Starting phenix.real_space_refine on Fri Feb 16 00:14:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4n_32309/02_2024/7w4n_32309_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4n_32309/02_2024/7w4n_32309.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4n_32309/02_2024/7w4n_32309_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/7w4n_32309/02_2024/7w4n_32309_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4n_32309/02_2024/7w4n_32309_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4n_32309/02_2024/7w4n_32309.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4n_32309/02_2024/7w4n_32309.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4n_32309/02_2024/7w4n_32309_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4n_32309/02_2024/7w4n_32309_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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 33 5.49 5 Mg 1 5.21 5 S 474 5.16 5 C 42929 2.51 5 N 11093 2.21 5 O 11918 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 38": "OE1" <-> "OE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "B GLU 89": "OE1" <-> "OE2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "B GLU 160": "OE1" <-> "OE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E GLU 109": "OE1" <-> "OE2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "F GLU 92": "OE1" <-> "OE2" Residue "G GLU 143": "OE1" <-> "OE2" Residue "H GLU 18": "OE1" <-> "OE2" Residue "H GLU 49": "OE1" <-> "OE2" Residue "H GLU 69": "OE1" <-> "OE2" Residue "H GLU 78": "OE1" <-> "OE2" Residue "H GLU 85": "OE1" <-> "OE2" Residue "H GLU 105": "OE1" <-> "OE2" Residue "H GLU 106": "OE1" <-> "OE2" Residue "I GLU 62": "OE1" <-> "OE2" Residue "I GLU 105": "OE1" <-> "OE2" Residue "J GLU 107": "OE1" <-> "OE2" Residue "J GLU 133": "OE1" <-> "OE2" Residue "J GLU 162": "OE1" <-> "OE2" Residue "J GLU 320": "OE1" <-> "OE2" Residue "K GLU 80": "OE1" <-> "OE2" Residue "L GLU 70": "OE1" <-> "OE2" Residue "L GLU 108": "OE1" <-> "OE2" Residue "L GLU 132": "OE1" <-> "OE2" Residue "L GLU 139": "OE1" <-> "OE2" Residue "M GLU 44": "OE1" <-> "OE2" Residue "M GLU 244": "OE1" <-> "OE2" Residue "M GLU 249": "OE1" <-> "OE2" Residue "M GLU 283": "OE1" <-> "OE2" Residue "M GLU 284": "OE1" <-> "OE2" Residue "M GLU 310": "OE1" <-> "OE2" Residue "M GLU 628": "OE1" <-> "OE2" Residue "M GLU 670": "OE1" <-> "OE2" Residue "N GLU 41": "OE1" <-> "OE2" Residue "N GLU 67": "OE1" <-> "OE2" Residue "O GLU 58": "OE1" <-> "OE2" Residue "O GLU 114": "OE1" <-> "OE2" Residue "O GLU 150": "OE1" <-> "OE2" Residue "O GLU 194": "OE1" <-> "OE2" Residue "O GLU 207": "OE1" <-> "OE2" Residue "O GLU 226": "OE1" <-> "OE2" Residue "P TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 215": "OE1" <-> "OE2" Residue "P GLU 222": "OE1" <-> "OE2" Residue "Q GLU 42": "OE1" <-> "OE2" Residue "Q GLU 45": "OE1" <-> "OE2" Residue "Q GLU 57": "OE1" <-> "OE2" Residue "Q GLU 100": "OE1" <-> "OE2" Residue "Q PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 205": "OE1" <-> "OE2" Residue "Q GLU 260": "OE1" <-> "OE2" Residue "Q GLU 315": "OE1" <-> "OE2" Residue "Q GLU 335": "OE1" <-> "OE2" Residue "Q GLU 336": "OE1" <-> "OE2" Residue "S GLU 4": "OE1" <-> "OE2" Residue "S GLU 49": "OE1" <-> "OE2" Residue "T GLU 61": "OE1" <-> "OE2" Residue "T GLU 73": "OE1" <-> "OE2" Residue "T GLU 78": "OE1" <-> "OE2" Residue "T TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 56": "OE1" <-> "OE2" Residue "W GLU 93": "OE1" <-> "OE2" Residue "W GLU 94": "OE1" <-> "OE2" Residue "W GLU 108": "OE1" <-> "OE2" Residue "W TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 131": "OE1" <-> "OE2" Residue "Y GLU 41": "OE1" <-> "OE2" Residue "Z GLU 15": "OE1" <-> "OE2" Residue "a GLU 97": "OE1" <-> "OE2" Residue "a GLU 108": "OE1" <-> "OE2" Residue "a GLU 145": "OE1" <-> "OE2" Residue "a GLU 148": "OE1" <-> "OE2" Residue "b GLU 8": "OE1" <-> "OE2" Residue "b GLU 27": "OE1" <-> "OE2" Residue "b GLU 99": "OE1" <-> "OE2" Residue "b GLU 112": "OE1" <-> "OE2" Residue "c GLU 46": "OE1" <-> "OE2" Residue "c GLU 63": "OE1" <-> "OE2" Residue "c GLU 103": "OE1" <-> "OE2" Residue "c GLU 148": "OE1" <-> "OE2" Residue "c GLU 177": "OE1" <-> "OE2" Residue "c GLU 185": "OE1" <-> "OE2" Residue "d GLU 12": "OE1" <-> "OE2" Residue "d GLU 79": "OE1" <-> "OE2" Residue "d GLU 130": "OE1" <-> "OE2" Residue "d PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 172": "OE1" <-> "OE2" Residue "e GLU 57": "OE1" <-> "OE2" Residue "e GLU 62": "OE1" <-> "OE2" Residue "e GLU 64": "OE1" <-> "OE2" Residue "e GLU 121": "OE1" <-> "OE2" Residue "e GLU 123": "OE1" <-> "OE2" Residue "e GLU 130": "OE1" <-> "OE2" Residue "e GLU 138": "OE1" <-> "OE2" Residue "f GLU 68": "OE1" <-> "OE2" Residue "g GLU 19": "OE1" <-> "OE2" Residue "g GLU 117": "OE1" <-> "OE2" Residue "h GLU 42": "OE1" <-> "OE2" Residue "h GLU 53": "OE1" <-> "OE2" Residue "h GLU 59": "OE1" <-> "OE2" Residue "i GLU 274": "OE1" <-> "OE2" Residue "i GLU 318": "OE1" <-> "OE2" Residue "l GLU 60": "OE1" <-> "OE2" Residue "l GLU 75": "OE1" <-> "OE2" Residue "l GLU 145": "OE1" <-> "OE2" Residue "l GLU 353": "OE1" <-> "OE2" Residue "l GLU 397": "OE1" <-> "OE2" Residue "l PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 445": "OE1" <-> "OE2" Residue "l GLU 559": "OE1" <-> "OE2" Residue "n GLU 33": "OE1" <-> "OE2" Residue "n GLU 48": "OE1" <-> "OE2" Residue "o GLU 46": "OE1" <-> "OE2" Residue "o GLU 118": "OE1" <-> "OE2" Residue "p GLU 54": "OE1" <-> "OE2" Residue "p GLU 68": "OE1" <-> "OE2" Residue "p GLU 69": "OE1" <-> "OE2" Residue "p GLU 84": "OE1" <-> "OE2" Residue "p GLU 95": "OE1" <-> "OE2" Residue "p GLU 123": "OE1" <-> "OE2" Residue "p GLU 152": "OE1" <-> "OE2" Residue "r GLU 378": "OE1" <-> "OE2" Residue "s GLU 24": "OE1" <-> "OE2" Residue "s GLU 59": "OE1" <-> "OE2" Residue "u GLU 6": "OE1" <-> "OE2" Residue "u GLU 11": "OE1" <-> "OE2" Residue "u GLU 155": "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 83": "OE1" <-> "OE2" Residue "v GLU 105": "OE1" <-> "OE2" Residue "w GLU 55": "OE1" <-> "OE2" Residue "w GLU 185": "OE1" <-> "OE2" Residue "w GLU 189": "OE1" <-> "OE2" Residue "w GLU 226": "OE1" <-> "OE2" Residue "w GLU 251": "OE1" <-> "OE2" Residue "w GLU 267": "OE1" <-> "OE2" Residue "w GLU 271": "OE1" <-> "OE2" Residue "w GLU 274": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 66477 Number of models: 1 Model: "" Number of chains: 65 Chain: "A" Number of atoms: 3313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3313 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 409} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "B" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1412 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "C" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1248 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 971 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "F" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 691 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "G" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 690 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ASP:plan': 3} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 910 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "I" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 11, 'TRANS': 85} Chain breaks: 1 Chain: "J" Number of atoms: 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 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 5292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5292 Classifications: {'peptide': 690} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 32, 'TRANS': 657} 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: "N" Number of atoms: 1201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1201 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 132} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 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: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1009 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 133} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "W" Number of atoms: 1173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1173 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain: "X" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 696 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Y" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 597 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 63} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "Z" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 674 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain: "a" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1165 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 10, 'TRANS': 129} Chain: "b" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 879 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 11, 'TRANS': 91} Chain breaks: 1 Chain: "c" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1315 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 20, 'TRANS': 135} Chain: "d" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1461 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 10, 'TRANS': 164} Chain: "e" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 890 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 10, 'TRANS': 96} Chain: "f" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 342 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 40} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "g" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1000 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 11, 'TRANS': 109} Chain: "h" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 867 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "i" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2710 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 328} Chain: "j" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 800 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 Chain: "k" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 748 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "l" Number of atoms: 4782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4782 Classifications: {'peptide': 603} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 574} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "m" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 946 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "n" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 479 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "o" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1062 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 11, 'TRANS': 116} Chain: "p" Number of atoms: 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: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1028 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "w" Number of atoms: 2570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2570 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'PEE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'PEE': 1, 'PLX': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "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: "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: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 91 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "g" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 113 Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 38 Chain: "j" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 245 Unusual residues: {'CDL': 2, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "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 2701 SG CYS A 382 47.514 49.457 172.207 1.00 34.54 S ATOM 3043 SG CYS A 425 46.957 45.590 177.604 1.00 34.55 S ATOM 2721 SG CYS A 385 44.414 44.909 171.925 1.00 33.51 S ATOM 2682 SG CYS A 379 42.277 49.638 176.128 1.00 32.08 S ATOM 3944 SG CYS B 113 35.932 67.547 138.535 1.00 20.35 S ATOM 3963 SG CYS B 116 40.912 64.860 142.167 1.00 11.60 S ATOM 3986 SG CYS B 119 41.995 67.965 136.847 1.00 0.86 S ATOM 4315 SG CYS B 162 39.454 62.122 137.201 1.00 21.44 S ATOM 4013 SG CYS B 123 48.097 70.866 132.249 1.00 2.33 S ATOM 4239 SG CYS B 152 46.112 69.585 126.357 1.00 10.29 S ATOM 4286 SG CYS B 158 44.183 65.532 130.868 1.00 9.22 S ATOM 4265 SG CYS B 155 50.300 65.878 129.358 1.00 11.42 S ATOM 5707 SG CYS C 166 52.398 70.009 121.922 1.00 19.61 S ATOM 4979 SG CYS C 72 53.358 71.566 115.785 1.00 13.40 S ATOM 4973 SG CYS C 71 58.146 70.015 118.325 1.00 4.18 S ATOM 5477 SG CYS C 136 55.070 74.587 120.711 1.00 22.05 S ATOM 14527 SG CYS M 131 40.621 64.157 154.103 1.00 13.61 S ATOM 14506 SG CYS M 128 43.969 59.732 150.719 1.00 20.39 S ATOM 14567 SG CYS M 137 46.175 62.976 156.097 1.00 8.70 S ATOM 14899 SG CYS M 179 44.810 62.271 167.223 1.00 30.01 S ATOM 15253 SG CYS M 226 41.716 65.297 163.273 1.00 21.02 S ATOM 14923 SG CYS M 182 39.441 64.814 169.350 1.00 29.29 S ATOM 14876 SG CYS M 176 39.036 59.684 165.573 1.00 15.99 S ATOM 14124 SG CYS M 78 56.268 57.220 170.386 1.00 27.96 S ATOM 14225 SG CYS M 92 54.636 59.205 172.963 1.00 35.74 S ATOM 14013 SG CYS M 64 50.220 59.290 170.767 1.00 34.46 S ATOM 14099 SG CYS M 75 51.226 57.752 167.573 1.00 22.00 S ATOM 21055 SG CYS O 135 31.374 31.454 179.360 1.00 69.65 S ATOM 21089 SG CYS O 140 31.210 27.985 180.192 1.00 76.20 S ATOM 21369 SG CYS O 176 35.794 33.022 182.034 1.00 69.17 S ATOM 21392 SG CYS O 180 36.235 29.734 182.310 1.00 81.56 S ATOM 28050 SG CYS T 86 28.525 53.836 145.750 1.00 42.13 S ATOM 28228 SG CYS T 111 29.717 57.078 146.809 1.00 38.08 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.66 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.66 Time building chain proxies: 26.24, per 1000 atoms: 0.39 Number of scatterers: 66477 At special positions: 0 Unit cell: (209.699, 229.461, 227.265, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 474 16.00 P 33 15.00 Mg 1 11.99 O 11918 8.00 N 11093 7.00 C 42929 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS F 24 " - pdb=" SG CYS F 58 " distance=2.03 Simple disulfide: pdb=" SG CYS V 95 " - pdb=" SG CYS V 115 " distance=2.24 Simple disulfide: pdb=" SG CYS d 113 " - pdb=" SG CYS d 125 " distance=2.18 Simple disulfide: pdb=" SG CYS h 33 " - pdb=" SG CYS h 66 " distance=2.04 Simple disulfide: pdb=" SG CYS h 43 " - pdb=" SG CYS h 56 " distance=2.04 Simple disulfide: pdb=" SG CYS u 88 " - pdb=" SG CYS u 100 " distance=2.03 Simple disulfide: pdb=" SG CYS v 69 " - pdb=" SG CYS v 80 " distance=2.02 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: 21.08 Conformation dependent library (CDL) restraints added in 9.1 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="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 135 " pdb=" SF4 A 501 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " pdb=" SF4 B 301 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 116 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " 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="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 71 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " pdb="FE3 SF4 C 301 " - pdb=" NE2 HIS Q 223 " pdb=" SF4 M 801 " pdb="FE3 SF4 M 801 " - pdb=" NE2 HIS M 124 " pdb="FE4 SF4 M 801 " - pdb=" SG CYS M 137 " pdb="FE1 SF4 M 801 " - pdb=" SG CYS M 131 " pdb="FE2 SF4 M 801 " - pdb=" SG CYS M 128 " 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=" NE2 HIS T 95 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 86 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 111 " 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15286 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 340 helices and 29 sheets defined 52.9% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.70 Creating SS restraints... Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 73 through 83 Processing helix chain 'A' and resid 95 through 103 removed outlier: 3.541A pdb=" N PHE A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N MET A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN A 103 " --> pdb=" O TRP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 132 Processing helix chain 'A' and resid 135 through 149 Processing helix chain 'A' and resid 163 through 178 Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 245 through 257 Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 296 through 303 Processing helix chain 'A' and resid 329 through 334 removed outlier: 4.766A 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: 3.676A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 419 removed outlier: 4.064A pdb=" N ASP A 410 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 457 Proline residue: A 434 - end of helix Proline residue: A 444 - end of helix Processing helix chain 'B' and resid 50 through 62 Processing helix chain 'B' and resid 64 through 78 Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 187 through 211 removed outlier: 5.934A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEU B 210 " --> pdb=" O GLN B 206 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N TYR B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 60 Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 86 through 89 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 114 through 122 Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 141 through 143 No H-bonds generated for 'chain 'C' and resid 141 through 143' Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 189 through 195 Processing helix chain 'E' and resid 25 through 49 Proline residue: E 44 - end of helix removed outlier: 3.519A pdb=" N HIS E 48 " --> pdb=" O PRO E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 70 removed outlier: 4.094A 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: 4.358A pdb=" N PHE E 106 " --> pdb=" O HIS E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 124 Processing helix chain 'F' and resid 28 through 47 removed outlier: 4.997A pdb=" N GLY F 32 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N TYR F 41 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N VAL F 42 " --> pdb=" O LYS F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 72 No H-bonds generated for 'chain 'F' and resid 70 through 72' Processing helix chain 'F' and resid 84 through 96 Processing helix chain 'G' and resid 76 through 89 Processing helix chain 'G' and resid 112 through 126 Processing helix chain 'G' and resid 132 through 135 No H-bonds generated for 'chain 'G' and resid 132 through 135' Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'H' and resid 20 through 37 removed outlier: 3.934A 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: 4.190A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N MET J 76 " --> pdb=" O HIS J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 97 removed outlier: 4.792A pdb=" N HIS J 93 " --> pdb=" O TYR J 89 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LEU J 94 " --> pdb=" O ASP J 90 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARG J 95 " --> pdb=" O THR J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 113 through 119 Processing helix chain 'J' and resid 141 through 145 Processing helix chain 'J' and resid 147 through 159 Processing helix chain 'J' and resid 179 through 194 Processing helix chain 'J' and resid 213 through 219 Processing helix chain 'J' and resid 242 through 254 Processing helix chain 'J' and resid 273 through 283 Processing helix chain 'J' and resid 317 through 323 Processing helix chain 'J' and resid 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: 4.811A pdb=" N ILE J 350 " --> pdb=" O GLU J 346 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLU J 351 " --> pdb=" O LEU J 347 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ARG J 355 " --> pdb=" O GLU J 351 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N HIS J 356 " --> pdb=" O VAL J 352 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 80 Processing helix chain 'K' and resid 85 through 96 removed outlier: 4.357A pdb=" N LYS K 95 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N PHE K 96 " --> pdb=" O GLU K 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 64 No H-bonds generated for 'chain 'L' and resid 62 through 64' 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 160 through 164 Processing helix chain 'M' and resid 49 through 56 removed outlier: 3.545A 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: 3.854A pdb=" N ILE M 225 " --> pdb=" O ILE M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 298 removed outlier: 5.157A pdb=" N TYR M 294 " --> pdb=" O THR M 290 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ASP M 295 " --> pdb=" O ARG M 291 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLY M 296 " --> pdb=" O PHE M 292 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU M 297 " --> pdb=" O ALA M 293 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS M 298 " --> pdb=" O TYR M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 319 through 332 removed outlier: 3.600A pdb=" N MET M 329 " --> pdb=" O ARG M 325 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 337 No H-bonds generated for 'chain 'M' and resid 335 through 337' Processing helix chain 'M' and resid 348 through 360 Processing helix chain 'M' and resid 382 through 385 Processing helix chain 'M' and resid 390 through 395 removed outlier: 3.808A pdb=" N VAL M 394 " --> pdb=" O THR M 390 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLU M 395 " --> pdb=" O ILE M 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 390 through 395' Processing helix chain 'M' and resid 407 through 410 No H-bonds generated for 'chain 'M' and resid 407 through 410' Processing helix chain 'M' and resid 412 through 424 Processing helix chain 'M' and resid 449 through 457 Processing helix chain 'M' and resid 461 through 468 Processing helix chain 'M' and resid 478 through 481 No H-bonds generated for 'chain 'M' and resid 478 through 481' Processing helix chain 'M' and resid 486 through 504 Processing helix chain 'M' and resid 520 through 528 removed outlier: 4.659A pdb=" N ALA M 524 " --> pdb=" O ALA M 520 " (cutoff:3.500A) Processing helix chain 'M' and resid 535 through 539 Processing helix chain 'M' and resid 557 through 559 No H-bonds generated for 'chain 'M' and resid 557 through 559' Processing helix chain 'M' and resid 619 through 629 Processing helix chain 'M' and resid 639 through 649 Processing helix chain 'M' and resid 651 through 653 No H-bonds generated for 'chain 'M' and resid 651 through 653' Processing helix chain 'M' and resid 665 through 673 removed outlier: 3.562A pdb=" N LYS M 673 " --> pdb=" O ASN M 669 " (cutoff:3.500A) 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 703 Processing helix chain 'M' and resid 705 through 715 Processing helix chain 'N' and resid 3 through 16 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: 4.327A pdb=" N LEU O 80 " --> pdb=" O ALA O 77 " (cutoff:3.500A) Proline residue: O 81 - end of helix Processing helix chain 'O' and resid 95 through 105 Processing helix chain 'O' and resid 109 through 118 Processing helix chain 'O' and resid 138 through 142 Processing helix chain 'O' and resid 146 through 156 Processing helix chain 'O' and resid 180 through 182 No H-bonds generated for 'chain 'O' and resid 180 through 182' Processing helix chain 'O' and resid 198 through 210 Processing helix chain 'P' and resid 52 through 68 Processing helix chain 'P' and resid 90 through 102 removed outlier: 4.289A pdb=" N ILE P 94 " --> pdb=" O ASP P 91 " (cutoff:3.500A) Proline residue: P 95 - end of helix Processing helix chain 'P' and resid 161 through 173 removed outlier: 3.589A pdb=" N ASN P 164 " --> pdb=" O LYS P 161 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TRP P 165 " --> pdb=" O ALA P 162 " (cutoff:3.500A) Processing helix chain 'P' and resid 243 through 245 No H-bonds generated for 'chain 'P' and resid 243 through 245' Processing helix chain 'Q' and resid 41 through 47 removed outlier: 4.222A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N PHE Q 47 " --> pdb=" O TRP Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 120 through 126 removed outlier: 3.784A pdb=" N GLU Q 125 " --> pdb=" O GLU Q 121 " (cutoff:3.500A) removed outlier: 4.178A 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: 4.115A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.720A 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: 4.245A 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: 4.458A pdb=" N GLY Q 295 " --> pdb=" O MET Q 292 " (cutoff:3.500A) Processing helix chain 'Q' and resid 302 through 305 No H-bonds generated for 'chain 'Q' and resid 302 through 305' Processing helix chain 'Q' and resid 311 through 313 No H-bonds generated for 'chain 'Q' and resid 311 through 313' Processing helix chain 'Q' and resid 326 through 349 Processing helix chain 'Q' and resid 368 through 373 Processing helix chain 'Q' and resid 375 through 386 Processing helix chain 'Q' and resid 427 through 438 removed outlier: 4.397A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N LYS Q 437 " --> pdb=" O ALA Q 433 " (cutoff:3.500A) Processing helix chain 'Q' and resid 444 through 454 removed outlier: 4.274A pdb=" N VAL Q 448 " --> pdb=" O LEU Q 444 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA Q 449 " --> pdb=" O ALA Q 445 " (cutoff:3.500A) Processing helix chain 'Q' and resid 458 through 462 Processing helix chain 'S' and resid 2 through 29 Proline residue: S 7 - end of helix Proline residue: S 19 - end of helix Processing helix chain 'S' and resid 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 73 Processing helix chain 'T' and resid 91 through 93 No H-bonds generated for 'chain 'T' and resid 91 through 93' Processing helix chain 'U' and resid 3 through 13 Processing helix chain 'U' and resid 17 through 35 Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 38 through 47 Processing helix chain 'U' and resid 79 through 83 Processing helix chain 'V' and resid 4 through 10 Processing helix chain 'V' and resid 18 through 43 Processing helix chain 'V' and resid 49 through 81 Processing helix chain 'V' and resid 87 through 105 Processing helix chain 'V' and resid 108 through 131 Processing helix chain 'W' and resid 32 through 99 Proline residue: W 73 - end of helix removed outlier: 3.793A pdb=" N LYS W 99 " --> pdb=" O ALA W 95 " (cutoff:3.500A) Processing helix chain 'W' and resid 121 through 124 No H-bonds generated for 'chain 'W' and resid 121 through 124' Processing helix chain 'W' and resid 130 through 142 removed outlier: 6.373A pdb=" N PHE W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ILE W 141 " --> pdb=" O THR W 137 " (cutoff:3.500A) Processing helix chain 'X' and resid 76 through 88 Processing helix chain 'X' and resid 112 through 126 Processing helix chain 'X' and resid 132 through 137 removed outlier: 4.410A pdb=" N LYS X 137 " --> pdb=" O ILE X 133 " (cutoff:3.500A) Processing helix chain 'X' and resid 141 through 151 Processing helix chain 'Y' and resid 52 through 75 Processing helix chain 'Y' and resid 78 through 81 No H-bonds generated for 'chain 'Y' and resid 78 through 81' Processing helix chain 'Y' and resid 89 through 91 No H-bonds generated for 'chain 'Y' and resid 89 through 91' Processing helix chain 'Z' and resid 19 through 21 No H-bonds generated for 'chain 'Z' and resid 19 through 21' Processing helix chain 'Z' and resid 28 through 39 removed outlier: 3.926A pdb=" N ARG Z 39 " --> pdb=" O LYS Z 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 46 through 48 No H-bonds generated for 'chain 'Z' and resid 46 through 48' Processing helix chain 'Z' and resid 50 through 53 Processing helix chain 'Z' and resid 56 through 58 No H-bonds generated for 'chain 'Z' and resid 56 through 58' 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: 3.687A 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: 3.543A 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 57 removed outlier: 4.608A 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: 6.290A pdb=" N GLU d 119 " --> pdb=" O GLN d 115 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N SER d 120 " --> pdb=" O ARG d 116 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TYR d 121 " --> pdb=" O GLU d 117 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ARG d 122 " --> pdb=" O GLY d 118 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLN d 123 " --> pdb=" O GLU d 119 " (cutoff:3.500A) Processing helix chain 'd' and resid 126 through 143 Processing helix chain 'd' and resid 152 through 174 Processing helix chain 'e' and resid 80 through 94 Processing helix chain 'e' and resid 98 through 107 removed outlier: 3.838A pdb=" N SER e 103 " --> pdb=" O LEU e 99 " (cutoff:3.500A) Processing helix chain 'e' and resid 115 through 131 Processing helix chain 'e' and resid 144 through 146 No H-bonds generated for 'chain 'e' and resid 144 through 146' Processing helix chain 'f' and resid 41 through 73 Processing helix chain 'g' and resid 4 through 6 No H-bonds generated for 'chain 'g' and resid 4 through 6' Processing helix chain 'g' and resid 19 through 22 removed outlier: 3.515A pdb=" N SER g 22 " --> pdb=" O GLU g 19 " (cutoff:3.500A) No H-bonds generated for '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 100 through 102 No H-bonds generated for 'chain 'g' and resid 100 through 102' Processing helix chain 'g' and resid 111 through 113 No H-bonds generated for 'chain 'g' and resid 111 through 113' Processing helix chain 'h' and resid 6 through 10 Processing helix chain 'h' and resid 16 through 18 No H-bonds generated for 'chain 'h' and resid 16 through 18' Processing helix chain 'h' and resid 26 through 28 No H-bonds generated for 'chain 'h' and resid 26 through 28' Processing helix chain 'h' and resid 34 through 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 removed outlier: 3.616A pdb=" N ILE i 41 " --> pdb=" O LEU i 37 " (cutoff:3.500A) Proline residue: i 42 - end of helix Processing helix chain 'i' and resid 50 through 80 Processing helix chain 'i' and resid 92 through 106 Processing helix chain 'i' and resid 113 through 121 removed outlier: 4.366A pdb=" N GLU i 117 " --> pdb=" O PHE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 144 removed outlier: 3.707A pdb=" N GLN i 134 " --> pdb=" O LEU i 130 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LYS i 135 " --> pdb=" O LEU i 131 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LEU i 136 " --> pdb=" O THR i 132 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ALA i 137 " --> pdb=" O TRP i 133 " (cutoff:3.500A) Proline residue: i 138 - end of helix Processing helix chain 'i' and resid 151 through 171 removed outlier: 3.911A pdb=" N LEU i 170 " --> pdb=" O GLY i 166 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ASN i 171 " --> pdb=" O TRP i 167 " (cutoff:3.500A) Processing helix chain 'i' and resid 175 through 193 removed outlier: 4.037A pdb=" N VAL i 193 " --> pdb=" O TRP i 189 " (cutoff:3.500A) Processing helix chain 'i' and resid 198 through 221 Processing helix chain 'i' and resid 227 through 235 removed outlier: 3.708A pdb=" N HIS i 232 " --> pdb=" O LEU i 228 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR i 233 " --> pdb=" O SER i 229 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N TRP i 234 " --> pdb=" O LEU i 230 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ASN i 235 " --> pdb=" O SER i 231 " (cutoff:3.500A) Processing helix chain 'i' and resid 238 through 251 Processing helix chain 'i' and resid 258 through 273 Proline residue: i 262 - end of helix Processing helix chain 'i' and resid 277 through 300 removed outlier: 4.448A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) Processing helix chain 'i' and resid 309 through 316 removed outlier: 3.602A pdb=" N MET i 313 " --> pdb=" O ASN i 310 " (cutoff:3.500A) Processing helix chain 'i' and resid 326 through 334 Processing helix chain 'i' and resid 340 through 345 removed outlier: 3.536A 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: 5.845A pdb=" N TRP j 77 " --> pdb=" O LEU j 73 " (cutoff:3.500A) Processing helix chain 'j' and resid 84 through 107 Processing helix chain 'k' and resid 3 through 21 Processing helix chain 'k' and resid 26 through 51 Processing helix chain 'k' and resid 54 through 85 removed outlier: 3.754A 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: 3.653A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR l 16 " --> pdb=" O LEU l 12 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE l 17 " --> pdb=" O THR l 13 " (cutoff:3.500A) Proline residue: l 18 - end of helix removed outlier: 4.893A pdb=" N ASN l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) Processing helix chain 'l' and resid 25 through 28 Processing helix chain 'l' and resid 32 through 57 removed outlier: 4.280A 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: 3.865A pdb=" N TRP l 106 " --> pdb=" O GLU l 102 " (cutoff:3.500A) Processing helix chain 'l' and resid 114 through 132 Processing helix chain 'l' and resid 137 through 155 removed outlier: 3.523A pdb=" N GLY l 148 " --> pdb=" O TRP l 144 " (cutoff:3.500A) Processing helix chain 'l' and resid 162 through 193 removed outlier: 3.907A 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: 4.192A pdb=" N MET l 237 " --> pdb=" O LEU l 233 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N GLU l 238 " --> pdb=" O PRO l 234 " (cutoff:3.500A) Processing helix chain 'l' and resid 241 through 250 removed outlier: 3.627A pdb=" N HIS l 248 " --> pdb=" O SER l 244 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N SER l 249 " --> pdb=" O ALA l 245 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER l 250 " --> pdb=" O LEU l 246 " (cutoff:3.500A) Processing helix chain 'l' and resid 253 through 262 removed outlier: 4.233A pdb=" N GLY l 256 " --> pdb=" O VAL l 253 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL l 257 " --> pdb=" O VAL l 254 " (cutoff:3.500A) Processing helix chain 'l' and resid 264 through 267 No H-bonds generated for 'chain 'l' and resid 264 through 267' Processing helix chain 'l' and resid 271 through 294 removed outlier: 4.433A pdb=" N THR l 294 " --> pdb=" O LEU l 290 " (cutoff:3.500A) Processing helix chain 'l' and resid 298 through 318 Processing helix chain 'l' and resid 322 through 349 removed outlier: 3.742A 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: 4.714A 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: 3.760A pdb=" N LEU l 457 " --> pdb=" O SER l 453 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N PHE l 466 " --> pdb=" O ILE l 462 " (cutoff:3.500A) Processing helix chain 'l' and resid 484 through 487 No H-bonds generated for 'chain 'l' and resid 484 through 487' Processing helix chain 'l' and resid 489 through 509 removed outlier: 3.596A pdb=" N THR l 507 " --> pdb=" O GLU l 503 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR l 508 " --> pdb=" O LEU l 504 " (cutoff:3.500A) removed outlier: 4.722A 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: 4.165A pdb=" N MET l 533 " --> pdb=" O PRO l 530 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU l 536 " --> pdb=" O MET l 533 " (cutoff:3.500A) Proline residue: l 537 - end of helix removed outlier: 4.462A pdb=" N SER l 543 " --> pdb=" O HIS l 540 " (cutoff:3.500A) Processing helix chain 'l' and resid 557 through 561 Processing helix chain 'l' and resid 563 through 578 Processing helix chain 'l' and resid 584 through 601 Processing helix chain 'm' and resid 5 through 21 Processing helix chain 'm' and resid 26 through 47 Processing helix chain 'm' and resid 50 through 74 removed outlier: 3.981A pdb=" N LEU m 61 " --> pdb=" O PHE m 57 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU m 65 " --> pdb=" O LEU m 61 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL m 66 " --> pdb=" O GLY m 62 " (cutoff:3.500A) Processing helix chain 'm' and resid 138 through 146 removed outlier: 4.217A 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: 6.445A pdb=" N VAL n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N HIS n 14 " --> pdb=" O ASP n 10 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE n 15 " --> pdb=" O HIS n 11 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU n 16 " --> pdb=" O TRP n 12 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N VAL n 17 " --> pdb=" O VAL n 13 " (cutoff:3.500A) Proline residue: n 18 - end of helix removed outlier: 3.827A pdb=" N LYS n 34 " --> pdb=" O ARG n 30 " (cutoff:3.500A) Processing helix chain 'o' and resid 16 through 18 No H-bonds generated for 'chain 'o' and resid 16 through 18' Processing helix chain 'o' and resid 20 through 23 No H-bonds generated for 'chain 'o' and resid 20 through 23' Processing helix chain 'o' and resid 27 through 51 Processing helix chain 'o' and resid 63 through 73 Processing helix chain 'o' and resid 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 49 Processing helix chain 'p' and resid 57 through 62 Processing helix chain 'p' and resid 66 through 73 Processing helix chain 'p' and resid 95 through 97 No H-bonds generated for 'chain 'p' and resid 95 through 97' Processing helix chain 'p' and resid 102 through 106 Processing helix chain 'p' and resid 109 through 113 Processing helix chain 'p' and resid 116 through 143 removed outlier: 3.936A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 3.763A 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: 4.303A pdb=" N LEU r 12 " --> pdb=" O THR r 8 " (cutoff:3.500A) Proline residue: r 13 - end of helix Processing helix chain 'r' and resid 23 through 42 removed outlier: 4.255A pdb=" N SER r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU r 42 " --> pdb=" O SER r 38 " (cutoff:3.500A) Processing helix chain 'r' and resid 62 through 83 removed outlier: 3.831A pdb=" N LEU r 73 " --> pdb=" O THR r 69 " (cutoff:3.500A) Proline residue: r 74 - end of helix removed outlier: 4.537A pdb=" N SER r 82 " --> pdb=" O MET r 78 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N HIS r 83 " --> pdb=" O ALA r 79 " (cutoff:3.500A) Processing helix chain 'r' and resid 89 through 111 removed outlier: 3.530A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 115 through 135 removed outlier: 4.893A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.464A 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 142 through 170 removed outlier: 3.894A pdb=" N THR r 153 " --> pdb=" O PHE r 149 " (cutoff:3.500A) Proline residue: r 159 - end of helix removed outlier: 3.565A pdb=" N VAL r 162 " --> pdb=" O LEU r 158 " (cutoff:3.500A) Processing helix chain 'r' and resid 176 through 181 Processing helix chain 'r' and resid 190 through 204 removed outlier: 4.316A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 222 removed outlier: 4.236A pdb=" N LYS r 218 " --> pdb=" O LEU r 214 " (cutoff:3.500A) Processing helix chain 'r' and resid 225 through 233 Processing helix chain 'r' and resid 237 through 249 removed outlier: 4.804A pdb=" N THR r 248 " --> pdb=" O MET r 244 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ILE r 249 " --> pdb=" O ARG r 245 " (cutoff:3.500A) Processing helix chain 'r' and resid 253 through 257 removed outlier: 3.940A pdb=" N MET r 257 " --> pdb=" O THR r 254 " (cutoff:3.500A) Processing helix chain 'r' and resid 259 through 277 removed outlier: 3.941A pdb=" N ILE r 270 " --> pdb=" O MET r 266 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER r 273 " --> pdb=" O MET r 269 " (cutoff:3.500A) removed outlier: 3.552A 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: 3.676A pdb=" N ARG r 336 " --> pdb=" O THR r 332 " (cutoff:3.500A) Processing helix chain 'r' and resid 348 through 351 No H-bonds generated for 'chain 'r' and resid 348 through 351' Processing helix chain 'r' and resid 353 through 366 Processing helix chain 'r' and resid 373 through 388 Processing helix chain 'r' and resid 392 through 415 removed outlier: 3.646A pdb=" N THR r 414 " --> pdb=" O MET r 410 " (cutoff:3.500A) Processing helix chain 'r' and resid 431 through 449 Proline residue: r 443 - end of helix removed outlier: 4.038A 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: 3.888A pdb=" N THR s 21 " --> pdb=" O VAL s 17 " (cutoff:3.500A) removed outlier: 4.290A 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: 4.395A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 123 removed outlier: 4.308A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 156 removed outlier: 3.877A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 168 removed outlier: 3.634A pdb=" N THR s 168 " --> pdb=" O LEU s 165 " (cutoff:3.500A) Processing helix chain 's' and resid 174 through 177 No H-bonds generated for 'chain 's' and resid 174 through 177' Processing helix chain 's' and resid 179 through 192 Processing helix chain 's' and resid 218 through 242 Processing helix chain 's' and resid 252 through 276 Processing helix chain 's' and resid 282 through 311 removed outlier: 5.280A pdb=" N LEU s 294 " --> pdb=" O TRP s 290 " (cutoff:3.500A) Proline residue: s 295 - end of helix Proline residue: s 308 - end of helix Processing helix chain 'u' and resid 22 through 27 Processing helix chain 'u' and resid 29 through 35 Processing helix chain 'u' and resid 37 through 50 Processing helix chain 'u' and resid 53 through 55 No H-bonds generated for 'chain 'u' and resid 53 through 55' Processing helix chain 'u' and resid 57 through 77 Processing helix chain 'u' and resid 79 through 91 Processing helix chain 'u' and resid 101 through 114 Processing helix chain 'v' and resid 3 through 10 Processing helix chain 'v' and resid 13 through 15 No H-bonds generated for 'chain 'v' and resid 13 through 15' Processing helix chain 'v' and resid 43 through 49 Processing helix chain 'v' and resid 60 through 72 Processing helix chain 'v' and resid 82 through 124 Processing helix chain 'w' and resid 40 through 45 Processing helix chain 'w' and resid 70 through 81 Processing helix chain 'w' and resid 94 through 96 No H-bonds generated for 'chain 'w' and resid 94 through 96' Processing helix chain 'w' and resid 114 through 119 Processing helix chain 'w' and resid 127 through 153 Processing helix chain 'w' and resid 167 through 175 Processing helix chain 'w' and resid 181 through 197 removed outlier: 5.164A 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 244 Processing helix chain 'w' and resid 246 through 250 Processing helix chain 'w' and resid 266 through 275 Processing helix chain 'w' and resid 283 through 285 No H-bonds generated for 'chain 'w' and resid 283 through 285' Processing helix chain 'w' and resid 288 through 298 Processing helix chain 'w' and resid 301 through 304 No H-bonds generated for 'chain 'w' and resid 301 through 304' Processing helix chain 'w' and resid 306 through 309 removed outlier: 4.000A pdb=" N THR w 309 " --> pdb=" O ASN w 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 306 through 309' Processing helix chain 'w' and resid 321 through 332 Processing helix chain 'w' and resid 352 through 354 No H-bonds generated for 'chain 'w' and resid 352 through 354' Processing sheet with id= A, first strand: chain 'A' and resid 240 through 244 removed outlier: 7.239A pdb=" N TYR A 112 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N ALA A 243 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL A 114 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALA A 153 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N VAL A 115 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TYR A 155 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ALA A 117 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TYR A 157 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASP A 194 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ILE A 156 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE A 196 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ILE A 158 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.203A 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: 6.026A pdb=" N GLU B 133 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 5.286A 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: 6.378A pdb=" N VAL C 102 " --> pdb=" O MET C 65 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N PHE C 67 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE C 104 " --> pdb=" O PHE C 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TYR C 129 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL C 105 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL C 131 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.345A 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 53 through 58 removed outlier: 6.517A pdb=" N ILE F 19 " --> pdb=" O LEU F 54 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ARG F 56 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ILE F 21 " --> pdb=" O ARG F 56 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N CYS F 58 " --> pdb=" O ILE F 21 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU F 23 " --> pdb=" O CYS F 58 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU F 18 " --> pdb=" O ARG F 68 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 262 through 265 removed outlier: 8.371A pdb=" N PHE J 263 " --> pdb=" O ALA J 198 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU J 164 " --> pdb=" O THR J 199 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ILE J 201 " --> pdb=" O LEU J 164 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N HIS J 166 " --> pdb=" O ILE J 201 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N SER J 168 " --> pdb=" O PRO J 203 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE J 167 " --> pdb=" O ASN J 128 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLN J 79 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N VAL J 58 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE J 81 " --> pdb=" O VAL J 58 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'L' and resid 144 through 147 Processing sheet with id= I, first strand: chain 'L' and resid 106 through 108 Processing sheet with id= J, first strand: chain 'M' and resid 32 through 36 Processing sheet with id= K, first strand: chain 'M' and resid 169 through 171 Processing sheet with id= L, first strand: chain 'M' and resid 196 through 198 Processing sheet with id= M, first strand: chain 'M' and resid 246 through 251 Processing sheet with id= N, first strand: chain 'M' and resid 306 through 308 Processing sheet with id= O, first strand: chain 'M' and resid 365 through 368 removed outlier: 4.773A pdb=" N SER M 365 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL M 544 " --> pdb=" O ALA M 339 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ILE M 341 " --> pdb=" O VAL M 544 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE M 546 " --> pdb=" O ILE M 341 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N PHE M 565 " --> pdb=" O LEU M 545 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N LEU M 547 " --> pdb=" O PHE M 565 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE M 567 " --> pdb=" O LEU M 547 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL M 582 " --> pdb=" O TYR M 568 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N GLY M 570 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU M 584 " --> pdb=" O GLY M 570 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'M' and resid 513 through 516 removed outlier: 8.301A pdb=" N ASN M 514 " --> pdb=" O PRO M 472 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL M 399 " --> pdb=" O MET M 473 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LYS M 428 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU M 402 " --> pdb=" O LYS M 428 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA M 430 " --> pdb=" O LEU M 402 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASP M 443 " --> pdb=" O LEU M 431 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'M' and resid 595 through 597 Processing sheet with id= R, first strand: chain 'N' and resid 60 through 63 removed outlier: 6.343A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N LEU N 38 " --> pdb=" O GLU N 50 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'O' and resid 169 through 174 removed outlier: 6.707A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N VAL O 134 " --> pdb=" O VAL O 174 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS O 135 " --> pdb=" O MET O 185 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N MET O 185 " --> pdb=" O CYS O 135 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'P' and resid 110 through 118 removed outlier: 6.756A pdb=" N ASN P 131 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LEU P 114 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL P 129 " --> pdb=" O LEU P 114 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA P 116 " --> pdb=" O GLU P 127 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLU P 127 " --> pdb=" O ALA P 116 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LEU P 84 " --> pdb=" O ARG P 140 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N TYR P 146 " --> pdb=" O ILE P 88 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'P' and resid 208 through 213 Processing sheet with id= V, first strand: chain 'Q' and resid 80 through 84 removed outlier: 3.594A pdb=" N ARG Q 96 " --> pdb=" O HIS Q 112 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N VAL Q 106 " --> pdb=" O SER Q 102 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'Q' and resid 394 through 402 Processing sheet with id= X, first strand: chain 'T' and resid 77 through 79 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: 6.459A 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: 6.510A pdb=" N VAL w 203 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ASP w 63 " --> pdb=" O VAL w 203 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL w 205 " --> pdb=" O ASP w 63 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLU w 254 " --> pdb=" O VAL w 204 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N TYR w 206 " --> pdb=" O GLU w 254 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU w 256 " --> pdb=" O TYR w 206 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ASP w 208 " --> pdb=" O LEU w 256 " (cutoff:3.500A) removed outlier: 6.851A 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 2910 hydrogen bonds defined for protein. 8214 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 21.62 Time building geometry restraints manager: 23.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.39: 27141 1.39 - 1.62: 40075 1.62 - 1.84: 834 1.84 - 2.06: 0 2.06 - 2.29: 80 Bond restraints: 68130 Sorted by residual: bond pdb=" C3D NAI A 503 " pdb=" C4D NAI A 503 " ideal model delta sigma weight residual 1.524 1.261 0.263 2.00e-02 2.50e+03 1.73e+02 bond pdb=" C1D NAI A 503 " pdb=" C2D NAI A 503 " ideal model delta sigma weight residual 1.528 1.289 0.239 2.00e-02 2.50e+03 1.43e+02 bond pdb=" C1B NAI A 503 " pdb=" C2B NAI A 503 " ideal model delta sigma weight residual 1.528 1.294 0.234 2.00e-02 2.50e+03 1.37e+02 bond pdb=" C1B NAI A 503 " pdb=" O4B NAI A 503 " ideal model delta sigma weight residual 1.397 1.629 -0.232 2.00e-02 2.50e+03 1.35e+02 bond pdb=" C3' ADP w 401 " pdb=" C4' ADP w 401 " ideal model delta sigma weight residual 1.524 1.298 0.226 2.00e-02 2.50e+03 1.28e+02 ... (remaining 68125 not shown) Histogram of bond angle deviations from ideal: 73.41 - 85.86: 76 85.86 - 98.30: 11 98.30 - 110.75: 23458 110.75 - 123.20: 65765 123.20 - 135.64: 2900 Bond angle restraints: 92210 Sorted by residual: angle pdb=" PA NDP J 401 " pdb=" O3 NDP J 401 " pdb=" PN NDP J 401 " ideal model delta sigma weight residual 107.74 124.20 -16.46 1.95e+00 2.62e-01 7.09e+01 angle pdb=" C11 CDL a 201 " pdb=" CA5 CDL a 201 " pdb=" OA6 CDL a 201 " ideal model delta sigma weight residual 111.33 121.75 -10.42 1.32e+00 5.72e-01 6.21e+01 angle pdb=" C51 CDL a 201 " pdb=" CB5 CDL a 201 " pdb=" OB6 CDL a 201 " ideal model delta sigma weight residual 111.33 121.45 -10.12 1.32e+00 5.72e-01 5.87e+01 angle pdb=" C11 CDL l 701 " pdb=" CA5 CDL l 701 " pdb=" OA6 CDL l 701 " ideal model delta sigma weight residual 111.33 120.99 -9.66 1.32e+00 5.72e-01 5.34e+01 angle pdb=" C5B NDP J 401 " pdb=" O5B NDP J 401 " pdb=" PA NDP J 401 " ideal model delta sigma weight residual 103.84 117.75 -13.91 1.91e+00 2.73e-01 5.27e+01 ... (remaining 92205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 39607 35.99 - 71.98: 1598 71.98 - 107.98: 91 107.98 - 143.97: 20 143.97 - 179.96: 13 Dihedral angle restraints: 41329 sinusoidal: 17627 harmonic: 23702 Sorted by residual: dihedral pdb=" CB CYS v 69 " pdb=" SG CYS v 69 " pdb=" SG CYS v 80 " pdb=" CB CYS v 80 " ideal model delta sinusoidal sigma weight residual 93.00 -178.28 -88.72 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" CB CYS u 88 " pdb=" SG CYS u 88 " pdb=" SG CYS u 100 " pdb=" CB CYS u 100 " ideal model delta sinusoidal sigma weight residual -86.00 -174.36 88.36 1 1.00e+01 1.00e-02 9.32e+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 77.55 -179.96 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 41326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 8915 0.078 - 0.155: 1061 0.155 - 0.233: 46 0.233 - 0.310: 8 0.310 - 0.388: 2 Chirality restraints: 10032 Sorted by residual: chirality pdb=" C3B NDP J 401 " pdb=" C2B NDP J 401 " pdb=" C4B NDP J 401 " pdb=" O3B NDP J 401 " both_signs ideal model delta sigma weight residual False -2.75 -2.36 -0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" C3D NDP J 401 " pdb=" C2D NDP J 401 " pdb=" C4D NDP J 401 " pdb=" O3D NDP J 401 " both_signs ideal model delta sigma weight residual False -2.71 -2.38 -0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" CA GLU p 143 " pdb=" N GLU p 143 " pdb=" C GLU p 143 " pdb=" CB GLU p 143 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 10029 not shown) Planarity restraints: 11549 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 UQ s 401 " 0.371 2.00e-02 2.50e+03 4.83e-01 2.92e+03 pdb=" C11 UQ s 401 " 0.179 2.00e-02 2.50e+03 pdb=" C7 UQ s 401 " 0.574 2.00e-02 2.50e+03 pdb=" C8 UQ s 401 " -0.699 2.00e-02 2.50e+03 pdb=" C9 UQ s 401 " -0.425 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 UQ s 401 " -0.401 2.00e-02 2.50e+03 3.61e-01 1.63e+03 pdb=" C18 UQ s 401 " 0.420 2.00e-02 2.50e+03 pdb=" C19 UQ s 401 " 0.393 2.00e-02 2.50e+03 pdb=" C20 UQ s 401 " -0.014 2.00e-02 2.50e+03 pdb=" C21 UQ s 401 " -0.397 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP J 401 " -0.008 2.00e-02 2.50e+03 2.05e-01 5.24e+02 pdb=" C3N NDP J 401 " 0.392 2.00e-02 2.50e+03 pdb=" C4N NDP J 401 " -0.098 2.00e-02 2.50e+03 pdb=" C7N NDP J 401 " -0.195 2.00e-02 2.50e+03 pdb=" N1N NDP J 401 " -0.091 2.00e-02 2.50e+03 ... (remaining 11546 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 503 2.57 - 3.15: 52744 3.15 - 3.73: 104625 3.73 - 4.32: 151116 4.32 - 4.90: 251173 Nonbonded interactions: 560161 Sorted by model distance: nonbonded pdb=" N GLU v 33 " pdb=" OE1 GLU v 33 " model vdw 1.982 2.520 nonbonded pdb=" O GLU b 122 " pdb=" OE1 GLU b 122 " model vdw 1.992 3.040 nonbonded pdb=" N GLU v 83 " pdb=" OE1 GLU v 83 " model vdw 2.152 2.520 nonbonded pdb=" O ASN l 351 " pdb=" ND2 ASN l 351 " model vdw 2.185 2.520 nonbonded pdb=" OD1 ASN A 185 " pdb=" N GLY A 190 " model vdw 2.196 2.520 ... (remaining 560156 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 145 or (resid 146 and (name N or name CA or nam \ e C or name O or name CB )) or resid 147 through 149 or (resid 150 through 153 a \ nd (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=0.66 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 8.510 Check model and map are aligned: 0.750 Set scattering table: 0.480 Process input model: 157.880 Find NCS groups from input model: 2.350 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 183.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 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 : 0.010 0.315 68130 Z= 0.648 Angle : 0.830 18.009 92210 Z= 0.427 Chirality : 0.051 0.388 10032 Planarity : 0.009 0.483 11549 Dihedral : 18.276 179.959 26022 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.86 % Favored : 96.11 % Rotamer: Outliers : 1.28 % Allowed : 17.63 % Favored : 81.09 % 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: 0.75 (0.09), residues: 8027 helix: 1.38 (0.08), residues: 4242 sheet: 0.32 (0.25), residues: 426 loop : -0.59 (0.11), residues: 3359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP c 145 HIS 0.007 0.001 HIS J 37 PHE 0.035 0.002 PHE i 292 TYR 0.023 0.002 TYR l 422 ARG 0.011 0.001 ARG g 51 *********************** 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 1151 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 1061 time to evaluate : 5.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 183 ASP cc_start: 0.8292 (p0) cc_final: 0.7890 (p0) REVERT: V 120 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8263 (mt) REVERT: X 108 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8822 (mp) REVERT: k 57 ASN cc_start: 0.9245 (m-40) cc_final: 0.8991 (m110) REVERT: n 30 ARG cc_start: 0.7855 (ttt90) cc_final: 0.6409 (ttt180) REVERT: w 274 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7284 (mp0) outliers start: 90 outliers final: 78 residues processed: 1141 average time/residue: 1.5442 time to fit residues: 2266.8094 Evaluate side-chains 1121 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 1040 time to evaluate : 5.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain J residue 374 THR Chi-restraints excluded: chain K residue 105 ARG Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 448 SER Chi-restraints excluded: chain M residue 487 THR Chi-restraints excluded: chain M residue 559 ASP Chi-restraints excluded: chain M residue 640 ASP Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain O residue 196 LEU Chi-restraints excluded: chain O residue 202 GLU Chi-restraints excluded: chain O residue 245 VAL Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 252 SER Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 373 THR Chi-restraints excluded: chain Q residue 409 VAL Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 84 ILE Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 100 THR Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 109 SER Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain Y residue 40 ILE Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 78 LEU Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 120 SER Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 101 GLU Chi-restraints excluded: chain g residue 60 LEU Chi-restraints excluded: chain i residue 108 LEU Chi-restraints excluded: chain i residue 300 SER Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 185 SER Chi-restraints excluded: chain l residue 543 SER Chi-restraints excluded: chain l residue 578 SER Chi-restraints excluded: chain l residue 598 SER Chi-restraints excluded: chain m residue 27 ILE Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain p residue 19 LEU Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 66 LEU Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 303 ILE Chi-restraints excluded: chain r residue 448 THR Chi-restraints excluded: chain s residue 17 VAL Chi-restraints excluded: chain s residue 73 ILE Chi-restraints excluded: chain s residue 144 VAL Chi-restraints excluded: chain u residue 14 LYS Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain v residue 33 GLU Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 274 GLU Chi-restraints excluded: chain w residue 312 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 669 optimal weight: 1.9990 chunk 601 optimal weight: 0.9990 chunk 333 optimal weight: 8.9990 chunk 205 optimal weight: 5.9990 chunk 405 optimal weight: 7.9990 chunk 321 optimal weight: 3.9990 chunk 621 optimal weight: 0.8980 chunk 240 optimal weight: 1.9990 chunk 377 optimal weight: 2.9990 chunk 462 optimal weight: 0.8980 chunk 720 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 277 ASN A 344 GLN A 456 GLN E 58 GLN E 70 ASN F 81 ASN H 110 ASN M 202 ASN ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 425 ASN ** O 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 63 GLN ** P 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 236 ASN T 74 GLN d 124 ASN h 70 GLN i 322 GLN m 46 ASN n 6 GLN o 79 ASN r 304 GLN u 95 GLN v 110 GLN w 111 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.0470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 68130 Z= 0.173 Angle : 0.531 10.438 92210 Z= 0.266 Chirality : 0.040 0.181 10032 Planarity : 0.004 0.064 11549 Dihedral : 13.914 179.679 10187 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.79 % Favored : 96.19 % Rotamer: Outliers : 2.78 % Allowed : 16.00 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.09), residues: 8027 helix: 1.64 (0.08), residues: 4246 sheet: 0.28 (0.25), residues: 432 loop : -0.52 (0.11), residues: 3349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.006 0.001 HIS J 37 PHE 0.030 0.001 PHE i 292 TYR 0.024 0.001 TYR r 406 ARG 0.007 0.000 ARG a 158 *********************** 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 1318 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1122 time to evaluate : 5.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 GLU cc_start: 0.7379 (tp30) cc_final: 0.7152 (tp30) REVERT: A 289 GLU cc_start: 0.7432 (tt0) cc_final: 0.7161 (tt0) REVERT: A 451 GLN cc_start: 0.7557 (tp40) cc_final: 0.7336 (tt0) REVERT: B 76 TYR cc_start: 0.8988 (OUTLIER) cc_final: 0.8071 (t80) REVERT: C 154 ASP cc_start: 0.8856 (OUTLIER) cc_final: 0.8593 (p0) REVERT: E 87 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8266 (tmtt) REVERT: F 31 GLN cc_start: 0.5582 (OUTLIER) cc_final: 0.5318 (tm-30) REVERT: F 57 GLU cc_start: 0.7931 (mp0) cc_final: 0.7655 (mm-30) REVERT: F 64 LYS cc_start: 0.8009 (mtpp) cc_final: 0.7595 (tppp) REVERT: G 115 GLN cc_start: 0.7748 (tm-30) cc_final: 0.7460 (tm-30) REVERT: G 118 ILE cc_start: 0.7945 (OUTLIER) cc_final: 0.7642 (mp) REVERT: J 79 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8782 (tt0) REVERT: J 238 GLN cc_start: 0.5632 (OUTLIER) cc_final: 0.5255 (tt0) REVERT: L 133 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.8328 (m-30) REVERT: M 381 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8065 (mm) REVERT: O 72 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.6545 (mp0) REVERT: O 88 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7418 (ttm110) REVERT: O 239 LYS cc_start: 0.7341 (mmmm) cc_final: 0.6423 (mmtp) REVERT: P 183 ASP cc_start: 0.8212 (p0) cc_final: 0.7934 (p0) REVERT: S 44 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.8845 (pt0) REVERT: V 72 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7393 (tm) REVERT: V 120 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8262 (mt) REVERT: W 24 ASN cc_start: 0.8350 (t0) cc_final: 0.8069 (t0) REVERT: d 76 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8073 (pt0) REVERT: d 161 GLN cc_start: 0.9050 (OUTLIER) cc_final: 0.8566 (pt0) REVERT: d 168 LYS cc_start: 0.8251 (ttmt) cc_final: 0.8043 (tppp) REVERT: e 148 GLN cc_start: 0.8497 (tp40) cc_final: 0.8210 (tp-100) REVERT: g 4 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8693 (mtm) REVERT: g 89 ASP cc_start: 0.9229 (m-30) cc_final: 0.8984 (m-30) REVERT: g 101 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6742 (mp0) REVERT: k 57 ASN cc_start: 0.9220 (m-40) cc_final: 0.8928 (m110) REVERT: l 331 MET cc_start: 0.9322 (mmp) cc_final: 0.9105 (mmt) REVERT: l 366 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.8802 (mtm) REVERT: l 383 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.7820 (tpt) REVERT: l 445 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7629 (mt-10) REVERT: n 30 ARG cc_start: 0.7866 (ttt90) cc_final: 0.6212 (ttt180) REVERT: v 21 ARG cc_start: 0.7243 (tpp-160) cc_final: 0.6912 (mtm-85) REVERT: v 35 LYS cc_start: 0.6993 (OUTLIER) cc_final: 0.6606 (tppp) REVERT: v 54 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.8033 (pt0) outliers start: 196 outliers final: 81 residues processed: 1210 average time/residue: 1.5318 time to fit residues: 2398.2727 Evaluate side-chains 1178 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 1075 time to evaluate : 6.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 31 GLN Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 238 GLN Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 133 ASP Chi-restraints excluded: chain L residue 144 SER Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain M residue 381 LEU Chi-restraints excluded: chain M residue 487 THR Chi-restraints excluded: chain M residue 556 THR Chi-restraints excluded: chain N residue 95 ASP Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 88 ARG Chi-restraints excluded: chain O residue 202 GLU Chi-restraints excluded: chain O residue 245 VAL Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 261 MET Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 409 VAL Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain V residue 4 THR Chi-restraints excluded: chain V residue 72 LEU Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 100 THR Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain Y residue 76 ASP Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain Z residue 42 ARG Chi-restraints excluded: chain c residue 78 LEU Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain d residue 76 GLU Chi-restraints excluded: chain d residue 136 SER Chi-restraints excluded: chain d residue 161 GLN Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain g residue 4 MET Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 101 GLU Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain j residue 8 LEU Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain l residue 61 MET Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 383 MET Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 581 LYS Chi-restraints excluded: chain m residue 2 THR Chi-restraints excluded: chain m residue 27 ILE Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 41 CYS Chi-restraints excluded: chain o residue 117 GLN Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 66 LEU Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 281 ASP Chi-restraints excluded: chain r residue 343 ILE Chi-restraints excluded: chain r residue 444 LEU Chi-restraints excluded: chain r residue 448 THR Chi-restraints excluded: chain s residue 225 MET Chi-restraints excluded: chain u residue 73 GLN Chi-restraints excluded: chain v residue 35 LYS Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 67 CYS Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 275 TYR 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: 9.9990 chunk 599 optimal weight: 8.9990 chunk 490 optimal weight: 7.9990 chunk 198 optimal weight: 9.9990 chunk 721 optimal weight: 3.9990 chunk 779 optimal weight: 6.9990 chunk 642 optimal weight: 7.9990 chunk 715 optimal weight: 3.9990 chunk 245 optimal weight: 10.0000 chunk 578 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 277 ASN A 344 GLN A 418 GLN A 436 GLN E 58 GLN E 70 ASN ** H 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 ASN K 79 HIS ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 678 GLN ** O 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 63 GLN ** P 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 236 ASN Q 147 ASN T 74 GLN d 23 GLN h 70 GLN i 150 ASN i 204 ASN i 310 ASN i 322 GLN l 109 HIS m 46 ASN n 6 GLN r 139 GLN r 304 GLN s 157 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 68130 Z= 0.514 Angle : 0.710 11.271 92210 Z= 0.358 Chirality : 0.050 0.242 10032 Planarity : 0.006 0.070 11549 Dihedral : 13.705 177.767 10090 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.75 % Favored : 95.23 % Rotamer: Outliers : 4.72 % Allowed : 16.07 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.09), residues: 8027 helix: 1.10 (0.08), residues: 4249 sheet: 0.04 (0.25), residues: 418 loop : -0.79 (0.10), residues: 3360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP l 144 HIS 0.010 0.002 HIS l 230 PHE 0.037 0.003 PHE i 292 TYR 0.024 0.002 TYR C 84 ARG 0.009 0.001 ARG l 357 *********************** 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 1411 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 333 poor density : 1078 time to evaluate : 6.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 GLU cc_start: 0.7476 (tp30) cc_final: 0.7210 (tp30) REVERT: A 343 VAL cc_start: 0.8607 (t) cc_final: 0.8391 (p) REVERT: C 154 ASP cc_start: 0.8863 (OUTLIER) cc_final: 0.8536 (p0) REVERT: E 87 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8395 (tmtt) REVERT: F 31 GLN cc_start: 0.6169 (OUTLIER) cc_final: 0.5646 (tm-30) REVERT: F 57 GLU cc_start: 0.7907 (mp0) cc_final: 0.7618 (mm-30) REVERT: G 122 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.7367 (mmp) REVERT: I 33 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8449 (mtpt) REVERT: J 37 HIS cc_start: 0.6468 (t-90) cc_final: 0.6236 (t70) REVERT: J 79 GLN cc_start: 0.9055 (OUTLIER) cc_final: 0.8817 (tt0) REVERT: J 174 ILE cc_start: 0.7414 (OUTLIER) cc_final: 0.7110 (tt) REVERT: J 238 GLN cc_start: 0.5971 (OUTLIER) cc_final: 0.5642 (tt0) REVERT: L 69 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7001 (pt0) REVERT: L 133 ASP cc_start: 0.8719 (OUTLIER) cc_final: 0.8407 (m-30) REVERT: M 58 MET cc_start: 0.8855 (tmt) cc_final: 0.8437 (tmt) REVERT: M 381 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8126 (mm) REVERT: N 5 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.7086 (tp40) REVERT: O 72 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.6887 (mp0) REVERT: O 88 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.7477 (ttm110) REVERT: O 169 PHE cc_start: 0.8483 (m-80) cc_final: 0.8175 (m-80) REVERT: O 185 MET cc_start: 0.8694 (ppp) cc_final: 0.8405 (ppp) REVERT: P 50 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7457 (ptm160) REVERT: P 183 ASP cc_start: 0.8204 (p0) cc_final: 0.7912 (p0) REVERT: Q 171 ARG cc_start: 0.9536 (OUTLIER) cc_final: 0.7738 (mtp85) REVERT: Q 335 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8320 (tm-30) REVERT: Q 367 LYS cc_start: 0.8888 (mttt) cc_final: 0.8652 (mttm) REVERT: Q 437 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8203 (ttmm) REVERT: S 44 GLN cc_start: 0.9296 (OUTLIER) cc_final: 0.8977 (pt0) REVERT: S 66 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8126 (mp) REVERT: S 69 ILE cc_start: 0.7602 (OUTLIER) cc_final: 0.7357 (mm) REVERT: V 41 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7760 (mp) REVERT: V 55 ARG cc_start: 0.7295 (ttm170) cc_final: 0.7015 (ttm170) REVERT: V 72 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7652 (tm) REVERT: V 131 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.7881 (mm-30) REVERT: X 108 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8791 (mp) REVERT: c 111 MET cc_start: 0.9290 (OUTLIER) cc_final: 0.8855 (ttp) REVERT: d 73 ASP cc_start: 0.8763 (p0) cc_final: 0.8541 (p0) REVERT: d 161 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.8685 (pt0) REVERT: f 46 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8321 (mp) REVERT: g 4 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.8851 (mtm) REVERT: g 101 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6672 (mp0) REVERT: h 24 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8312 (tp30) REVERT: h 61 ASP cc_start: 0.9057 (m-30) cc_final: 0.8815 (m-30) REVERT: h 83 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7039 (ttp-170) REVERT: k 57 ASN cc_start: 0.9254 (m-40) cc_final: 0.9007 (m110) REVERT: l 21 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8891 (mtm) REVERT: l 351 ASN cc_start: 0.8846 (t0) cc_final: 0.8599 (t0) REVERT: l 366 MET cc_start: 0.9230 (OUTLIER) cc_final: 0.8863 (mtm) REVERT: l 525 MET cc_start: 0.9172 (OUTLIER) cc_final: 0.8412 (mpp) REVERT: l 596 MET cc_start: 0.7914 (mtt) cc_final: 0.7704 (mtp) REVERT: m 76 THR cc_start: 0.6781 (m) cc_final: 0.6415 (p) REVERT: n 30 ARG cc_start: 0.8130 (ttt90) cc_final: 0.6482 (ttt180) REVERT: p 48 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.7749 (t80) REVERT: p 141 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7979 (mt0) REVERT: r 103 GLN cc_start: 0.9361 (OUTLIER) cc_final: 0.8834 (tt0) REVERT: r 114 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8260 (tm-30) REVERT: r 378 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8491 (tt0) REVERT: v 12 ASP cc_start: 0.8059 (t0) cc_final: 0.7768 (t0) REVERT: v 35 LYS cc_start: 0.7064 (OUTLIER) cc_final: 0.6825 (tppp) REVERT: w 173 MET cc_start: 0.9116 (mtt) cc_final: 0.8910 (mtt) REVERT: w 197 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7649 (mt-10) outliers start: 333 outliers final: 156 residues processed: 1240 average time/residue: 1.5007 time to fit residues: 2411.6547 Evaluate side-chains 1230 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 1032 time to evaluate : 6.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 31 GLN Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 174 ILE Chi-restraints excluded: chain J residue 238 GLN Chi-restraints excluded: chain J residue 266 VAL Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 133 ASP Chi-restraints excluded: chain L residue 144 SER Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 379 THR Chi-restraints excluded: chain M residue 381 LEU Chi-restraints excluded: chain M residue 400 ILE Chi-restraints excluded: chain M residue 487 THR Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 556 THR Chi-restraints excluded: chain M residue 645 ARG Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 95 ASP Chi-restraints excluded: chain N residue 132 LYS Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 88 ARG Chi-restraints excluded: chain O residue 196 LEU Chi-restraints excluded: chain O residue 202 GLU Chi-restraints excluded: chain O residue 245 VAL Chi-restraints excluded: chain O residue 246 GLN Chi-restraints excluded: chain P residue 50 ARG Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 96 ARG Chi-restraints excluded: chain Q residue 171 ARG Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 261 MET Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 335 GLU Chi-restraints excluded: chain Q residue 409 VAL Chi-restraints excluded: chain Q residue 437 LYS Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 69 ILE Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain T residue 49 ASP Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 84 ILE Chi-restraints excluded: chain T residue 119 ARG Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain V residue 4 THR Chi-restraints excluded: chain V residue 6 LEU Chi-restraints excluded: chain V residue 27 SER Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain V residue 72 LEU Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain V residue 131 GLU Chi-restraints excluded: chain W residue 4 SER Chi-restraints excluded: chain W residue 27 ARG Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Y residue 76 ASP Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Y residue 100 LEU Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain Z residue 42 ARG Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 78 LEU Chi-restraints excluded: chain c residue 111 MET Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain d residue 76 GLU Chi-restraints excluded: chain d residue 127 LYS Chi-restraints excluded: chain d residue 136 SER Chi-restraints excluded: chain d residue 161 GLN Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 137 MET Chi-restraints excluded: chain f residue 46 LEU Chi-restraints excluded: chain f residue 60 LYS Chi-restraints excluded: chain g residue 4 MET Chi-restraints excluded: chain g residue 19 GLU Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 101 GLU Chi-restraints excluded: chain h residue 24 GLU Chi-restraints excluded: chain h residue 83 ARG Chi-restraints excluded: chain h residue 88 LYS Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 347 ASN Chi-restraints excluded: chain j residue 8 LEU Chi-restraints excluded: chain j residue 20 ILE Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain l residue 21 MET Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 61 MET Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 184 LEU Chi-restraints excluded: chain l residue 293 ILE Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 496 MET Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 511 LEU Chi-restraints excluded: chain l residue 525 MET Chi-restraints excluded: chain l residue 571 MET Chi-restraints excluded: chain l residue 581 LYS Chi-restraints excluded: chain m residue 2 THR Chi-restraints excluded: chain m residue 5 ILE Chi-restraints excluded: chain m residue 27 ILE Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 41 CYS Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain o residue 50 GLN Chi-restraints excluded: chain p residue 19 LEU Chi-restraints excluded: chain p residue 48 PHE Chi-restraints excluded: chain p residue 141 GLN Chi-restraints excluded: chain r residue 50 LEU Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 66 LEU Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 281 ASP Chi-restraints excluded: chain r residue 303 ILE Chi-restraints excluded: chain r residue 343 ILE Chi-restraints excluded: chain r residue 378 GLU Chi-restraints excluded: chain r residue 448 THR Chi-restraints excluded: chain r residue 452 LYS Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 65 THR Chi-restraints excluded: chain s residue 144 VAL Chi-restraints excluded: chain s residue 200 LEU Chi-restraints excluded: chain s residue 225 MET Chi-restraints excluded: chain v residue 22 MET Chi-restraints excluded: chain v residue 35 LYS Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 61 THR Chi-restraints excluded: chain w residue 67 CYS Chi-restraints excluded: chain w residue 197 GLU Chi-restraints excluded: chain w residue 275 TYR Chi-restraints excluded: chain w residue 312 VAL Chi-restraints excluded: chain w residue 354 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 712 optimal weight: 0.8980 chunk 542 optimal weight: 2.9990 chunk 374 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 344 optimal weight: 2.9990 chunk 484 optimal weight: 2.9990 chunk 724 optimal weight: 2.9990 chunk 766 optimal weight: 0.9980 chunk 378 optimal weight: 0.9990 chunk 686 optimal weight: 0.8980 chunk 206 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 436 GLN A 456 GLN E 58 GLN G 115 GLN H 110 ASN J 238 GLN ** J 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 522 GLN M 678 GLN O 153 GLN P 63 GLN P 75 GLN P 105 ASN ** P 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 124 ASN P 236 ASN T 74 GLN W 24 ASN c 127 ASN h 70 GLN i 150 ASN i 322 GLN n 6 GLN r 139 GLN r 251 ASN r 304 GLN s 157 ASN u 95 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 68130 Z= 0.186 Angle : 0.542 11.676 92210 Z= 0.273 Chirality : 0.041 0.193 10032 Planarity : 0.005 0.065 11549 Dihedral : 12.662 178.701 10083 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.65 % Favored : 96.32 % Rotamer: Outliers : 3.57 % Allowed : 17.84 % Favored : 78.58 % 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: 0.77 (0.09), residues: 8027 helix: 1.49 (0.08), residues: 4259 sheet: 0.17 (0.25), residues: 417 loop : -0.69 (0.11), residues: 3351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP u 86 HIS 0.007 0.001 HIS p 76 PHE 0.042 0.001 PHE l 340 TYR 0.021 0.001 TYR r 406 ARG 0.008 0.000 ARG a 158 *********************** 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 1344 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 1092 time to evaluate : 6.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 GLU cc_start: 0.7363 (tp30) cc_final: 0.7118 (tp30) REVERT: A 292 MET cc_start: 0.7268 (OUTLIER) cc_final: 0.6903 (ttt) REVERT: A 332 CYS cc_start: 0.8002 (p) cc_final: 0.7750 (p) REVERT: A 451 GLN cc_start: 0.7810 (tp40) cc_final: 0.7487 (tt0) REVERT: C 142 TYR cc_start: 0.9385 (OUTLIER) cc_final: 0.9130 (t80) REVERT: C 154 ASP cc_start: 0.8859 (OUTLIER) cc_final: 0.8582 (p0) REVERT: E 87 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8274 (tmtt) REVERT: G 115 GLN cc_start: 0.7893 (tm-30) cc_final: 0.7576 (tm-30) REVERT: G 124 ASP cc_start: 0.7914 (p0) cc_final: 0.7707 (p0) REVERT: G 128 PHE cc_start: 0.7265 (p90) cc_final: 0.6791 (p90) REVERT: G 139 MET cc_start: 0.6563 (OUTLIER) cc_final: 0.6014 (mmt) REVERT: I 18 ARG cc_start: 0.8384 (mtt90) cc_final: 0.7955 (mpt-90) REVERT: I 33 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8382 (mtpt) REVERT: J 318 LYS cc_start: 0.7602 (OUTLIER) cc_final: 0.7036 (ttpm) REVERT: L 69 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6928 (pt0) REVERT: L 133 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.8331 (m-30) REVERT: M 58 MET cc_start: 0.8834 (tmt) cc_final: 0.8298 (tmt) REVERT: M 381 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8077 (mm) REVERT: M 470 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7422 (tptp) REVERT: N 5 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.7105 (tp40) REVERT: O 72 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.6843 (mp0) REVERT: O 169 PHE cc_start: 0.8499 (m-80) cc_final: 0.8226 (m-80) REVERT: P 50 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7383 (ptm160) REVERT: P 183 ASP cc_start: 0.8255 (p0) cc_final: 0.7958 (p0) REVERT: Q 437 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8113 (ttmm) REVERT: U 31 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8378 (mp) REVERT: V 41 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7557 (mp) REVERT: V 55 ARG cc_start: 0.7279 (ttm170) cc_final: 0.7036 (ttm170) REVERT: V 72 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7439 (tm) REVERT: V 134 GLN cc_start: 0.8919 (mt0) cc_final: 0.8647 (mt0) REVERT: W 25 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8026 (mp) REVERT: Z 91 GLN cc_start: 0.5490 (OUTLIER) cc_final: 0.3519 (tp40) REVERT: d 73 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.8337 (p0) REVERT: d 76 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8103 (OUTLIER) REVERT: d 161 GLN cc_start: 0.9081 (OUTLIER) cc_final: 0.8569 (pt0) REVERT: e 114 MET cc_start: 0.8738 (mmm) cc_final: 0.8345 (mmm) REVERT: g 4 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8757 (mtm) REVERT: g 101 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6666 (mp0) REVERT: h 24 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8207 (tp30) REVERT: h 61 ASP cc_start: 0.9031 (m-30) cc_final: 0.8720 (m-30) REVERT: i 318 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7707 (mm-30) REVERT: k 3 LEU cc_start: 0.8012 (mp) cc_final: 0.7762 (mm) REVERT: k 57 ASN cc_start: 0.9245 (m-40) cc_final: 0.8974 (m110) REVERT: l 176 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.8784 (mmt90) REVERT: l 366 MET cc_start: 0.9189 (OUTLIER) cc_final: 0.8930 (mtm) REVERT: m 76 THR cc_start: 0.6712 (m) cc_final: 0.6369 (p) REVERT: n 30 ARG cc_start: 0.8017 (ttt90) cc_final: 0.6307 (ttt180) REVERT: p 48 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.7479 (t80) REVERT: p 139 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.8610 (tm-30) REVERT: r 103 GLN cc_start: 0.9209 (OUTLIER) cc_final: 0.8680 (tt0) REVERT: u 64 ASN cc_start: 0.8598 (OUTLIER) cc_final: 0.8321 (t0) REVERT: v 35 LYS cc_start: 0.7039 (OUTLIER) cc_final: 0.6776 (tppp) REVERT: w 210 PRO cc_start: 0.8154 (Cg_exo) cc_final: 0.7835 (Cg_endo) outliers start: 252 outliers final: 105 residues processed: 1229 average time/residue: 1.5051 time to fit residues: 2390.8808 Evaluate side-chains 1188 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1050 time to evaluate : 5.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 48 LYS Chi-restraints excluded: chain I residue 64 MET Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 318 LYS Chi-restraints excluded: chain J residue 374 THR Chi-restraints excluded: chain K residue 105 ARG Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 133 ASP Chi-restraints excluded: chain L residue 144 SER Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 381 LEU Chi-restraints excluded: chain M residue 470 LYS Chi-restraints excluded: chain M residue 487 THR Chi-restraints excluded: chain M residue 559 ASP Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 95 ASP Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 245 VAL Chi-restraints excluded: chain P residue 50 ARG Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 238 LEU Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 373 THR Chi-restraints excluded: chain Q residue 409 VAL Chi-restraints excluded: chain Q residue 437 LYS Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain V residue 6 LEU Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain V residue 72 LEU Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 25 LEU Chi-restraints excluded: chain W residue 27 ARG Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain Y residue 76 ASP Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain Z residue 42 ARG Chi-restraints excluded: chain Z residue 91 GLN Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 78 LEU Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 73 ASP Chi-restraints excluded: chain d residue 76 GLU Chi-restraints excluded: chain d residue 119 GLU Chi-restraints excluded: chain d residue 127 LYS Chi-restraints excluded: chain d residue 136 SER Chi-restraints excluded: chain d residue 161 GLN Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain f residue 60 LYS Chi-restraints excluded: chain g residue 4 MET Chi-restraints excluded: chain g residue 19 GLU Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 60 LEU Chi-restraints excluded: chain g residue 101 GLU Chi-restraints excluded: chain g residue 115 LEU Chi-restraints excluded: chain h residue 24 GLU Chi-restraints excluded: chain i residue 86 ILE Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 318 GLU Chi-restraints excluded: chain i residue 347 ASN Chi-restraints excluded: chain j residue 8 LEU Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 176 ARG Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 496 MET Chi-restraints excluded: chain l residue 511 LEU Chi-restraints excluded: chain l residue 571 MET Chi-restraints excluded: chain l residue 581 LYS Chi-restraints excluded: chain m residue 2 THR Chi-restraints excluded: chain m residue 27 ILE Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 41 CYS Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain o residue 9 SER Chi-restraints excluded: chain o residue 117 GLN Chi-restraints excluded: chain p residue 43 LEU Chi-restraints excluded: chain p residue 48 PHE Chi-restraints excluded: chain p residue 139 GLN Chi-restraints excluded: chain r residue 50 LEU Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 66 LEU Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 448 THR Chi-restraints excluded: chain s residue 65 THR Chi-restraints excluded: chain s residue 200 LEU Chi-restraints excluded: chain u residue 64 ASN Chi-restraints excluded: chain v residue 22 MET Chi-restraints excluded: chain v residue 35 LYS Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 67 CYS Chi-restraints excluded: chain w residue 100 ASP Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 275 TYR Chi-restraints excluded: chain w residue 293 ARG Chi-restraints excluded: chain w residue 312 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 638 optimal weight: 4.9990 chunk 435 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 570 optimal weight: 6.9990 chunk 316 optimal weight: 8.9990 chunk 654 optimal weight: 0.0570 chunk 529 optimal weight: 0.3980 chunk 0 optimal weight: 20.0000 chunk 391 optimal weight: 3.9990 chunk 688 optimal weight: 4.9990 chunk 193 optimal weight: 5.9990 overall best weight: 2.8904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN E 58 GLN H 110 ASN M 678 GLN O 144 ASN P 63 GLN P 105 ASN P 236 ASN T 74 GLN h 70 GLN i 150 ASN i 204 ASN n 6 GLN r 139 GLN r 251 ASN r 304 GLN s 157 ASN v 76 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 68130 Z= 0.315 Angle : 0.601 10.651 92210 Z= 0.302 Chirality : 0.044 0.207 10032 Planarity : 0.005 0.067 11549 Dihedral : 12.407 178.496 10077 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.42 % Favored : 95.55 % Rotamer: Outliers : 4.14 % Allowed : 18.01 % Favored : 77.85 % 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: 0.67 (0.09), residues: 8027 helix: 1.40 (0.08), residues: 4261 sheet: 0.09 (0.25), residues: 416 loop : -0.73 (0.11), residues: 3350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP l 144 HIS 0.008 0.001 HIS J 37 PHE 0.035 0.002 PHE i 292 TYR 0.020 0.002 TYR Y 44 ARG 0.005 0.000 ARG C 195 *********************** 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 1365 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 1073 time to evaluate : 6.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 GLU cc_start: 0.7320 (tp30) cc_final: 0.7071 (tp30) REVERT: A 292 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.7001 (ttt) REVERT: A 343 VAL cc_start: 0.8561 (t) cc_final: 0.8354 (p) REVERT: A 451 GLN cc_start: 0.7833 (tp40) cc_final: 0.7615 (tp40) REVERT: C 142 TYR cc_start: 0.9374 (OUTLIER) cc_final: 0.9128 (t80) REVERT: C 154 ASP cc_start: 0.8827 (OUTLIER) cc_final: 0.8541 (p0) REVERT: E 87 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8323 (tmtt) REVERT: F 64 LYS cc_start: 0.7860 (mtpm) cc_final: 0.7505 (tppt) REVERT: G 115 GLN cc_start: 0.7902 (tm-30) cc_final: 0.7568 (tm-30) REVERT: I 33 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8410 (mtpt) REVERT: J 318 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.7027 (tttm) REVERT: L 69 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6924 (pt0) REVERT: L 133 ASP cc_start: 0.8585 (OUTLIER) cc_final: 0.8310 (m-30) REVERT: M 58 MET cc_start: 0.8846 (tmt) cc_final: 0.8404 (tmt) REVERT: M 381 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8050 (mm) REVERT: O 72 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.6929 (mp0) REVERT: O 143 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7691 (mmt90) REVERT: O 169 PHE cc_start: 0.8518 (m-80) cc_final: 0.8230 (m-80) REVERT: O 185 MET cc_start: 0.8599 (ppp) cc_final: 0.8142 (ptp) REVERT: P 50 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7351 (ptm160) REVERT: P 183 ASP cc_start: 0.8352 (p0) cc_final: 0.7991 (p0) REVERT: Q 171 ARG cc_start: 0.9529 (OUTLIER) cc_final: 0.8073 (mtp85) REVERT: Q 192 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8965 (tp) REVERT: Q 335 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8018 (tm-30) REVERT: Q 437 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8157 (ttmm) REVERT: T 74 GLN cc_start: 0.9029 (mm-40) cc_final: 0.8757 (mm110) REVERT: U 31 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8386 (mp) REVERT: V 41 ILE cc_start: 0.8020 (OUTLIER) cc_final: 0.7578 (mp) REVERT: V 55 ARG cc_start: 0.7253 (ttm170) cc_final: 0.7008 (ttm170) REVERT: V 72 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7526 (tm) REVERT: V 134 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8655 (mt0) REVERT: Z 91 GLN cc_start: 0.5690 (OUTLIER) cc_final: 0.3509 (tp40) REVERT: d 73 ASP cc_start: 0.8713 (p0) cc_final: 0.8428 (p0) REVERT: d 76 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8104 (pt0) REVERT: d 79 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7337 (tp30) REVERT: d 161 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8574 (pt0) REVERT: e 55 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7614 (pp) REVERT: g 4 MET cc_start: 0.9130 (OUTLIER) cc_final: 0.8830 (mtm) REVERT: g 101 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.6737 (mp0) REVERT: h 24 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8229 (tp30) REVERT: i 318 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7706 (mm-30) REVERT: k 57 ASN cc_start: 0.9225 (m-40) cc_final: 0.8950 (m110) REVERT: l 21 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8854 (mtm) REVERT: l 46 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9102 (tm) REVERT: l 61 MET cc_start: 0.8952 (mtm) cc_final: 0.8745 (mtm) REVERT: l 176 ARG cc_start: 0.9144 (OUTLIER) cc_final: 0.8803 (mmt90) REVERT: l 366 MET cc_start: 0.9235 (OUTLIER) cc_final: 0.9000 (mtm) REVERT: l 471 ASN cc_start: 0.8808 (m-40) cc_final: 0.8310 (m110) REVERT: n 30 ARG cc_start: 0.7959 (ttt90) cc_final: 0.6329 (ttt180) REVERT: o 39 ILE cc_start: 0.9082 (pt) cc_final: 0.8803 (mt) REVERT: p 48 PHE cc_start: 0.8284 (OUTLIER) cc_final: 0.7679 (t80) REVERT: p 139 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8653 (tm-30) REVERT: r 103 GLN cc_start: 0.9318 (OUTLIER) cc_final: 0.8780 (tt0) REVERT: r 114 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8001 (tm-30) REVERT: r 116 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.9102 (tp) REVERT: v 35 LYS cc_start: 0.7183 (OUTLIER) cc_final: 0.6972 (tppp) REVERT: w 197 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7562 (mt-10) REVERT: w 210 PRO cc_start: 0.8220 (Cg_exo) cc_final: 0.7918 (Cg_endo) outliers start: 292 outliers final: 148 residues processed: 1227 average time/residue: 1.5099 time to fit residues: 2402.5924 Evaluate side-chains 1233 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1045 time to evaluate : 5.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 318 LYS Chi-restraints excluded: chain J residue 374 THR Chi-restraints excluded: chain K residue 105 ARG Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 133 ASP Chi-restraints excluded: chain L residue 144 SER Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 379 THR Chi-restraints excluded: chain M residue 381 LEU Chi-restraints excluded: chain M residue 389 THR Chi-restraints excluded: chain M residue 473 MET Chi-restraints excluded: chain M residue 487 THR Chi-restraints excluded: chain M residue 556 THR Chi-restraints excluded: chain M residue 559 ASP Chi-restraints excluded: chain N residue 95 ASP Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 132 LYS Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 143 ARG Chi-restraints excluded: chain O residue 245 VAL Chi-restraints excluded: chain P residue 50 ARG Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain Q residue 171 ARG Chi-restraints excluded: chain Q residue 192 LEU Chi-restraints excluded: chain Q residue 238 LEU Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 335 GLU Chi-restraints excluded: chain Q residue 373 THR Chi-restraints excluded: chain Q residue 409 VAL Chi-restraints excluded: chain Q residue 437 LYS Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 84 ILE Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain V residue 4 THR Chi-restraints excluded: chain V residue 6 LEU Chi-restraints excluded: chain V residue 27 SER Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain V residue 72 LEU Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain V residue 134 GLN Chi-restraints excluded: chain W residue 4 SER Chi-restraints excluded: chain W residue 27 ARG Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 103 ASP Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 102 SER Chi-restraints excluded: chain X residue 136 GLU Chi-restraints excluded: chain Y residue 76 ASP Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Y residue 100 LEU Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain Z residue 42 ARG Chi-restraints excluded: chain Z residue 91 GLN Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 78 LEU Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain d residue 76 GLU Chi-restraints excluded: chain d residue 79 GLU Chi-restraints excluded: chain d residue 127 LYS Chi-restraints excluded: chain d residue 136 SER Chi-restraints excluded: chain d residue 161 GLN Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain f residue 60 LYS Chi-restraints excluded: chain g residue 4 MET Chi-restraints excluded: chain g residue 19 GLU Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 60 LEU Chi-restraints excluded: chain g residue 101 GLU Chi-restraints excluded: chain h residue 24 GLU Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 318 GLU Chi-restraints excluded: chain i residue 347 ASN Chi-restraints excluded: chain j residue 8 LEU Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 14 ILE Chi-restraints excluded: chain l residue 21 MET Chi-restraints excluded: chain l residue 46 LEU Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 176 ARG Chi-restraints excluded: chain l residue 293 ILE Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 482 MET Chi-restraints excluded: chain l residue 496 MET Chi-restraints excluded: chain l residue 511 LEU Chi-restraints excluded: chain l residue 571 MET Chi-restraints excluded: chain l residue 581 LYS Chi-restraints excluded: chain m residue 2 THR Chi-restraints excluded: chain m residue 5 ILE Chi-restraints excluded: chain m residue 27 ILE Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 41 CYS Chi-restraints excluded: chain m residue 127 ILE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 16 LEU Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 50 GLN Chi-restraints excluded: chain o residue 117 GLN Chi-restraints excluded: chain p residue 19 LEU Chi-restraints excluded: chain p residue 48 PHE Chi-restraints excluded: chain p residue 139 GLN Chi-restraints excluded: chain r residue 50 LEU Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 66 LEU Chi-restraints excluded: chain r residue 80 SER Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 281 ASP Chi-restraints excluded: chain r residue 303 ILE Chi-restraints excluded: chain r residue 343 ILE Chi-restraints excluded: chain r residue 448 THR Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 65 THR Chi-restraints excluded: chain s residue 144 VAL Chi-restraints excluded: chain s residue 200 LEU Chi-restraints excluded: chain u residue 87 THR Chi-restraints excluded: chain v residue 22 MET Chi-restraints excluded: chain v residue 35 LYS Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 67 CYS Chi-restraints excluded: chain w residue 100 ASP Chi-restraints excluded: chain w residue 197 GLU Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 275 TYR Chi-restraints excluded: chain w residue 293 ARG Chi-restraints excluded: chain w residue 312 VAL Chi-restraints excluded: chain w residue 354 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 257 optimal weight: 4.9990 chunk 690 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 450 optimal weight: 5.9990 chunk 189 optimal weight: 3.9990 chunk 767 optimal weight: 5.9990 chunk 636 optimal weight: 7.9990 chunk 355 optimal weight: 0.0070 chunk 63 optimal weight: 0.7980 chunk 253 optimal weight: 0.0070 chunk 402 optimal weight: 0.0570 overall best weight: 0.5736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN E 58 GLN F 31 GLN H 110 ASN J 238 GLN ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 300 GLN M 678 GLN P 63 GLN P 105 ASN P 236 ASN Q 147 ASN Q 431 HIS h 70 GLN i 150 ASN ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 6 GLN r 139 GLN r 192 ASN r 304 GLN s 124 ASN s 157 ASN s 284 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 68130 Z= 0.144 Angle : 0.514 10.474 92210 Z= 0.258 Chirality : 0.039 0.174 10032 Planarity : 0.004 0.063 11549 Dihedral : 11.585 179.579 10077 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.70 % Favored : 96.28 % Rotamer: Outliers : 2.94 % Allowed : 19.61 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.10), residues: 8027 helix: 1.70 (0.08), residues: 4260 sheet: 0.14 (0.25), residues: 432 loop : -0.60 (0.11), residues: 3335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP u 86 HIS 0.006 0.001 HIS J 37 PHE 0.030 0.001 PHE A 262 TYR 0.025 0.001 TYR l 422 ARG 0.009 0.000 ARG a 158 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1311 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 1104 time to evaluate : 6.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.7226 (OUTLIER) cc_final: 0.6910 (ttt) REVERT: A 332 CYS cc_start: 0.7988 (p) cc_final: 0.7714 (p) REVERT: A 451 GLN cc_start: 0.7794 (tp40) cc_final: 0.7593 (tp40) REVERT: B 149 MET cc_start: 0.9351 (mmm) cc_final: 0.9052 (mmm) REVERT: F 64 LYS cc_start: 0.7758 (mtpm) cc_final: 0.7480 (tppt) REVERT: G 115 GLN cc_start: 0.7923 (tm-30) cc_final: 0.7600 (tm-30) REVERT: G 128 PHE cc_start: 0.7060 (p90) cc_final: 0.6765 (p90) REVERT: I 18 ARG cc_start: 0.8185 (mtt90) cc_final: 0.7969 (mpt-90) REVERT: I 33 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8357 (mtpt) REVERT: L 133 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.8293 (m-30) REVERT: M 58 MET cc_start: 0.8817 (tmt) cc_final: 0.8250 (tmt) REVERT: M 381 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.8003 (mm) REVERT: O 42 ARG cc_start: 0.7862 (mtm-85) cc_final: 0.7648 (mtm-85) REVERT: O 169 PHE cc_start: 0.8488 (m-80) cc_final: 0.8221 (m-80) REVERT: P 164 ASN cc_start: 0.8890 (t0) cc_final: 0.8688 (t0) REVERT: P 183 ASP cc_start: 0.8291 (p0) cc_final: 0.8011 (p0) REVERT: U 34 SER cc_start: 0.8927 (p) cc_final: 0.8719 (m) REVERT: V 41 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7578 (mp) REVERT: V 72 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7371 (tm) REVERT: V 134 GLN cc_start: 0.8911 (mt0) cc_final: 0.8617 (mt0) REVERT: Y 76 ASP cc_start: 0.7444 (m-30) cc_final: 0.7143 (m-30) REVERT: d 76 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8116 (OUTLIER) REVERT: d 127 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8419 (mmmt) REVERT: d 161 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8595 (pt0) REVERT: g 4 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8742 (mtm) REVERT: g 101 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.6840 (mp0) REVERT: h 24 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8085 (tp30) REVERT: i 318 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7706 (mm-30) REVERT: k 57 ASN cc_start: 0.9197 (m-40) cc_final: 0.8892 (m110) REVERT: l 176 ARG cc_start: 0.9101 (OUTLIER) cc_final: 0.8864 (mmt90) REVERT: n 30 ARG cc_start: 0.7858 (ttt90) cc_final: 0.6404 (ttp80) REVERT: o 39 ILE cc_start: 0.9006 (pt) cc_final: 0.8783 (mt) REVERT: o 85 LYS cc_start: 0.8607 (tttt) cc_final: 0.8302 (tttm) REVERT: p 48 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.7513 (t80) REVERT: p 160 GLU cc_start: 0.7136 (tp30) cc_final: 0.6901 (mm-30) REVERT: r 207 MET cc_start: 0.9322 (mmm) cc_final: 0.8823 (mmt) REVERT: u 110 CYS cc_start: 0.8438 (OUTLIER) cc_final: 0.7523 (t) REVERT: w 160 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7686 (mp0) REVERT: w 210 PRO cc_start: 0.8101 (Cg_exo) cc_final: 0.7802 (Cg_endo) outliers start: 207 outliers final: 94 residues processed: 1221 average time/residue: 1.5202 time to fit residues: 2407.9882 Evaluate side-chains 1182 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 1072 time to evaluate : 5.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain I residue 48 LYS Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 374 THR Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 133 ASP Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 381 LEU Chi-restraints excluded: chain M residue 559 ASP Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 95 ASP Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 222 ARG Chi-restraints excluded: chain O residue 245 VAL Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain Q residue 238 LEU Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 409 VAL Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain T residue 84 ILE Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain V residue 6 LEU Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain V residue 72 LEU Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 27 ARG Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 103 ASP Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain Z residue 15 GLU Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain Z residue 42 ARG Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 76 GLU Chi-restraints excluded: chain d residue 127 LYS Chi-restraints excluded: chain d residue 136 SER Chi-restraints excluded: chain d residue 161 GLN Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain f residue 60 LYS Chi-restraints excluded: chain g residue 4 MET Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 101 GLU Chi-restraints excluded: chain h residue 24 GLU Chi-restraints excluded: chain i residue 68 MET Chi-restraints excluded: chain i residue 86 ILE Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 318 GLU Chi-restraints excluded: chain j residue 8 LEU Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain k residue 58 MET Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 176 ARG Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 496 MET Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 511 LEU Chi-restraints excluded: chain l residue 581 LYS Chi-restraints excluded: chain l residue 598 SER Chi-restraints excluded: chain m residue 27 ILE Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 41 CYS Chi-restraints excluded: chain o residue 117 GLN Chi-restraints excluded: chain p residue 43 LEU Chi-restraints excluded: chain p residue 48 PHE Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 281 ASP Chi-restraints excluded: chain r residue 303 ILE Chi-restraints excluded: chain r residue 448 THR Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 200 LEU Chi-restraints excluded: chain u residue 110 CYS Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 67 CYS Chi-restraints excluded: chain w residue 160 GLU Chi-restraints excluded: chain w residue 275 TYR Chi-restraints excluded: chain w residue 293 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 739 optimal weight: 0.1980 chunk 86 optimal weight: 9.9990 chunk 437 optimal weight: 5.9990 chunk 560 optimal weight: 3.9990 chunk 434 optimal weight: 1.9990 chunk 645 optimal weight: 0.6980 chunk 428 optimal weight: 4.9990 chunk 764 optimal weight: 9.9990 chunk 478 optimal weight: 8.9990 chunk 465 optimal weight: 5.9990 chunk 352 optimal weight: 0.6980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN E 58 GLN E 70 ASN H 110 ASN ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 678 GLN ** P 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 236 ASN T 74 GLN c 127 ASN h 70 GLN ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 6 GLN r 139 GLN r 304 GLN s 157 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 68130 Z= 0.200 Angle : 0.541 10.534 92210 Z= 0.269 Chirality : 0.041 0.179 10032 Planarity : 0.004 0.068 11549 Dihedral : 11.421 179.839 10069 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.95 % Favored : 96.03 % Rotamer: Outliers : 3.15 % Allowed : 19.90 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.10), residues: 8027 helix: 1.70 (0.08), residues: 4268 sheet: 0.24 (0.26), residues: 415 loop : -0.61 (0.11), residues: 3344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP c 145 HIS 0.007 0.001 HIS J 37 PHE 0.038 0.001 PHE A 262 TYR 0.020 0.001 TYR G 147 ARG 0.009 0.000 ARG a 158 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1302 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1080 time to evaluate : 5.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.7219 (OUTLIER) cc_final: 0.6899 (ttt) REVERT: A 451 GLN cc_start: 0.7797 (tp40) cc_final: 0.7589 (tp40) REVERT: B 149 MET cc_start: 0.9361 (mmm) cc_final: 0.9137 (mmm) REVERT: G 89 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7274 (mt) REVERT: G 105 MET cc_start: 0.5972 (mpm) cc_final: 0.5431 (mpt) REVERT: G 115 GLN cc_start: 0.7901 (tm-30) cc_final: 0.7577 (tm-30) REVERT: G 128 PHE cc_start: 0.7137 (p90) cc_final: 0.6774 (p90) REVERT: I 18 ARG cc_start: 0.8215 (mtt90) cc_final: 0.7999 (mpt-90) REVERT: I 33 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8380 (mtpt) REVERT: L 69 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6923 (pt0) REVERT: L 133 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.8292 (m-30) REVERT: M 58 MET cc_start: 0.8828 (tmt) cc_final: 0.8276 (tmt) REVERT: O 42 ARG cc_start: 0.7834 (mtm-85) cc_final: 0.7583 (mtm-85) REVERT: O 169 PHE cc_start: 0.8497 (m-80) cc_final: 0.8251 (m-80) REVERT: P 183 ASP cc_start: 0.8296 (p0) cc_final: 0.8027 (p0) REVERT: Q 437 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8110 (ttmm) REVERT: U 31 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8357 (mp) REVERT: U 34 SER cc_start: 0.8925 (p) cc_final: 0.8723 (m) REVERT: V 41 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7575 (mp) REVERT: V 72 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7411 (tm) REVERT: V 134 GLN cc_start: 0.8915 (mt0) cc_final: 0.8624 (mt0) REVERT: Y 76 ASP cc_start: 0.7579 (OUTLIER) cc_final: 0.7279 (m-30) REVERT: Z 91 GLN cc_start: 0.5705 (OUTLIER) cc_final: 0.3609 (tp40) REVERT: b 27 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8071 (mt-10) REVERT: d 76 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8123 (OUTLIER) REVERT: d 161 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8619 (pt0) REVERT: g 4 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8790 (mtm) REVERT: g 101 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.6857 (mp0) REVERT: h 24 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8215 (mm-30) REVERT: i 69 MET cc_start: 0.9092 (mtp) cc_final: 0.8810 (mtp) REVERT: i 318 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7679 (mm-30) REVERT: k 57 ASN cc_start: 0.9212 (m-40) cc_final: 0.8915 (m110) REVERT: l 176 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.8814 (mmt90) REVERT: n 30 ARG cc_start: 0.7854 (ttt90) cc_final: 0.6395 (ttp80) REVERT: o 39 ILE cc_start: 0.9037 (pt) cc_final: 0.8787 (mt) REVERT: o 85 LYS cc_start: 0.8644 (tttt) cc_final: 0.8342 (tttm) REVERT: p 48 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.7682 (t80) REVERT: p 139 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8581 (tm-30) REVERT: p 160 GLU cc_start: 0.7123 (tp30) cc_final: 0.6879 (mm-30) REVERT: r 103 GLN cc_start: 0.9182 (OUTLIER) cc_final: 0.8684 (tt0) REVERT: u 110 CYS cc_start: 0.8430 (OUTLIER) cc_final: 0.7527 (t) REVERT: w 160 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7747 (mp0) REVERT: w 210 PRO cc_start: 0.8185 (Cg_exo) cc_final: 0.7921 (Cg_endo) outliers start: 222 outliers final: 117 residues processed: 1208 average time/residue: 1.5395 time to fit residues: 2411.3477 Evaluate side-chains 1198 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 1059 time to evaluate : 6.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 374 THR Chi-restraints excluded: chain K residue 105 ARG Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 133 ASP Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 379 THR Chi-restraints excluded: chain M residue 559 ASP Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 95 ASP Chi-restraints excluded: chain O residue 207 GLU Chi-restraints excluded: chain O residue 245 VAL Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 238 LEU Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 409 VAL Chi-restraints excluded: chain Q residue 437 LYS Chi-restraints excluded: chain S residue 69 ILE Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain T residue 68 ILE Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 84 ILE Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain V residue 6 LEU Chi-restraints excluded: chain V residue 16 THR Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain V residue 72 LEU Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 27 ARG Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 103 ASP Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Y residue 76 ASP Chi-restraints excluded: chain Z residue 15 GLU Chi-restraints excluded: chain Z residue 42 ARG Chi-restraints excluded: chain Z residue 91 GLN Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 110 ASP Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain d residue 76 GLU Chi-restraints excluded: chain d residue 127 LYS Chi-restraints excluded: chain d residue 136 SER Chi-restraints excluded: chain d residue 161 GLN Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain f residue 60 LYS Chi-restraints excluded: chain g residue 4 MET Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 101 GLU Chi-restraints excluded: chain h residue 24 GLU Chi-restraints excluded: chain i residue 86 ILE Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 318 GLU Chi-restraints excluded: chain i residue 347 ASN Chi-restraints excluded: chain j residue 8 LEU Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain k residue 58 MET Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 61 MET Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 176 ARG Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 511 LEU Chi-restraints excluded: chain l residue 581 LYS Chi-restraints excluded: chain m residue 27 ILE Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 41 CYS Chi-restraints excluded: chain m residue 50 SER Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 50 GLN Chi-restraints excluded: chain o residue 117 GLN Chi-restraints excluded: chain p residue 43 LEU Chi-restraints excluded: chain p residue 48 PHE Chi-restraints excluded: chain p residue 139 GLN Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 281 ASP Chi-restraints excluded: chain r residue 303 ILE Chi-restraints excluded: chain r residue 448 THR Chi-restraints excluded: chain s residue 65 THR Chi-restraints excluded: chain s residue 144 VAL Chi-restraints excluded: chain s residue 200 LEU Chi-restraints excluded: chain u residue 110 CYS Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 67 CYS Chi-restraints excluded: chain w residue 160 GLU Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 275 TYR Chi-restraints excluded: chain w residue 293 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 472 optimal weight: 0.9990 chunk 305 optimal weight: 5.9990 chunk 456 optimal weight: 4.9990 chunk 230 optimal weight: 9.9990 chunk 150 optimal weight: 10.0000 chunk 148 optimal weight: 8.9990 chunk 485 optimal weight: 8.9990 chunk 520 optimal weight: 2.9990 chunk 377 optimal weight: 5.9990 chunk 71 optimal weight: 0.0070 chunk 600 optimal weight: 8.9990 overall best weight: 3.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN E 58 GLN F 31 GLN H 110 ASN ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 678 GLN N 69 ASN N 112 ASN ** P 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 236 ASN T 74 GLN W 24 ASN h 70 GLN j 83 ASN l 109 HIS ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 6 GLN r 192 ASN r 304 GLN s 157 ASN w 107 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 68130 Z= 0.319 Angle : 0.615 10.685 92210 Z= 0.307 Chirality : 0.044 0.209 10032 Planarity : 0.005 0.066 11549 Dihedral : 11.616 179.078 10067 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.40 % Favored : 95.58 % Rotamer: Outliers : 3.38 % Allowed : 19.83 % Favored : 76.80 % 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: 0.76 (0.09), residues: 8027 helix: 1.48 (0.08), residues: 4251 sheet: 0.17 (0.26), residues: 421 loop : -0.69 (0.11), residues: 3355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP c 145 HIS 0.008 0.001 HIS J 37 PHE 0.049 0.002 PHE m 57 TYR 0.022 0.002 TYR P 64 ARG 0.009 0.000 ARG a 158 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1310 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 1072 time to evaluate : 6.116 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.7276 (OUTLIER) cc_final: 0.6968 (ttt) REVERT: A 343 VAL cc_start: 0.8536 (t) cc_final: 0.8307 (p) REVERT: A 451 GLN cc_start: 0.7792 (tp40) cc_final: 0.7541 (tp40) REVERT: C 142 TYR cc_start: 0.9375 (OUTLIER) cc_final: 0.9101 (t80) REVERT: C 154 ASP cc_start: 0.8791 (OUTLIER) cc_final: 0.8488 (p0) REVERT: E 87 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8333 (tmtt) REVERT: G 89 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7325 (mt) REVERT: G 115 GLN cc_start: 0.7838 (tm-30) cc_final: 0.7516 (tm-30) REVERT: I 18 ARG cc_start: 0.8262 (mtt90) cc_final: 0.7993 (mpt-90) REVERT: I 33 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8412 (mtpt) REVERT: K 93 LEU cc_start: 0.8164 (mt) cc_final: 0.7900 (mp) REVERT: L 69 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7150 (pt0) REVERT: L 133 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.8320 (m-30) REVERT: M 58 MET cc_start: 0.8852 (tmt) cc_final: 0.8397 (tmt) REVERT: O 42 ARG cc_start: 0.7797 (mtm-85) cc_final: 0.7525 (mtm-85) REVERT: O 169 PHE cc_start: 0.8518 (m-80) cc_final: 0.8236 (m-80) REVERT: P 50 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7320 (ptm160) REVERT: P 183 ASP cc_start: 0.8257 (p0) cc_final: 0.7943 (p0) REVERT: Q 437 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8167 (ttmm) REVERT: U 31 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8376 (mp) REVERT: U 63 MET cc_start: 0.7969 (mtp) cc_final: 0.7733 (mtp) REVERT: V 72 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7528 (tm) REVERT: V 134 GLN cc_start: 0.8941 (mt0) cc_final: 0.8660 (mt0) REVERT: V 140 LYS cc_start: 0.8833 (tttt) cc_final: 0.8628 (pttt) REVERT: Y 76 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7303 (m-30) REVERT: Z 91 GLN cc_start: 0.5949 (OUTLIER) cc_final: 0.3748 (tp40) REVERT: b 27 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8027 (mt-10) REVERT: d 76 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8116 (pt0) REVERT: d 161 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8579 (pt0) REVERT: e 55 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7565 (pp) REVERT: g 4 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.8842 (mtm) REVERT: g 101 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.6886 (mp0) REVERT: h 24 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8237 (tp30) REVERT: h 61 ASP cc_start: 0.9038 (m-30) cc_final: 0.8794 (m-30) REVERT: h 71 LYS cc_start: 0.8778 (mttt) cc_final: 0.8360 (mtpp) REVERT: i 318 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7653 (mm-30) REVERT: k 57 ASN cc_start: 0.9231 (m-40) cc_final: 0.8978 (m110) REVERT: l 176 ARG cc_start: 0.9159 (OUTLIER) cc_final: 0.8839 (mmt90) REVERT: l 307 SER cc_start: 0.9225 (OUTLIER) cc_final: 0.8899 (m) REVERT: l 351 ASN cc_start: 0.8760 (t0) cc_final: 0.8543 (t0) REVERT: l 471 ASN cc_start: 0.8827 (m-40) cc_final: 0.8338 (m110) REVERT: n 30 ARG cc_start: 0.7957 (ttt90) cc_final: 0.6339 (ttt180) REVERT: o 39 ILE cc_start: 0.9084 (pt) cc_final: 0.8828 (mt) REVERT: p 48 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7755 (t80) REVERT: p 139 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8671 (tm-30) REVERT: r 103 GLN cc_start: 0.9305 (OUTLIER) cc_final: 0.8803 (tt0) REVERT: r 184 HIS cc_start: 0.7373 (OUTLIER) cc_final: 0.6905 (p90) REVERT: u 110 CYS cc_start: 0.8477 (OUTLIER) cc_final: 0.7479 (t) REVERT: w 160 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.6901 (mp0) REVERT: w 197 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7562 (mt-10) REVERT: w 210 PRO cc_start: 0.8203 (Cg_exo) cc_final: 0.7912 (Cg_endo) outliers start: 238 outliers final: 135 residues processed: 1202 average time/residue: 1.4956 time to fit residues: 2340.5910 Evaluate side-chains 1211 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1046 time to evaluate : 5.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 266 VAL Chi-restraints excluded: chain J residue 374 THR Chi-restraints excluded: chain K residue 105 ARG Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 133 ASP Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 379 THR Chi-restraints excluded: chain M residue 389 THR Chi-restraints excluded: chain M residue 559 ASP Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 95 ASP Chi-restraints excluded: chain N residue 132 LYS Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 207 GLU Chi-restraints excluded: chain O residue 245 VAL Chi-restraints excluded: chain P residue 50 ARG Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain Q residue 238 LEU Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 409 VAL Chi-restraints excluded: chain Q residue 437 LYS Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain T residue 49 ASP Chi-restraints excluded: chain T residue 84 ILE Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain V residue 6 LEU Chi-restraints excluded: chain V residue 16 THR Chi-restraints excluded: chain V residue 72 LEU Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 27 ARG Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 102 SER Chi-restraints excluded: chain X residue 136 GLU Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Y residue 76 ASP Chi-restraints excluded: chain Y residue 100 LEU Chi-restraints excluded: chain Z residue 42 ARG Chi-restraints excluded: chain Z residue 91 GLN Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain d residue 76 GLU Chi-restraints excluded: chain d residue 127 LYS Chi-restraints excluded: chain d residue 136 SER Chi-restraints excluded: chain d residue 161 GLN Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain f residue 60 LYS Chi-restraints excluded: chain g residue 4 MET Chi-restraints excluded: chain g residue 19 GLU Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 101 GLU Chi-restraints excluded: chain h residue 24 GLU Chi-restraints excluded: chain i residue 86 ILE Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 318 GLU Chi-restraints excluded: chain i residue 347 ASN Chi-restraints excluded: chain j residue 8 LEU Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain k residue 58 MET Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 61 MET Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 176 ARG Chi-restraints excluded: chain l residue 307 SER Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 496 MET Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 511 LEU Chi-restraints excluded: chain l residue 581 LYS Chi-restraints excluded: chain l residue 598 SER Chi-restraints excluded: chain m residue 2 THR Chi-restraints excluded: chain m residue 5 ILE Chi-restraints excluded: chain m residue 27 ILE Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 41 CYS Chi-restraints excluded: chain m residue 50 SER Chi-restraints excluded: chain m residue 127 ILE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 16 LEU Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 50 GLN Chi-restraints excluded: chain o residue 117 GLN Chi-restraints excluded: chain p residue 19 LEU Chi-restraints excluded: chain p residue 43 LEU Chi-restraints excluded: chain p residue 48 PHE Chi-restraints excluded: chain p residue 139 GLN Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 80 SER Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 184 HIS Chi-restraints excluded: chain r residue 281 ASP Chi-restraints excluded: chain r residue 303 ILE Chi-restraints excluded: chain r residue 448 THR Chi-restraints excluded: chain s residue 8 SER Chi-restraints excluded: chain s residue 65 THR Chi-restraints excluded: chain s residue 144 VAL Chi-restraints excluded: chain s residue 200 LEU Chi-restraints excluded: chain u residue 110 CYS Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 67 CYS Chi-restraints excluded: chain w residue 100 ASP Chi-restraints excluded: chain w residue 160 GLU Chi-restraints excluded: chain w residue 197 GLU Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 275 TYR Chi-restraints excluded: chain w residue 293 ARG Chi-restraints excluded: chain w residue 312 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 695 optimal weight: 1.9990 chunk 732 optimal weight: 2.9990 chunk 668 optimal weight: 4.9990 chunk 712 optimal weight: 0.8980 chunk 428 optimal weight: 2.9990 chunk 310 optimal weight: 2.9990 chunk 559 optimal weight: 3.9990 chunk 218 optimal weight: 1.9990 chunk 643 optimal weight: 1.9990 chunk 673 optimal weight: 2.9990 chunk 709 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN E 58 GLN H 110 ASN J 238 GLN ** J 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 678 GLN P 236 ASN S 44 GLN S 68 ASN T 74 GLN c 127 ASN h 70 GLN ** j 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 6 GLN r 139 GLN r 192 ASN r 304 GLN s 157 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 68130 Z= 0.203 Angle : 0.557 10.560 92210 Z= 0.278 Chirality : 0.041 0.187 10032 Planarity : 0.005 0.066 11549 Dihedral : 11.238 179.453 10067 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.05 % Favored : 95.93 % Rotamer: Outliers : 2.64 % Allowed : 20.89 % Favored : 76.47 % 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: 0.90 (0.09), residues: 8027 helix: 1.61 (0.08), residues: 4264 sheet: 0.19 (0.26), residues: 420 loop : -0.66 (0.11), residues: 3343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP c 145 HIS 0.007 0.001 HIS J 37 PHE 0.049 0.001 PHE m 57 TYR 0.020 0.001 TYR r 406 ARG 0.009 0.000 ARG a 158 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1247 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1061 time to evaluate : 6.065 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.7215 (OUTLIER) cc_final: 0.6893 (ttt) REVERT: A 337 MET cc_start: 0.7974 (mmm) cc_final: 0.7754 (mtp) REVERT: A 343 VAL cc_start: 0.8541 (t) cc_final: 0.8282 (p) REVERT: A 451 GLN cc_start: 0.7788 (tp40) cc_final: 0.7562 (tp40) REVERT: C 154 ASP cc_start: 0.8810 (OUTLIER) cc_final: 0.8516 (p0) REVERT: E 87 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8280 (tmtt) REVERT: G 89 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7263 (mt) REVERT: G 105 MET cc_start: 0.6095 (mpm) cc_final: 0.5617 (mpt) REVERT: G 115 GLN cc_start: 0.7833 (tm-30) cc_final: 0.7515 (tm-30) REVERT: G 128 PHE cc_start: 0.7098 (p90) cc_final: 0.6755 (p90) REVERT: I 18 ARG cc_start: 0.8242 (mtt90) cc_final: 0.8025 (mpt-90) REVERT: I 33 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8384 (mtpt) REVERT: J 140 ASP cc_start: 0.7677 (p0) cc_final: 0.7426 (p0) REVERT: L 133 ASP cc_start: 0.8607 (OUTLIER) cc_final: 0.8342 (m-30) REVERT: M 58 MET cc_start: 0.8841 (tmt) cc_final: 0.8362 (tmt) REVERT: O 42 ARG cc_start: 0.7759 (mtm-85) cc_final: 0.7498 (mtm-85) REVERT: O 72 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.6881 (mp0) REVERT: O 169 PHE cc_start: 0.8501 (m-80) cc_final: 0.8227 (m-80) REVERT: P 183 ASP cc_start: 0.8239 (p0) cc_final: 0.8001 (p0) REVERT: Q 437 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8096 (ttmm) REVERT: U 31 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8306 (mp) REVERT: U 63 MET cc_start: 0.7994 (mtp) cc_final: 0.7750 (mtp) REVERT: V 72 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7415 (tm) REVERT: V 134 GLN cc_start: 0.8922 (mt0) cc_final: 0.8641 (mt0) REVERT: V 140 LYS cc_start: 0.8844 (tttt) cc_final: 0.8623 (pttt) REVERT: Z 91 GLN cc_start: 0.5881 (OUTLIER) cc_final: 0.3712 (tp40) REVERT: b 27 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8090 (mt-10) REVERT: d 76 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8111 (pt0) REVERT: d 161 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8571 (pt0) REVERT: g 4 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.8801 (mtm) REVERT: g 101 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.6853 (mp0) REVERT: g 108 LYS cc_start: 0.7740 (mmmt) cc_final: 0.7002 (ptpt) REVERT: h 24 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8244 (mm-30) REVERT: h 61 ASP cc_start: 0.9020 (m-30) cc_final: 0.8761 (m-30) REVERT: h 71 LYS cc_start: 0.8704 (mttt) cc_final: 0.8294 (mtpp) REVERT: i 318 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7660 (mm-30) REVERT: k 57 ASN cc_start: 0.9219 (m-40) cc_final: 0.8947 (m110) REVERT: l 176 ARG cc_start: 0.9141 (OUTLIER) cc_final: 0.8821 (mmt90) REVERT: l 351 ASN cc_start: 0.8793 (t0) cc_final: 0.8554 (t0) REVERT: m 3 MET cc_start: 0.4226 (mmp) cc_final: 0.3048 (mpp) REVERT: n 30 ARG cc_start: 0.7868 (ttt90) cc_final: 0.6302 (ttt180) REVERT: o 39 ILE cc_start: 0.9036 (pt) cc_final: 0.8822 (mt) REVERT: p 48 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7698 (t80) REVERT: p 139 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8565 (tm-30) REVERT: p 160 GLU cc_start: 0.7174 (tp30) cc_final: 0.6944 (mm-30) REVERT: r 103 GLN cc_start: 0.9194 (OUTLIER) cc_final: 0.8695 (tt0) REVERT: r 114 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.7920 (tm-30) REVERT: u 110 CYS cc_start: 0.8443 (OUTLIER) cc_final: 0.7517 (t) REVERT: w 160 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.6889 (mp0) REVERT: w 197 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7529 (mt-10) REVERT: w 210 PRO cc_start: 0.8166 (Cg_exo) cc_final: 0.7877 (Cg_endo) outliers start: 186 outliers final: 122 residues processed: 1176 average time/residue: 1.5447 time to fit residues: 2355.4100 Evaluate side-chains 1194 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1047 time to evaluate : 5.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 374 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 133 ASP Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 379 THR Chi-restraints excluded: chain M residue 389 THR Chi-restraints excluded: chain M residue 559 ASP Chi-restraints excluded: chain M residue 678 GLN Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 95 ASP Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 207 GLU Chi-restraints excluded: chain O residue 245 VAL Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 238 LEU Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 409 VAL Chi-restraints excluded: chain Q residue 437 LYS Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain T residue 84 ILE Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain V residue 6 LEU Chi-restraints excluded: chain V residue 16 THR Chi-restraints excluded: chain V residue 72 LEU Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 27 ARG Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Y residue 100 LEU Chi-restraints excluded: chain Z residue 15 GLU Chi-restraints excluded: chain Z residue 42 ARG Chi-restraints excluded: chain Z residue 91 GLN Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 76 GLU Chi-restraints excluded: chain d residue 127 LYS Chi-restraints excluded: chain d residue 136 SER Chi-restraints excluded: chain d residue 161 GLN Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain f residue 60 LYS Chi-restraints excluded: chain g residue 4 MET Chi-restraints excluded: chain g residue 19 GLU Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 101 GLU Chi-restraints excluded: chain g residue 115 LEU Chi-restraints excluded: chain h residue 24 GLU Chi-restraints excluded: chain i residue 86 ILE Chi-restraints excluded: chain i residue 154 MET Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 318 GLU Chi-restraints excluded: chain i residue 347 ASN Chi-restraints excluded: chain j residue 8 LEU Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain k residue 58 MET Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 61 MET Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 176 ARG Chi-restraints excluded: chain l residue 186 MET Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 511 LEU Chi-restraints excluded: chain l residue 562 LEU Chi-restraints excluded: chain l residue 581 LYS Chi-restraints excluded: chain l residue 598 SER Chi-restraints excluded: chain m residue 2 THR Chi-restraints excluded: chain m residue 5 ILE Chi-restraints excluded: chain m residue 27 ILE Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 41 CYS Chi-restraints excluded: chain m residue 50 SER Chi-restraints excluded: chain m residue 127 ILE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 16 LEU Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 50 GLN Chi-restraints excluded: chain o residue 117 GLN Chi-restraints excluded: chain p residue 43 LEU Chi-restraints excluded: chain p residue 48 PHE Chi-restraints excluded: chain p residue 139 GLN Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 281 ASP Chi-restraints excluded: chain r residue 303 ILE Chi-restraints excluded: chain r residue 448 THR Chi-restraints excluded: chain s residue 8 SER Chi-restraints excluded: chain s residue 65 THR Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 144 VAL Chi-restraints excluded: chain s residue 200 LEU Chi-restraints excluded: chain u residue 110 CYS Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 67 CYS Chi-restraints excluded: chain w residue 100 ASP Chi-restraints excluded: chain w residue 160 GLU Chi-restraints excluded: chain w residue 197 GLU Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 275 TYR Chi-restraints excluded: chain w residue 293 ARG Chi-restraints excluded: chain w residue 312 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 467 optimal weight: 4.9990 chunk 753 optimal weight: 0.0060 chunk 459 optimal weight: 0.9990 chunk 357 optimal weight: 0.0470 chunk 523 optimal weight: 1.9990 chunk 790 optimal weight: 1.9990 chunk 727 optimal weight: 5.9990 chunk 629 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 485 optimal weight: 8.9990 chunk 385 optimal weight: 5.9990 overall best weight: 1.0100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 303 HIS E 58 GLN H 110 ASN I 29 GLN P 63 GLN ** P 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 236 ASN S 68 ASN T 74 GLN W 24 ASN c 127 ASN d 55 GLN h 70 GLN ** j 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 6 GLN r 304 GLN s 157 ASN w 223 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 68130 Z= 0.170 Angle : 0.549 15.512 92210 Z= 0.272 Chirality : 0.040 0.304 10032 Planarity : 0.004 0.063 11549 Dihedral : 10.956 179.716 10067 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.09 % Favored : 95.89 % Rotamer: Outliers : 2.37 % Allowed : 21.27 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.10), residues: 8027 helix: 1.72 (0.08), residues: 4262 sheet: 0.16 (0.26), residues: 427 loop : -0.58 (0.11), residues: 3338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP c 145 HIS 0.006 0.001 HIS J 37 PHE 0.049 0.001 PHE m 57 TYR 0.022 0.001 TYR l 422 ARG 0.010 0.000 ARG a 158 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1241 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1074 time to evaluate : 5.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.7152 (OUTLIER) cc_final: 0.6870 (ttt) REVERT: A 337 MET cc_start: 0.7942 (mmm) cc_final: 0.7734 (mtp) REVERT: A 451 GLN cc_start: 0.7796 (tp40) cc_final: 0.7569 (tp40) REVERT: C 154 ASP cc_start: 0.8792 (OUTLIER) cc_final: 0.8518 (p0) REVERT: E 87 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8230 (tmtt) REVERT: E 94 ILE cc_start: 0.7819 (OUTLIER) cc_final: 0.7577 (mp) REVERT: G 89 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7299 (mt) REVERT: G 105 MET cc_start: 0.5985 (mpm) cc_final: 0.5616 (mpt) REVERT: G 115 GLN cc_start: 0.7826 (tm-30) cc_final: 0.7471 (tm-30) REVERT: G 128 PHE cc_start: 0.7084 (p90) cc_final: 0.6752 (p90) REVERT: G 139 MET cc_start: 0.5854 (tpp) cc_final: 0.5297 (tpt) REVERT: G 143 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7342 (mp0) REVERT: I 18 ARG cc_start: 0.8211 (mtt90) cc_final: 0.8004 (mpt-90) REVERT: I 33 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8368 (mtpt) REVERT: J 140 ASP cc_start: 0.7672 (p0) cc_final: 0.7439 (p0) REVERT: L 133 ASP cc_start: 0.8554 (OUTLIER) cc_final: 0.8285 (m-30) REVERT: M 58 MET cc_start: 0.8829 (tmt) cc_final: 0.8318 (tmt) REVERT: O 42 ARG cc_start: 0.7747 (mtm-85) cc_final: 0.7503 (mtm-85) REVERT: O 72 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.6840 (mp0) REVERT: Q 171 ARG cc_start: 0.9500 (OUTLIER) cc_final: 0.8307 (mtp85) REVERT: Q 437 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8071 (ttmm) REVERT: S 68 ASN cc_start: 0.8587 (OUTLIER) cc_final: 0.8118 (t0) REVERT: T 74 GLN cc_start: 0.9014 (mm-40) cc_final: 0.8762 (mm110) REVERT: U 31 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8335 (mp) REVERT: U 34 SER cc_start: 0.8929 (p) cc_final: 0.8714 (m) REVERT: U 63 MET cc_start: 0.8033 (mtp) cc_final: 0.7807 (mtp) REVERT: V 72 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7396 (tm) REVERT: V 134 GLN cc_start: 0.8913 (mt0) cc_final: 0.8599 (mt0) REVERT: V 140 LYS cc_start: 0.8843 (tttt) cc_final: 0.8643 (pttt) REVERT: Y 76 ASP cc_start: 0.7521 (m-30) cc_final: 0.7224 (m-30) REVERT: Z 91 GLN cc_start: 0.5857 (OUTLIER) cc_final: 0.3703 (tp40) REVERT: b 27 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8043 (mt-10) REVERT: d 127 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8433 (mmmt) REVERT: d 161 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.8603 (pt0) REVERT: g 4 MET cc_start: 0.9062 (OUTLIER) cc_final: 0.8777 (mtm) REVERT: g 101 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.6996 (mp0) REVERT: h 24 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8191 (mm-30) REVERT: h 71 LYS cc_start: 0.8729 (mttt) cc_final: 0.8308 (mtpp) REVERT: i 187 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8563 (mmp) REVERT: i 318 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7665 (mm-30) REVERT: k 57 ASN cc_start: 0.9212 (m-40) cc_final: 0.8945 (m110) REVERT: l 176 ARG cc_start: 0.9144 (OUTLIER) cc_final: 0.8820 (mmt90) REVERT: l 351 ASN cc_start: 0.8768 (t0) cc_final: 0.8535 (t0) REVERT: m 3 MET cc_start: 0.4151 (mmp) cc_final: 0.2974 (mpp) REVERT: n 30 ARG cc_start: 0.7833 (ttt90) cc_final: 0.6383 (ttp80) REVERT: o 39 ILE cc_start: 0.9005 (pt) cc_final: 0.8793 (mt) REVERT: o 85 LYS cc_start: 0.8683 (tttt) cc_final: 0.8410 (tttm) REVERT: p 48 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7580 (t80) REVERT: p 139 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8568 (tm-30) REVERT: p 160 GLU cc_start: 0.7145 (tp30) cc_final: 0.6907 (mm-30) REVERT: r 103 GLN cc_start: 0.9162 (OUTLIER) cc_final: 0.8648 (tt0) REVERT: u 110 CYS cc_start: 0.8434 (OUTLIER) cc_final: 0.7513 (t) REVERT: w 197 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7556 (mt-10) REVERT: w 210 PRO cc_start: 0.8154 (Cg_exo) cc_final: 0.7894 (Cg_endo) outliers start: 167 outliers final: 114 residues processed: 1169 average time/residue: 1.5510 time to fit residues: 2348.9198 Evaluate side-chains 1198 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1057 time to evaluate : 5.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 374 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 133 ASP Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 389 THR Chi-restraints excluded: chain M residue 559 ASP Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 95 ASP Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 207 GLU Chi-restraints excluded: chain O residue 245 VAL Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain Q residue 171 ARG Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 238 LEU Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 409 VAL Chi-restraints excluded: chain Q residue 437 LYS Chi-restraints excluded: chain S residue 68 ASN Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain T residue 84 ILE Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain V residue 6 LEU Chi-restraints excluded: chain V residue 16 THR Chi-restraints excluded: chain V residue 72 LEU Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 4 SER Chi-restraints excluded: chain W residue 27 ARG Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Y residue 100 LEU Chi-restraints excluded: chain Z residue 42 ARG Chi-restraints excluded: chain Z residue 91 GLN Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 76 GLU Chi-restraints excluded: chain d residue 127 LYS Chi-restraints excluded: chain d residue 136 SER Chi-restraints excluded: chain d residue 161 GLN Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain f residue 60 LYS Chi-restraints excluded: chain g residue 4 MET Chi-restraints excluded: chain g residue 19 GLU Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 101 GLU Chi-restraints excluded: chain g residue 115 LEU Chi-restraints excluded: chain h residue 24 GLU Chi-restraints excluded: chain i residue 86 ILE Chi-restraints excluded: chain i residue 154 MET Chi-restraints excluded: chain i residue 187 MET Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 318 GLU Chi-restraints excluded: chain i residue 347 ASN Chi-restraints excluded: chain j residue 8 LEU Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain k residue 58 MET Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 61 MET Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 176 ARG Chi-restraints excluded: chain l residue 186 MET Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 496 MET Chi-restraints excluded: chain l residue 511 LEU Chi-restraints excluded: chain l residue 562 LEU Chi-restraints excluded: chain l residue 581 LYS Chi-restraints excluded: chain m residue 2 THR Chi-restraints excluded: chain m residue 5 ILE Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 57 PHE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 50 GLN Chi-restraints excluded: chain o residue 117 GLN Chi-restraints excluded: chain p residue 43 LEU Chi-restraints excluded: chain p residue 48 PHE Chi-restraints excluded: chain p residue 139 GLN Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 281 ASP Chi-restraints excluded: chain r residue 303 ILE Chi-restraints excluded: chain r residue 448 THR Chi-restraints excluded: chain s residue 8 SER Chi-restraints excluded: chain s residue 65 THR Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 144 VAL Chi-restraints excluded: chain s residue 200 LEU Chi-restraints excluded: chain u residue 110 CYS Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 67 CYS Chi-restraints excluded: chain w residue 100 ASP Chi-restraints excluded: chain w residue 197 GLU Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 275 TYR Chi-restraints excluded: chain w residue 293 ARG Chi-restraints excluded: chain w residue 312 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 499 optimal weight: 0.9990 chunk 670 optimal weight: 7.9990 chunk 192 optimal weight: 8.9990 chunk 580 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 174 optimal weight: 8.9990 chunk 630 optimal weight: 9.9990 chunk 263 optimal weight: 7.9990 chunk 647 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN E 58 GLN F 25 GLN H 110 ASN ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 678 GLN O 69 ASN ** P 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 236 ASN S 68 ASN W 24 ASN h 70 GLN ** j 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 6 GLN r 139 GLN r 192 ASN r 304 GLN s 157 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.120785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.093734 restraints weight = 89056.511| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 1.29 r_work: 0.2820 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.118 68130 Z= 0.432 Angle : 0.673 11.579 92210 Z= 0.336 Chirality : 0.047 0.323 10032 Planarity : 0.006 0.064 11549 Dihedral : 11.392 179.033 10065 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.77 % Favored : 95.20 % Rotamer: Outliers : 2.84 % Allowed : 20.95 % Favored : 76.22 % 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: 0.62 (0.09), residues: 8027 helix: 1.35 (0.08), residues: 4261 sheet: 0.17 (0.26), residues: 423 loop : -0.75 (0.11), residues: 3343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP c 145 HIS 0.015 0.002 HIS Q 223 PHE 0.058 0.002 PHE m 57 TYR 0.022 0.002 TYR C 84 ARG 0.009 0.001 ARG a 158 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30542.36 seconds wall clock time: 527 minutes 53.06 seconds (31673.06 seconds total)