Starting phenix.real_space_refine on Thu Feb 15 22:22:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4k_32306/02_2024/7w4k_32306_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4k_32306/02_2024/7w4k_32306.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4k_32306/02_2024/7w4k_32306_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4k_32306/02_2024/7w4k_32306_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4k_32306/02_2024/7w4k_32306_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4k_32306/02_2024/7w4k_32306.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4k_32306/02_2024/7w4k_32306.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4k_32306/02_2024/7w4k_32306_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4k_32306/02_2024/7w4k_32306_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 30 5.49 5 Mg 1 5.21 5 S 473 5.16 5 C 42875 2.51 5 N 11085 2.21 5 O 11881 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 119": "OE1" <-> "OE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 301": "OE1" <-> "OE2" Residue "A GLU 377": "OE1" <-> "OE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B GLU 110": "OE1" <-> "OE2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "B GLU 160": "OE1" <-> "OE2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "C PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "E GLU 34": "OE1" <-> "OE2" Residue "E GLU 65": "OE1" <-> "OE2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "F GLU 43": "OE1" <-> "OE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "G GLU 136": "OE1" <-> "OE2" Residue "H GLU 18": "OE1" <-> "OE2" Residue "H GLU 62": "OE1" <-> "OE2" Residue "H GLU 70": "OE1" <-> "OE2" Residue "I GLU 105": "OE1" <-> "OE2" Residue "J GLU 133": "OE1" <-> "OE2" Residue "J GLU 142": "OE1" <-> "OE2" Residue "J GLU 158": "OE1" <-> "OE2" Residue "J GLU 197": "OE1" <-> "OE2" Residue "J GLU 320": "OE1" <-> "OE2" Residue "J GLU 336": "OE1" <-> "OE2" Residue "K PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 69": "OE1" <-> "OE2" Residue "M GLU 118": "OE1" <-> "OE2" Residue "M GLU 155": "OE1" <-> "OE2" Residue "M GLU 249": "OE1" <-> "OE2" Residue "M GLU 468": "OE1" <-> "OE2" Residue "M GLU 535": "OE1" <-> "OE2" Residue "M GLU 591": "OE1" <-> "OE2" Residue "M GLU 647": "OE1" <-> "OE2" Residue "N PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 136": "OE1" <-> "OE2" Residue "O GLU 46": "OE1" <-> "OE2" Residue "O GLU 64": "OE1" <-> "OE2" Residue "O GLU 72": "OE1" <-> "OE2" Residue "O GLU 103": "OE1" <-> "OE2" Residue "O GLU 114": "OE1" <-> "OE2" Residue "O GLU 202": "OE1" <-> "OE2" Residue "O GLU 203": "OE1" <-> "OE2" Residue "P PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 154": "OE1" <-> "OE2" Residue "P GLU 209": "OE1" <-> "OE2" Residue "P GLU 225": "OE1" <-> "OE2" Residue "Q GLU 42": "OE1" <-> "OE2" Residue "Q GLU 104": "OE1" <-> "OE2" Residue "Q GLU 156": "OE1" <-> "OE2" Residue "Q GLU 205": "OE1" <-> "OE2" Residue "Q GLU 259": "OE1" <-> "OE2" Residue "Q GLU 315": "OE1" <-> "OE2" Residue "Q GLU 335": "OE1" <-> "OE2" Residue "S GLU 67": "OE1" <-> "OE2" Residue "T GLU 73": "OE1" <-> "OE2" Residue "W GLU 56": "OE1" <-> "OE2" Residue "W GLU 78": "OE1" <-> "OE2" Residue "W GLU 92": "OE1" <-> "OE2" Residue "W GLU 94": "OE1" <-> "OE2" Residue "W GLU 108": "OE1" <-> "OE2" Residue "W GLU 123": "OE1" <-> "OE2" Residue "W GLU 131": "OE1" <-> "OE2" Residue "X GLU 77": "OE1" <-> "OE2" Residue "X GLU 129": "OE1" <-> "OE2" Residue "X GLU 136": "OE1" <-> "OE2" Residue "Y GLU 96": "OE1" <-> "OE2" Residue "Z GLU 49": "OE1" <-> "OE2" Residue "a GLU 103": "OE1" <-> "OE2" Residue "a GLU 134": "OE1" <-> "OE2" Residue "a GLU 145": "OE1" <-> "OE2" Residue "a GLU 153": "OE1" <-> "OE2" Residue "a GLU 155": "OE1" <-> "OE2" Residue "b GLU 8": "OE1" <-> "OE2" Residue "b GLU 17": "OE1" <-> "OE2" Residue "b TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 99": "OE1" <-> "OE2" Residue "b GLU 115": "OE1" <-> "OE2" Residue "c GLU 46": "OE1" <-> "OE2" Residue "c GLU 63": "OE1" <-> "OE2" Residue "c GLU 148": "OE1" <-> "OE2" Residue "c GLU 169": "OE1" <-> "OE2" Residue "c GLU 185": "OE1" <-> "OE2" Residue "d GLU 67": "OE1" <-> "OE2" Residue "e GLU 57": "OE1" <-> "OE2" Residue "e GLU 64": "OE1" <-> "OE2" Residue "e GLU 151": "OE1" <-> "OE2" Residue "f GLU 64": "OE1" <-> "OE2" Residue "g GLU 19": "OE1" <-> "OE2" Residue "g GLU 117": "OE1" <-> "OE2" Residue "h GLU 39": "OE1" <-> "OE2" Residue "h GLU 42": "OE1" <-> "OE2" Residue "h GLU 53": "OE1" <-> "OE2" Residue "h GLU 55": "OE1" <-> "OE2" Residue "h GLU 65": "OE1" <-> "OE2" Residue "i GLU 34": "OE1" <-> "OE2" Residue "i GLU 318": "OE1" <-> "OE2" Residue "j GLU 68": "OE1" <-> "OE2" Residue "j GLU 105": "OE1" <-> "OE2" Residue "l GLU 60": "OE1" <-> "OE2" Residue "l GLU 75": "OE1" <-> "OE2" Residue "l GLU 145": "OE1" <-> "OE2" Residue "l ASP 355": "OD1" <-> "OD2" Residue "l TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 397": "OE1" <-> "OE2" Residue "l GLU 445": "OE1" <-> "OE2" Residue "m GLU 170": "OE1" <-> "OE2" Residue "n GLU 33": "OE1" <-> "OE2" Residue "n GLU 54": "OE1" <-> "OE2" Residue "o GLU 61": "OE1" <-> "OE2" Residue "o GLU 113": "OE1" <-> "OE2" Residue "p GLU 54": "OE1" <-> "OE2" Residue "p GLU 68": "OE1" <-> "OE2" Residue "p GLU 70": "OE1" <-> "OE2" Residue "p GLU 95": "OE1" <-> "OE2" Residue "p GLU 134": "OE1" <-> "OE2" Residue "r TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 378": "OE1" <-> "OE2" Residue "s GLU 59": "OE1" <-> "OE2" Residue "s GLU 227": "OE1" <-> "OE2" Residue "u GLU 80": "OE1" <-> "OE2" Residue "u GLU 109": "OE1" <-> "OE2" Residue "u GLU 153": "OE1" <-> "OE2" Residue "v GLU 45": "OE1" <-> "OE2" Residue "v GLU 91": "OE1" <-> "OE2" Residue "w GLU 47": "OE1" <-> "OE2" Residue "w GLU 76": "OE1" <-> "OE2" Residue "w GLU 185": "OE1" <-> "OE2" Residue "w GLU 226": "OE1" <-> "OE2" Residue "w GLU 238": "OE1" <-> "OE2" Residue "w GLU 274": "OE1" <-> "OE2" Residue "w GLU 303": "OE1" <-> "OE2" Residue "w GLU 316": "OE1" <-> "OE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 66374 Number of models: 1 Model: "" Number of chains: 64 Chain: "A" Number of atoms: 3314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3314 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 409} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "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: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 81} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 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: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 906 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} 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: "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: 2355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2355 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 280} Chain breaks: 3 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: "K" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 355 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 3, 'TRANS': 38} Chain: "L" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1016 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "M" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5296 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 32, 'TRANS': 657} Chain: "N" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1204 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} Chain: "O" Number of atoms: 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: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 640 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 71} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "V" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1015 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 133} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "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: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 870 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 91} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "c" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1311 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 135} 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: "d" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1461 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 10, 'TRANS': 164} Chain: "e" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 890 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 10, 'TRANS': 96} Chain: "f" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 342 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 40} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "g" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1000 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 11, 'TRANS': 109} Chain: "h" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 867 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "i" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2706 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 328} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "j" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 800 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 Chain: "k" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 748 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "l" Number of atoms: 4782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4782 Classifications: {'peptide': 603} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 574} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 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: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 948 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "n" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 466 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 53} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 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: 1529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1529 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 160} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 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: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2579 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 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: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'PEE': 1, 'PLX': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' MG': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 143 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "i" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 152 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 192 Unusual residues: {'CDL': 1, 'PEE': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 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: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 155 Unusual residues: {'PEE': 1, 'PLX': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {' UQ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {' UQ:plan-11': 1, ' UQ:plan-2': 1, ' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 35 Chain: "w" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2702 SG CYS A 382 48.192 49.378 172.147 1.00 32.18 S ATOM 3044 SG CYS A 425 47.641 45.218 177.341 1.00 37.56 S ATOM 2722 SG CYS A 385 45.053 44.657 171.667 1.00 46.50 S ATOM 2683 SG CYS A 379 42.986 49.404 175.968 1.00 34.48 S ATOM 3945 SG CYS B 113 36.343 67.577 138.335 1.00 37.87 S ATOM 3964 SG CYS B 116 41.554 64.799 141.799 1.00 15.66 S ATOM 3987 SG CYS B 119 42.430 67.963 136.593 1.00 12.29 S ATOM 4316 SG CYS B 162 39.719 62.066 136.995 1.00 21.29 S ATOM 4014 SG CYS B 123 48.312 70.906 132.228 1.00 33.68 S ATOM 4240 SG CYS B 152 46.515 69.599 126.252 1.00 21.87 S ATOM 4287 SG CYS B 158 44.520 65.530 130.649 1.00 14.68 S ATOM 4266 SG CYS B 155 50.683 65.874 129.270 1.00 14.45 S ATOM 5708 SG CYS C 166 52.667 69.902 121.905 1.00 15.33 S ATOM 4974 SG CYS C 71 57.428 69.783 117.758 1.00 15.66 S ATOM 4980 SG CYS C 72 53.749 71.855 115.764 1.00 9.16 S ATOM 4974 SG CYS C 71 57.428 69.783 117.758 1.00 15.66 S ATOM 5478 SG CYS C 136 55.282 74.574 120.696 1.00 28.44 S ATOM 14504 SG CYS M 131 40.933 63.977 154.066 1.00 27.80 S ATOM 14483 SG CYS M 128 44.423 59.642 150.582 1.00 23.96 S ATOM 14544 SG CYS M 137 46.699 62.872 155.935 1.00 13.77 S ATOM 14876 SG CYS M 179 45.378 62.041 167.192 1.00 28.27 S ATOM 15230 SG CYS M 226 42.229 64.951 163.163 1.00 25.41 S ATOM 14900 SG CYS M 182 39.956 64.752 169.200 1.00 34.29 S ATOM 14853 SG CYS M 176 39.705 59.358 165.411 1.00 32.70 S ATOM 14101 SG CYS M 78 56.887 57.100 170.443 1.00 27.18 S ATOM 14202 SG CYS M 92 55.183 58.963 172.960 1.00 33.84 S ATOM 13990 SG CYS M 64 50.770 59.177 170.683 1.00 45.02 S ATOM 14076 SG CYS M 75 51.830 57.504 167.491 1.00 11.31 S ATOM 21039 SG CYS O 135 32.064 31.185 179.054 1.00 56.73 S ATOM 21073 SG CYS O 140 32.025 27.626 179.929 1.00 80.16 S ATOM 21353 SG CYS O 176 36.584 32.713 181.680 1.00 68.84 S ATOM 21376 SG CYS O 180 36.887 29.220 181.797 1.00 71.10 S ATOM 28034 SG CYS T 86 29.159 53.538 145.515 1.00 30.55 S ATOM 28212 SG CYS T 111 30.133 56.942 146.516 1.00 28.27 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.69 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.69 Time building chain proxies: 28.02, per 1000 atoms: 0.42 Number of scatterers: 66374 At special positions: 0 Unit cell: (210.797, 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 473 16.00 P 30 15.00 Mg 1 11.99 O 11881 8.00 N 11085 7.00 C 42875 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=2.68 Simple disulfide: pdb=" SG CYS d 113 " - pdb=" SG CYS d 125 " distance=2.03 Simple disulfide: pdb=" SG CYS h 33 " - pdb=" SG CYS h 66 " distance=2.03 Simple disulfide: pdb=" SG CYS h 43 " - pdb=" SG CYS h 56 " distance=2.04 Simple disulfide: pdb=" SG CYS u 88 " - pdb=" SG CYS u 100 " distance=2.02 Simple disulfide: pdb=" SG CYS v 69 " - pdb=" SG CYS v 80 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 20.89 Conformation dependent library (CDL) restraints added in 9.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " 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="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 140 " 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="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb=" SF4 B 301 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 116 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " pdb=" SF4 C 301 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 71 " pdb="FE3 SF4 C 301 " - pdb=" NE2 HIS Q 223 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb=" SF4 M 801 " pdb="FE3 SF4 M 801 " - pdb=" NE2 HIS M 124 " pdb="FE1 SF4 M 801 " - pdb=" SG CYS M 131 " pdb="FE2 SF4 M 801 " - pdb=" SG CYS M 128 " pdb="FE4 SF4 M 801 " - pdb=" SG CYS M 137 " pdb=" SF4 M 802 " pdb="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " pdb="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 111 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 86 " pdb="ZN ZN T 201 " - pdb=" NE2 HIS T 95 " 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: 336 helices and 29 sheets defined 52.7% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.57 Creating SS restraints... Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 73 through 83 Processing helix chain 'A' and resid 95 through 103 removed outlier: 3.502A pdb=" N ASN A 103 " --> pdb=" O TRP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 132 Processing helix chain 'A' and resid 135 through 149 Processing helix chain 'A' and resid 163 through 179 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 263 Processing helix chain 'A' and resid 296 through 303 Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 329 through 332 No H-bonds generated for 'chain 'A' and resid 329 through 332' 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: 3.714A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 419 removed outlier: 3.989A 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: 5.836A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LEU B 210 " --> pdb=" O GLN B 206 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N TYR B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 59 removed outlier: 3.553A pdb=" N VAL C 47 " --> pdb=" O GLY C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 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 111 through 123 Proline residue: C 115 - end of helix removed outlier: 3.510A pdb=" N GLN C 123 " --> pdb=" O LYS C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 141 through 143 No H-bonds generated for 'chain 'C' and resid 141 through 143' Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 189 through 194 Processing helix chain 'E' and resid 25 through 49 Proline residue: E 44 - end of helix Processing helix chain 'E' and resid 56 through 70 removed outlier: 4.320A 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: 4.252A 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 30 through 47 removed outlier: 5.941A pdb=" N TYR F 41 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 5.646A 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: 3.956A 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: 4.309A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N MET J 76 " --> pdb=" O HIS J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 97 removed outlier: 4.946A pdb=" N HIS J 93 " --> pdb=" O TYR J 89 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N LEU J 94 " --> pdb=" O ASP J 90 " (cutoff:3.500A) removed outlier: 4.170A 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 218 Processing helix chain 'J' and resid 242 through 254 Processing helix chain 'J' and resid 273 through 283 Processing helix chain 'J' and resid 317 through 322 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: 4.705A pdb=" N ILE J 350 " --> pdb=" O GLU J 346 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLU J 351 " --> pdb=" O LEU J 347 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ARG J 355 " --> pdb=" O GLU J 351 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N HIS J 356 " --> pdb=" O VAL J 352 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 80 removed outlier: 3.566A pdb=" N GLU K 80 " --> pdb=" O GLN K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 96 removed outlier: 4.346A pdb=" N LYS K 95 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N PHE K 96 " --> pdb=" O GLU K 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 71 No H-bonds generated for 'chain 'L' and resid 69 through 71' Processing helix chain 'L' and resid 131 through 141 Processing helix chain 'L' and resid 160 through 162 No H-bonds generated for 'chain 'L' and resid 160 through 162' Processing helix chain 'M' and resid 49 through 56 Processing helix chain 'M' and resid 107 through 121 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: 3.529A pdb=" N ILE M 222 " --> pdb=" O SER M 219 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE M 225 " --> pdb=" O ILE M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 298 removed outlier: 5.025A pdb=" N TYR M 294 " --> pdb=" O THR M 290 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASP M 295 " --> pdb=" O ARG M 291 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N GLY M 296 " --> pdb=" O PHE M 292 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU M 297 " --> pdb=" O ALA M 293 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LYS M 298 " --> pdb=" O TYR M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 319 through 332 removed outlier: 3.727A 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: 3.766A pdb=" N VAL M 394 " --> pdb=" O THR M 390 " (cutoff:3.500A) removed outlier: 4.521A 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 483 removed outlier: 4.341A pdb=" N ARG M 483 " --> pdb=" O SER M 479 " (cutoff:3.500A) Processing helix chain 'M' and resid 486 through 504 Processing helix chain 'M' and resid 522 through 527 Processing helix chain 'M' and resid 535 through 539 Processing helix chain 'M' and resid 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 Processing helix chain 'M' and resid 691 through 693 No H-bonds generated for 'chain 'M' and resid 691 through 693' Processing helix chain 'M' and resid 699 through 702 No H-bonds generated for 'chain 'M' and resid 699 through 702' Processing helix chain 'M' and resid 705 through 715 Processing helix chain 'N' and resid 3 through 17 removed outlier: 3.766A pdb=" N HIS N 17 " --> pdb=" O GLN N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 30 Processing helix chain 'N' and resid 79 through 81 No H-bonds generated for 'chain 'N' and resid 79 through 81' Processing helix chain 'N' and resid 84 through 90 Processing helix chain 'O' and resid 57 through 69 Processing helix chain 'O' and resid 75 through 90 removed outlier: 4.463A pdb=" N LEU O 80 " --> pdb=" O ALA O 77 " (cutoff:3.500A) Proline residue: O 81 - end of helix Processing helix chain 'O' and resid 95 through 105 Processing helix chain 'O' and resid 109 through 118 Processing helix chain 'O' and resid 138 through 142 Processing helix chain 'O' and resid 145 through 156 Processing helix chain 'O' and resid 198 through 210 Processing helix chain 'P' and resid 52 through 68 Processing helix chain 'P' and resid 90 through 102 removed outlier: 3.505A pdb=" N VAL P 93 " --> pdb=" O PRO P 90 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ILE P 94 " --> pdb=" O ASP P 91 " (cutoff:3.500A) Proline residue: P 95 - end of helix Processing helix chain 'P' and resid 161 through 174 removed outlier: 3.549A pdb=" N ASN P 164 " --> pdb=" O LYS P 161 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N TRP P 165 " --> pdb=" O ALA P 162 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE P 174 " --> pdb=" O TRP P 171 " (cutoff:3.500A) Processing helix chain 'P' and resid 243 through 245 No H-bonds generated for 'chain 'P' and resid 243 through 245' Processing helix chain 'Q' and resid 41 through 47 removed outlier: 4.118A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N PHE Q 47 " --> pdb=" O TRP Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 120 through 126 removed outlier: 3.669A pdb=" N GLU Q 125 " --> pdb=" O GLU Q 121 " (cutoff:3.500A) removed outlier: 4.130A 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: 4.113A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.702A 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: 4.188A 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 removed outlier: 3.609A pdb=" N MET Q 261 " --> pdb=" O GLU Q 257 " (cutoff:3.500A) 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: 4.652A 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 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: 4.366A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LYS Q 437 " --> pdb=" O ALA Q 433 " (cutoff:3.500A) Processing helix chain 'Q' and resid 444 through 454 removed outlier: 4.438A pdb=" N VAL Q 448 " --> pdb=" O LEU Q 444 " (cutoff:3.500A) removed outlier: 4.072A 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 34 Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 37 through 47 removed outlier: 3.542A pdb=" N ASN U 40 " --> pdb=" O PRO U 37 " (cutoff:3.500A) Processing helix chain 'U' and resid 79 through 83 Processing helix chain 'V' and resid 4 through 11 Processing helix chain 'V' and resid 18 through 43 Processing helix chain 'V' and resid 49 through 81 Processing helix chain 'V' and resid 87 through 100 Processing helix chain 'V' and resid 108 through 131 removed outlier: 4.088A pdb=" N CYS V 115 " --> pdb=" O GLY V 111 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA V 116 " --> pdb=" O ALA V 112 " (cutoff:3.500A) Processing helix chain 'W' and resid 32 through 99 Proline residue: W 73 - end of helix removed outlier: 3.810A 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: 6.148A pdb=" N PHE W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ILE W 141 " --> pdb=" O THR W 137 " (cutoff:3.500A) Processing helix chain 'X' and resid 76 through 88 Processing helix chain 'X' and resid 112 through 126 Processing helix chain 'X' and resid 132 through 135 No H-bonds generated for 'chain 'X' and resid 132 through 135' Processing helix chain 'X' and resid 141 through 152 Processing helix chain 'Y' and resid 52 through 75 Processing helix chain 'Y' and resid 77 through 81 Processing helix chain 'Y' and resid 89 through 91 No H-bonds generated for 'chain 'Y' and resid 89 through 91' Processing helix chain 'Z' and resid 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: 3.663A pdb=" N ARG Z 39 " --> pdb=" O LYS Z 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 47 through 53 removed outlier: 4.608A pdb=" N TRP Z 51 " --> pdb=" O ASN Z 48 " (cutoff:3.500A) Processing helix chain 'Z' and resid 63 through 67 Processing helix chain 'Z' and resid 71 through 89 Processing helix chain 'a' and resid 62 through 92 Proline residue: a 81 - end of helix Processing helix chain 'a' and resid 109 through 111 No H-bonds generated for 'chain 'a' and resid 109 through 111' Processing helix chain 'a' and resid 116 through 125 Processing helix chain 'a' and resid 129 through 163 Processing helix chain 'a' and resid 176 through 178 No H-bonds generated for 'chain 'a' and resid 176 through 178' Processing helix chain 'b' and resid 6 through 26 Processing helix chain 'b' and resid 65 through 74 Processing helix chain 'b' and resid 76 through 88 Processing helix chain 'b' and resid 90 through 92 No H-bonds generated for 'chain 'b' and resid 90 through 92' Processing helix chain 'c' and resid 34 through 36 No H-bonds generated for 'chain 'c' and resid 34 through 36' Processing helix chain 'c' and resid 45 through 54 Processing helix chain 'c' and resid 126 through 149 Processing helix chain 'd' and resid 29 through 58 removed outlier: 4.735A pdb=" N ARG d 43 " --> pdb=" O LEU d 39 " (cutoff:3.500A) Proline residue: d 44 - end of helix Processing helix chain 'd' and resid 74 through 76 No H-bonds generated for 'chain 'd' and resid 74 through 76' Processing helix chain 'd' and resid 82 through 124 removed outlier: 3.865A pdb=" N GLY d 118 " --> pdb=" O GLN d 114 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLU d 119 " --> pdb=" O GLN d 115 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N SER d 120 " --> pdb=" O ARG d 116 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TYR d 121 " --> pdb=" O GLU d 117 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ARG d 122 " --> pdb=" O GLY d 118 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLN d 123 " --> pdb=" O GLU d 119 " (cutoff:3.500A) Processing helix chain 'd' and resid 126 through 143 Processing helix chain 'd' and resid 152 through 174 Processing helix chain 'e' and resid 66 through 69 No H-bonds generated for 'chain 'e' and resid 66 through 69' Processing helix chain 'e' and resid 80 through 94 Processing helix chain 'e' and resid 98 through 107 removed outlier: 4.164A 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 Processing helix chain 'g' and resid 31 through 50 Processing helix chain 'g' and resid 60 through 98 Processing helix chain 'g' and resid 111 through 113 No H-bonds generated for 'chain 'g' and resid 111 through 113' Processing helix chain 'h' and resid 6 through 10 Processing helix chain 'h' and resid 16 through 18 No H-bonds generated for 'chain 'h' and resid 16 through 18' Processing helix chain 'h' and resid 26 through 28 No H-bonds generated for 'chain 'h' and resid 26 through 28' Processing helix chain 'h' and resid 34 through 43 Processing helix chain 'h' and resid 49 through 55 Processing helix chain 'h' and resid 57 through 68 Processing helix chain 'h' and resid 70 through 89 Processing helix chain 'i' and resid 3 through 22 Processing helix chain 'i' and resid 26 through 44 removed outlier: 3.631A 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 132 Processing helix chain 'i' and resid 134 through 144 removed outlier: 3.560A pdb=" N ALA i 137 " --> pdb=" O GLN i 134 " (cutoff:3.500A) Proline residue: i 138 - end of helix Processing helix chain 'i' and resid 151 through 171 removed outlier: 3.977A pdb=" N LEU i 170 " --> pdb=" O GLY i 166 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASN i 171 " --> pdb=" O TRP i 167 " (cutoff:3.500A) Processing helix chain 'i' and resid 175 through 193 removed outlier: 4.153A 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: 3.643A pdb=" N HIS i 232 " --> pdb=" O LEU i 228 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR i 233 " --> pdb=" O SER i 229 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N TRP i 234 " --> pdb=" O LEU i 230 " (cutoff:3.500A) removed outlier: 5.526A 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: 4.340A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) Processing helix chain 'i' and resid 309 through 316 removed outlier: 3.543A pdb=" N MET i 313 " --> pdb=" O ASN i 310 " (cutoff:3.500A) Processing helix chain 'i' and resid 326 through 332 Processing helix chain 'i' and resid 337 through 345 Proline residue: i 341 - end of helix 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: 5.894A pdb=" N TRP j 77 " --> pdb=" O LEU j 73 " (cutoff:3.500A) Processing helix chain 'j' and resid 84 through 107 Processing helix chain 'k' and resid 3 through 21 Processing helix chain 'k' and resid 26 through 50 Processing helix chain 'k' and resid 54 through 85 removed outlier: 3.807A 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: 3.787A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR l 16 " --> pdb=" O LEU l 12 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE l 17 " --> pdb=" O THR l 13 " (cutoff:3.500A) Proline residue: l 18 - end of helix removed outlier: 4.706A 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 56 removed outlier: 4.292A 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: 3.881A pdb=" N TRP l 106 " --> pdb=" O GLU l 102 " (cutoff:3.500A) Processing helix chain 'l' and resid 114 through 133 Processing helix chain 'l' and resid 137 through 155 removed outlier: 3.623A pdb=" N GLY l 148 " --> pdb=" O TRP l 144 " (cutoff:3.500A) Processing helix chain 'l' and resid 162 through 192 removed outlier: 3.976A pdb=" N GLY l 181 " --> pdb=" O ILE l 177 " (cutoff:3.500A) Processing helix chain 'l' and resid 198 through 204 Processing helix chain 'l' and resid 210 through 224 Processing helix chain 'l' and resid 227 through 229 No H-bonds generated for 'chain 'l' and resid 227 through 229' Processing helix chain 'l' and resid 231 through 238 removed outlier: 4.146A pdb=" N MET l 237 " --> pdb=" O LEU l 233 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLU l 238 " --> pdb=" O PRO l 234 " (cutoff:3.500A) Processing helix chain 'l' and resid 241 through 250 removed outlier: 3.632A pdb=" N HIS l 248 " --> pdb=" O SER l 244 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N SER l 249 " --> pdb=" O ALA l 245 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER l 250 " --> pdb=" O LEU l 246 " (cutoff:3.500A) Processing helix chain 'l' and resid 255 through 262 Processing helix chain 'l' and resid 264 through 269 removed outlier: 4.333A pdb=" N THR l 269 " --> pdb=" O PRO l 265 " (cutoff:3.500A) Processing helix chain 'l' and resid 271 through 294 removed outlier: 4.355A 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: 3.642A 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 387 through 400 removed outlier: 4.166A pdb=" N SER l 391 " --> pdb=" O THR l 387 " (cutoff:3.500A) removed outlier: 4.298A 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: 3.636A pdb=" N LEU l 457 " --> pdb=" O SER l 453 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.396A 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: 3.614A pdb=" N THR l 507 " --> pdb=" O GLU l 503 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR l 508 " --> pdb=" O LEU l 504 " (cutoff:3.500A) removed outlier: 4.863A 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: 4.231A pdb=" N MET l 533 " --> pdb=" O PRO l 530 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N LEU l 536 " --> pdb=" O MET l 533 " (cutoff:3.500A) Proline residue: l 537 - end of helix removed outlier: 4.641A 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: 3.948A pdb=" N LEU m 61 " --> pdb=" O PHE m 57 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU m 65 " --> pdb=" O LEU m 61 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL m 66 " --> pdb=" O GLY m 62 " (cutoff:3.500A) Processing helix chain 'm' and resid 138 through 146 removed outlier: 4.213A 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 7 through 34 removed outlier: 6.258A pdb=" N VAL n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N HIS n 14 " --> pdb=" O ASP n 10 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE n 15 " --> pdb=" O HIS n 11 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU n 16 " --> pdb=" O TRP n 12 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL n 17 " --> pdb=" O VAL n 13 " (cutoff:3.500A) Proline residue: n 18 - end of helix removed outlier: 3.846A 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 Processing helix chain 'o' and resid 27 through 51 Processing helix chain 'o' and resid 63 through 73 Processing helix chain 'o' and resid 77 through 79 No H-bonds generated for 'chain 'o' and resid 77 through 79' Processing helix chain 'o' and resid 84 through 118 Proline residue: o 97 - end of helix Processing helix chain 'p' and resid 12 through 30 Processing helix chain 'p' and resid 34 through 51 removed outlier: 3.606A pdb=" N GLU p 50 " --> pdb=" O ALA p 46 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N HIS p 51 " --> pdb=" O ARG p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 57 through 62 Processing helix chain 'p' and resid 66 through 73 Processing helix chain 'p' and resid 101 through 106 Processing helix chain 'p' and resid 109 through 113 Processing helix chain 'p' and resid 116 through 143 removed outlier: 3.837A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 3.874A 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: 4.220A 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: 4.197A pdb=" N SER r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU r 42 " --> pdb=" O SER r 38 " (cutoff:3.500A) Processing helix chain 'r' and resid 62 through 83 removed outlier: 3.857A pdb=" N LEU r 73 " --> pdb=" O THR r 69 " (cutoff:3.500A) Proline residue: r 74 - end of helix removed outlier: 4.607A pdb=" N SER r 82 " --> pdb=" O MET r 78 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N HIS r 83 " --> pdb=" O ALA r 79 " (cutoff:3.500A) Processing helix chain 'r' and resid 89 through 111 removed outlier: 3.666A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 115 through 135 removed outlier: 4.621A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.509A 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: 4.034A pdb=" N THR r 153 " --> pdb=" O PHE r 149 " (cutoff:3.500A) Proline residue: r 159 - end of helix removed outlier: 3.597A 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: 4.343A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 222 removed outlier: 4.172A pdb=" N LYS r 218 " --> pdb=" O LEU r 214 " (cutoff:3.500A) Processing helix chain 'r' and resid 225 through 233 Processing helix chain 'r' and resid 237 through 246 Processing helix chain 'r' and resid 253 through 257 removed outlier: 3.881A pdb=" N MET r 257 " --> pdb=" O THR r 254 " (cutoff:3.500A) Processing helix chain 'r' and resid 259 through 277 removed outlier: 4.031A pdb=" N ILE r 270 " --> pdb=" O MET r 266 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER r 273 " --> pdb=" O MET r 269 " (cutoff:3.500A) removed outlier: 3.686A 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: 3.752A 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: 3.737A 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: 4.136A 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: 3.798A pdb=" N THR s 21 " --> pdb=" O VAL s 17 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU s 22 " --> pdb=" O ALA s 18 " (cutoff:3.500A) Processing helix chain 's' and resid 47 through 57 Processing helix chain 's' and resid 68 through 86 Proline residue: s 75 - end of helix removed outlier: 4.642A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 123 removed outlier: 4.431A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 156 removed outlier: 3.888A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 168 removed outlier: 3.660A 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 310 removed outlier: 5.236A 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 97 through 114 removed outlier: 3.971A pdb=" N CYS u 100 " --> pdb=" O PHE u 97 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG u 101 " --> pdb=" O ARG u 98 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LYS u 102 " --> pdb=" O HIS u 99 " (cutoff:3.500A) Processing helix chain 'v' and resid 3 through 10 Processing helix chain 'v' and resid 13 through 15 No H-bonds generated for 'chain 'v' and resid 13 through 15' Processing helix chain 'v' and resid 27 through 29 No H-bonds generated for 'chain 'v' and resid 27 through 29' Processing helix chain 'v' and resid 43 through 49 Processing helix chain 'v' and resid 60 through 72 Processing helix chain 'v' and resid 82 through 124 Processing helix chain 'w' and resid 40 through 45 Processing helix chain 'w' and resid 70 through 81 Processing helix chain 'w' and resid 94 through 97 Processing helix chain 'w' and resid 114 through 119 Processing helix chain 'w' and resid 127 through 153 Processing helix chain 'w' and resid 167 through 175 Processing helix chain 'w' and resid 181 through 197 removed outlier: 5.484A 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: 4.025A 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 333 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: 7.453A pdb=" N TYR A 112 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N ALA A 243 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL A 114 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA A 153 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL A 115 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TYR A 155 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ALA A 117 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR A 157 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ASP A 194 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ILE A 156 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N PHE A 196 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE A 158 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.241A 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: 5.982A pdb=" N GLU B 133 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 5.163A 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: 6.290A pdb=" N VAL C 102 " --> pdb=" O MET C 65 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N PHE C 67 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE C 104 " --> pdb=" O PHE C 67 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TYR C 129 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL C 105 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL C 131 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE C 161 " --> pdb=" O SER C 132 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'F' and resid 52 through 58 removed outlier: 6.944A pdb=" N ARG F 68 " --> pdb=" O ARG F 17 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ILE F 19 " --> pdb=" O TRP F 66 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP F 66 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ILE F 21 " --> pdb=" O LYS F 64 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LYS F 64 " --> pdb=" O ILE F 21 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 262 through 265 removed outlier: 6.523A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE J 167 " --> pdb=" O ASN J 128 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLN J 79 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N VAL J 58 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE J 81 " --> pdb=" O VAL J 58 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'L' and resid 144 through 147 Processing sheet with id= I, first strand: chain 'L' and resid 106 through 108 Processing sheet with id= J, first strand: chain 'M' and resid 32 through 36 Processing sheet with id= K, first strand: chain 'M' and resid 169 through 171 Processing sheet with id= L, first strand: chain 'M' and resid 196 through 198 Processing sheet with id= M, first strand: chain 'M' and resid 246 through 251 Processing sheet with id= N, first strand: chain 'M' and resid 306 through 308 Processing sheet with id= O, first strand: chain 'M' and resid 366 through 368 removed outlier: 8.689A pdb=" N CYS M 367 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ALA M 340 " --> pdb=" O CYS M 367 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL M 544 " --> pdb=" O ALA M 339 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N ILE M 341 " --> pdb=" O VAL M 544 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N PHE M 546 " --> pdb=" O ILE M 341 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N PHE M 565 " --> pdb=" O LEU M 545 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU M 547 " --> pdb=" O PHE M 565 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE M 567 " --> pdb=" O LEU M 547 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL M 582 " --> pdb=" O TYR M 568 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N GLY M 570 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU M 584 " --> pdb=" O GLY M 570 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'M' and resid 513 through 516 removed outlier: 8.279A pdb=" N ASN M 514 " --> pdb=" O PRO M 472 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL M 399 " --> pdb=" O MET M 473 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LYS M 428 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU M 402 " --> pdb=" O LYS M 428 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA M 430 " --> pdb=" O LEU M 402 " (cutoff:3.500A) removed outlier: 6.590A 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: 6.484A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 5.579A 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: 6.835A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N VAL O 134 " --> pdb=" O VAL O 174 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N CYS O 135 " --> pdb=" O MET O 185 " (cutoff:3.500A) removed outlier: 5.551A 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: 6.849A pdb=" N ASN P 131 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LEU P 114 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL P 129 " --> pdb=" O LEU P 114 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA P 116 " --> pdb=" O GLU P 127 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLU P 127 " --> pdb=" O ALA P 116 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU P 84 " --> pdb=" O ARG P 142 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N LYS P 144 " --> pdb=" O LEU P 84 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE P 86 " --> pdb=" O LYS P 144 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N TYR P 146 " --> pdb=" O ILE P 86 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N ILE P 88 " --> pdb=" O TYR P 146 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'P' and resid 208 through 213 Processing sheet with id= V, first strand: chain 'Q' and resid 80 through 84 removed outlier: 3.731A pdb=" N ARG Q 96 " --> pdb=" O HIS Q 112 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 5.506A 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: 6.295A 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: 6.593A pdb=" N VAL w 203 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ASP w 63 " --> pdb=" O VAL w 203 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL w 205 " --> pdb=" O ASP w 63 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLU w 254 " --> pdb=" O VAL w 204 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N TYR w 206 " --> pdb=" O GLU w 254 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU w 256 " --> pdb=" O TYR w 206 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ASP w 208 " --> pdb=" O LEU w 256 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N TYR w 258 " --> pdb=" O ASP w 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'w' and resid 84 through 86 2904 hydrogen bonds defined for protein. 8115 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 22.52 Time building geometry restraints manager: 23.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.41: 27397 1.41 - 1.63: 39720 1.63 - 1.86: 829 1.86 - 2.09: 0 2.09 - 2.31: 80 Bond restraints: 68026 Sorted by residual: bond pdb=" C3D NAI A 503 " pdb=" C4D NAI A 503 " ideal model delta sigma weight residual 1.524 1.262 0.262 2.00e-02 2.50e+03 1.71e+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=" O4B NAI A 503 " ideal model delta sigma weight residual 1.397 1.633 -0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1B NAI A 503 " pdb=" C2B NAI A 503 " ideal model delta sigma weight residual 1.528 1.297 0.231 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C3' ADP w 401 " pdb=" C4' ADP w 401 " ideal model delta sigma weight residual 1.524 1.299 0.225 2.00e-02 2.50e+03 1.27e+02 ... (remaining 68021 not shown) Histogram of bond angle deviations from ideal: 73.32 - 85.78: 76 85.78 - 98.23: 3 98.23 - 110.68: 22241 110.68 - 123.14: 66595 123.14 - 135.59: 3166 Bond angle restraints: 92081 Sorted by residual: angle pdb=" N HIS Q 233 " pdb=" CA HIS Q 233 " pdb=" C HIS Q 233 " ideal model delta sigma weight residual 111.28 122.26 -10.98 1.09e+00 8.42e-01 1.01e+02 angle pdb=" C MET C 124 " pdb=" N PRO C 125 " pdb=" CA PRO C 125 " ideal model delta sigma weight residual 119.85 128.14 -8.29 1.01e+00 9.80e-01 6.73e+01 angle pdb=" N ASP P 102 " pdb=" CA ASP P 102 " pdb=" C ASP P 102 " ideal model delta sigma weight residual 111.36 120.07 -8.71 1.09e+00 8.42e-01 6.38e+01 angle pdb=" N LEU b 111 " pdb=" CA LEU b 111 " pdb=" C LEU b 111 " ideal model delta sigma weight residual 111.28 119.79 -8.51 1.09e+00 8.42e-01 6.09e+01 angle pdb=" C5B NDP J 401 " pdb=" O5B NDP J 401 " pdb=" PA NDP J 401 " ideal model delta sigma weight residual 103.84 118.48 -14.64 1.91e+00 2.73e-01 5.84e+01 ... (remaining 92076 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 39774 35.90 - 71.79: 1350 71.79 - 107.69: 93 107.69 - 143.58: 26 143.58 - 179.48: 13 Dihedral angle restraints: 41256 sinusoidal: 17554 harmonic: 23702 Sorted by residual: dihedral pdb=" C10 FMN A 502 " pdb=" C1' FMN A 502 " pdb=" N10 FMN A 502 " pdb=" C2' FMN A 502 " ideal model delta sinusoidal sigma weight residual -102.41 77.07 -179.48 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP w 401 " pdb=" O5' ADP w 401 " pdb=" PA ADP w 401 " pdb=" O2A ADP w 401 " ideal model delta sinusoidal sigma weight residual -60.00 102.39 -162.38 1 2.00e+01 2.50e-03 4.69e+01 dihedral pdb=" CB CYS F 24 " pdb=" SG CYS F 24 " pdb=" SG CYS F 58 " pdb=" CB CYS F 58 " ideal model delta sinusoidal sigma weight residual -86.00 -142.52 56.52 1 1.00e+01 1.00e-02 4.30e+01 ... (remaining 41253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 9649 0.100 - 0.199: 346 0.199 - 0.299: 26 0.299 - 0.398: 6 0.398 - 0.498: 2 Chirality restraints: 10029 Sorted by residual: chirality pdb=" CA GLN P 107 " pdb=" N GLN P 107 " pdb=" C GLN P 107 " pdb=" CB GLN P 107 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.20e+00 chirality pdb=" CA TRP c 89 " pdb=" N TRP c 89 " pdb=" C TRP c 89 " pdb=" CB TRP c 89 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" CA GLN Q 234 " pdb=" N GLN Q 234 " pdb=" C GLN Q 234 " pdb=" CB GLN Q 234 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.93e+00 ... (remaining 10026 not shown) Planarity restraints: 11528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 UQ s 401 " -0.216 2.00e-02 2.50e+03 4.84e-01 2.92e+03 pdb=" C11 UQ s 401 " -0.346 2.00e-02 2.50e+03 pdb=" C7 UQ s 401 " -0.569 2.00e-02 2.50e+03 pdb=" C8 UQ s 401 " 0.708 2.00e-02 2.50e+03 pdb=" C9 UQ s 401 " 0.422 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD 2MR Q 118 " 0.173 2.00e-02 2.50e+03 2.96e-01 1.53e+03 pdb=" NE 2MR Q 118 " -0.265 2.00e-02 2.50e+03 pdb=" CZ 2MR Q 118 " 0.121 2.00e-02 2.50e+03 pdb=" NH1 2MR Q 118 " 0.506 2.00e-02 2.50e+03 pdb=" NH2 2MR Q 118 " 0.123 2.00e-02 2.50e+03 pdb=" CQ1 2MR Q 118 " -0.396 2.00e-02 2.50e+03 pdb=" CQ2 2MR Q 118 " -0.262 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 UQ s 401 " -0.278 2.00e-02 2.50e+03 2.74e-01 9.37e+02 pdb=" C18 UQ s 401 " 0.243 2.00e-02 2.50e+03 pdb=" C19 UQ s 401 " 0.369 2.00e-02 2.50e+03 pdb=" C20 UQ s 401 " -0.014 2.00e-02 2.50e+03 pdb=" C21 UQ s 401 " -0.320 2.00e-02 2.50e+03 ... (remaining 11525 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 388 2.50 - 3.10: 47260 3.10 - 3.70: 101598 3.70 - 4.30: 151350 4.30 - 4.90: 253332 Nonbonded interactions: 553928 Sorted by model distance: nonbonded pdb=" OE1 GLN A 456 " pdb=" ND1 HIS A 457 " model vdw 1.897 2.520 nonbonded pdb=" O ASN l 579 " pdb=" OD1 ASN l 579 " model vdw 2.194 3.040 nonbonded pdb=" O ASN J 215 " pdb=" OG SER J 219 " model vdw 2.199 2.440 nonbonded pdb=" OD1 ASN A 185 " pdb=" N GLY A 190 " model vdw 2.200 2.520 nonbonded pdb=" OG SER J 204 " pdb=" O GLN J 238 " model vdw 2.203 2.440 ... (remaining 553923 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 131 or (resid 132 and (name N or name CA or nam \ e C or name O or name CB )) or resid 133 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=0.69 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 8.230 Check model and map are aligned: 0.750 Set scattering table: 0.450 Process input model: 159.900 Find NCS groups from input model: 2.360 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 175.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.310 68026 Z= 0.447 Angle : 0.757 17.718 92081 Z= 0.396 Chirality : 0.045 0.498 10029 Planarity : 0.009 0.484 11528 Dihedral : 17.808 179.480 25949 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.00 % Favored : 95.93 % Rotamer: Outliers : 0.41 % Allowed : 13.64 % Favored : 85.95 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.09), residues: 8027 helix: 1.63 (0.08), residues: 4209 sheet: 0.52 (0.25), residues: 417 loop : -0.46 (0.11), residues: 3401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP l 407 HIS 0.014 0.001 HIS W 112 PHE 0.030 0.001 PHE i 292 TYR 0.025 0.001 TYR l 422 ARG 0.009 0.000 ARG e 88 *********************** 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 1133 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 1104 time to evaluate : 5.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8134 (tm-30) REVERT: G 94 ASP cc_start: 0.6295 (p0) cc_final: 0.5880 (p0) REVERT: V 108 TYR cc_start: 0.6755 (OUTLIER) cc_final: 0.6455 (t80) REVERT: l 186 MET cc_start: 0.9182 (mtp) cc_final: 0.8981 (mtp) outliers start: 29 outliers final: 14 residues processed: 1118 average time/residue: 0.6574 time to fit residues: 1247.9940 Evaluate side-chains 1102 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1086 time to evaluate : 5.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain T residue 49 ASP Chi-restraints excluded: chain V residue 95 CYS Chi-restraints excluded: chain V residue 101 LEU Chi-restraints excluded: chain V residue 106 ARG Chi-restraints excluded: chain V residue 108 TYR Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain s residue 84 THR Chi-restraints excluded: chain w residue 54 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 669 optimal weight: 4.9990 chunk 601 optimal weight: 0.9990 chunk 333 optimal weight: 4.9990 chunk 205 optimal weight: 9.9990 chunk 405 optimal weight: 0.9980 chunk 321 optimal weight: 5.9990 chunk 621 optimal weight: 1.9990 chunk 240 optimal weight: 3.9990 chunk 377 optimal weight: 6.9990 chunk 462 optimal weight: 10.0000 chunk 720 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN E 51 GLN ** H 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 ASN O 69 ASN ** O 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 ASN P 107 GLN S 68 ASN Y 49 GLN ** d 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 25 GLN l 72 GLN ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 103 GLN r 180 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.0557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 68026 Z= 0.225 Angle : 0.558 13.076 92081 Z= 0.278 Chirality : 0.041 0.184 10029 Planarity : 0.005 0.069 11528 Dihedral : 13.762 179.490 10031 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.89 % Favored : 96.06 % Rotamer: Outliers : 2.06 % Allowed : 13.80 % Favored : 84.14 % 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: 1.06 (0.09), residues: 8027 helix: 1.67 (0.08), residues: 4219 sheet: 0.50 (0.26), residues: 417 loop : -0.47 (0.11), residues: 3391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP u 86 HIS 0.007 0.001 HIS Q 223 PHE 0.027 0.001 PHE i 292 TYR 0.024 0.001 TYR l 422 ARG 0.010 0.000 ARG H 96 *********************** 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 1269 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 1124 time to evaluate : 6.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.7786 (tm-30) REVERT: F 43 GLU cc_start: 0.7278 (pm20) cc_final: 0.7025 (pm20) REVERT: G 94 ASP cc_start: 0.6462 (p0) cc_final: 0.5866 (p0) REVERT: J 357 ARG cc_start: 0.7893 (mtt180) cc_final: 0.7527 (mtt180) REVERT: M 443 ASP cc_start: 0.6999 (m-30) cc_final: 0.6673 (m-30) REVERT: M 535 GLU cc_start: 0.7278 (mp0) cc_final: 0.7061 (tt0) REVERT: O 156 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8330 (mt) REVERT: O 185 MET cc_start: 0.7817 (ppp) cc_final: 0.7548 (ppp) REVERT: S 69 ILE cc_start: 0.7647 (tp) cc_final: 0.7394 (tp) REVERT: V 108 TYR cc_start: 0.6825 (OUTLIER) cc_final: 0.6311 (t80) REVERT: V 110 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.7295 (mm) REVERT: X 117 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8044 (mt-10) REVERT: X 122 MET cc_start: 0.8620 (mmt) cc_final: 0.8273 (mmt) REVERT: e 88 ARG cc_start: 0.8721 (mtt180) cc_final: 0.8512 (mtt-85) REVERT: g 4 MET cc_start: 0.8389 (mtm) cc_final: 0.8061 (mtm) REVERT: i 95 MET cc_start: 0.8512 (tpt) cc_final: 0.8290 (tpt) REVERT: i 244 MET cc_start: 0.8854 (ttm) cc_final: 0.8644 (ttm) REVERT: l 486 MET cc_start: 0.8187 (ttm) cc_final: 0.7935 (ttp) REVERT: p 18 ARG cc_start: 0.8270 (mpt-90) cc_final: 0.7814 (mtt-85) REVERT: p 57 MET cc_start: 0.3497 (ptp) cc_final: 0.0361 (ttp) REVERT: p 118 TYR cc_start: 0.8855 (t80) cc_final: 0.8433 (t80) REVERT: r 231 LEU cc_start: 0.9392 (mt) cc_final: 0.9163 (mt) REVERT: s 234 MET cc_start: 0.8907 (mmt) cc_final: 0.8649 (mmm) REVERT: v 105 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7372 (tm-30) REVERT: w 307 TYR cc_start: 0.8969 (m-80) cc_final: 0.8627 (m-80) outliers start: 145 outliers final: 87 residues processed: 1200 average time/residue: 0.6423 time to fit residues: 1305.8377 Evaluate side-chains 1162 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 1070 time to evaluate : 5.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 103 SER Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain M residue 74 ASN Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 204 MET Chi-restraints excluded: chain M residue 556 THR Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain O residue 226 GLU Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 197 MET Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain V residue 19 HIS Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain V residue 108 TYR Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain W residue 20 ASP Chi-restraints excluded: chain W residue 109 SER Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain X residue 124 ASP Chi-restraints excluded: chain Z residue 27 THR Chi-restraints excluded: chain Z residue 62 SER Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain a residue 151 LEU Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 125 SER Chi-restraints excluded: chain d residue 87 GLU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain h residue 76 LEU Chi-restraints excluded: chain i residue 15 SER Chi-restraints excluded: chain i residue 154 MET Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain k residue 44 SER Chi-restraints excluded: chain k residue 63 LEU Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 252 MET Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain m residue 72 THR Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain o residue 57 LEU Chi-restraints excluded: chain o residue 86 THR Chi-restraints excluded: chain o residue 120 LYS Chi-restraints excluded: chain p residue 144 THR Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 296 LEU Chi-restraints excluded: chain u residue 21 SER Chi-restraints excluded: chain u residue 22 SER Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 92 SER Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain u residue 133 THR Chi-restraints excluded: chain u residue 171 THR Chi-restraints excluded: chain v residue 105 GLU Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 203 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 400 optimal weight: 8.9990 chunk 223 optimal weight: 7.9990 chunk 599 optimal weight: 0.0470 chunk 490 optimal weight: 0.5980 chunk 198 optimal weight: 0.0980 chunk 721 optimal weight: 4.9990 chunk 779 optimal weight: 7.9990 chunk 642 optimal weight: 3.9990 chunk 715 optimal weight: 2.9990 chunk 245 optimal weight: 9.9990 chunk 578 optimal weight: 1.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN E 51 GLN ** H 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 ASN P 196 HIS S 68 ASN T 59 GLN Y 49 GLN Z 33 GLN ** d 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 48 ASN g 63 GLN ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 180 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 68026 Z= 0.170 Angle : 0.519 12.278 92081 Z= 0.259 Chirality : 0.040 0.187 10029 Planarity : 0.004 0.061 11528 Dihedral : 12.827 179.237 10013 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.85 % Favored : 96.11 % Rotamer: Outliers : 2.23 % Allowed : 14.79 % Favored : 82.98 % 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: 1.17 (0.10), residues: 8027 helix: 1.78 (0.08), residues: 4215 sheet: 0.45 (0.26), residues: 416 loop : -0.44 (0.11), residues: 3396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.007 0.001 HIS r 180 PHE 0.030 0.001 PHE i 292 TYR 0.023 0.001 TYR l 422 ARG 0.009 0.000 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1291 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1134 time to evaluate : 5.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.7975 (tm-30) REVERT: E 65 GLU cc_start: 0.7824 (tp30) cc_final: 0.7299 (tt0) REVERT: F 40 ARG cc_start: 0.7316 (OUTLIER) cc_final: 0.5929 (ptp-170) REVERT: G 94 ASP cc_start: 0.6544 (p0) cc_final: 0.5932 (p0) REVERT: M 369 GLU cc_start: 0.7738 (tp30) cc_final: 0.7361 (tp30) REVERT: M 443 ASP cc_start: 0.6932 (m-30) cc_final: 0.6589 (m-30) REVERT: M 468 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7221 (pp20) REVERT: M 535 GLU cc_start: 0.7243 (mp0) cc_final: 0.7008 (tt0) REVERT: O 156 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8502 (mm) REVERT: O 185 MET cc_start: 0.7908 (ppp) cc_final: 0.7570 (ppp) REVERT: P 128 ILE cc_start: 0.9337 (OUTLIER) cc_final: 0.8713 (mm) REVERT: V 108 TYR cc_start: 0.6701 (OUTLIER) cc_final: 0.6461 (t80) REVERT: V 110 ILE cc_start: 0.7505 (OUTLIER) cc_final: 0.7185 (mm) REVERT: X 88 LYS cc_start: 0.7980 (mtmt) cc_final: 0.7637 (mttm) REVERT: X 117 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8211 (mt-10) REVERT: X 122 MET cc_start: 0.8568 (mmt) cc_final: 0.8208 (mmt) REVERT: e 88 ARG cc_start: 0.8724 (mtt180) cc_final: 0.8479 (mtt-85) REVERT: f 65 ASP cc_start: 0.8354 (m-30) cc_final: 0.8134 (m-30) REVERT: g 76 TYR cc_start: 0.8766 (m-80) cc_final: 0.8066 (m-80) REVERT: p 18 ARG cc_start: 0.8283 (mpt-90) cc_final: 0.7944 (mtt-85) REVERT: p 57 MET cc_start: 0.3503 (ptp) cc_final: 0.0398 (ttp) REVERT: r 231 LEU cc_start: 0.9388 (mt) cc_final: 0.9150 (mt) REVERT: s 103 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8478 (mp) REVERT: s 234 MET cc_start: 0.8919 (mmt) cc_final: 0.8659 (mmm) REVERT: u 64 ASN cc_start: 0.8433 (OUTLIER) cc_final: 0.8071 (t0) REVERT: v 34 ARG cc_start: 0.4749 (tpt170) cc_final: 0.4349 (tpt90) REVERT: v 105 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7814 (tm-30) REVERT: w 160 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6428 (mp0) REVERT: w 307 TYR cc_start: 0.8915 (m-80) cc_final: 0.8618 (m-80) outliers start: 157 outliers final: 102 residues processed: 1223 average time/residue: 0.6751 time to fit residues: 1413.3336 Evaluate side-chains 1188 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1076 time to evaluate : 5.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain J residue 206 ILE Chi-restraints excluded: chain K residue 103 SER Chi-restraints excluded: chain M residue 74 ASN Chi-restraints excluded: chain M residue 204 MET Chi-restraints excluded: chain M residue 365 SER Chi-restraints excluded: chain M residue 556 THR Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain O residue 226 GLU Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 128 ILE Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 197 MET Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain T residue 49 ASP Chi-restraints excluded: chain V residue 19 HIS Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain V residue 106 ARG Chi-restraints excluded: chain V residue 108 TYR Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain W residue 20 ASP Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain X residue 124 ASP Chi-restraints excluded: chain Z residue 62 SER Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain a residue 151 LEU Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 87 GLU Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain i residue 154 MET Chi-restraints excluded: chain i residue 237 MET Chi-restraints excluded: chain i residue 251 MET Chi-restraints excluded: chain i residue 343 LEU Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain k residue 44 SER Chi-restraints excluded: chain k residue 63 LEU Chi-restraints excluded: chain k residue 78 LEU Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 252 MET Chi-restraints excluded: chain l residue 293 ILE Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain m residue 72 THR Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain o residue 86 THR Chi-restraints excluded: chain o residue 120 LYS Chi-restraints excluded: chain p residue 85 SER Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain s residue 103 LEU Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain s residue 296 LEU Chi-restraints excluded: chain u residue 21 SER Chi-restraints excluded: chain u residue 22 SER Chi-restraints excluded: chain u residue 64 ASN Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 92 SER Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain u residue 133 THR Chi-restraints excluded: chain u residue 144 SER Chi-restraints excluded: chain u residue 171 THR Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 105 GLU Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 60 ILE Chi-restraints excluded: chain w residue 63 ASP Chi-restraints excluded: chain w residue 160 GLU Chi-restraints excluded: chain w residue 163 ILE Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 208 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 712 optimal weight: 7.9990 chunk 542 optimal weight: 0.8980 chunk 374 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 344 optimal weight: 0.7980 chunk 484 optimal weight: 0.8980 chunk 724 optimal weight: 5.9990 chunk 766 optimal weight: 0.9990 chunk 378 optimal weight: 5.9990 chunk 686 optimal weight: 0.9990 chunk 206 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN E 51 GLN I 21 GLN P 51 ASN ** Q 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 68 ASN Y 49 GLN i 134 GLN ** k 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 135 ASN ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 180 HIS w 176 GLN w 300 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 68026 Z= 0.156 Angle : 0.508 11.224 92081 Z= 0.252 Chirality : 0.040 0.181 10029 Planarity : 0.004 0.057 11528 Dihedral : 12.089 179.930 10013 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.72 % Favored : 96.24 % Rotamer: Outliers : 2.64 % Allowed : 15.32 % Favored : 82.04 % 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: 1.25 (0.10), residues: 8027 helix: 1.85 (0.08), residues: 4215 sheet: 0.43 (0.26), residues: 412 loop : -0.39 (0.11), residues: 3400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.007 0.001 HIS r 180 PHE 0.028 0.001 PHE i 292 TYR 0.023 0.001 TYR l 422 ARG 0.010 0.000 ARG w 139 *********************** 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 1308 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1122 time to evaluate : 5.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.7925 (tm-30) REVERT: B 76 TYR cc_start: 0.8695 (OUTLIER) cc_final: 0.8009 (t80) REVERT: B 198 GLU cc_start: 0.8377 (tp30) cc_final: 0.8135 (tp30) REVERT: C 77 MET cc_start: 0.9216 (OUTLIER) cc_final: 0.8983 (ptp) REVERT: C 142 TYR cc_start: 0.9414 (OUTLIER) cc_final: 0.8735 (t80) REVERT: E 65 GLU cc_start: 0.7871 (tp30) cc_final: 0.7259 (tt0) REVERT: F 40 ARG cc_start: 0.7197 (OUTLIER) cc_final: 0.5929 (ptp-170) REVERT: G 94 ASP cc_start: 0.6481 (p0) cc_final: 0.5856 (p0) REVERT: J 212 ARG cc_start: 0.6445 (mpp80) cc_final: 0.6204 (mtm180) REVERT: J 275 ASP cc_start: 0.5927 (OUTLIER) cc_final: 0.5705 (m-30) REVERT: L 86 ASN cc_start: 0.8247 (t0) cc_final: 0.8046 (m110) REVERT: M 369 GLU cc_start: 0.7772 (tp30) cc_final: 0.7376 (tp30) REVERT: M 443 ASP cc_start: 0.6922 (m-30) cc_final: 0.6580 (m-30) REVERT: M 535 GLU cc_start: 0.7223 (mp0) cc_final: 0.6965 (tt0) REVERT: O 156 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8499 (mm) REVERT: O 185 MET cc_start: 0.7952 (ppp) cc_final: 0.7617 (ppp) REVERT: O 196 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8314 (mp) REVERT: P 128 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.8682 (mm) REVERT: S 69 ILE cc_start: 0.7714 (tp) cc_final: 0.7497 (tp) REVERT: T 59 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7826 (pt0) REVERT: V 108 TYR cc_start: 0.6685 (OUTLIER) cc_final: 0.6442 (t80) REVERT: V 110 ILE cc_start: 0.7385 (OUTLIER) cc_final: 0.7082 (mm) REVERT: X 88 LYS cc_start: 0.7986 (mtmt) cc_final: 0.7651 (mttm) REVERT: X 117 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8221 (mt-10) REVERT: Y 43 ARG cc_start: 0.8415 (mmt-90) cc_final: 0.8033 (mmt90) REVERT: b 8 GLU cc_start: 0.6765 (mt-10) cc_final: 0.6516 (mt-10) REVERT: c 185 GLU cc_start: 0.4885 (tp30) cc_final: 0.4585 (tp30) REVERT: f 65 ASP cc_start: 0.8381 (m-30) cc_final: 0.8060 (m-30) REVERT: g 76 TYR cc_start: 0.8758 (m-80) cc_final: 0.8008 (m-80) REVERT: i 18 MET cc_start: 0.8555 (mmm) cc_final: 0.8342 (mmm) REVERT: p 18 ARG cc_start: 0.8227 (mpt-90) cc_final: 0.7787 (mtt-85) REVERT: p 57 MET cc_start: 0.3526 (ptp) cc_final: 0.0414 (ttp) REVERT: p 160 GLU cc_start: 0.7334 (tp30) cc_final: 0.6889 (tt0) REVERT: r 121 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.9017 (mm) REVERT: r 231 LEU cc_start: 0.9420 (mt) cc_final: 0.9203 (mt) REVERT: s 234 MET cc_start: 0.8872 (mmt) cc_final: 0.8612 (mmm) REVERT: u 64 ASN cc_start: 0.8431 (OUTLIER) cc_final: 0.8106 (t0) REVERT: v 105 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7849 (tm-30) REVERT: w 160 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6429 (mp0) outliers start: 186 outliers final: 118 residues processed: 1235 average time/residue: 0.6764 time to fit residues: 1436.0222 Evaluate side-chains 1208 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1074 time to evaluate : 5.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 21 GLN Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain J residue 206 ILE Chi-restraints excluded: chain J residue 275 ASP Chi-restraints excluded: chain K residue 103 SER Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 74 ASN Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 556 THR Chi-restraints excluded: chain M residue 658 ASP Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 196 LEU Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain O residue 226 GLU Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 128 ILE Chi-restraints excluded: chain Q residue 98 VAL Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 197 MET Chi-restraints excluded: chain Q residue 253 PHE Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain T residue 59 GLN Chi-restraints excluded: chain V residue 19 HIS Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain V residue 108 TYR Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain Z residue 62 SER Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain a residue 151 LEU Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain b residue 91 THR Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 141 LEU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 87 GLU Chi-restraints excluded: chain d residue 131 GLN Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 92 MET Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain i residue 15 SER Chi-restraints excluded: chain i residue 237 MET Chi-restraints excluded: chain i residue 251 MET Chi-restraints excluded: chain i residue 343 LEU Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain k residue 44 SER Chi-restraints excluded: chain k residue 63 LEU Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 252 MET Chi-restraints excluded: chain l residue 293 ILE Chi-restraints excluded: chain l residue 315 VAL Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain m residue 72 THR Chi-restraints excluded: chain m residue 127 ILE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain o residue 86 THR Chi-restraints excluded: chain o residue 120 LYS Chi-restraints excluded: chain p residue 56 ASP Chi-restraints excluded: chain r residue 121 LEU Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain s residue 296 LEU Chi-restraints excluded: chain u residue 21 SER Chi-restraints excluded: chain u residue 22 SER Chi-restraints excluded: chain u residue 64 ASN Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 92 SER Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain u residue 133 THR Chi-restraints excluded: chain u residue 144 SER Chi-restraints excluded: chain u residue 171 THR Chi-restraints excluded: chain v residue 105 GLU Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 60 ILE Chi-restraints excluded: chain w residue 63 ASP Chi-restraints excluded: chain w residue 160 GLU Chi-restraints excluded: chain w residue 163 ILE Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 208 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 638 optimal weight: 5.9990 chunk 435 optimal weight: 0.2980 chunk 11 optimal weight: 3.9990 chunk 570 optimal weight: 10.0000 chunk 316 optimal weight: 6.9990 chunk 654 optimal weight: 8.9990 chunk 529 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 391 optimal weight: 3.9990 chunk 688 optimal weight: 6.9990 chunk 193 optimal weight: 10.0000 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 GLN E 45 ASN E 51 GLN I 21 GLN J 138 ASN ** J 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 69 ASN ** O 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 454 GLN S 68 ASN Y 49 GLN Z 9 HIS ** c 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 135 ASN l 320 ASN ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 180 HIS r 255 ASN u 64 ASN u 95 GLN u 143 HIS w 300 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 68026 Z= 0.410 Angle : 0.661 12.577 92081 Z= 0.331 Chirality : 0.046 0.223 10029 Planarity : 0.005 0.064 11528 Dihedral : 12.070 176.437 10013 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.85 % Favored : 95.12 % Rotamer: Outliers : 3.31 % Allowed : 15.99 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.09), residues: 8027 helix: 1.36 (0.08), residues: 4227 sheet: 0.28 (0.25), residues: 422 loop : -0.66 (0.11), residues: 3378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP u 86 HIS 0.010 0.002 HIS N 87 PHE 0.032 0.002 PHE i 292 TYR 0.024 0.002 TYR B 145 ARG 0.011 0.001 ARG J 179 *********************** 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 1341 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 1108 time to evaluate : 7.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8084 (tm-30) REVERT: B 76 TYR cc_start: 0.8868 (OUTLIER) cc_final: 0.8154 (t80) REVERT: B 145 TYR cc_start: 0.9484 (t80) cc_final: 0.9082 (t80) REVERT: C 77 MET cc_start: 0.9230 (OUTLIER) cc_final: 0.9000 (ptp) REVERT: F 40 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.6058 (ptp-170) REVERT: G 94 ASP cc_start: 0.6588 (p0) cc_final: 0.5952 (p0) REVERT: J 212 ARG cc_start: 0.6406 (mpp80) cc_final: 0.6189 (mtm180) REVERT: J 275 ASP cc_start: 0.6026 (OUTLIER) cc_final: 0.5557 (m-30) REVERT: L 86 ASN cc_start: 0.8640 (t0) cc_final: 0.8391 (m-40) REVERT: L 156 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8370 (mttp) REVERT: M 369 GLU cc_start: 0.7730 (tp30) cc_final: 0.7343 (tp30) REVERT: M 498 GLN cc_start: 0.8130 (tp-100) cc_final: 0.7917 (tp40) REVERT: O 156 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8328 (mm) REVERT: O 185 MET cc_start: 0.8165 (ppp) cc_final: 0.7842 (ppp) REVERT: O 196 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8037 (mp) REVERT: P 128 ILE cc_start: 0.9354 (OUTLIER) cc_final: 0.8781 (mm) REVERT: Q 438 MET cc_start: 0.9148 (mtp) cc_final: 0.8832 (mtp) REVERT: S 4 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.7722 (mp0) REVERT: T 59 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7934 (pt0) REVERT: V 17 GLU cc_start: 0.6651 (mm-30) cc_final: 0.5628 (mt-10) REVERT: V 108 TYR cc_start: 0.6823 (OUTLIER) cc_final: 0.6511 (t80) REVERT: W 50 MET cc_start: 0.9150 (mmm) cc_final: 0.8944 (mmt) REVERT: X 117 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8295 (mt-10) REVERT: a 186 THR cc_start: 0.8849 (m) cc_final: 0.8587 (p) REVERT: b 87 LYS cc_start: 0.8951 (ttmm) cc_final: 0.8543 (ttmt) REVERT: c 47 GLU cc_start: 0.8177 (pt0) cc_final: 0.7946 (pt0) REVERT: e 83 ASP cc_start: 0.9033 (OUTLIER) cc_final: 0.8728 (t0) REVERT: f 65 ASP cc_start: 0.8302 (m-30) cc_final: 0.7875 (m-30) REVERT: g 66 TYR cc_start: 0.8950 (OUTLIER) cc_final: 0.8692 (m-80) REVERT: h 89 GLU cc_start: 0.5798 (tm-30) cc_final: 0.5275 (tt0) REVERT: h 91 LYS cc_start: 0.7933 (tttt) cc_final: 0.7724 (tttt) REVERT: i 339 MET cc_start: 0.8798 (mmm) cc_final: 0.8557 (mmm) REVERT: l 271 LYS cc_start: 0.8034 (tttt) cc_final: 0.7693 (tttp) REVERT: l 385 TYR cc_start: 0.8669 (m-80) cc_final: 0.8379 (m-80) REVERT: p 57 MET cc_start: 0.3924 (ptp) cc_final: 0.1362 (ttp) REVERT: p 160 GLU cc_start: 0.7403 (tp30) cc_final: 0.6946 (tt0) REVERT: s 150 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.8740 (tp) REVERT: u 149 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7929 (mp0) REVERT: v 34 ARG cc_start: 0.4937 (tpt170) cc_final: 0.4013 (tpt90) REVERT: v 105 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7746 (tm-30) REVERT: w 160 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.6526 (mp0) outliers start: 233 outliers final: 151 residues processed: 1253 average time/residue: 0.6323 time to fit residues: 1346.1085 Evaluate side-chains 1226 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 1057 time to evaluate : 5.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 457 HIS Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain J residue 138 ASN Chi-restraints excluded: chain J residue 140 ASP Chi-restraints excluded: chain J residue 174 ILE Chi-restraints excluded: chain J residue 275 ASP Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 103 SER Chi-restraints excluded: chain L residue 156 LYS Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain M residue 74 ASN Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 204 MET Chi-restraints excluded: chain M residue 239 THR Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 365 SER Chi-restraints excluded: chain M residue 556 THR Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 122 GLN Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 196 LEU Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain O residue 206 ASP Chi-restraints excluded: chain O residue 234 LEU Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 128 ILE Chi-restraints excluded: chain Q residue 98 VAL Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 197 MET Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 4 GLU Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain T residue 59 GLN Chi-restraints excluded: chain U residue 22 SER Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain V residue 19 HIS Chi-restraints excluded: chain V residue 69 ILE Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain V residue 106 ARG Chi-restraints excluded: chain V residue 108 TYR Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 20 ASP Chi-restraints excluded: chain W residue 109 SER Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 27 THR Chi-restraints excluded: chain Z residue 62 SER Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain b residue 91 THR Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 141 LEU Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 87 GLU Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 66 TYR Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 76 LEU Chi-restraints excluded: chain h residue 77 SER Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain i residue 15 SER Chi-restraints excluded: chain i residue 132 THR Chi-restraints excluded: chain i residue 237 MET Chi-restraints excluded: chain i residue 251 MET Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain i residue 343 LEU Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 82 ASN Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain k residue 34 GLU Chi-restraints excluded: chain k residue 44 SER Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 293 ILE Chi-restraints excluded: chain l residue 315 VAL Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 393 ASP Chi-restraints excluded: chain l residue 401 MET Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain m residue 127 ILE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain o residue 86 THR Chi-restraints excluded: chain o residue 120 LYS Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 56 ASP Chi-restraints excluded: chain p residue 85 SER Chi-restraints excluded: chain p residue 114 MET Chi-restraints excluded: chain p residue 144 THR Chi-restraints excluded: chain r residue 126 LEU Chi-restraints excluded: chain r residue 138 ASN Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain s residue 103 LEU Chi-restraints excluded: chain s residue 150 LEU Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain s residue 296 LEU Chi-restraints excluded: chain u residue 21 SER Chi-restraints excluded: chain u residue 22 SER Chi-restraints excluded: chain u residue 64 ASN Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 92 SER Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain u residue 133 THR Chi-restraints excluded: chain u residue 144 SER Chi-restraints excluded: chain u residue 149 GLU Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 46 MET Chi-restraints excluded: chain v residue 105 GLU Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 60 ILE Chi-restraints excluded: chain w residue 63 ASP Chi-restraints excluded: chain w residue 160 GLU Chi-restraints excluded: chain w residue 163 ILE Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 203 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 257 optimal weight: 0.9980 chunk 690 optimal weight: 1.9990 chunk 151 optimal weight: 9.9990 chunk 450 optimal weight: 7.9990 chunk 189 optimal weight: 3.9990 chunk 767 optimal weight: 0.5980 chunk 636 optimal weight: 5.9990 chunk 355 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 253 optimal weight: 0.9990 chunk 402 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN E 51 GLN O 69 ASN O 133 GLN S 68 ASN T 65 ASN Y 49 GLN Y 57 GLN ** d 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 123 GLN ** r 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 180 HIS r 440 HIS v 43 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 68026 Z= 0.173 Angle : 0.532 10.711 92081 Z= 0.267 Chirality : 0.040 0.195 10029 Planarity : 0.004 0.060 11528 Dihedral : 11.395 178.479 10012 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.96 % Favored : 95.99 % Rotamer: Outliers : 2.65 % Allowed : 17.25 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.09), residues: 8027 helix: 1.65 (0.08), residues: 4210 sheet: 0.35 (0.25), residues: 425 loop : -0.57 (0.11), residues: 3392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP u 86 HIS 0.008 0.001 HIS r 180 PHE 0.029 0.001 PHE i 292 TYR 0.023 0.001 TYR l 422 ARG 0.011 0.000 ARG H 96 *********************** 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 1299 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 1112 time to evaluate : 6.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8001 (tm-30) REVERT: B 76 TYR cc_start: 0.8745 (OUTLIER) cc_final: 0.7991 (t80) REVERT: B 145 TYR cc_start: 0.9425 (t80) cc_final: 0.9013 (t80) REVERT: C 77 MET cc_start: 0.9227 (OUTLIER) cc_final: 0.8978 (ptp) REVERT: C 142 TYR cc_start: 0.9439 (OUTLIER) cc_final: 0.8742 (t80) REVERT: E 65 GLU cc_start: 0.7889 (tp30) cc_final: 0.7365 (tt0) REVERT: F 40 ARG cc_start: 0.7185 (OUTLIER) cc_final: 0.5934 (ptp-170) REVERT: G 94 ASP cc_start: 0.6598 (p0) cc_final: 0.5938 (p0) REVERT: J 205 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.7297 (t70) REVERT: J 275 ASP cc_start: 0.5972 (OUTLIER) cc_final: 0.5746 (m-30) REVERT: L 156 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8267 (mttp) REVERT: M 498 GLN cc_start: 0.8067 (tp-100) cc_final: 0.7863 (tp-100) REVERT: N 11 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8138 (mm) REVERT: O 133 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7221 (mt0) REVERT: O 156 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8347 (mm) REVERT: O 185 MET cc_start: 0.8129 (ppp) cc_final: 0.7802 (ppp) REVERT: O 196 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8166 (mp) REVERT: P 128 ILE cc_start: 0.9308 (OUTLIER) cc_final: 0.8912 (mm) REVERT: Q 438 MET cc_start: 0.9092 (mtp) cc_final: 0.8742 (mtp) REVERT: T 59 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7862 (pt0) REVERT: W 50 MET cc_start: 0.9088 (mmm) cc_final: 0.8863 (mmt) REVERT: W 85 GLN cc_start: 0.8721 (tt0) cc_final: 0.8486 (tt0) REVERT: X 88 LYS cc_start: 0.8034 (mtmt) cc_final: 0.7755 (mttm) REVERT: X 117 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8340 (mt-10) REVERT: Z 35 LYS cc_start: 0.8088 (mmtt) cc_final: 0.7541 (mmtt) REVERT: b 8 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6680 (mt-10) REVERT: b 87 LYS cc_start: 0.8905 (ttmm) cc_final: 0.8605 (ttmt) REVERT: d 104 ASN cc_start: 0.9348 (m-40) cc_final: 0.9130 (m-40) REVERT: e 83 ASP cc_start: 0.8860 (OUTLIER) cc_final: 0.8556 (t0) REVERT: e 123 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8231 (mt-10) REVERT: f 65 ASP cc_start: 0.8289 (m-30) cc_final: 0.7851 (m-30) REVERT: g 76 TYR cc_start: 0.8889 (m-80) cc_final: 0.8218 (m-80) REVERT: h 89 GLU cc_start: 0.5815 (tm-30) cc_final: 0.5110 (tt0) REVERT: i 18 MET cc_start: 0.8641 (mmm) cc_final: 0.8430 (mmm) REVERT: j 23 TRP cc_start: 0.6627 (m100) cc_final: 0.5916 (m100) REVERT: k 10 MET cc_start: 0.7992 (mtp) cc_final: 0.7599 (mtt) REVERT: l 271 LYS cc_start: 0.7910 (tttt) cc_final: 0.7590 (tttp) REVERT: m 27 ILE cc_start: 0.7043 (OUTLIER) cc_final: 0.6793 (mp) REVERT: p 57 MET cc_start: 0.4070 (ptp) cc_final: 0.1608 (ttp) REVERT: p 160 GLU cc_start: 0.7484 (tp30) cc_final: 0.6996 (tt0) REVERT: r 271 MET cc_start: 0.9108 (mmm) cc_final: 0.8756 (mmp) REVERT: r 398 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.7514 (mtt) REVERT: s 150 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.9000 (tp) REVERT: s 235 ASN cc_start: 0.9007 (m110) cc_final: 0.8742 (m-40) REVERT: u 149 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7938 (mp0) REVERT: v 78 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7635 (pp) REVERT: v 105 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7763 (tm-30) REVERT: w 160 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6487 (mp0) REVERT: w 214 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8209 (tt) outliers start: 187 outliers final: 119 residues processed: 1230 average time/residue: 0.6378 time to fit residues: 1341.0352 Evaluate side-chains 1213 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 1071 time to evaluate : 5.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 58 GLN Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain J residue 116 ILE Chi-restraints excluded: chain J residue 140 ASP Chi-restraints excluded: chain J residue 205 ASP Chi-restraints excluded: chain J residue 275 ASP Chi-restraints excluded: chain K residue 103 SER Chi-restraints excluded: chain L residue 156 LYS Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain M residue 74 ASN Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 260 ASN Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 365 SER Chi-restraints excluded: chain M residue 556 THR Chi-restraints excluded: chain M residue 658 ASP Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain O residue 133 GLN Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 196 LEU Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 128 ILE Chi-restraints excluded: chain Q residue 98 VAL Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 197 MET Chi-restraints excluded: chain Q residue 253 PHE Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain S residue 68 ASN Chi-restraints excluded: chain T residue 59 GLN Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 19 HIS Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 20 ASP Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain Z residue 20 LYS Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain b residue 91 THR Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 87 GLU Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain i residue 15 SER Chi-restraints excluded: chain i residue 237 MET Chi-restraints excluded: chain i residue 251 MET Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 19 LEU Chi-restraints excluded: chain k residue 44 SER Chi-restraints excluded: chain k residue 63 LEU Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 293 ILE Chi-restraints excluded: chain l residue 315 VAL Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain m residue 27 ILE Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain m residue 126 VAL Chi-restraints excluded: chain m residue 127 ILE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain o residue 86 THR Chi-restraints excluded: chain o residue 120 LYS Chi-restraints excluded: chain p residue 56 ASP Chi-restraints excluded: chain p residue 85 SER Chi-restraints excluded: chain r residue 23 ILE Chi-restraints excluded: chain r residue 398 MET Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 59 GLU Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain s residue 103 LEU Chi-restraints excluded: chain s residue 150 LEU Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain s residue 296 LEU Chi-restraints excluded: chain u residue 21 SER Chi-restraints excluded: chain u residue 22 SER Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 92 SER Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain u residue 133 THR Chi-restraints excluded: chain u residue 144 SER Chi-restraints excluded: chain u residue 149 GLU Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 20 LEU Chi-restraints excluded: chain v residue 46 MET Chi-restraints excluded: chain v residue 61 HIS Chi-restraints excluded: chain v residue 78 LEU Chi-restraints excluded: chain v residue 105 GLU Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 60 ILE Chi-restraints excluded: chain w residue 63 ASP Chi-restraints excluded: chain w residue 160 GLU Chi-restraints excluded: chain w residue 163 ILE Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 214 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 739 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 437 optimal weight: 1.9990 chunk 560 optimal weight: 4.9990 chunk 434 optimal weight: 4.9990 chunk 645 optimal weight: 5.9990 chunk 428 optimal weight: 0.6980 chunk 764 optimal weight: 9.9990 chunk 478 optimal weight: 0.0270 chunk 465 optimal weight: 4.9990 chunk 352 optimal weight: 0.9990 overall best weight: 1.1444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN E 51 GLN ** J 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 ASN ** O 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 381 HIS S 68 ASN Y 49 GLN c 84 GLN l 135 ASN ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 123 GLN r 139 GLN r 144 ASN ** r 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 251 ASN u 95 GLN ** w 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 329 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 68026 Z= 0.176 Angle : 0.530 10.734 92081 Z= 0.264 Chirality : 0.040 0.226 10029 Planarity : 0.004 0.058 11528 Dihedral : 11.033 178.701 10010 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.10 % Favored : 95.86 % Rotamer: Outliers : 2.48 % Allowed : 17.48 % Favored : 80.04 % 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: 1.07 (0.10), residues: 8027 helix: 1.73 (0.08), residues: 4205 sheet: 0.34 (0.25), residues: 431 loop : -0.52 (0.11), residues: 3391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.008 0.001 HIS O 131 PHE 0.028 0.001 PHE i 292 TYR 0.023 0.001 TYR l 422 ARG 0.011 0.000 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1277 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 1102 time to evaluate : 5.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8073 (tm-30) REVERT: B 76 TYR cc_start: 0.8752 (OUTLIER) cc_final: 0.7965 (t80) REVERT: B 145 TYR cc_start: 0.9445 (t80) cc_final: 0.9037 (t80) REVERT: C 77 MET cc_start: 0.9229 (OUTLIER) cc_final: 0.8991 (ptp) REVERT: C 142 TYR cc_start: 0.9435 (OUTLIER) cc_final: 0.8715 (t80) REVERT: E 65 GLU cc_start: 0.7902 (tp30) cc_final: 0.7331 (tt0) REVERT: F 40 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.6056 (ptp-170) REVERT: G 87 LEU cc_start: 0.7025 (OUTLIER) cc_final: 0.6682 (mm) REVERT: G 94 ASP cc_start: 0.6630 (p0) cc_final: 0.5946 (p0) REVERT: G 105 MET cc_start: 0.6694 (mmt) cc_final: 0.6424 (mmt) REVERT: J 205 ASP cc_start: 0.7594 (OUTLIER) cc_final: 0.7310 (t70) REVERT: J 275 ASP cc_start: 0.5968 (OUTLIER) cc_final: 0.5745 (m-30) REVERT: L 156 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8356 (mttp) REVERT: M 498 GLN cc_start: 0.8122 (tp-100) cc_final: 0.7919 (tp-100) REVERT: N 11 LEU cc_start: 0.8633 (tp) cc_final: 0.8136 (mm) REVERT: N 53 LYS cc_start: 0.8298 (mtmm) cc_final: 0.7895 (mttt) REVERT: O 156 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8428 (mm) REVERT: O 185 MET cc_start: 0.8165 (ppp) cc_final: 0.7841 (ppp) REVERT: O 196 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8179 (mp) REVERT: P 128 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.8890 (mm) REVERT: Q 438 MET cc_start: 0.9109 (mtp) cc_final: 0.8749 (mtp) REVERT: T 59 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7926 (pt0) REVERT: W 50 MET cc_start: 0.9070 (mmm) cc_final: 0.8863 (mmt) REVERT: W 85 GLN cc_start: 0.8772 (tt0) cc_final: 0.8545 (tt0) REVERT: W 109 SER cc_start: 0.8849 (t) cc_final: 0.8549 (p) REVERT: X 88 LYS cc_start: 0.8032 (mtmt) cc_final: 0.7778 (mttm) REVERT: Y 43 ARG cc_start: 0.8473 (mmt-90) cc_final: 0.8054 (mmt90) REVERT: b 8 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6725 (mt-10) REVERT: b 87 LYS cc_start: 0.8930 (ttmm) cc_final: 0.8576 (ttmt) REVERT: b 121 LYS cc_start: 0.6761 (ttmt) cc_final: 0.6494 (ttmt) REVERT: c 47 GLU cc_start: 0.8129 (pt0) cc_final: 0.7913 (pt0) REVERT: d 104 ASN cc_start: 0.9347 (m-40) cc_final: 0.9129 (m-40) REVERT: e 83 ASP cc_start: 0.8873 (OUTLIER) cc_final: 0.8565 (t0) REVERT: e 123 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8219 (mt-10) REVERT: f 65 ASP cc_start: 0.8281 (m-30) cc_final: 0.7815 (m-30) REVERT: g 76 TYR cc_start: 0.8825 (m-80) cc_final: 0.8168 (m-80) REVERT: h 89 GLU cc_start: 0.5940 (tm-30) cc_final: 0.5174 (tt0) REVERT: j 23 TRP cc_start: 0.6660 (m100) cc_final: 0.5936 (m100) REVERT: k 10 MET cc_start: 0.7916 (mtp) cc_final: 0.7504 (mtt) REVERT: p 45 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8195 (ttt90) REVERT: p 57 MET cc_start: 0.4021 (ptp) cc_final: 0.1582 (ttp) REVERT: p 160 GLU cc_start: 0.7487 (tp30) cc_final: 0.7016 (tt0) REVERT: p 177 ARG cc_start: 0.8659 (ptp-110) cc_final: 0.8313 (ptp-110) REVERT: r 231 LEU cc_start: 0.9478 (mt) cc_final: 0.9200 (mt) REVERT: r 398 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.7509 (mtt) REVERT: s 150 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8938 (tp) REVERT: s 235 ASN cc_start: 0.8998 (m110) cc_final: 0.8741 (m-40) REVERT: u 149 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7956 (mp0) REVERT: v 34 ARG cc_start: 0.4783 (tpt170) cc_final: 0.4455 (tpt90) REVERT: v 51 LEU cc_start: 0.6779 (OUTLIER) cc_final: 0.6379 (mp) REVERT: v 78 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7588 (pp) REVERT: v 105 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7860 (tm-30) REVERT: w 160 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.6470 (mp0) REVERT: w 214 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8200 (tt) outliers start: 175 outliers final: 133 residues processed: 1215 average time/residue: 0.6870 time to fit residues: 1423.0545 Evaluate side-chains 1228 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1072 time to evaluate : 5.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 58 GLN Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 48 ASN Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain J residue 116 ILE Chi-restraints excluded: chain J residue 205 ASP Chi-restraints excluded: chain J residue 275 ASP Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 103 SER Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 156 LYS Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain M residue 74 ASN Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 204 MET Chi-restraints excluded: chain M residue 260 ASN Chi-restraints excluded: chain M residue 365 SER Chi-restraints excluded: chain M residue 513 MET Chi-restraints excluded: chain M residue 556 THR Chi-restraints excluded: chain M residue 658 ASP Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 196 LEU Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 128 ILE Chi-restraints excluded: chain Q residue 98 VAL Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 197 MET Chi-restraints excluded: chain Q residue 253 PHE Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain T residue 59 GLN Chi-restraints excluded: chain U residue 22 SER Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain V residue 19 HIS Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain V residue 108 TYR Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 49 SER Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain Z residue 62 SER Chi-restraints excluded: chain a residue 100 ASP Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain b residue 91 THR Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 87 GLU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 92 MET Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain i residue 15 SER Chi-restraints excluded: chain i residue 146 SER Chi-restraints excluded: chain i residue 237 MET Chi-restraints excluded: chain i residue 251 MET Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain k residue 44 SER Chi-restraints excluded: chain k residue 63 LEU Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 184 LEU Chi-restraints excluded: chain l residue 293 ILE Chi-restraints excluded: chain l residue 315 VAL Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain m residue 72 THR Chi-restraints excluded: chain m residue 126 VAL Chi-restraints excluded: chain m residue 127 ILE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain o residue 86 THR Chi-restraints excluded: chain o residue 120 LYS Chi-restraints excluded: chain p residue 45 ARG Chi-restraints excluded: chain p residue 56 ASP Chi-restraints excluded: chain p residue 85 SER Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 398 MET Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 59 GLU Chi-restraints excluded: chain s residue 150 LEU Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain s residue 296 LEU Chi-restraints excluded: chain u residue 21 SER Chi-restraints excluded: chain u residue 22 SER Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 92 SER Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain u residue 133 THR Chi-restraints excluded: chain u residue 144 SER Chi-restraints excluded: chain u residue 149 GLU Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 20 LEU Chi-restraints excluded: chain v residue 38 GLU Chi-restraints excluded: chain v residue 46 MET Chi-restraints excluded: chain v residue 51 LEU Chi-restraints excluded: chain v residue 61 HIS Chi-restraints excluded: chain v residue 78 LEU Chi-restraints excluded: chain v residue 105 GLU Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 60 ILE Chi-restraints excluded: chain w residue 63 ASP Chi-restraints excluded: chain w residue 160 GLU Chi-restraints excluded: chain w residue 163 ILE Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 214 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 472 optimal weight: 6.9990 chunk 305 optimal weight: 9.9990 chunk 456 optimal weight: 0.7980 chunk 230 optimal weight: 8.9990 chunk 150 optimal weight: 7.9990 chunk 148 optimal weight: 0.6980 chunk 485 optimal weight: 6.9990 chunk 520 optimal weight: 4.9990 chunk 377 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 600 optimal weight: 7.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN E 51 GLN G 142 GLN ** I 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 69 ASN ** O 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 83 ASN ** Q 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 8 GLN Y 49 GLN ** c 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 83 GLN i 134 GLN l 135 ASN l 320 ASN ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 123 GLN p 66 GLN ** r 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 95 GLN w 300 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 68026 Z= 0.367 Angle : 0.640 13.116 92081 Z= 0.319 Chirality : 0.045 0.277 10029 Planarity : 0.005 0.058 11528 Dihedral : 11.280 176.170 10010 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.86 % Favored : 95.09 % Rotamer: Outliers : 3.00 % Allowed : 17.36 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.09), residues: 8027 helix: 1.40 (0.08), residues: 4215 sheet: 0.15 (0.25), residues: 433 loop : -0.73 (0.11), residues: 3379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP u 86 HIS 0.009 0.001 HIS l 230 PHE 0.032 0.002 PHE i 292 TYR 0.021 0.002 TYR Y 44 ARG 0.014 0.001 ARG H 96 *********************** 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 1303 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 1092 time to evaluate : 5.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8076 (tm-30) REVERT: B 76 TYR cc_start: 0.8915 (OUTLIER) cc_final: 0.8258 (t80) REVERT: B 145 TYR cc_start: 0.9555 (t80) cc_final: 0.9209 (t80) REVERT: E 99 GLN cc_start: 0.8857 (mp10) cc_final: 0.8656 (mp10) REVERT: F 40 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.6006 (ptp-170) REVERT: G 94 ASP cc_start: 0.6573 (p0) cc_final: 0.5784 (p0) REVERT: I 21 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7750 (tp40) REVERT: J 205 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.7397 (t70) REVERT: J 275 ASP cc_start: 0.6044 (OUTLIER) cc_final: 0.5615 (m-30) REVERT: L 156 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8511 (mttp) REVERT: N 11 LEU cc_start: 0.8720 (tp) cc_final: 0.8222 (mm) REVERT: N 41 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.7592 (tp30) REVERT: O 156 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8438 (mm) REVERT: O 185 MET cc_start: 0.8337 (ppp) cc_final: 0.7985 (tmm) REVERT: O 196 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8111 (mp) REVERT: P 128 ILE cc_start: 0.9338 (OUTLIER) cc_final: 0.8989 (mm) REVERT: Q 438 MET cc_start: 0.9144 (mtp) cc_final: 0.8839 (mtp) REVERT: S 4 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7955 (mp0) REVERT: T 58 ARG cc_start: 0.8194 (mtm110) cc_final: 0.7912 (mtm180) REVERT: T 59 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7899 (pt0) REVERT: V 17 GLU cc_start: 0.6689 (mm-30) cc_final: 0.5725 (mt-10) REVERT: W 85 GLN cc_start: 0.8795 (tt0) cc_final: 0.8556 (tt0) REVERT: X 117 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8338 (mt-10) REVERT: b 87 LYS cc_start: 0.9016 (ttmm) cc_final: 0.8615 (ttmt) REVERT: c 53 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7462 (tttt) REVERT: e 83 ASP cc_start: 0.8999 (OUTLIER) cc_final: 0.8634 (t0) REVERT: e 123 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8216 (mt-10) REVERT: f 65 ASP cc_start: 0.8310 (m-30) cc_final: 0.7853 (m-30) REVERT: h 89 GLU cc_start: 0.6271 (tm-30) cc_final: 0.5444 (tt0) REVERT: i 339 MET cc_start: 0.8791 (mmm) cc_final: 0.8545 (mmm) REVERT: j 23 TRP cc_start: 0.6836 (m100) cc_final: 0.6143 (m100) REVERT: k 10 MET cc_start: 0.8155 (mtp) cc_final: 0.7714 (mtt) REVERT: m 27 ILE cc_start: 0.7135 (OUTLIER) cc_final: 0.6919 (mp) REVERT: p 45 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8214 (ttt90) REVERT: p 57 MET cc_start: 0.4379 (ptp) cc_final: 0.1961 (ttp) REVERT: p 160 GLU cc_start: 0.7584 (tp30) cc_final: 0.7113 (tt0) REVERT: p 177 ARG cc_start: 0.8740 (ptp-110) cc_final: 0.8431 (ptp-110) REVERT: s 150 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8814 (tp) REVERT: u 73 GLN cc_start: 0.8282 (mt0) cc_final: 0.8025 (mt0) REVERT: u 149 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7997 (mt-10) REVERT: v 78 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7813 (pp) REVERT: v 105 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7856 (tm-30) REVERT: w 160 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.6573 (mp0) REVERT: w 214 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8315 (tt) outliers start: 211 outliers final: 162 residues processed: 1227 average time/residue: 0.6364 time to fit residues: 1325.4438 Evaluate side-chains 1234 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1049 time to evaluate : 5.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 457 HIS Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 58 GLN Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 21 GLN Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain J residue 116 ILE Chi-restraints excluded: chain J residue 140 ASP Chi-restraints excluded: chain J residue 205 ASP Chi-restraints excluded: chain J residue 275 ASP Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 103 SER Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 156 LYS Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain M residue 74 ASN Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 260 ASN Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 365 SER Chi-restraints excluded: chain M residue 513 MET Chi-restraints excluded: chain M residue 556 THR Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 658 ASP Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 122 GLN Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 196 LEU Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 128 ILE Chi-restraints excluded: chain P residue 153 ILE Chi-restraints excluded: chain Q residue 98 VAL Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 197 MET Chi-restraints excluded: chain Q residue 222 MET Chi-restraints excluded: chain Q residue 253 PHE Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 417 SER Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 4 GLU Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain T residue 59 GLN Chi-restraints excluded: chain U residue 22 SER Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 19 HIS Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 49 SER Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain Z residue 62 SER Chi-restraints excluded: chain Z residue 68 LEU Chi-restraints excluded: chain a residue 100 ASP Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain b residue 91 THR Chi-restraints excluded: chain c residue 53 LYS Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 141 LEU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 52 ILE Chi-restraints excluded: chain d residue 87 GLU Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 77 SER Chi-restraints excluded: chain i residue 15 SER Chi-restraints excluded: chain i residue 146 SER Chi-restraints excluded: chain i residue 237 MET Chi-restraints excluded: chain i residue 251 MET Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain i residue 347 ASN Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 19 LEU Chi-restraints excluded: chain j residue 30 TYR Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 82 ASN Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain k residue 34 GLU Chi-restraints excluded: chain k residue 44 SER Chi-restraints excluded: chain k residue 63 LEU Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 293 ILE Chi-restraints excluded: chain l residue 315 VAL Chi-restraints excluded: chain l residue 355 ASP Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain m residue 27 ILE Chi-restraints excluded: chain m residue 127 ILE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain o residue 86 THR Chi-restraints excluded: chain o residue 120 LYS Chi-restraints excluded: chain o residue 123 GLN Chi-restraints excluded: chain p residue 45 ARG Chi-restraints excluded: chain p residue 56 ASP Chi-restraints excluded: chain p residue 85 SER Chi-restraints excluded: chain r residue 23 ILE Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 126 LEU Chi-restraints excluded: chain r residue 398 MET Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 3 MET Chi-restraints excluded: chain s residue 103 LEU Chi-restraints excluded: chain s residue 150 LEU Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain s residue 296 LEU Chi-restraints excluded: chain u residue 21 SER Chi-restraints excluded: chain u residue 22 SER Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 92 SER Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain u residue 133 THR Chi-restraints excluded: chain u residue 144 SER Chi-restraints excluded: chain u residue 149 GLU Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 20 LEU Chi-restraints excluded: chain v residue 46 MET Chi-restraints excluded: chain v residue 61 HIS Chi-restraints excluded: chain v residue 78 LEU Chi-restraints excluded: chain v residue 105 GLU Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 60 ILE Chi-restraints excluded: chain w residue 63 ASP Chi-restraints excluded: chain w residue 160 GLU Chi-restraints excluded: chain w residue 163 ILE Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 214 ILE Chi-restraints excluded: chain w residue 248 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 695 optimal weight: 0.9980 chunk 732 optimal weight: 9.9990 chunk 668 optimal weight: 0.6980 chunk 712 optimal weight: 0.9990 chunk 428 optimal weight: 0.9980 chunk 310 optimal weight: 3.9990 chunk 559 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 chunk 643 optimal weight: 1.9990 chunk 673 optimal weight: 0.8980 chunk 709 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 393 ASN E 45 ASN E 51 GLN J 331 HIS L 86 ASN M 498 GLN O 69 ASN Y 49 GLN i 83 GLN i 134 GLN l 135 ASN ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 78 GLN r 139 GLN r 169 ASN ** w 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.107 68026 Z= 0.165 Angle : 0.538 12.405 92081 Z= 0.268 Chirality : 0.040 0.216 10029 Planarity : 0.004 0.059 11528 Dihedral : 10.766 178.305 10010 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.92 % Favored : 96.04 % Rotamer: Outliers : 2.20 % Allowed : 18.30 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.09), residues: 8027 helix: 1.66 (0.08), residues: 4195 sheet: 0.37 (0.25), residues: 425 loop : -0.59 (0.11), residues: 3407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP u 86 HIS 0.005 0.001 HIS J 37 PHE 0.028 0.001 PHE i 292 TYR 0.025 0.001 TYR l 422 ARG 0.013 0.000 ARG H 96 *********************** 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 1262 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1107 time to evaluate : 5.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8048 (tm-30) REVERT: A 344 GLN cc_start: 0.7767 (mp10) cc_final: 0.7523 (mp10) REVERT: B 76 TYR cc_start: 0.8753 (OUTLIER) cc_final: 0.7961 (t80) REVERT: B 145 TYR cc_start: 0.9485 (t80) cc_final: 0.9105 (t80) REVERT: E 65 GLU cc_start: 0.7900 (tp30) cc_final: 0.7392 (tt0) REVERT: F 40 ARG cc_start: 0.7484 (OUTLIER) cc_final: 0.6225 (ptp-170) REVERT: G 87 LEU cc_start: 0.6966 (OUTLIER) cc_final: 0.6628 (mm) REVERT: G 94 ASP cc_start: 0.6568 (p0) cc_final: 0.5749 (p0) REVERT: H 94 MET cc_start: 0.8366 (mmm) cc_final: 0.7901 (mtp) REVERT: J 205 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.7238 (t70) REVERT: J 212 ARG cc_start: 0.6788 (mpp80) cc_final: 0.6185 (mtm180) REVERT: J 275 ASP cc_start: 0.5989 (OUTLIER) cc_final: 0.5779 (m-30) REVERT: L 156 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8455 (mmtp) REVERT: N 11 LEU cc_start: 0.8571 (tp) cc_final: 0.8078 (mm) REVERT: N 32 ASP cc_start: 0.8309 (t0) cc_final: 0.8038 (m-30) REVERT: N 41 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.7532 (tp30) REVERT: N 53 LYS cc_start: 0.8331 (mtmm) cc_final: 0.7912 (mttt) REVERT: O 156 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8451 (mm) REVERT: O 185 MET cc_start: 0.8213 (ppp) cc_final: 0.7991 (ppp) REVERT: O 196 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8170 (mp) REVERT: P 128 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.8891 (mm) REVERT: Q 438 MET cc_start: 0.9051 (mtp) cc_final: 0.8656 (mtp) REVERT: S 4 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8065 (mp0) REVERT: T 58 ARG cc_start: 0.8084 (mtm110) cc_final: 0.7870 (mtm180) REVERT: T 59 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7810 (pt0) REVERT: V 17 GLU cc_start: 0.6540 (mm-30) cc_final: 0.5558 (mt-10) REVERT: W 85 GLN cc_start: 0.8745 (tt0) cc_final: 0.8506 (tt0) REVERT: W 109 SER cc_start: 0.8998 (t) cc_final: 0.8564 (p) REVERT: X 88 LYS cc_start: 0.8035 (mtmt) cc_final: 0.7779 (mttm) REVERT: Y 43 ARG cc_start: 0.8447 (mmt-90) cc_final: 0.8021 (mmt90) REVERT: b 4 TYR cc_start: 0.8384 (m-10) cc_final: 0.8103 (m-10) REVERT: b 87 LYS cc_start: 0.8945 (ttmm) cc_final: 0.8611 (ttmt) REVERT: c 53 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7429 (tttt) REVERT: d 104 ASN cc_start: 0.9334 (m-40) cc_final: 0.9109 (m-40) REVERT: e 83 ASP cc_start: 0.8852 (OUTLIER) cc_final: 0.8532 (t0) REVERT: f 65 ASP cc_start: 0.8257 (m-30) cc_final: 0.7828 (m-30) REVERT: h 89 GLU cc_start: 0.6243 (tm-30) cc_final: 0.5363 (tt0) REVERT: j 23 TRP cc_start: 0.6822 (m100) cc_final: 0.6022 (m100) REVERT: k 10 MET cc_start: 0.8023 (mtp) cc_final: 0.7641 (mtt) REVERT: p 57 MET cc_start: 0.4135 (ptp) cc_final: 0.1892 (ttp) REVERT: p 160 GLU cc_start: 0.7561 (tp30) cc_final: 0.7103 (tt0) REVERT: r 231 LEU cc_start: 0.9450 (mt) cc_final: 0.9161 (mt) REVERT: r 271 MET cc_start: 0.9103 (mmm) cc_final: 0.8754 (mmp) REVERT: r 398 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.7475 (mtt) REVERT: s 150 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8912 (tp) REVERT: s 235 ASN cc_start: 0.8976 (m110) cc_final: 0.8594 (m-40) REVERT: v 15 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.6713 (mptp) REVERT: v 38 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7335 (pm20) REVERT: v 78 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7482 (pp) REVERT: v 105 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7875 (tm-30) REVERT: w 160 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.6492 (mp0) REVERT: w 214 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.8103 (tt) outliers start: 155 outliers final: 116 residues processed: 1204 average time/residue: 0.6476 time to fit residues: 1321.9995 Evaluate side-chains 1213 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 1074 time to evaluate : 5.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 58 GLN Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain J residue 205 ASP Chi-restraints excluded: chain J residue 275 ASP Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 156 LYS Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 74 ASN Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 260 ASN Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 556 THR Chi-restraints excluded: chain M residue 658 ASP Chi-restraints excluded: chain N residue 39 VAL Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 196 LEU Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 128 ILE Chi-restraints excluded: chain Q residue 98 VAL Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 197 MET Chi-restraints excluded: chain Q residue 253 PHE Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 417 SER Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 4 GLU Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain T residue 59 GLN Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain V residue 19 HIS Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 20 ASP Chi-restraints excluded: chain W residue 49 SER Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain a residue 100 ASP Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain b residue 91 THR Chi-restraints excluded: chain c residue 53 LYS Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 87 GLU Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 77 SER Chi-restraints excluded: chain i residue 15 SER Chi-restraints excluded: chain i residue 146 SER Chi-restraints excluded: chain i residue 237 MET Chi-restraints excluded: chain i residue 251 MET Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain k residue 44 SER Chi-restraints excluded: chain k residue 63 LEU 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 315 VAL Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain m residue 127 ILE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain o residue 86 THR Chi-restraints excluded: chain o residue 120 LYS Chi-restraints excluded: chain p residue 85 SER Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 398 MET Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 3 MET Chi-restraints excluded: chain s residue 103 LEU Chi-restraints excluded: chain s residue 150 LEU Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain s residue 296 LEU Chi-restraints excluded: chain u residue 22 SER Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 92 SER Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain u residue 133 THR Chi-restraints excluded: chain u residue 144 SER Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 15 LYS Chi-restraints excluded: chain v residue 20 LEU Chi-restraints excluded: chain v residue 38 GLU Chi-restraints excluded: chain v residue 46 MET Chi-restraints excluded: chain v residue 61 HIS Chi-restraints excluded: chain v residue 78 LEU Chi-restraints excluded: chain v residue 105 GLU Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 60 ILE Chi-restraints excluded: chain w residue 63 ASP Chi-restraints excluded: chain w residue 160 GLU Chi-restraints excluded: chain w residue 163 ILE Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 214 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 467 optimal weight: 0.9980 chunk 753 optimal weight: 0.4980 chunk 459 optimal weight: 2.9990 chunk 357 optimal weight: 2.9990 chunk 523 optimal weight: 4.9990 chunk 790 optimal weight: 5.9990 chunk 727 optimal weight: 3.9990 chunk 629 optimal weight: 0.0470 chunk 65 optimal weight: 0.0570 chunk 485 optimal weight: 6.9990 chunk 385 optimal weight: 0.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 45 ASN E 51 GLN I 21 GLN ** S 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 49 GLN i 134 GLN ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 123 GLN ** v 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.148 68026 Z= 0.178 Angle : 0.610 59.200 92081 Z= 0.322 Chirality : 0.041 0.645 10029 Planarity : 0.004 0.134 11528 Dihedral : 10.760 178.333 10010 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.90 % Favored : 96.06 % Rotamer: Outliers : 2.10 % Allowed : 18.44 % Favored : 79.46 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.09), residues: 8027 helix: 1.67 (0.08), residues: 4192 sheet: 0.38 (0.25), residues: 425 loop : -0.58 (0.11), residues: 3410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP u 86 HIS 0.006 0.001 HIS G 103 PHE 0.027 0.001 PHE i 292 TYR 0.024 0.001 TYR l 422 ARG 0.012 0.000 ARG H 96 ********************** 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 1220 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1072 time to evaluate : 5.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8046 (tm-30) REVERT: B 76 TYR cc_start: 0.8760 (OUTLIER) cc_final: 0.7960 (t80) REVERT: B 145 TYR cc_start: 0.9486 (t80) cc_final: 0.9105 (t80) REVERT: E 65 GLU cc_start: 0.7899 (tp30) cc_final: 0.7376 (tt0) REVERT: F 40 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.6221 (ptp-170) REVERT: G 87 LEU cc_start: 0.6960 (OUTLIER) cc_final: 0.6632 (mm) REVERT: G 94 ASP cc_start: 0.6563 (p0) cc_final: 0.5747 (p0) REVERT: G 124 ASP cc_start: 0.7546 (p0) cc_final: 0.7256 (p0) REVERT: H 94 MET cc_start: 0.8376 (mmm) cc_final: 0.7909 (mtp) REVERT: J 205 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.7239 (t70) REVERT: J 212 ARG cc_start: 0.6796 (mpp80) cc_final: 0.6185 (mtm180) REVERT: J 275 ASP cc_start: 0.5986 (OUTLIER) cc_final: 0.5778 (m-30) REVERT: L 156 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8452 (mmtp) REVERT: N 11 LEU cc_start: 0.8569 (tp) cc_final: 0.8076 (mm) REVERT: N 32 ASP cc_start: 0.8309 (t0) cc_final: 0.8038 (m-30) REVERT: N 41 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.7530 (tp30) REVERT: N 53 LYS cc_start: 0.8330 (mtmm) cc_final: 0.7913 (mttt) REVERT: O 156 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8451 (mm) REVERT: O 185 MET cc_start: 0.8216 (ppp) cc_final: 0.7999 (ppp) REVERT: O 196 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8170 (mp) REVERT: P 128 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.8890 (mm) REVERT: Q 438 MET cc_start: 0.9050 (mtp) cc_final: 0.8652 (mtp) REVERT: S 4 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8066 (mp0) REVERT: T 58 ARG cc_start: 0.8061 (mtm110) cc_final: 0.7852 (mtm180) REVERT: T 59 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7809 (pt0) REVERT: V 17 GLU cc_start: 0.6538 (mm-30) cc_final: 0.5558 (mt-10) REVERT: W 85 GLN cc_start: 0.8740 (tt0) cc_final: 0.8504 (tt0) REVERT: W 109 SER cc_start: 0.8900 (t) cc_final: 0.8561 (p) REVERT: X 88 LYS cc_start: 0.8037 (mtmt) cc_final: 0.7778 (mttm) REVERT: Y 43 ARG cc_start: 0.8437 (mmt-90) cc_final: 0.8020 (mmt90) REVERT: b 4 TYR cc_start: 0.8385 (m-10) cc_final: 0.8106 (m-10) REVERT: b 87 LYS cc_start: 0.8966 (ttmm) cc_final: 0.8686 (ttmt) REVERT: c 53 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7436 (tttt) REVERT: d 104 ASN cc_start: 0.9329 (m-40) cc_final: 0.9107 (m-40) REVERT: e 83 ASP cc_start: 0.8848 (OUTLIER) cc_final: 0.8533 (t0) REVERT: f 65 ASP cc_start: 0.8265 (m-30) cc_final: 0.7827 (m-30) REVERT: h 89 GLU cc_start: 0.6244 (tm-30) cc_final: 0.5363 (tt0) REVERT: j 23 TRP cc_start: 0.6825 (m100) cc_final: 0.6021 (m100) REVERT: k 10 MET cc_start: 0.7988 (mtp) cc_final: 0.7642 (mtt) REVERT: p 57 MET cc_start: 0.4122 (ptp) cc_final: 0.1888 (ttp) REVERT: p 160 GLU cc_start: 0.7557 (tp30) cc_final: 0.7102 (tt0) REVERT: r 231 LEU cc_start: 0.9448 (mt) cc_final: 0.9160 (mt) REVERT: r 271 MET cc_start: 0.9099 (mmm) cc_final: 0.8750 (mmp) REVERT: r 398 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.7482 (mtt) REVERT: s 150 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8933 (tp) REVERT: s 235 ASN cc_start: 0.8975 (m110) cc_final: 0.8590 (m-40) REVERT: v 15 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.6673 (mptp) REVERT: v 38 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7335 (pm20) REVERT: v 78 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7484 (pp) REVERT: v 105 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7873 (tm-30) REVERT: w 160 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.6528 (mp0) REVERT: w 214 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.8101 (tt) outliers start: 148 outliers final: 121 residues processed: 1164 average time/residue: 0.6467 time to fit residues: 1282.9826 Evaluate side-chains 1214 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1070 time to evaluate : 5.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 58 GLN Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 21 GLN Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain J residue 140 ASP Chi-restraints excluded: chain J residue 205 ASP Chi-restraints excluded: chain J residue 275 ASP Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain L residue 156 LYS Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 74 ASN Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 260 ASN Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 556 THR Chi-restraints excluded: chain M residue 658 ASP Chi-restraints excluded: chain N residue 39 VAL Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 196 LEU Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 128 ILE Chi-restraints excluded: chain Q residue 98 VAL Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 197 MET Chi-restraints excluded: chain Q residue 198 THR Chi-restraints excluded: chain Q residue 253 PHE Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 417 SER Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 4 GLU Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain T residue 59 GLN Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain V residue 19 HIS Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 20 ASP Chi-restraints excluded: chain W residue 49 SER Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain a residue 100 ASP Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain c residue 53 LYS Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 87 GLU Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 77 SER Chi-restraints excluded: chain i residue 15 SER Chi-restraints excluded: chain i residue 146 SER Chi-restraints excluded: chain i residue 237 MET Chi-restraints excluded: chain i residue 251 MET Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain k residue 22 TYR Chi-restraints excluded: chain k residue 44 SER 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 315 VAL Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain m residue 127 ILE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain o residue 86 THR Chi-restraints excluded: chain o residue 120 LYS Chi-restraints excluded: chain p residue 85 SER Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 398 MET Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 3 MET Chi-restraints excluded: chain s residue 103 LEU Chi-restraints excluded: chain s residue 150 LEU Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain s residue 296 LEU Chi-restraints excluded: chain u residue 22 SER Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 92 SER Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain u residue 133 THR Chi-restraints excluded: chain u residue 144 SER Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 15 LYS Chi-restraints excluded: chain v residue 20 LEU Chi-restraints excluded: chain v residue 38 GLU Chi-restraints excluded: chain v residue 46 MET Chi-restraints excluded: chain v residue 61 HIS Chi-restraints excluded: chain v residue 78 LEU Chi-restraints excluded: chain v residue 105 GLU Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 60 ILE Chi-restraints excluded: chain w residue 63 ASP Chi-restraints excluded: chain w residue 160 GLU Chi-restraints excluded: chain w residue 163 ILE Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 208 ASP Chi-restraints excluded: chain w residue 214 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 499 optimal weight: 4.9990 chunk 670 optimal weight: 0.0070 chunk 192 optimal weight: 1.9990 chunk 580 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 174 optimal weight: 5.9990 chunk 630 optimal weight: 0.0470 chunk 263 optimal weight: 0.0030 chunk 647 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 116 optimal weight: 0.7980 overall best weight: 0.5708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 45 ASN E 51 GLN I 21 GLN ** O 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 49 GLN i 134 GLN ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 123 GLN ** v 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.133901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.110183 restraints weight = 98806.841| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.43 r_work: 0.3090 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.213 68026 Z= 0.196 Angle : 0.642 59.197 92081 Z= 0.347 Chirality : 0.040 0.269 10029 Planarity : 0.004 0.104 11528 Dihedral : 10.758 178.334 10010 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.90 % Favored : 96.06 % Rotamer: Outliers : 2.07 % Allowed : 18.48 % Favored : 79.44 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.09), residues: 8027 helix: 1.68 (0.08), residues: 4192 sheet: 0.38 (0.25), residues: 425 loop : -0.58 (0.11), residues: 3410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP u 86 HIS 0.006 0.001 HIS G 103 PHE 0.027 0.001 PHE i 292 TYR 0.025 0.001 TYR G 147 ARG 0.010 0.000 ARG H 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19889.85 seconds wall clock time: 347 minutes 45.42 seconds (20865.42 seconds total)