.48 % Favored : 95.49 % Rotamer: Outliers : 3.14 % Allowed : 18.93 % Favored : 77.93 % Cbeta Deviations : 0.01 % 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: 0.82 (0.09), residues: 8027 helix: 1.47 (0.08), residues: 4300 sheet: 0.25 (0.26), residues: 406 loop : -0.62 (0.11), residues: 3321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 75 HIS 0.005 0.001 HIS J 37 PHE 0.026 0.001 PHE i 292 TYR 0.028 0.001 TYR A 63 ARG 0.009 0.000 ARG F 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20497.41 seconds wall clock time: 358 minutes 20.60 seconds (21500.60 seconds total)