Starting phenix.real_space_refine on Sat Jan 20 06:22:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2l_32264/01_2024/7w2l_32264_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2l_32264/01_2024/7w2l_32264.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2l_32264/01_2024/7w2l_32264_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2l_32264/01_2024/7w2l_32264_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2l_32264/01_2024/7w2l_32264_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2l_32264/01_2024/7w2l_32264.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2l_32264/01_2024/7w2l_32264.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2l_32264/01_2024/7w2l_32264_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2l_32264/01_2024/7w2l_32264_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 36 5.49 5 Mg 1 5.21 5 S 473 5.16 5 C 42939 2.51 5 N 11065 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 119": "OE1" <-> "OE2" Residue "A GLU 129": "OE1" <-> "OE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "B GLU 160": "OE1" <-> "OE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "E GLU 34": "OE1" <-> "OE2" Residue "E GLU 91": "OE1" <-> "OE2" Residue "F GLU 38": "OE1" <-> "OE2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "H GLU 54": "OE1" <-> "OE2" Residue "J GLU 135": "OE1" <-> "OE2" Residue "J PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 158": "OE1" <-> "OE2" Residue "J GLU 162": "OE1" <-> "OE2" Residue "J PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 346": "OE1" <-> "OE2" Residue "K GLU 80": "OE1" <-> "OE2" Residue "K PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 92": "OE1" <-> "OE2" Residue "L GLU 69": "OE1" <-> "OE2" Residue "L GLU 108": "OE1" <-> "OE2" Residue "L GLU 148": "OE1" <-> "OE2" Residue "M GLU 67": "OE1" <-> "OE2" Residue "M GLU 161": "OE1" <-> "OE2" Residue "M GLU 217": "OE1" <-> "OE2" Residue "M GLU 369": "OE1" <-> "OE2" Residue "M GLU 370": "OE1" <-> "OE2" Residue "M GLU 395": "OE1" <-> "OE2" Residue "M GLU 468": "OE1" <-> "OE2" Residue "M GLU 535": "OE1" <-> "OE2" Residue "M GLU 591": "OE1" <-> "OE2" Residue "M GLU 647": "OE1" <-> "OE2" Residue "N PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 136": "OE1" <-> "OE2" Residue "O GLU 162": "OE1" <-> "OE2" Residue "O GLU 173": "OE1" <-> "OE2" Residue "O GLU 202": "OE1" <-> "OE2" Residue "O GLU 203": "OE1" <-> "OE2" Residue "O GLU 207": "OE1" <-> "OE2" Residue "P GLU 85": "OE1" <-> "OE2" Residue "P PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 194": "OE1" <-> "OE2" Residue "P GLU 225": "OE1" <-> "OE2" Residue "P GLU 240": "OE1" <-> "OE2" Residue "Q GLU 42": "OE1" <-> "OE2" Residue "Q GLU 45": "OE1" <-> "OE2" Residue "Q PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 212": "OE1" <-> "OE2" Residue "Q GLU 315": "OE1" <-> "OE2" Residue "S GLU 4": "OE1" <-> "OE2" Residue "S GLU 35": "OE1" <-> "OE2" Residue "S GLU 49": "OE1" <-> "OE2" Residue "T GLU 73": "OE1" <-> "OE2" Residue "W GLU 56": "OE1" <-> "OE2" Residue "W GLU 89": "OE1" <-> "OE2" Residue "W GLU 123": "OE1" <-> "OE2" Residue "X GLU 77": "OE1" <-> "OE2" Residue "X GLU 136": "OE1" <-> "OE2" Residue "X GLU 156": "OE1" <-> "OE2" Residue "Z GLU 30": "OE1" <-> "OE2" Residue "Z GLU 34": "OE1" <-> "OE2" Residue "Z GLU 49": "OE1" <-> "OE2" Residue "a GLU 97": "OE1" <-> "OE2" Residue "a GLU 103": "OE1" <-> "OE2" Residue "a GLU 108": "OE1" <-> "OE2" Residue "a GLU 145": "OE1" <-> "OE2" Residue "a GLU 148": "OE1" <-> "OE2" Residue "a GLU 153": "OE1" <-> "OE2" Residue "a GLU 155": "OE1" <-> "OE2" Residue "b GLU 17": "OE1" <-> "OE2" Residue "b GLU 115": "OE1" <-> "OE2" Residue "b GLU 122": "OE1" <-> "OE2" Residue "c GLU 148": "OE1" <-> "OE2" Residue "c GLU 185": "OE1" <-> "OE2" Residue "d GLU 12": "OE1" <-> "OE2" Residue "d GLU 50": "OE1" <-> "OE2" Residue "d GLU 89": "OE1" <-> "OE2" Residue "d GLU 101": "OE1" <-> "OE2" Residue "d GLU 128": "OE1" <-> "OE2" Residue "d GLU 130": "OE1" <-> "OE2" Residue "d PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 57": "OE1" <-> "OE2" Residue "e GLU 64": "OE1" <-> "OE2" Residue "e GLU 68": "OE1" <-> "OE2" Residue "e GLU 116": "OE1" <-> "OE2" Residue "e GLU 121": "OE1" <-> "OE2" Residue "e GLU 123": "OE1" <-> "OE2" Residue "f GLU 64": "OE1" <-> "OE2" Residue "g GLU 113": "OE1" <-> "OE2" Residue "h GLU 24": "OE1" <-> "OE2" Residue "h GLU 59": "OE1" <-> "OE2" Residue "i GLU 34": "OE1" <-> "OE2" Residue "j GLU 112": "OE1" <-> "OE2" Residue "k GLU 34": "OE1" <-> "OE2" Residue "k GLU 70": "OE1" <-> "OE2" Residue "l GLU 60": "OE1" <-> "OE2" Residue "l GLU 75": "OE1" <-> "OE2" Residue "l GLU 145": "OE1" <-> "OE2" Residue "l GLU 207": "OE1" <-> "OE2" Residue "l GLU 353": "OE1" <-> "OE2" Residue "l GLU 397": "OE1" <-> "OE2" Residue "m GLU 138": "OE1" <-> "OE2" Residue "n GLU 54": "OE1" <-> "OE2" Residue "o GLU 35": "OE1" <-> "OE2" Residue "o GLU 46": "OE1" <-> "OE2" Residue "o GLU 61": "OE1" <-> "OE2" Residue "o GLU 113": "OE1" <-> "OE2" Residue "p PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 50": "OE1" <-> "OE2" Residue "p GLU 68": "OE1" <-> "OE2" Residue "p GLU 69": "OE1" <-> "OE2" Residue "p GLU 70": "OE1" <-> "OE2" Residue "p GLU 123": "OE1" <-> "OE2" Residue "p GLU 134": "OE1" <-> "OE2" Residue "p GLU 136": "OE1" <-> "OE2" Residue "p GLU 152": "OE1" <-> "OE2" Residue "p GLU 160": "OE1" <-> "OE2" Residue "r GLU 87": "OE1" <-> "OE2" Residue "r GLU 114": "OE1" <-> "OE2" Residue "r GLU 123": "OE1" <-> "OE2" Residue "s GLU 24": "OE1" <-> "OE2" Residue "s GLU 59": "OE1" <-> "OE2" Residue "s GLU 227": "OE1" <-> "OE2" Residue "u GLU 17": "OE1" <-> "OE2" Residue "u GLU 58": "OE1" <-> "OE2" Residue "u PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 109": "OE1" <-> "OE2" Residue "v GLU 16": "OE1" <-> "OE2" Residue "v GLU 33": "OE1" <-> "OE2" Residue "v GLU 36": "OE1" <-> "OE2" Residue "v PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 91": "OE1" <-> "OE2" Residue "v GLU 103": "OE1" <-> "OE2" Residue "v GLU 105": "OE1" <-> "OE2" Residue "v GLU 116": "OE1" <-> "OE2" Residue "w GLU 115": "OE1" <-> "OE2" Residue "w GLU 185": "OE1" <-> "OE2" Residue "w GLU 251": "OE1" <-> "OE2" Residue "w GLU 254": "OE1" <-> "OE2" Residue "w GLU 262": "OE1" <-> "OE2" Residue "w GLU 267": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 66472 Number of models: 1 Model: "" Number of chains: 66 Chain: "A" Number of atoms: 3314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3314 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 409} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 963 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 108} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 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: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 683 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 910 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "I" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 762 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 85} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 2359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2359 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 16, 'TRANS': 280} Chain breaks: 3 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: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1013 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 118} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 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: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1671 Classifications: {'peptide': 217} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 195} Chain: "P" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1738 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "Q" Number of atoms: 3377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3377 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 27, 'TRANS': 391} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 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: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1017 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 133} 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: "W" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1154 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 8, 'TRANS': 133} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 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: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 577 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 63} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 22 Chain: "Z" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 663 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 80} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "a" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1152 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 129} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "b" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 875 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 91} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "c" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1315 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 20, 'TRANS': 135} Chain: "d" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1457 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 164} 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: "e" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 890 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 10, 'TRANS': 96} Chain: "f" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 342 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 40} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "g" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1000 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 11, 'TRANS': 109} Chain: "h" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 867 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "i" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2706 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 328} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "j" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 800 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 Chain: "k" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 748 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "l" Number of atoms: 4785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4785 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 28, 'TRANS': 574} Chain: "m" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 948 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "n" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 456 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 53} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "o" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1054 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 116} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "p" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1534 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 17, 'TRANS': 160} Chain: "r" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3631 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Chain: "s" Number of atoms: 2394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2394 Classifications: {'peptide': 303} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 281} Chain breaks: 1 Chain: "u" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1398 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "v" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1020 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 28 Chain: "w" Number of atoms: 2567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2567 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 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: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "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: "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: "U" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 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: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 130 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 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: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 99 Unusual residues: {'PEE': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 203 Unusual residues: {'CDL': 1, 'PEE': 1, 'PLX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {' UQ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {' UQ:plan-11': 1, ' UQ:plan-2': 1, ' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 35 Chain: "w" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2702 SG CYS A 382 49.108 48.274 170.154 1.00 26.43 S ATOM 3044 SG CYS A 425 48.252 44.577 175.603 1.00 10.10 S ATOM 2722 SG CYS A 385 46.011 43.963 169.726 1.00 23.82 S ATOM 2683 SG CYS A 379 43.653 48.820 173.631 1.00 23.38 S ATOM 3945 SG CYS B 113 40.255 65.562 135.216 1.00 22.82 S ATOM 3964 SG CYS B 116 45.114 62.881 139.200 1.00 15.66 S ATOM 3987 SG CYS B 119 46.471 65.667 133.981 1.00 13.00 S ATOM 4316 SG CYS B 162 43.677 59.937 134.234 1.00 4.42 S ATOM 4014 SG CYS B 123 52.773 68.523 129.873 1.00 0.00 S ATOM 4240 SG CYS B 152 51.306 66.896 123.746 1.00 13.01 S ATOM 4287 SG CYS B 158 48.988 63.240 128.355 1.00 0.00 S ATOM 4266 SG CYS B 155 55.182 63.316 127.065 1.00 0.00 S ATOM 5708 SG CYS C 166 57.946 67.109 119.901 1.00 0.64 S ATOM 4980 SG CYS C 72 59.396 68.749 113.756 1.00 5.18 S ATOM 4974 SG CYS C 71 63.425 66.626 116.310 1.00 3.35 S ATOM 5478 SG CYS C 136 60.678 71.545 118.615 1.00 2.73 S ATOM 14495 SG CYS M 131 43.692 62.511 151.242 1.00 5.37 S ATOM 14474 SG CYS M 128 47.394 58.028 148.122 1.00 0.42 S ATOM 14535 SG CYS M 137 49.179 61.268 153.605 1.00 0.00 S ATOM 14867 SG CYS M 179 46.993 61.130 164.636 1.00 12.28 S ATOM 15221 SG CYS M 226 44.206 63.938 160.214 1.00 19.95 S ATOM 14891 SG CYS M 182 41.541 63.585 166.222 1.00 4.63 S ATOM 14844 SG CYS M 176 41.369 58.372 162.550 1.00 12.05 S ATOM 14092 SG CYS M 78 58.179 55.898 168.768 1.00 13.49 S ATOM 14193 SG CYS M 92 56.335 57.950 171.102 1.00 12.84 S ATOM 13981 SG CYS M 64 52.129 58.113 168.550 1.00 19.50 S ATOM 14067 SG CYS M 75 53.274 56.319 165.490 1.00 3.16 S ATOM 21030 SG CYS O 135 32.242 31.129 176.662 1.00 43.49 S ATOM 21064 SG CYS O 140 31.893 27.651 177.541 1.00 54.24 S ATOM 21344 SG CYS O 176 36.516 32.531 179.576 1.00 44.46 S ATOM 21367 SG CYS O 180 36.853 29.247 180.158 1.00 52.69 S ATOM 28025 SG CYS T 86 32.241 52.205 142.079 1.00 13.79 S ATOM 28203 SG CYS T 111 33.360 55.499 143.399 1.00 16.75 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.59 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.59 Time building chain proxies: 26.74, per 1000 atoms: 0.40 Number of scatterers: 66472 At special positions: 0 Unit cell: (223.434, 221.285, 225.582, 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 473 16.00 P 36 15.00 Mg 1 11.99 O 11929 8.00 N 11065 7.00 C 42939 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS F 24 " - pdb=" SG CYS F 58 " distance=2.03 Simple disulfide: pdb=" SG CYS V 18 " - pdb=" SG CYS V 75 " distance=2.71 Simple disulfide: pdb=" SG CYS V 95 " - pdb=" SG CYS V 115 " distance=2.34 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 v 69 " - pdb=" SG CYS v 80 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.32 Conformation dependent library (CDL) restraints added in 9.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 92 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 64 " pdb=" FES O 301 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 180 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 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="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb=" SF4 B 301 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 116 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " pdb=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " pdb=" SF4 C 301 " pdb="FE3 SF4 C 301 " - pdb=" NE2 HIS Q 223 " pdb="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="FE2 SF4 M 801 " - pdb=" SG CYS M 128 " pdb="FE4 SF4 M 801 " - pdb=" SG CYS M 137 " 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="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " pdb="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 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: 341 helices and 29 sheets defined 52.8% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.52 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 58 Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 73 through 82 Processing helix chain 'A' and resid 95 through 103 removed outlier: 3.741A pdb=" N MET A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN A 103 " --> pdb=" O TRP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 132 Processing helix chain 'A' and resid 135 through 149 Processing helix chain 'A' and resid 163 through 178 Processing helix chain 'A' and resid 204 through 207 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 245 through 257 Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 259 through 263 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: 4.456A 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: 3.973A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 419 removed outlier: 3.982A pdb=" N ASP A 410 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 457 Proline residue: A 434 - end of helix Proline residue: A 444 - end of helix Processing helix chain 'B' and resid 50 through 62 Processing helix chain 'B' and resid 64 through 77 Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 187 through 211 removed outlier: 5.880A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU B 210 " --> pdb=" O GLN B 206 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N TYR B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 60 removed outlier: 3.720A pdb=" N VAL C 47 " --> pdb=" O GLY C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 79 Processing helix chain 'C' and resid 86 through 89 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 114 through 123 Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 141 through 143 No H-bonds generated for 'chain 'C' and resid 141 through 143' Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 189 through 194 Processing helix chain 'E' and resid 25 through 49 Proline residue: E 44 - end of helix Processing helix chain 'E' and resid 56 through 70 removed outlier: 4.282A pdb=" N ASN E 70 " --> pdb=" O MET E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 94 Processing helix chain 'E' and resid 100 through 106 removed outlier: 4.359A pdb=" N PHE E 106 " --> pdb=" O HIS E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 124 Processing helix chain 'F' and resid 31 through 47 removed outlier: 6.399A pdb=" N VAL F 42 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N GLU F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 72 No H-bonds generated for 'chain 'F' and resid 70 through 72' Processing helix chain 'F' and resid 84 through 96 Processing helix chain 'G' and resid 76 through 89 Processing helix chain 'G' and resid 112 through 126 Processing helix chain 'G' and resid 132 through 135 No H-bonds generated for 'chain 'G' and resid 132 through 135' Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'H' and resid 20 through 37 removed outlier: 4.039A pdb=" N GLN H 37 " --> pdb=" O ASP H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 60 Processing helix chain 'H' and resid 66 through 72 Processing helix chain 'H' and resid 77 through 97 Processing helix chain 'I' and resid 6 through 16 Processing helix chain 'I' and resid 54 through 56 No H-bonds generated for 'chain 'I' and resid 54 through 56' Processing helix chain 'I' and resid 60 through 62 No H-bonds generated for 'chain 'I' and resid 60 through 62' Processing helix chain 'J' and resid 38 through 40 No H-bonds generated for 'chain 'J' and resid 38 through 40' Processing helix chain 'J' and resid 64 through 76 removed outlier: 4.156A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N MET J 76 " --> pdb=" O HIS J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 97 removed outlier: 3.504A pdb=" N MET J 92 " --> pdb=" O TYR J 89 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N HIS J 93 " --> pdb=" O ASP J 90 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 113 through 119 Processing helix chain 'J' and resid 141 through 145 Processing helix chain 'J' and resid 147 through 159 Processing helix chain 'J' and resid 179 through 194 Processing helix chain 'J' and resid 214 through 218 Processing helix chain 'J' and resid 242 through 254 Processing helix chain 'J' and resid 273 through 283 Processing helix chain 'J' and resid 317 through 323 Processing helix chain 'J' and resid 336 through 338 No H-bonds generated for 'chain 'J' and resid 336 through 338' Processing helix chain 'J' and resid 345 through 356 removed outlier: 4.092A pdb=" N ILE J 350 " --> pdb=" O GLU J 346 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLU J 351 " --> pdb=" O LEU J 347 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ARG J 355 " --> pdb=" O GLU J 351 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N HIS J 356 " --> pdb=" O VAL J 352 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 80 removed outlier: 3.771A 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: 4.533A pdb=" N LYS K 95 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 4.844A 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 141 Processing helix chain 'L' and resid 161 through 164 Processing helix chain 'M' and resid 49 through 56 removed outlier: 3.576A pdb=" N VAL M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 122 Processing helix chain 'M' and resid 138 through 146 Processing helix chain 'M' and resid 173 through 175 No H-bonds generated for 'chain 'M' and resid 173 through 175' Processing helix chain 'M' and resid 181 through 188 Processing helix chain 'M' and resid 201 through 203 No H-bonds generated for 'chain 'M' and resid 201 through 203' Processing helix chain 'M' and resid 219 through 225 removed outlier: 3.984A pdb=" N ILE M 225 " --> pdb=" O ILE M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 298 removed outlier: 5.091A pdb=" N TYR M 294 " --> pdb=" O THR M 290 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASP M 295 " --> pdb=" O ARG M 291 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N GLY M 296 " --> pdb=" O PHE M 292 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU M 297 " --> pdb=" O ALA M 293 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LYS M 298 " --> pdb=" O TYR M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 319 through 332 removed outlier: 3.621A pdb=" N MET M 329 " --> pdb=" O ARG M 325 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 337 No H-bonds generated for 'chain 'M' and resid 335 through 337' Processing helix chain 'M' and resid 348 through 360 Processing helix chain 'M' and resid 378 through 380 No H-bonds generated for 'chain 'M' and resid 378 through 380' Processing helix chain 'M' and resid 382 through 385 Processing helix chain 'M' and resid 392 through 395 Processing helix chain 'M' and resid 407 through 410 No H-bonds generated for 'chain 'M' and resid 407 through 410' Processing helix chain 'M' and resid 412 through 424 Processing helix chain 'M' and resid 449 through 457 Processing helix chain 'M' and resid 461 through 468 Processing helix chain 'M' and resid 478 through 483 removed outlier: 4.395A pdb=" N ARG M 483 " --> pdb=" O SER M 479 " (cutoff:3.500A) Processing helix chain 'M' and resid 486 through 503 Processing helix chain 'M' and resid 522 through 527 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 589 through 591 No H-bonds generated for 'chain 'M' and resid 589 through 591' Processing helix chain 'M' and resid 619 through 629 Processing helix chain 'M' and resid 639 through 649 Processing helix chain 'M' and resid 651 through 653 No H-bonds generated for 'chain 'M' and resid 651 through 653' Processing helix chain 'M' and resid 665 through 672 Processing helix chain 'M' and resid 691 through 693 No H-bonds generated for 'chain 'M' and resid 691 through 693' Processing helix chain 'M' and resid 699 through 702 No H-bonds generated for 'chain 'M' and resid 699 through 702' Processing helix chain 'M' and resid 705 through 715 Processing helix chain 'N' and resid 3 through 17 removed outlier: 3.669A pdb=" N HIS N 17 " --> pdb=" O GLN N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 30 Processing helix chain 'N' and resid 79 through 81 No H-bonds generated for 'chain 'N' and resid 79 through 81' Processing helix chain 'N' and resid 84 through 90 Processing helix chain 'O' and resid 57 through 69 Processing helix chain 'O' and resid 75 through 90 removed outlier: 4.490A 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 145 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: 3.669A pdb=" N VAL P 93 " --> pdb=" O PRO P 90 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ILE P 94 " --> pdb=" O ASP P 91 " (cutoff:3.500A) Proline residue: P 95 - end of helix Processing helix chain 'P' and resid 161 through 174 removed outlier: 3.981A pdb=" N TRP P 165 " --> pdb=" O ALA P 162 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE P 174 " --> pdb=" O TRP P 171 " (cutoff:3.500A) Processing helix chain 'P' and resid 243 through 245 No H-bonds generated for 'chain 'P' and resid 243 through 245' Processing helix chain 'Q' and resid 41 through 47 removed outlier: 3.914A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N PHE Q 47 " --> pdb=" O TRP Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 58 through 60 No H-bonds generated for 'chain 'Q' and resid 58 through 60' Processing helix chain 'Q' and resid 120 through 126 removed outlier: 3.891A pdb=" N GLU Q 125 " --> pdb=" O GLU Q 121 " (cutoff:3.500A) removed outlier: 4.071A 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: 4.040A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.611A 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: 4.252A 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: 4.347A 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 439 removed outlier: 4.511A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LYS Q 437 " --> pdb=" O ALA Q 433 " (cutoff:3.500A) Processing helix chain 'Q' and resid 446 through 454 Processing helix chain 'Q' and resid 458 through 462 Processing helix chain 'S' and resid 2 through 29 Proline residue: S 7 - end of helix Proline residue: S 19 - end of helix Processing helix chain 'S' and resid 44 through 55 Processing helix chain 'S' and resid 66 through 68 No H-bonds generated for 'chain 'S' and resid 66 through 68' Processing helix chain 'T' and resid 50 through 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 34 Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 39 through 47 Processing helix chain 'U' and resid 79 through 83 Processing helix chain 'V' and resid 3 through 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: 3.600A pdb=" N THR V 121 " --> pdb=" O TYR V 117 " (cutoff:3.500A) Processing helix chain 'W' and resid 32 through 97 Proline residue: W 73 - end of helix Processing helix chain 'W' and resid 121 through 125 Processing helix chain 'W' and resid 130 through 142 removed outlier: 6.373A pdb=" N PHE W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE W 141 " --> pdb=" O THR W 137 " (cutoff:3.500A) Processing helix chain 'X' and resid 76 through 88 Processing helix chain 'X' and resid 112 through 126 Processing helix chain 'X' and resid 132 through 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 77 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 28 through 39 removed outlier: 3.688A pdb=" N ARG Z 39 " --> pdb=" O LYS Z 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 47 through 53 removed outlier: 3.649A pdb=" N ALA Z 50 " --> pdb=" O ARG Z 47 " (cutoff:3.500A) removed outlier: 4.790A 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: 3.839A 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 removed outlier: 3.532A pdb=" N GLN b 26 " --> pdb=" O TRP b 22 " (cutoff:3.500A) Processing helix chain 'b' and resid 65 through 74 Processing helix chain 'b' and resid 76 through 88 Processing helix chain 'c' and resid 34 through 36 No H-bonds generated for 'chain 'c' and resid 34 through 36' Processing helix chain 'c' and resid 45 through 54 Processing helix chain 'c' and resid 109 through 111 No H-bonds generated for 'chain 'c' and resid 109 through 111' Processing helix chain 'c' and resid 126 through 149 Processing helix chain 'd' and resid 29 through 58 removed outlier: 4.733A pdb=" N ARG d 43 " --> pdb=" O LEU d 39 " (cutoff:3.500A) Proline residue: d 44 - end of helix Processing helix chain 'd' and resid 74 through 76 No H-bonds generated for 'chain 'd' and resid 74 through 76' Processing helix chain 'd' and resid 82 through 124 removed outlier: 3.992A pdb=" N GLY d 118 " --> pdb=" O GLN d 114 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLU d 119 " --> pdb=" O GLN d 115 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N SER d 120 " --> pdb=" O ARG d 116 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TYR d 121 " --> pdb=" O GLU d 117 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ARG d 122 " --> pdb=" O GLY d 118 " (cutoff:3.500A) removed outlier: 6.355A 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 Processing helix chain 'e' and resid 115 through 131 Processing helix chain 'e' and resid 144 through 146 No H-bonds generated for 'chain 'e' and resid 144 through 146' Processing helix chain 'f' and resid 41 through 73 Processing helix chain 'g' and resid 4 through 6 No H-bonds generated for 'chain 'g' and resid 4 through 6' Processing helix chain 'g' and resid 19 through 22 Processing helix chain 'g' and resid 31 through 50 Processing helix chain 'g' and resid 60 through 98 Processing helix chain 'g' and resid 111 through 113 No H-bonds generated for 'chain 'g' and resid 111 through 113' Processing helix chain 'h' and resid 6 through 10 Processing helix chain 'h' and resid 16 through 18 No H-bonds generated for 'chain 'h' and resid 16 through 18' Processing helix chain 'h' and resid 26 through 28 No H-bonds generated for 'chain 'h' and resid 26 through 28' Processing helix chain 'h' and resid 34 through 44 Processing helix chain 'h' and resid 49 through 55 Processing helix chain 'h' and resid 57 through 68 Processing helix chain 'h' and resid 70 through 89 Processing helix chain 'i' and resid 3 through 22 Processing helix chain 'i' and resid 26 through 44 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: 4.391A pdb=" N GLU i 117 " --> pdb=" O PHE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 144 removed outlier: 3.852A pdb=" N GLN i 134 " --> pdb=" O LEU i 130 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LYS i 135 " --> pdb=" O LEU i 131 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU i 136 " --> pdb=" O THR i 132 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ALA i 137 " --> pdb=" O TRP i 133 " (cutoff:3.500A) Proline residue: i 138 - end of helix Processing helix chain 'i' and resid 146 through 148 No H-bonds generated for 'chain 'i' and resid 146 through 148' Processing helix chain 'i' and resid 151 through 171 removed outlier: 3.921A pdb=" N LEU i 170 " --> pdb=" O GLY i 166 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASN i 171 " --> pdb=" O TRP i 167 " (cutoff:3.500A) Processing helix chain 'i' and resid 175 through 191 Processing helix chain 'i' and resid 198 through 221 Processing helix chain 'i' and resid 227 through 235 removed outlier: 3.811A pdb=" N HIS i 232 " --> pdb=" O LEU i 228 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N THR i 233 " --> pdb=" O SER i 229 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N TRP i 234 " --> pdb=" O LEU i 230 " (cutoff:3.500A) removed outlier: 5.567A 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: 4.359A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) Processing helix chain 'i' and resid 309 through 316 Processing helix chain 'i' and resid 326 through 332 Processing helix chain 'i' and resid 337 through 345 Proline residue: i 341 - end of helix removed outlier: 3.553A pdb=" N SER i 344 " --> pdb=" O PRO i 341 " (cutoff:3.500A) 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: 5.687A 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 54 through 85 removed outlier: 3.648A 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: 3.764A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR l 16 " --> pdb=" O LEU l 12 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE l 17 " --> pdb=" O THR l 13 " (cutoff:3.500A) Proline residue: l 18 - end of helix removed outlier: 4.942A pdb=" N ASN l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) Processing helix chain 'l' and resid 26 through 28 No H-bonds generated for 'chain 'l' and resid 26 through 28' Processing helix chain 'l' and resid 32 through 57 removed outlier: 4.240A 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: 3.895A 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 157 removed outlier: 3.647A pdb=" N TRP l 157 " --> pdb=" O LEU l 153 " (cutoff:3.500A) Processing helix chain 'l' and resid 162 through 192 removed outlier: 4.022A pdb=" N GLY l 181 " --> pdb=" O ILE l 177 " (cutoff:3.500A) Processing helix chain 'l' and resid 198 through 203 Processing helix chain 'l' and resid 210 through 224 Processing helix chain 'l' and resid 227 through 229 No H-bonds generated for 'chain 'l' and resid 227 through 229' Processing helix chain 'l' and resid 231 through 238 removed outlier: 3.956A pdb=" N MET l 237 " --> pdb=" O LEU l 233 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N GLU l 238 " --> pdb=" O PRO l 234 " (cutoff:3.500A) Processing helix chain 'l' and resid 241 through 246 Processing helix chain 'l' and resid 255 through 262 Processing helix chain 'l' and resid 264 through 269 removed outlier: 4.351A pdb=" N THR l 269 " --> pdb=" O PRO l 265 " (cutoff:3.500A) Processing helix chain 'l' and resid 271 through 294 removed outlier: 4.394A 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: 3.709A 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: 4.856A 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: 3.726A pdb=" N LEU l 457 " --> pdb=" O SER l 453 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.431A 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: 4.306A pdb=" N THR l 508 " --> pdb=" O LEU l 504 " (cutoff:3.500A) removed outlier: 4.629A 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: 4.133A pdb=" N MET l 533 " --> pdb=" O PRO l 530 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU l 536 " --> pdb=" O MET l 533 " (cutoff:3.500A) Proline residue: l 537 - end of helix removed outlier: 4.497A 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 removed outlier: 3.580A pdb=" N SER l 590 " --> pdb=" O LEU l 586 " (cutoff:3.500A) 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: 3.867A pdb=" N LEU m 61 " --> pdb=" O PHE m 57 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU m 65 " --> pdb=" O LEU m 61 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N VAL m 66 " --> pdb=" O GLY m 62 " (cutoff:3.500A) Processing helix chain 'm' and resid 138 through 146 removed outlier: 4.104A 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: 6.606A pdb=" N VAL n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N HIS n 14 " --> pdb=" O ASP n 10 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ILE n 15 " --> pdb=" O HIS n 11 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU n 16 " --> pdb=" O TRP n 12 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL n 17 " --> pdb=" O VAL n 13 " (cutoff:3.500A) Proline residue: n 18 - end of helix removed outlier: 3.594A 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 22 No H-bonds generated for 'chain 'o' and resid 20 through 22' Processing helix chain 'o' and resid 27 through 51 Processing helix chain 'o' and resid 63 through 73 Processing helix chain 'o' and resid 77 through 79 No H-bonds generated for 'chain 'o' and resid 77 through 79' Processing helix chain 'o' and resid 84 through 118 Proline residue: o 97 - end of helix Processing helix chain 'p' and resid 12 through 30 Processing helix chain 'p' and resid 34 through 47 Processing helix chain 'p' and resid 57 through 62 Processing helix chain 'p' and resid 66 through 73 Processing helix chain 'p' and resid 102 through 106 Processing helix chain 'p' and resid 109 through 113 Processing helix chain 'p' and resid 116 through 143 removed outlier: 3.871A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 3.953A 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: 4.413A pdb=" N LEU r 12 " --> pdb=" O THR r 8 " (cutoff:3.500A) Proline residue: r 13 - end of helix Processing helix chain 'r' and resid 23 through 42 removed outlier: 3.645A pdb=" N LEU r 39 " --> pdb=" O SER r 35 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N SER r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU r 42 " --> pdb=" O SER r 38 " (cutoff:3.500A) Processing helix chain 'r' and resid 62 through 83 removed outlier: 3.833A pdb=" N LEU r 73 " --> pdb=" O THR r 69 " (cutoff:3.500A) Proline residue: r 74 - end of helix removed outlier: 4.770A pdb=" N SER r 82 " --> pdb=" O MET r 78 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N HIS r 83 " --> pdb=" O ALA r 79 " (cutoff:3.500A) Processing helix chain 'r' and resid 89 through 111 removed outlier: 3.706A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 115 through 135 removed outlier: 4.543A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.427A 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: 3.505A pdb=" N ALA r 145 " --> pdb=" O ARG r 142 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR r 152 " --> pdb=" O PHE r 149 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU r 158 " --> pdb=" O ALA r 155 " (cutoff:3.500A) Proline residue: r 159 - end of helix removed outlier: 3.664A 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: 4.455A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS r 206 " --> pdb=" O ALA r 202 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 221 removed outlier: 4.160A pdb=" N LYS r 218 " --> pdb=" O LEU r 214 " (cutoff:3.500A) Processing helix chain 'r' and resid 225 through 233 Processing helix chain 'r' and resid 235 through 248 removed outlier: 4.723A pdb=" N GLY r 239 " --> pdb=" O LEU r 235 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY r 240 " --> pdb=" O LEU r 236 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N THR r 248 " --> pdb=" O MET r 244 " (cutoff:3.500A) Processing helix chain 'r' and resid 253 through 257 Processing helix chain 'r' and resid 259 through 277 removed outlier: 3.864A pdb=" N ILE r 270 " --> pdb=" O MET r 266 " (cutoff:3.500A) removed outlier: 3.718A 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: 3.811A pdb=" N ARG r 336 " --> pdb=" O THR r 332 " (cutoff:3.500A) Processing helix chain 'r' and resid 348 through 351 No H-bonds generated for 'chain 'r' and resid 348 through 351' Processing helix chain 'r' and resid 353 through 366 Processing helix chain 'r' and resid 373 through 388 Processing helix chain 'r' and resid 390 through 415 removed outlier: 3.620A pdb=" N ILE r 393 " --> pdb=" O ASN r 390 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR r 413 " --> pdb=" O MET r 410 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR r 414 " --> pdb=" O LEU r 411 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN r 415 " --> pdb=" O ILE r 412 " (cutoff:3.500A) Processing helix chain 'r' and resid 431 through 449 Proline residue: r 443 - end of helix removed outlier: 4.119A 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 31 Proline residue: s 12 - end of helix removed outlier: 3.610A pdb=" N THR s 21 " --> pdb=" O VAL s 17 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU s 22 " --> pdb=" O ALA s 18 " (cutoff:3.500A) Processing helix chain 's' and resid 47 through 56 Processing helix chain 's' and resid 68 through 86 Proline residue: s 75 - end of helix removed outlier: 4.509A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 123 removed outlier: 4.387A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 156 removed outlier: 3.856A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) Processing helix chain 's' and resid 162 through 168 removed outlier: 3.622A 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 274 Processing helix chain 's' and resid 282 through 310 removed outlier: 4.735A pdb=" N LEU s 294 " --> pdb=" O TRP s 290 " (cutoff:3.500A) Proline residue: s 295 - end of helix Proline residue: s 308 - end of helix Processing helix chain 'u' and resid 10 through 13 Processing helix chain 'u' and resid 22 through 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 91 removed outlier: 3.927A pdb=" N LEU u 57 " --> pdb=" O ARG u 54 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLU u 58 " --> pdb=" O ARG u 55 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL u 63 " --> pdb=" O GLY u 60 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N CYS u 78 " --> pdb=" O LYS u 75 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ALA u 79 " --> pdb=" O ARG u 76 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLU u 80 " --> pdb=" O HIS u 77 " (cutoff:3.500A) Proline residue: u 81 - end of helix removed outlier: 3.863A pdb=" N THR u 87 " --> pdb=" O GLU u 84 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR u 91 " --> pdb=" O CYS u 88 " (cutoff:3.500A) Processing helix chain 'u' and resid 101 through 112 Processing helix chain 'v' and resid 3 through 10 Processing helix chain 'v' and resid 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 44 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 96 No H-bonds generated for 'chain 'w' and resid 94 through 96' Processing helix chain 'w' and resid 114 through 119 Processing helix chain 'w' and resid 127 through 153 Processing helix chain 'w' and resid 166 through 175 removed outlier: 3.735A pdb=" N ARG w 175 " --> pdb=" O ALA w 172 " (cutoff:3.500A) Processing helix chain 'w' and resid 181 through 197 removed outlier: 5.403A pdb=" N GLU w 197 " --> pdb=" O VAL w 193 " (cutoff:3.500A) Processing helix chain 'w' and resid 211 through 221 Processing helix chain 'w' and resid 226 through 228 No H-bonds generated for 'chain 'w' and resid 226 through 228' Processing helix chain 'w' and resid 231 through 243 Processing helix chain 'w' and resid 245 through 250 Processing helix chain 'w' and resid 261 through 263 No H-bonds generated for 'chain 'w' and resid 261 through 263' Processing helix chain 'w' and resid 266 through 275 Processing helix chain 'w' and resid 288 through 298 Processing helix chain 'w' and resid 301 through 304 No H-bonds generated for 'chain 'w' and resid 301 through 304' Processing helix chain 'w' and resid 307 through 309 No H-bonds generated for 'chain 'w' and resid 307 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: 6.814A pdb=" N TYR A 112 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ALA A 243 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL A 114 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA A 153 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N VAL A 115 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N TYR A 155 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ALA A 117 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TYR A 157 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ASP A 194 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE A 156 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N PHE A 196 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE A 158 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.136A 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: 6.081A pdb=" N GLU B 133 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 5.304A 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: 6.331A pdb=" N VAL C 102 " --> pdb=" O MET C 65 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N PHE C 67 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE C 104 " --> pdb=" O PHE C 67 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR C 129 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N VAL C 105 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL C 131 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.421A 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: 6.898A pdb=" N ARG F 68 " --> pdb=" O ARG F 17 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE F 19 " --> pdb=" O TRP F 66 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N TRP F 66 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ILE F 21 " --> pdb=" O LYS F 64 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LYS F 64 " --> pdb=" O ILE F 21 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 262 through 265 removed outlier: 6.559A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE J 167 " --> pdb=" O ASN J 128 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLN J 79 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N VAL J 58 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE J 81 " --> pdb=" O VAL J 58 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'L' and resid 144 through 147 Processing sheet with id= I, first strand: chain 'L' and resid 106 through 108 Processing sheet with id= J, first strand: chain 'M' and resid 32 through 36 Processing sheet with id= K, first strand: chain 'M' and resid 79 through 81 Processing sheet with id= L, first strand: chain 'M' and resid 169 through 171 Processing sheet with id= M, first strand: chain 'M' and resid 196 through 198 Processing sheet with id= N, first strand: chain 'M' and resid 246 through 251 Processing sheet with id= O, first strand: chain 'M' and resid 306 through 308 Processing sheet with id= P, first strand: chain 'M' and resid 366 through 368 removed outlier: 8.456A pdb=" N CYS M 367 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ALA M 340 " --> pdb=" O CYS M 367 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL M 544 " --> pdb=" O ALA M 339 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N ILE M 341 " --> pdb=" O VAL M 544 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N PHE M 546 " --> pdb=" O ILE M 341 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N PHE M 565 " --> pdb=" O LEU M 545 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU M 547 " --> pdb=" O PHE M 565 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE M 567 " --> pdb=" O LEU M 547 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL M 582 " --> pdb=" O TYR M 568 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N GLY M 570 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU M 584 " --> pdb=" O GLY M 570 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'M' and resid 513 through 516 removed outlier: 8.208A pdb=" N ASN M 514 " --> pdb=" O PRO M 472 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL M 399 " --> pdb=" O MET M 473 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LYS M 428 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LEU M 402 " --> pdb=" O LYS M 428 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA M 430 " --> pdb=" O LEU M 402 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ASP M 443 " --> pdb=" O LEU M 431 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'M' and resid 595 through 597 Processing sheet with id= S, first strand: chain 'N' and resid 60 through 63 removed outlier: 6.480A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N LEU N 38 " --> pdb=" O GLU N 50 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'O' and resid 169 through 174 removed outlier: 6.500A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N VAL O 134 " --> pdb=" O VAL O 174 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'P' and resid 110 through 118 removed outlier: 6.822A pdb=" N ASN P 131 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU P 114 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL P 129 " --> pdb=" O LEU P 114 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA P 116 " --> pdb=" O GLU P 127 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLU P 127 " --> pdb=" O ALA P 116 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LEU P 84 " --> pdb=" O ARG P 140 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N TYR P 146 " --> pdb=" O ILE P 88 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'P' and resid 208 through 213 Processing sheet with id= W, first strand: chain 'Q' and resid 80 through 84 removed outlier: 3.606A pdb=" N ARG Q 96 " --> pdb=" O HIS Q 112 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N VAL Q 106 " --> pdb=" O SER Q 102 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'Q' and resid 394 through 402 Processing sheet with id= Y, first strand: chain 'T' and resid 83 through 86 Processing sheet with id= Z, first strand: chain 'l' and resid 69 through 71 Processing sheet with id= AA, first strand: chain 'l' and resid 62 through 67 removed outlier: 6.451A pdb=" N LEU l 78 " --> pdb=" O ASN l 65 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'w' and resid 60 through 64 removed outlier: 6.523A pdb=" N VAL w 203 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ASP w 63 " --> pdb=" O VAL w 203 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N VAL w 205 " --> pdb=" O ASP w 63 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLU w 254 " --> pdb=" O VAL w 204 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N TYR w 206 " --> pdb=" O GLU w 254 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU w 256 " --> pdb=" O TYR w 206 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ASP w 208 " --> pdb=" O LEU w 256 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TYR w 258 " --> pdb=" O ASP w 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'w' and resid 84 through 86 2904 hydrogen bonds defined for protein. 8001 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 22.77 Time building geometry restraints manager: 23.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 27236 1.40 - 1.62: 39963 1.62 - 1.85: 841 1.85 - 2.07: 1 2.07 - 2.29: 80 Bond restraints: 68121 Sorted by residual: bond pdb=" C3D NAI A 503 " pdb=" C4D NAI A 503 " ideal model delta sigma weight residual 1.524 1.266 0.258 2.00e-02 2.50e+03 1.67e+02 bond pdb=" C1D NAI A 503 " pdb=" C2D NAI A 503 " ideal model delta sigma weight residual 1.528 1.286 0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C1B NAI A 503 " pdb=" O4B NAI A 503 " ideal model delta sigma weight residual 1.397 1.634 -0.237 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C1B NAI A 503 " pdb=" C2B NAI A 503 " ideal model delta sigma weight residual 1.528 1.299 0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C3' ADP w 401 " pdb=" C4' ADP w 401 " ideal model delta sigma weight residual 1.524 1.299 0.225 2.00e-02 2.50e+03 1.26e+02 ... (remaining 68116 not shown) Histogram of bond angle deviations from ideal: 73.59 - 86.02: 76 86.02 - 98.46: 5 98.46 - 110.89: 24695 110.89 - 123.32: 64939 123.32 - 135.75: 2479 Bond angle restraints: 92194 Sorted by residual: angle pdb=" N MET Q 144 " pdb=" CA MET Q 144 " pdb=" C MET Q 144 " ideal model delta sigma weight residual 111.28 121.91 -10.63 1.09e+00 8.42e-01 9.50e+01 angle pdb=" C5B NDP J 401 " pdb=" O5B NDP J 401 " pdb=" PA NDP J 401 " ideal model delta sigma weight residual 103.84 118.50 -14.66 1.91e+00 2.73e-01 5.86e+01 angle pdb=" PA NDP J 401 " pdb=" O3 NDP J 401 " pdb=" PN NDP J 401 " ideal model delta sigma weight residual 107.74 122.64 -14.90 1.95e+00 2.62e-01 5.81e+01 angle pdb=" C11 CDL a 201 " pdb=" CA5 CDL a 201 " pdb=" OA6 CDL a 201 " ideal model delta sigma weight residual 111.33 121.05 -9.72 1.32e+00 5.72e-01 5.41e+01 angle pdb=" C51 CDL g 202 " pdb=" CB5 CDL g 202 " pdb=" OB6 CDL g 202 " ideal model delta sigma weight residual 111.33 120.71 -9.38 1.32e+00 5.72e-01 5.03e+01 ... (remaining 92189 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.55: 39762 35.55 - 71.09: 1419 71.09 - 106.64: 125 106.64 - 142.18: 21 142.18 - 177.73: 12 Dihedral angle restraints: 41339 sinusoidal: 17638 harmonic: 23701 Sorted by residual: dihedral pdb=" C TYR l 587 " pdb=" N TYR l 587 " pdb=" CA TYR l 587 " pdb=" CB TYR l 587 " ideal model delta harmonic sigma weight residual -122.60 -143.86 21.26 0 2.50e+00 1.60e-01 7.23e+01 dihedral pdb=" N TYR l 587 " pdb=" C TYR l 587 " pdb=" CA TYR l 587 " pdb=" CB TYR l 587 " ideal model delta harmonic sigma weight residual 122.80 143.98 -21.18 0 2.50e+00 1.60e-01 7.18e+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 -102.41 75.32 -177.73 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 41336 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.177: 9998 0.177 - 0.353: 29 0.353 - 0.530: 1 0.530 - 0.706: 0 0.706 - 0.883: 1 Chirality restraints: 10029 Sorted by residual: chirality pdb=" CA TYR l 587 " pdb=" N TYR l 587 " pdb=" C TYR l 587 " pdb=" CB TYR l 587 " both_signs ideal model delta sigma weight residual False 2.51 1.63 0.88 2.00e-01 2.50e+01 1.95e+01 chirality pdb=" C3B NDP J 401 " pdb=" C2B NDP J 401 " pdb=" C4B NDP J 401 " pdb=" O3B NDP J 401 " both_signs ideal model delta sigma weight residual False -2.75 -2.35 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" CA TRP l 557 " pdb=" N TRP l 557 " pdb=" C TRP l 557 " pdb=" CB TRP l 557 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.03e+00 ... (remaining 10026 not shown) Planarity restraints: 11540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 UQ s 401 " 0.226 2.00e-02 2.50e+03 4.88e-01 2.98e+03 pdb=" C11 UQ s 401 " 0.338 2.00e-02 2.50e+03 pdb=" C7 UQ s 401 " 0.578 2.00e-02 2.50e+03 pdb=" C8 UQ s 401 " -0.715 2.00e-02 2.50e+03 pdb=" C9 UQ s 401 " -0.426 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 UQ s 401 " -0.308 2.00e-02 2.50e+03 2.95e-01 1.08e+03 pdb=" C18 UQ s 401 " 0.283 2.00e-02 2.50e+03 pdb=" C19 UQ s 401 " 0.376 2.00e-02 2.50e+03 pdb=" C20 UQ s 401 " -0.010 2.00e-02 2.50e+03 pdb=" C21 UQ s 401 " -0.342 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP J 401 " 0.192 2.00e-02 2.50e+03 1.98e-01 4.88e+02 pdb=" C3N NDP J 401 " -0.359 2.00e-02 2.50e+03 pdb=" C4N NDP J 401 " 0.146 2.00e-02 2.50e+03 pdb=" C7N NDP J 401 " 0.073 2.00e-02 2.50e+03 pdb=" N1N NDP J 401 " -0.052 2.00e-02 2.50e+03 ... (remaining 11537 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 4275 2.73 - 3.28: 66999 3.28 - 3.82: 113384 3.82 - 4.36: 142551 4.36 - 4.90: 238661 Nonbonded interactions: 565870 Sorted by model distance: nonbonded pdb=" N GLU W 131 " pdb=" OE1 GLU W 131 " model vdw 2.192 2.520 nonbonded pdb=" OG SER J 204 " pdb=" O GLN J 238 " model vdw 2.200 2.440 nonbonded pdb=" O ASP A 50 " pdb=" NH2 ARG A 59 " model vdw 2.203 2.520 nonbonded pdb=" OD2 ASP N 32 " pdb=" NH2 ARG N 58 " model vdw 2.207 2.520 nonbonded pdb=" OH TYR w 143 " pdb=" O LEU w 199 " model vdw 2.214 2.440 ... (remaining 565865 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 138 or (resid 139 and (name N or name CA or nam \ e C or name O or name CB )) or resid 140 through 142 or (resid 143 through 144 a \ nd (name N or name CA or name C or name O or name CB )) or resid 145 through 149 \ or (resid 150 through 153 and (name N or name 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=0.59 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: 1.530 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: 0.060 Extract box with map and model: 8.850 Check model and map are aligned: 0.760 Set scattering table: 0.480 Process input model: 160.520 Find NCS groups from input model: 2.760 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:14.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 189.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.311 68121 Z= 0.428 Angle : 0.798 17.291 92194 Z= 0.412 Chirality : 0.045 0.883 10029 Planarity : 0.008 0.488 11540 Dihedral : 17.979 177.727 26032 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.77 % Favored : 96.16 % Rotamer: Outliers : 0.23 % Allowed : 12.77 % Favored : 87.00 % 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: 0.79 (0.09), residues: 8027 helix: 1.41 (0.08), residues: 4238 sheet: 0.33 (0.26), residues: 408 loop : -0.55 (0.11), residues: 3381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.009 0.001 HIS J 37 PHE 0.032 0.001 PHE i 292 TYR 0.027 0.001 TYR l 422 ARG 0.009 0.001 ARG C 98 *********************** 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 1159 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1143 time to evaluate : 5.913 Fit side-chains revert: symmetry clash REVERT: F 38 GLU cc_start: 0.7763 (tt0) cc_final: 0.7512 (tp30) REVERT: F 39 LYS cc_start: 0.7728 (mmtt) cc_final: 0.7338 (mttp) REVERT: I 33 LYS cc_start: 0.8677 (mmtm) cc_final: 0.8438 (mmtm) REVERT: M 97 MET cc_start: 0.8339 (mtt) cc_final: 0.8129 (mtm) REVERT: M 329 MET cc_start: 0.7946 (mmm) cc_final: 0.7723 (mpt) REVERT: N 122 GLN cc_start: 0.8548 (mp10) cc_final: 0.8304 (mp10) REVERT: S 59 ARG cc_start: 0.8444 (mtm-85) cc_final: 0.8242 (mpp-170) REVERT: V 40 SER cc_start: 0.7465 (t) cc_final: 0.7111 (m) REVERT: V 101 LEU cc_start: 0.7769 (tt) cc_final: 0.7523 (tm) REVERT: V 117 TYR cc_start: 0.7729 (m-80) cc_final: 0.7472 (m-80) REVERT: W 50 MET cc_start: 0.9041 (mmm) cc_final: 0.8805 (tpt) REVERT: X 82 ARG cc_start: 0.8206 (mtp180) cc_final: 0.7911 (mtp180) REVERT: a 69 LYS cc_start: 0.8572 (mttm) cc_final: 0.8316 (mtpm) REVERT: e 116 GLU cc_start: 0.7649 (pt0) cc_final: 0.7335 (tt0) REVERT: f 70 LYS cc_start: 0.8461 (mtpt) cc_final: 0.8211 (mtpp) REVERT: h 42 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7777 (mm-30) REVERT: h 87 ILE cc_start: 0.8299 (mm) cc_final: 0.8046 (mm) REVERT: i 322 GLN cc_start: 0.7211 (pt0) cc_final: 0.6819 (pm20) REVERT: i 323 MET cc_start: 0.7861 (mtm) cc_final: 0.7537 (ptp) REVERT: i 329 MET cc_start: 0.9170 (mmt) cc_final: 0.8896 (mpp) REVERT: k 92 ASN cc_start: 0.7644 (m110) cc_final: 0.7417 (m-40) REVERT: l 176 ARG cc_start: 0.8720 (mmt-90) cc_final: 0.8506 (mmt90) REVERT: l 571 MET cc_start: 0.8879 (ttp) cc_final: 0.8673 (tmm) REVERT: l 601 LEU cc_start: 0.5498 (mp) cc_final: 0.5020 (tt) REVERT: o 108 ASP cc_start: 0.8931 (t0) cc_final: 0.8673 (t0) REVERT: p 179 MET cc_start: 0.7313 (mpp) cc_final: 0.7056 (mpp) REVERT: r 302 MET cc_start: 0.9376 (mmp) cc_final: 0.9110 (mmp) REVERT: s 43 TYR cc_start: 0.8015 (m-80) cc_final: 0.7659 (m-80) REVERT: v 100 LYS cc_start: 0.8217 (mttt) cc_final: 0.7941 (mttm) outliers start: 16 outliers final: 7 residues processed: 1148 average time/residue: 1.5292 time to fit residues: 2262.8164 Evaluate side-chains 1076 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1069 time to evaluate : 5.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain M residue 30 ASN Chi-restraints excluded: chain Q residue 141 TYR Chi-restraints excluded: chain Y residue 78 ASP Chi-restraints excluded: chain d residue 34 THR Chi-restraints excluded: chain l residue 554 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 669 optimal weight: 5.9990 chunk 601 optimal weight: 1.9990 chunk 333 optimal weight: 5.9990 chunk 205 optimal weight: 6.9990 chunk 405 optimal weight: 8.9990 chunk 321 optimal weight: 4.9990 chunk 621 optimal weight: 0.8980 chunk 240 optimal weight: 4.9990 chunk 377 optimal weight: 6.9990 chunk 462 optimal weight: 10.0000 chunk 720 optimal weight: 8.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 ASN K 78 HIS M 278 HIS ** M 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 182 ASN S 46 ASN V 79 GLN ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 189 ASN c 56 ASN d 115 GLN ** d 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 319 HIS l 2 ASN ** l 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 79 ASN p 51 HIS ** p 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 157 ASN v 65 GLN w 215 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.0775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 68121 Z= 0.400 Angle : 0.650 11.155 92194 Z= 0.327 Chirality : 0.046 0.207 10029 Planarity : 0.006 0.069 11540 Dihedral : 14.265 177.294 10167 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.14 % Favored : 95.81 % Rotamer: Outliers : 2.99 % Allowed : 14.81 % Favored : 82.20 % 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: 0.55 (0.09), residues: 8027 helix: 1.22 (0.08), residues: 4236 sheet: 0.26 (0.27), residues: 404 loop : -0.67 (0.11), residues: 3387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP M 422 HIS 0.012 0.001 HIS p 76 PHE 0.037 0.002 PHE i 292 TYR 0.035 0.002 TYR l 587 ARG 0.008 0.001 ARG W 68 *********************** 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 1297 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 1087 time to evaluate : 6.098 Fit side-chains revert: symmetry clash REVERT: A 323 SER cc_start: 0.8599 (t) cc_final: 0.8381 (m) REVERT: A 456 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7709 (mp10) REVERT: C 99 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8306 (pt0) REVERT: E 31 ARG cc_start: 0.8359 (mtt180) cc_final: 0.8143 (mtt180) REVERT: E 45 ASN cc_start: 0.7952 (OUTLIER) cc_final: 0.7638 (m-40) REVERT: F 25 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8108 (tt0) REVERT: F 38 GLU cc_start: 0.7762 (tt0) cc_final: 0.7527 (tp30) REVERT: F 39 LYS cc_start: 0.7648 (mmtt) cc_final: 0.7314 (mttp) REVERT: I 33 LYS cc_start: 0.8676 (mmtm) cc_final: 0.8442 (mmtm) REVERT: I 109 ASP cc_start: 0.8180 (t70) cc_final: 0.7881 (t0) REVERT: M 97 MET cc_start: 0.8341 (mtt) cc_final: 0.8099 (mtm) REVERT: M 329 MET cc_start: 0.8001 (mmm) cc_final: 0.7757 (mpt) REVERT: M 513 MET cc_start: 0.8378 (tpt) cc_final: 0.7951 (tpt) REVERT: M 636 TYR cc_start: 0.8398 (OUTLIER) cc_final: 0.7790 (p90) REVERT: M 663 ASN cc_start: 0.7747 (t0) cc_final: 0.7476 (t0) REVERT: N 122 GLN cc_start: 0.8562 (mp10) cc_final: 0.8329 (mp10) REVERT: S 1 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8292 (mmm) REVERT: S 59 ARG cc_start: 0.8539 (mtm-85) cc_final: 0.8233 (mpp-170) REVERT: U 16 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7768 (mp0) REVERT: V 117 TYR cc_start: 0.7797 (m-80) cc_final: 0.7593 (m-80) REVERT: W 50 MET cc_start: 0.9100 (mmm) cc_final: 0.8844 (tpt) REVERT: W 98 MET cc_start: 0.8422 (mmp) cc_final: 0.8126 (mmt) REVERT: Z 15 GLU cc_start: 0.6220 (OUTLIER) cc_final: 0.5805 (pm20) REVERT: a 69 LYS cc_start: 0.8595 (mttm) cc_final: 0.8349 (mtpm) REVERT: e 116 GLU cc_start: 0.7646 (pt0) cc_final: 0.7363 (tt0) REVERT: f 70 LYS cc_start: 0.8650 (mtpt) cc_final: 0.8434 (mtpp) REVERT: h 87 ILE cc_start: 0.8461 (mm) cc_final: 0.8200 (mm) REVERT: i 200 MET cc_start: 0.9328 (OUTLIER) cc_final: 0.8460 (mpt) REVERT: i 244 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8671 (ttm) REVERT: i 322 GLN cc_start: 0.7282 (pt0) cc_final: 0.6940 (pm20) REVERT: i 323 MET cc_start: 0.7973 (mtm) cc_final: 0.7591 (ptp) REVERT: i 329 MET cc_start: 0.9250 (mmt) cc_final: 0.9038 (mpp) REVERT: l 380 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9198 (tp) REVERT: l 383 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8755 (tpt) REVERT: l 571 MET cc_start: 0.8956 (ttp) cc_final: 0.8672 (tmm) REVERT: l 601 LEU cc_start: 0.5530 (mp) cc_final: 0.5132 (tt) REVERT: o 30 ARG cc_start: 0.7968 (mmt90) cc_final: 0.7033 (mmt180) REVERT: o 42 ARG cc_start: 0.8147 (ptm-80) cc_final: 0.7882 (ptt-90) REVERT: r 139 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8051 (mm110) REVERT: s 24 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8221 (tm-30) REVERT: v 29 TYR cc_start: 0.7581 (t80) cc_final: 0.7314 (t80) REVERT: v 53 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8875 (tp) REVERT: v 105 GLU cc_start: 0.7981 (tp30) cc_final: 0.7508 (tm-30) outliers start: 210 outliers final: 100 residues processed: 1193 average time/residue: 1.5273 time to fit residues: 2361.2303 Evaluate side-chains 1149 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 1034 time to evaluate : 5.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain J residue 158 GLU Chi-restraints excluded: chain J residue 319 VAL Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 30 ASN Chi-restraints excluded: chain M residue 74 ASN Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 426 ASP Chi-restraints excluded: chain M residue 487 THR Chi-restraints excluded: chain M residue 498 GLN Chi-restraints excluded: chain M residue 534 VAL Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 556 THR Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 654 VAL Chi-restraints excluded: chain N residue 68 MET Chi-restraints excluded: chain N residue 101 LYS Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 141 SER 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 156 SER Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain U residue 16 GLU Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 86 ASP Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 154 VAL Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain Y residue 78 ASP Chi-restraints excluded: chain Z residue 15 GLU Chi-restraints excluded: chain Z residue 67 LEU Chi-restraints excluded: chain a residue 58 LYS Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 182 VAL Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 34 THR Chi-restraints excluded: chain d residue 38 ASP Chi-restraints excluded: chain d residue 75 THR Chi-restraints excluded: chain e residue 124 ARG Chi-restraints excluded: chain e residue 143 ASP Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain i residue 45 MET Chi-restraints excluded: chain i residue 200 MET Chi-restraints excluded: chain i residue 244 MET Chi-restraints excluded: chain i residue 281 LEU Chi-restraints excluded: chain i residue 347 ASN Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain l residue 62 ILE Chi-restraints excluded: chain l residue 159 HIS Chi-restraints excluded: chain l residue 252 MET Chi-restraints excluded: chain l residue 267 MET Chi-restraints excluded: chain l residue 380 LEU Chi-restraints excluded: chain l residue 383 MET Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 480 THR Chi-restraints excluded: chain l residue 498 PHE Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 578 SER Chi-restraints excluded: chain m residue 11 THR Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain o residue 86 THR Chi-restraints excluded: chain p residue 132 SER Chi-restraints excluded: chain p residue 140 LEU Chi-restraints excluded: chain p residue 151 THR Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 58 SER Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 139 GLN Chi-restraints excluded: chain r residue 350 THR Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 144 VAL Chi-restraints excluded: chain s residue 258 ASN Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 62 LEU Chi-restraints excluded: chain u residue 66 CYS Chi-restraints excluded: chain u residue 78 CYS Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain u residue 118 VAL Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 133 SER Chi-restraints excluded: chain w residue 194 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 400 optimal weight: 5.9990 chunk 223 optimal weight: 0.9990 chunk 599 optimal weight: 0.3980 chunk 490 optimal weight: 0.0970 chunk 198 optimal weight: 3.9990 chunk 721 optimal weight: 0.3980 chunk 779 optimal weight: 6.9990 chunk 642 optimal weight: 8.9990 chunk 715 optimal weight: 0.9990 chunk 245 optimal weight: 3.9990 chunk 578 optimal weight: 3.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS F 76 ASN K 75 ASN K 78 HIS K 79 HIS L 86 ASN ** M 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 54 GLN c 56 ASN d 23 GLN d 131 GLN e 86 ASN g 63 GLN l 226 GLN l 446 ASN o 79 ASN p 51 HIS r 81 GLN r 139 GLN v 65 GLN w 155 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 68121 Z= 0.145 Angle : 0.515 10.856 92194 Z= 0.260 Chirality : 0.039 0.172 10029 Planarity : 0.004 0.057 11540 Dihedral : 13.108 179.933 10163 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.46 % Favored : 96.50 % Rotamer: Outliers : 2.49 % Allowed : 16.65 % Favored : 80.86 % 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: 0.94 (0.09), residues: 8027 helix: 1.56 (0.08), residues: 4230 sheet: 0.23 (0.26), residues: 413 loop : -0.48 (0.11), residues: 3384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.010 0.001 HIS K 78 PHE 0.028 0.001 PHE i 292 TYR 0.025 0.001 TYR l 422 ARG 0.006 0.000 ARG f 71 *********************** 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 1328 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 1153 time to evaluate : 5.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7639 (mp10) REVERT: B 110 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.7705 (tp30) REVERT: C 99 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8316 (pt0) REVERT: C 195 ARG cc_start: 0.8396 (mpp80) cc_final: 0.8063 (mtt180) REVERT: F 38 GLU cc_start: 0.7733 (tt0) cc_final: 0.7492 (tp30) REVERT: F 39 LYS cc_start: 0.7696 (mmtt) cc_final: 0.7404 (mttp) REVERT: H 71 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7800 (mt0) REVERT: I 33 LYS cc_start: 0.8666 (mmtm) cc_final: 0.8410 (mmtm) REVERT: J 97 MET cc_start: 0.9459 (mtt) cc_final: 0.9159 (mtt) REVERT: L 73 LYS cc_start: 0.8295 (ptpt) cc_final: 0.7825 (ptmt) REVERT: L 78 ARG cc_start: 0.8798 (ttt-90) cc_final: 0.8536 (ttt-90) REVERT: M 97 MET cc_start: 0.8326 (mtt) cc_final: 0.8084 (mtm) REVERT: M 329 MET cc_start: 0.7950 (mmm) cc_final: 0.7724 (mpt) REVERT: M 543 LYS cc_start: 0.7865 (mttp) cc_final: 0.7481 (mptt) REVERT: M 636 TYR cc_start: 0.8304 (OUTLIER) cc_final: 0.7612 (p90) REVERT: M 663 ASN cc_start: 0.7697 (t0) cc_final: 0.7485 (t0) REVERT: N 122 GLN cc_start: 0.8559 (mp10) cc_final: 0.8351 (mp10) REVERT: O 202 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7826 (mp0) REVERT: P 234 ASP cc_start: 0.8640 (m-30) cc_final: 0.8332 (m-30) REVERT: Q 308 TYR cc_start: 0.8723 (OUTLIER) cc_final: 0.7479 (p90) REVERT: S 1 MET cc_start: 0.8635 (mmm) cc_final: 0.8371 (tpp) REVERT: S 59 ARG cc_start: 0.8425 (mtm-85) cc_final: 0.8151 (mpp-170) REVERT: U 16 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7683 (mp0) REVERT: V 40 SER cc_start: 0.7427 (t) cc_final: 0.7058 (m) REVERT: V 110 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7833 (mp) REVERT: V 117 TYR cc_start: 0.7758 (m-80) cc_final: 0.7475 (m-80) REVERT: W 50 MET cc_start: 0.9057 (mmm) cc_final: 0.8828 (tpt) REVERT: W 98 MET cc_start: 0.8172 (mmp) cc_final: 0.7878 (mmt) REVERT: Z 15 GLU cc_start: 0.6089 (OUTLIER) cc_final: 0.5721 (pm20) REVERT: a 69 LYS cc_start: 0.8575 (mttm) cc_final: 0.8341 (mtpm) REVERT: a 106 VAL cc_start: 0.8929 (m) cc_final: 0.8665 (p) REVERT: a 176 LYS cc_start: 0.8764 (ptmt) cc_final: 0.8212 (ttpp) REVERT: e 83 ASP cc_start: 0.8509 (OUTLIER) cc_final: 0.7767 (t0) REVERT: e 116 GLU cc_start: 0.7567 (pt0) cc_final: 0.7305 (tt0) REVERT: f 70 LYS cc_start: 0.8464 (mtpt) cc_final: 0.8254 (mtpp) REVERT: h 87 ILE cc_start: 0.8373 (mm) cc_final: 0.8145 (mm) REVERT: h 101 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7605 (mmtp) REVERT: i 244 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8567 (ttm) REVERT: i 304 MET cc_start: 0.9175 (mtm) cc_final: 0.8937 (mtp) REVERT: i 322 GLN cc_start: 0.7266 (pt0) cc_final: 0.6927 (pm20) REVERT: i 323 MET cc_start: 0.8034 (mtm) cc_final: 0.7582 (ptp) REVERT: k 97 GLN cc_start: 0.6343 (OUTLIER) cc_final: 0.5966 (mt0) REVERT: l 571 MET cc_start: 0.8860 (ttp) cc_final: 0.8625 (tmm) REVERT: l 601 LEU cc_start: 0.5269 (mp) cc_final: 0.4847 (tt) REVERT: o 30 ARG cc_start: 0.7974 (mmt90) cc_final: 0.7075 (mmt180) REVERT: o 42 ARG cc_start: 0.8097 (ptm-80) cc_final: 0.7867 (ptt-90) REVERT: o 108 ASP cc_start: 0.8910 (t70) cc_final: 0.8647 (t0) REVERT: p 48 PHE cc_start: 0.7412 (OUTLIER) cc_final: 0.6514 (t80) REVERT: r 45 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7574 (pp) REVERT: r 337 VAL cc_start: 0.8625 (t) cc_final: 0.8306 (m) REVERT: s 11 ILE cc_start: 0.8874 (mm) cc_final: 0.8671 (mt) REVERT: u 91 TYR cc_start: 0.9260 (t80) cc_final: 0.8897 (t80) REVERT: v 29 TYR cc_start: 0.7515 (t80) cc_final: 0.7214 (t80) REVERT: v 53 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8701 (tp) REVERT: v 105 GLU cc_start: 0.7943 (tp30) cc_final: 0.7551 (tm-30) outliers start: 175 outliers final: 71 residues processed: 1253 average time/residue: 1.4926 time to fit residues: 2440.2725 Evaluate side-chains 1148 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1060 time to evaluate : 5.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 129 THR 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 F residue 27 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 71 GLN Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain J residue 118 LYS Chi-restraints excluded: chain J residue 158 GLU Chi-restraints excluded: chain J residue 317 ASP Chi-restraints excluded: chain J residue 319 VAL Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 317 THR Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 403 VAL Chi-restraints excluded: chain M residue 426 ASP Chi-restraints excluded: chain M residue 498 GLN Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 556 THR Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 68 MET Chi-restraints excluded: chain N residue 135 GLN Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 202 GLU Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 409 VAL Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain U residue 16 GLU Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 39 THR Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 86 ASP Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain Y residue 78 ASP Chi-restraints excluded: chain Z residue 15 GLU Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 182 VAL Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 34 THR Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain e residue 143 ASP Chi-restraints excluded: chain f residue 46 LEU Chi-restraints excluded: chain h residue 101 LYS Chi-restraints excluded: chain i residue 244 MET Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain i residue 281 LEU Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 62 ILE Chi-restraints excluded: chain l residue 267 MET Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 578 SER Chi-restraints excluded: chain l residue 584 ILE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain p residue 48 PHE Chi-restraints excluded: chain p residue 132 SER Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 367 LEU Chi-restraints excluded: chain r residue 375 LEU Chi-restraints excluded: chain s residue 258 ASN Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 78 CYS Chi-restraints excluded: chain u residue 121 ASP Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 133 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 712 optimal weight: 5.9990 chunk 542 optimal weight: 0.9990 chunk 374 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 344 optimal weight: 10.0000 chunk 484 optimal weight: 6.9990 chunk 724 optimal weight: 0.9980 chunk 766 optimal weight: 8.9990 chunk 378 optimal weight: 8.9990 chunk 686 optimal weight: 7.9990 chunk 206 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 ASN K 78 HIS L 163 ASN M 460 HIS ** M 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 116 ASN P 138 ASN V 89 ASN Z 21 GLN c 56 ASN c 84 GLN d 131 GLN e 86 ASN g 63 GLN i 171 ASN p 51 HIS p 124 GLN u 16 GLN v 65 GLN w 155 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 68121 Z= 0.285 Angle : 0.569 11.190 92194 Z= 0.286 Chirality : 0.043 0.189 10029 Planarity : 0.005 0.054 11540 Dihedral : 12.799 178.506 10161 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.96 % Favored : 96.00 % Rotamer: Outliers : 3.29 % Allowed : 17.07 % Favored : 79.64 % 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: 1.50 (0.08), residues: 4234 sheet: 0.26 (0.26), residues: 406 loop : -0.51 (0.11), residues: 3387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 422 HIS 0.009 0.001 HIS K 78 PHE 0.034 0.002 PHE i 292 TYR 0.026 0.002 TYR l 587 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 1309 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 1078 time to evaluate : 5.942 Fit side-chains revert: symmetry clash REVERT: A 456 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7697 (mp10) REVERT: B 110 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.7780 (tp30) REVERT: C 66 THR cc_start: 0.7621 (OUTLIER) cc_final: 0.7257 (t) REVERT: C 98 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.6207 (ptp-170) REVERT: C 99 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8332 (pt0) REVERT: F 38 GLU cc_start: 0.7721 (tt0) cc_final: 0.7463 (tp30) REVERT: F 39 LYS cc_start: 0.7830 (mmtt) cc_final: 0.7476 (mttp) REVERT: G 115 GLN cc_start: 0.8049 (tm-30) cc_final: 0.7761 (tm130) REVERT: G 124 ASP cc_start: 0.7602 (p0) cc_final: 0.7396 (p0) REVERT: I 33 LYS cc_start: 0.8660 (mmtm) cc_final: 0.8399 (mmtm) REVERT: I 109 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.7785 (t0) REVERT: J 118 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7925 (tttt) REVERT: M 97 MET cc_start: 0.8322 (mtt) cc_final: 0.8066 (mtm) REVERT: M 329 MET cc_start: 0.7999 (mmm) cc_final: 0.7771 (mpt) REVERT: M 636 TYR cc_start: 0.8347 (OUTLIER) cc_final: 0.7640 (p90) REVERT: N 122 GLN cc_start: 0.8565 (mp10) cc_final: 0.8363 (mp10) REVERT: O 202 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7714 (mp0) REVERT: O 222 ARG cc_start: 0.8114 (ttp80) cc_final: 0.7852 (ttp80) REVERT: P 234 ASP cc_start: 0.8673 (m-30) cc_final: 0.8361 (m-30) REVERT: Q 308 TYR cc_start: 0.8785 (OUTLIER) cc_final: 0.7469 (p90) REVERT: S 59 ARG cc_start: 0.8412 (mtm-85) cc_final: 0.8114 (mpp-170) REVERT: T 46 ASP cc_start: 0.7344 (OUTLIER) cc_final: 0.7095 (m-30) REVERT: U 16 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7676 (mp0) REVERT: V 83 LYS cc_start: 0.7045 (mmtp) cc_final: 0.6481 (mmmt) REVERT: V 110 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7877 (mp) REVERT: V 117 TYR cc_start: 0.7746 (m-80) cc_final: 0.7501 (m-80) REVERT: W 50 MET cc_start: 0.9094 (mmm) cc_final: 0.8872 (tpt) REVERT: Z 15 GLU cc_start: 0.6201 (OUTLIER) cc_final: 0.5972 (pm20) REVERT: a 69 LYS cc_start: 0.8579 (mttm) cc_final: 0.8326 (mtpm) REVERT: a 176 LYS cc_start: 0.8836 (ptmt) cc_final: 0.8276 (ttpp) REVERT: c 37 PHE cc_start: 0.8643 (OUTLIER) cc_final: 0.8369 (m-10) REVERT: c 143 MET cc_start: 0.9019 (mmm) cc_final: 0.8815 (mmm) REVERT: e 83 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.7961 (t0) REVERT: e 116 GLU cc_start: 0.7628 (pt0) cc_final: 0.7340 (tt0) REVERT: f 70 LYS cc_start: 0.8452 (mtpt) cc_final: 0.8237 (mtpp) REVERT: h 87 ILE cc_start: 0.8520 (mm) cc_final: 0.8293 (mm) REVERT: h 101 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7527 (mmtp) REVERT: i 200 MET cc_start: 0.9333 (OUTLIER) cc_final: 0.8263 (mpt) REVERT: i 304 MET cc_start: 0.9206 (mtm) cc_final: 0.8981 (mtp) REVERT: i 322 GLN cc_start: 0.7275 (pt0) cc_final: 0.6944 (pm20) REVERT: i 323 MET cc_start: 0.8031 (mtm) cc_final: 0.7593 (ptp) REVERT: k 97 GLN cc_start: 0.6416 (OUTLIER) cc_final: 0.5994 (mt0) REVERT: l 383 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8629 (tpt) REVERT: l 571 MET cc_start: 0.8922 (ttp) cc_final: 0.8696 (tmm) REVERT: l 601 LEU cc_start: 0.5284 (mp) cc_final: 0.4865 (tt) REVERT: o 30 ARG cc_start: 0.7996 (mmt90) cc_final: 0.7141 (mmt180) REVERT: p 48 PHE cc_start: 0.7468 (OUTLIER) cc_final: 0.6412 (t80) REVERT: p 160 GLU cc_start: 0.6643 (OUTLIER) cc_final: 0.6307 (tt0) REVERT: r 17 MET cc_start: 0.8748 (mmm) cc_final: 0.8437 (mmm) REVERT: r 45 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7619 (pp) REVERT: r 263 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.8919 (mmm) REVERT: u 76 ARG cc_start: 0.7724 (ttm110) cc_final: 0.7492 (ttp80) REVERT: u 91 TYR cc_start: 0.9273 (t80) cc_final: 0.8948 (t80) REVERT: v 29 TYR cc_start: 0.7475 (t80) cc_final: 0.7079 (t80) REVERT: v 53 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8773 (tp) REVERT: v 105 GLU cc_start: 0.7982 (tp30) cc_final: 0.7520 (tm-30) outliers start: 231 outliers final: 118 residues processed: 1208 average time/residue: 1.4676 time to fit residues: 2317.0066 Evaluate side-chains 1190 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1047 time to evaluate : 5.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain J residue 118 LYS Chi-restraints excluded: chain J residue 158 GLU Chi-restraints excluded: chain J residue 317 ASP Chi-restraints excluded: chain J residue 319 VAL Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain M residue 30 ASN Chi-restraints excluded: chain M residue 74 ASN Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 299 ARG Chi-restraints excluded: chain M residue 317 THR Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 403 VAL Chi-restraints excluded: chain M residue 426 ASP Chi-restraints excluded: chain M residue 487 THR Chi-restraints excluded: chain M residue 498 GLN Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 556 THR Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 68 MET Chi-restraints excluded: chain N residue 101 LYS Chi-restraints excluded: chain N residue 135 GLN Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 202 GLU Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain P residue 156 SER Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 409 VAL Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 46 ASP Chi-restraints excluded: chain U residue 16 GLU Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 39 THR Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 86 ASP Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain W residue 120 MET Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 89 LEU Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain X residue 154 VAL Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain Y residue 78 ASP Chi-restraints excluded: chain Z residue 15 GLU Chi-restraints excluded: chain a residue 58 LYS Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain c residue 37 PHE Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 182 VAL Chi-restraints excluded: chain d residue 34 THR Chi-restraints excluded: chain d residue 38 ASP Chi-restraints excluded: chain d residue 75 THR Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain e residue 143 ASP Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain h residue 101 LYS Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain i residue 187 MET Chi-restraints excluded: chain i residue 200 MET Chi-restraints excluded: chain i residue 237 MET Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain i residue 308 THR Chi-restraints excluded: chain i residue 347 ASN Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain k residue 44 SER Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 62 ILE Chi-restraints excluded: chain l residue 159 HIS Chi-restraints excluded: chain l residue 267 MET Chi-restraints excluded: chain l residue 383 MET Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 480 THR Chi-restraints excluded: chain l residue 526 LEU Chi-restraints excluded: chain l residue 578 SER Chi-restraints excluded: chain l residue 584 ILE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain o residue 86 THR Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain p residue 48 PHE Chi-restraints excluded: chain p residue 132 SER Chi-restraints excluded: chain p residue 140 LEU Chi-restraints excluded: chain p residue 151 THR Chi-restraints excluded: chain p residue 160 GLU Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 58 SER Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 263 MET Chi-restraints excluded: chain r residue 313 THR Chi-restraints excluded: chain r residue 367 LEU Chi-restraints excluded: chain r residue 375 LEU Chi-restraints excluded: chain s residue 144 VAL Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 258 ASN Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 66 CYS Chi-restraints excluded: chain u residue 78 CYS Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain u residue 118 VAL Chi-restraints excluded: chain u residue 121 ASP Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 133 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 638 optimal weight: 4.9990 chunk 435 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 570 optimal weight: 8.9990 chunk 316 optimal weight: 4.9990 chunk 654 optimal weight: 3.9990 chunk 529 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 391 optimal weight: 9.9990 chunk 688 optimal weight: 6.9990 chunk 193 optimal weight: 4.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS B 206 GLN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 78 HIS L 86 ASN ** M 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 663 ASN N 116 ASN P 82 ASN a 170 GLN c 56 ASN d 23 GLN d 124 ASN d 131 GLN l 59 GLN l 226 GLN p 51 HIS ** p 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 16 GLN v 65 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 68121 Z= 0.423 Angle : 0.656 11.160 92194 Z= 0.330 Chirality : 0.046 0.229 10029 Planarity : 0.005 0.065 11540 Dihedral : 12.889 177.343 10159 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.25 % Favored : 95.70 % Rotamer: Outliers : 4.13 % Allowed : 17.16 % Favored : 78.71 % 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: 0.49 (0.09), residues: 8027 helix: 1.17 (0.08), residues: 4249 sheet: 0.08 (0.26), residues: 404 loop : -0.70 (0.11), residues: 3374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 422 HIS 0.010 0.002 HIS J 37 PHE 0.037 0.002 PHE i 292 TYR 0.032 0.002 TYR l 587 ARG 0.008 0.001 ARG r 336 *********************** 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 1374 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 290 poor density : 1084 time to evaluate : 5.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.8128 (mmm) REVERT: A 184 LYS cc_start: 0.7454 (OUTLIER) cc_final: 0.6378 (tmtt) REVERT: A 241 THR cc_start: 0.9159 (OUTLIER) cc_final: 0.8822 (m) REVERT: A 331 VAL cc_start: 0.8369 (OUTLIER) cc_final: 0.8146 (t) REVERT: C 67 PHE cc_start: 0.8853 (OUTLIER) cc_final: 0.8195 (m-80) REVERT: C 98 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.6371 (ptp-170) REVERT: C 99 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8370 (mt0) REVERT: C 195 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8081 (ttm-80) REVERT: E 45 ASN cc_start: 0.7948 (OUTLIER) cc_final: 0.7585 (m-40) REVERT: E 75 ASP cc_start: 0.8484 (t0) cc_final: 0.8251 (t0) REVERT: E 114 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7495 (mmp-170) REVERT: F 38 GLU cc_start: 0.7699 (tt0) cc_final: 0.7448 (tp30) REVERT: F 39 LYS cc_start: 0.7728 (mmtt) cc_final: 0.7407 (mttp) REVERT: I 33 LYS cc_start: 0.8720 (mmtm) cc_final: 0.8473 (mmtm) REVERT: I 109 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7936 (t0) REVERT: I 110 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8264 (tm-30) REVERT: J 79 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8825 (tp40) REVERT: J 97 MET cc_start: 0.9515 (mtt) cc_final: 0.9290 (mtt) REVERT: J 118 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8158 (ttpt) REVERT: M 97 MET cc_start: 0.8365 (mtt) cc_final: 0.8111 (mtm) REVERT: M 329 MET cc_start: 0.8053 (mmm) cc_final: 0.7814 (mpt) REVERT: M 636 TYR cc_start: 0.8496 (OUTLIER) cc_final: 0.7895 (p90) REVERT: N 144 TYR cc_start: 0.7516 (OUTLIER) cc_final: 0.6364 (p90) REVERT: O 222 ARG cc_start: 0.8072 (ttp80) cc_final: 0.7784 (ttp80) REVERT: P 154 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7978 (tm-30) REVERT: P 234 ASP cc_start: 0.8702 (m-30) cc_final: 0.8390 (m-30) REVERT: Q 84 PHE cc_start: 0.7400 (m-80) cc_final: 0.7177 (m-80) REVERT: Q 308 TYR cc_start: 0.8925 (OUTLIER) cc_final: 0.7628 (p90) REVERT: S 59 ARG cc_start: 0.8425 (mtm-85) cc_final: 0.8131 (mpp-170) REVERT: T 46 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.7068 (m-30) REVERT: U 16 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7680 (mp0) REVERT: V 83 LYS cc_start: 0.6912 (mmtp) cc_final: 0.6633 (mmmt) REVERT: V 110 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.7973 (mp) REVERT: W 50 MET cc_start: 0.9123 (mmm) cc_final: 0.8870 (tpt) REVERT: a 64 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.8021 (m-30) REVERT: a 69 LYS cc_start: 0.8595 (mttm) cc_final: 0.8339 (mtpm) REVERT: a 141 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8061 (tt0) REVERT: a 176 LYS cc_start: 0.8899 (ptmt) cc_final: 0.8447 (ttpp) REVERT: c 37 PHE cc_start: 0.8658 (OUTLIER) cc_final: 0.8323 (m-10) REVERT: e 116 GLU cc_start: 0.7693 (pt0) cc_final: 0.7399 (tt0) REVERT: h 65 GLU cc_start: 0.8878 (tp30) cc_final: 0.8639 (tp30) REVERT: h 101 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.7568 (mmtp) REVERT: i 200 MET cc_start: 0.9348 (OUTLIER) cc_final: 0.8612 (mpt) REVERT: i 244 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8672 (ttm) REVERT: i 274 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8644 (mt-10) REVERT: i 322 GLN cc_start: 0.7288 (pt0) cc_final: 0.6951 (pm20) REVERT: i 323 MET cc_start: 0.7806 (mtm) cc_final: 0.7282 (mtt) REVERT: i 329 MET cc_start: 0.9215 (mmt) cc_final: 0.8985 (mpp) REVERT: k 21 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.6922 (mpt) REVERT: k 97 GLN cc_start: 0.6625 (OUTLIER) cc_final: 0.6168 (mt0) REVERT: l 150 MET cc_start: 0.9061 (tpp) cc_final: 0.8824 (tpp) REVERT: l 383 MET cc_start: 0.9082 (OUTLIER) cc_final: 0.8799 (tpt) REVERT: l 601 LEU cc_start: 0.5458 (mp) cc_final: 0.4947 (tt) REVERT: m 47 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.8339 (t80) REVERT: o 30 ARG cc_start: 0.8043 (mmt90) cc_final: 0.7206 (mmt180) REVERT: p 48 PHE cc_start: 0.7550 (OUTLIER) cc_final: 0.6352 (t80) REVERT: p 52 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7624 (ttmt) REVERT: p 160 GLU cc_start: 0.6671 (OUTLIER) cc_final: 0.6333 (tt0) REVERT: r 45 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7616 (pp) REVERT: r 263 MET cc_start: 0.9230 (OUTLIER) cc_final: 0.8917 (mmm) REVERT: u 76 ARG cc_start: 0.7753 (ttm110) cc_final: 0.7542 (ttp80) REVERT: v 29 TYR cc_start: 0.7520 (t80) cc_final: 0.7059 (t80) REVERT: v 53 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8873 (tp) REVERT: v 105 GLU cc_start: 0.8048 (tp30) cc_final: 0.7488 (tm-30) outliers start: 290 outliers final: 151 residues processed: 1258 average time/residue: 1.3682 time to fit residues: 2242.6466 Evaluate side-chains 1227 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1039 time to evaluate : 4.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 195 ARG Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 114 ARG Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain I residue 110 GLN Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 118 LYS Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 158 GLU Chi-restraints excluded: chain J residue 317 ASP Chi-restraints excluded: chain J residue 319 VAL Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 30 ASN Chi-restraints excluded: chain M residue 74 ASN Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 317 THR Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 382 ARG Chi-restraints excluded: chain M residue 403 VAL Chi-restraints excluded: chain M residue 487 THR Chi-restraints excluded: chain M residue 498 GLN Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 556 THR Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 654 VAL Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 68 MET Chi-restraints excluded: chain N residue 101 LYS Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain N residue 144 TYR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain O residue 232 THR Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain P residue 156 SER Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 409 VAL Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 46 ASP Chi-restraints excluded: chain U residue 16 GLU Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 39 THR Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 86 ASP Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain W residue 120 MET Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 89 LEU Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain X residue 154 VAL Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain Y residue 78 ASP Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 67 LEU Chi-restraints excluded: chain a residue 58 LYS Chi-restraints excluded: chain a residue 64 ASP Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 141 GLN Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 37 PHE Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 182 VAL Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 34 THR Chi-restraints excluded: chain d residue 38 ASP Chi-restraints excluded: chain d residue 75 THR Chi-restraints excluded: chain d residue 168 LYS Chi-restraints excluded: chain e residue 124 ARG Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain e residue 143 ASP Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain h residue 101 LYS Chi-restraints excluded: chain i residue 45 MET Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain i residue 183 SER Chi-restraints excluded: chain i residue 187 MET Chi-restraints excluded: chain i residue 200 MET Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 244 MET Chi-restraints excluded: chain i residue 274 GLU Chi-restraints excluded: chain i residue 280 THR Chi-restraints excluded: chain i residue 281 LEU Chi-restraints excluded: chain i residue 308 THR Chi-restraints excluded: chain i residue 347 ASN Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 21 MET Chi-restraints excluded: chain k residue 22 TYR Chi-restraints excluded: chain k residue 44 SER Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 62 ILE Chi-restraints excluded: chain l residue 159 HIS Chi-restraints excluded: chain l residue 267 MET Chi-restraints excluded: chain l residue 383 MET Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 480 THR Chi-restraints excluded: chain l residue 498 PHE Chi-restraints excluded: chain l residue 526 LEU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 578 SER Chi-restraints excluded: chain l residue 584 ILE Chi-restraints excluded: chain m residue 11 THR Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain m residue 47 PHE Chi-restraints excluded: chain m residue 74 MET Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 52 ASN Chi-restraints excluded: chain o residue 86 THR Chi-restraints excluded: chain p residue 48 PHE Chi-restraints excluded: chain p residue 52 LYS Chi-restraints excluded: chain p residue 132 SER Chi-restraints excluded: chain p residue 140 LEU Chi-restraints excluded: chain p residue 151 THR Chi-restraints excluded: chain p residue 160 GLU Chi-restraints excluded: chain r residue 15 THR Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 58 SER Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 263 MET Chi-restraints excluded: chain r residue 313 THR Chi-restraints excluded: chain r residue 375 LEU Chi-restraints excluded: chain s residue 144 VAL Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 66 CYS Chi-restraints excluded: chain u residue 78 CYS Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain u residue 112 LEU Chi-restraints excluded: chain u residue 118 VAL Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 133 SER Chi-restraints excluded: chain w residue 168 VAL Chi-restraints excluded: chain w residue 194 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 257 optimal weight: 0.0040 chunk 690 optimal weight: 4.9990 chunk 151 optimal weight: 20.0000 chunk 450 optimal weight: 6.9990 chunk 189 optimal weight: 0.7980 chunk 767 optimal weight: 7.9990 chunk 636 optimal weight: 3.9990 chunk 355 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 253 optimal weight: 0.6980 chunk 402 optimal weight: 1.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: