Starting phenix.real_space_refine on Sat Jan 20 11:17:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2f_31644/01_2024/7v2f_31644_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2f_31644/01_2024/7v2f_31644.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2f_31644/01_2024/7v2f_31644_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2f_31644/01_2024/7v2f_31644_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2f_31644/01_2024/7v2f_31644_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2f_31644/01_2024/7v2f_31644.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2f_31644/01_2024/7v2f_31644.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2f_31644/01_2024/7v2f_31644_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2f_31644/01_2024/7v2f_31644_updated.pdb" } resolution = 3.1 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 43 5.49 5 Mg 1 5.21 5 S 473 5.16 5 C 43276 2.51 5 N 11093 2.21 5 O 12024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 79": "OE1" <-> "OE2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A ARG 88": "NH1" <-> "NH2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "B GLU 110": "OE1" <-> "OE2" Residue "B GLU 111": "OE1" <-> "OE2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "C TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 34": "OE1" <-> "OE2" Residue "E GLU 65": "OE1" <-> "OE2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 91": "OE1" <-> "OE2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "H GLU 18": "OE1" <-> "OE2" Residue "H GLU 54": "OE1" <-> "OE2" Residue "H GLU 69": "OE1" <-> "OE2" Residue "H GLU 85": "OE1" <-> "OE2" Residue "H GLU 105": "OE1" <-> "OE2" Residue "J ARG 85": "NH1" <-> "NH2" Residue "J GLU 107": "OE1" <-> "OE2" Residue "J GLU 133": "OE1" <-> "OE2" Residue "J GLU 135": "OE1" <-> "OE2" Residue "J GLU 142": "OE1" <-> "OE2" Residue "J GLU 158": "OE1" <-> "OE2" Residue "J PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 346": "OE1" <-> "OE2" Residue "K GLU 80": "OE1" <-> "OE2" Residue "M GLU 67": "OE1" <-> "OE2" Residue "M GLU 118": "OE1" <-> "OE2" Residue "M GLU 284": "OE1" <-> "OE2" Residue "M GLU 468": "OE1" <-> "OE2" Residue "M GLU 716": "OE1" <-> "OE2" Residue "N GLU 50": "OE1" <-> "OE2" Residue "O GLU 103": "OE1" <-> "OE2" Residue "O GLU 150": "OE1" <-> "OE2" Residue "O GLU 202": "OE1" <-> "OE2" Residue "P GLU 85": "OE1" <-> "OE2" Residue "P GLU 215": "OE1" <-> "OE2" Residue "P GLU 222": "OE1" <-> "OE2" Residue "Q GLU 42": "OE1" <-> "OE2" Residue "Q GLU 45": "OE1" <-> "OE2" Residue "Q GLU 100": "OE1" <-> "OE2" Residue "Q GLU 246": "OE1" <-> "OE2" Residue "Q TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 315": "OE1" <-> "OE2" Residue "Q GLU 336": "OE1" <-> "OE2" Residue "S GLU 35": "OE1" <-> "OE2" Residue "S GLU 49": "OE1" <-> "OE2" Residue "T GLU 73": "OE1" <-> "OE2" Residue "T GLU 78": "OE1" <-> "OE2" Residue "U GLU 16": "OE1" <-> "OE2" Residue "V PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 131": "OE1" <-> "OE2" Residue "W GLU 66": "OE1" <-> "OE2" Residue "W GLU 78": "OE1" <-> "OE2" Residue "W GLU 93": "OE1" <-> "OE2" Residue "W GLU 94": "OE1" <-> "OE2" Residue "W GLU 123": "OE1" <-> "OE2" Residue "X GLU 96": "OE1" <-> "OE2" Residue "X GLU 117": "OE1" <-> "OE2" Residue "X GLU 136": "OE1" <-> "OE2" Residue "X GLU 143": "OE1" <-> "OE2" Residue "Y GLU 59": "OE1" <-> "OE2" Residue "Z GLU 34": "OE1" <-> "OE2" Residue "Z GLU 49": "OE1" <-> "OE2" Residue "a GLU 103": "OE1" <-> "OE2" Residue "a GLU 108": "OE1" <-> "OE2" Residue "a GLU 143": "OE1" <-> "OE2" Residue "a GLU 145": "OE1" <-> "OE2" Residue "a GLU 148": "OE1" <-> "OE2" Residue "a GLU 155": "OE1" <-> "OE2" Residue "b GLU 27": "OE1" <-> "OE2" Residue "b GLU 99": "OE1" <-> "OE2" Residue "c GLU 47": "OE1" <-> "OE2" Residue "c GLU 63": "OE1" <-> "OE2" Residue "c GLU 85": "OE1" <-> "OE2" Residue "c GLU 103": "OE1" <-> "OE2" Residue "c GLU 185": "OE1" <-> "OE2" Residue "d GLU 87": "OE1" <-> "OE2" Residue "d GLU 130": "OE1" <-> "OE2" Residue "e GLU 68": "OE1" <-> "OE2" Residue "e GLU 116": "OE1" <-> "OE2" Residue "e GLU 121": "OE1" <-> "OE2" Residue "e GLU 123": "OE1" <-> "OE2" Residue "g GLU 113": "OE1" <-> "OE2" Residue "g GLU 116": "OE1" <-> "OE2" Residue "h GLU 39": "OE1" <-> "OE2" Residue "h GLU 59": "OE1" <-> "OE2" Residue "h GLU 102": "OE1" <-> "OE2" Residue "i GLU 34": "OE1" <-> "OE2" Residue "i GLU 54": "OE1" <-> "OE2" Residue "i GLU 117": "OE1" <-> "OE2" Residue "i GLU 318": "OE1" <-> "OE2" Residue "j GLU 68": "OE1" <-> "OE2" Residue "k GLU 70": "OE1" <-> "OE2" Residue "l GLU 75": "OE1" <-> "OE2" Residue "l GLU 102": "OE1" <-> "OE2" Residue "l GLU 145": "OE1" <-> "OE2" Residue "l GLU 207": "OE1" <-> "OE2" Residue "l GLU 238": "OE1" <-> "OE2" Residue "l GLU 353": "OE1" <-> "OE2" Residue "l GLU 397": "OE1" <-> "OE2" Residue "l GLU 445": "OE1" <-> "OE2" Residue "m GLU 138": "OE1" <-> "OE2" Residue "n GLU 33": "OE1" <-> "OE2" Residue "n GLU 54": "OE1" <-> "OE2" Residue "o TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 61": "OE1" <-> "OE2" Residue "o GLU 113": "OE1" <-> "OE2" Residue "p GLU 69": "OE1" <-> "OE2" Residue "p GLU 95": "OE1" <-> "OE2" Residue "p GLU 123": "OE1" <-> "OE2" Residue "p GLU 134": "OE1" <-> "OE2" Residue "p GLU 176": "OE1" <-> "OE2" Residue "r GLU 87": "OE1" <-> "OE2" Residue "r GLU 222": "OE1" <-> "OE2" Residue "r GLU 335": "OE1" <-> "OE2" Residue "s GLU 24": "OE1" <-> "OE2" Residue "s GLU 170": "OE1" <-> "OE2" Residue "s GLU 227": "OE1" <-> "OE2" Residue "u GLU 6": "OE1" <-> "OE2" Residue "u GLU 17": "OE1" <-> "OE2" Residue "u GLU 80": "OE1" <-> "OE2" Residue "v GLU 16": "OE1" <-> "OE2" Residue "v GLU 38": "OE1" <-> "OE2" Residue "v GLU 45": "OE1" <-> "OE2" Residue "v GLU 91": "OE1" <-> "OE2" Residue "v GLU 101": "OE1" <-> "OE2" Residue "w GLU 47": "OE1" <-> "OE2" Residue "w GLU 160": "OE1" <-> "OE2" Residue "w GLU 189": "OE1" <-> "OE2" Residue "w GLU 197": "OE1" <-> "OE2" Residue "w GLU 213": "OE1" <-> "OE2" Residue "w GLU 226": "OE1" <-> "OE2" Residue "w GLU 267": "OE1" <-> "OE2" Residue "w GLU 333": "OE1" <-> "OE2" Residue "w GLU 345": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 66939 Number of models: 1 Model: "" Number of chains: 67 Chain: "A" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3318 Classifications: {'peptide': 431} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 409} Chain: "B" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1412 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "C" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1248 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 145} Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 971 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "F" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 691 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "G" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 693 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 910 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "I" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 11, 'TRANS': 85} Chain breaks: 1 Chain: "J" Number of atoms: 2359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2359 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 16, 'TRANS': 280} Chain breaks: 3 Chain: "K" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 355 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 3, 'TRANS': 38} Chain: "L" Number of atoms: 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: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 643 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 11, 'TRANS': 71} Chain: "V" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1021 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "W" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1167 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, '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: "X" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 699 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 600 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 6, 'TRANS': 63} Chain: "Z" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 674 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain: "a" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1165 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 10, 'TRANS': 129} Chain: "b" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 879 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 11, 'TRANS': 91} Chain breaks: 1 Chain: "c" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1315 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 20, 'TRANS': 135} Chain: "d" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1461 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 10, 'TRANS': 164} Chain: "e" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 890 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 10, 'TRANS': 96} Chain: "f" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 342 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 40} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "g" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1000 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 11, 'TRANS': 109} Chain: "h" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 867 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "i" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2710 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 328} Chain: "j" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 800 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 Chain: "k" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 748 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "l" Number of atoms: 4785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4785 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 28, 'TRANS': 574} Chain: "m" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 951 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "n" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 479 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "o" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1062 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 11, 'TRANS': 116} Chain: "p" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1534 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 17, 'TRANS': 160} Chain: "r" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3631 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Chain: "s" Number of atoms: 2394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2394 Classifications: {'peptide': 303} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 281} Chain breaks: 1 Chain: "u" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1398 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "v" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1012 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 36 Chain: "w" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2583 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 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: "N" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 305 Unusual residues: {'CDL': 2, 'PEE': 2, 'PLX': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "X" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 91 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "e" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 118 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Chain: "j" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 338 Unusual residues: {'CDL': 2, 'PEE': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 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: "n" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 130 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "r" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 97 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "s" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {' UQ': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {' UQ:plan-11': 1, ' UQ:plan-2': 1, ' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 35 Chain: "w" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2706 SG CYS A 382 48.135 48.231 183.502 1.00 12.56 S ATOM 3048 SG CYS A 425 47.684 44.741 189.120 1.00 17.81 S ATOM 2726 SG CYS A 385 44.694 44.054 183.754 1.00 15.03 S ATOM 2687 SG CYS A 379 43.290 49.265 187.814 1.00 16.08 S ATOM 3949 SG CYS B 113 36.031 65.527 149.684 1.00 28.65 S ATOM 3968 SG CYS B 116 40.983 62.336 153.008 1.00 28.65 S ATOM 3991 SG CYS B 119 41.999 65.050 147.553 1.00 28.65 S ATOM 4320 SG CYS B 162 38.734 59.572 148.503 1.00 28.65 S ATOM 4018 SG CYS B 123 48.013 67.124 142.430 1.00 28.65 S ATOM 4244 SG CYS B 152 45.437 65.605 136.698 1.00 28.65 S ATOM 4291 SG CYS B 158 43.527 62.202 141.675 1.00 28.65 S ATOM 4270 SG CYS B 155 49.463 61.689 139.690 1.00 28.65 S ATOM 5712 SG CYS C 166 51.494 64.825 132.088 1.00 28.65 S ATOM 4984 SG CYS C 72 52.083 66.338 125.728 1.00 11.08 S ATOM 4978 SG CYS C 71 55.883 63.591 127.608 1.00 11.39 S ATOM 5482 SG CYS C 136 54.475 69.342 130.305 1.00 20.64 S ATOM 14538 SG CYS M 131 41.257 62.515 165.112 1.00 22.94 S ATOM 14517 SG CYS M 128 44.137 57.602 161.783 1.00 28.65 S ATOM 14578 SG CYS M 137 46.954 60.853 166.793 1.00 15.42 S ATOM 14910 SG CYS M 179 46.350 61.045 177.949 1.00 28.65 S ATOM 15264 SG CYS M 226 43.154 63.984 173.941 1.00 19.45 S ATOM 14934 SG CYS M 182 41.404 64.206 180.127 1.00 28.65 S ATOM 14887 SG CYS M 176 40.274 58.774 176.756 1.00 20.94 S ATOM 14135 SG CYS M 78 57.481 54.944 180.602 1.00 17.45 S ATOM 14236 SG CYS M 92 56.120 57.041 183.117 1.00 12.00 S ATOM 14024 SG CYS M 64 51.680 57.676 181.332 1.00 28.65 S ATOM 14110 SG CYS M 75 52.145 55.742 178.144 1.00 16.94 S ATOM 21073 SG CYS O 135 31.016 32.726 192.592 1.00 47.88 S ATOM 21107 SG CYS O 140 30.663 29.379 193.591 1.00 50.11 S ATOM 21387 SG CYS O 176 35.692 33.871 195.023 1.00 48.14 S ATOM 21410 SG CYS O 180 35.480 30.182 195.423 1.00 57.41 S ATOM 28068 SG CYS T 86 27.929 52.911 158.025 1.00 15.04 S ATOM 28246 SG CYS T 111 29.451 56.281 158.981 1.00 16.86 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.50 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.50 Time building chain proxies: 26.29, per 1000 atoms: 0.39 Number of scatterers: 66939 At special positions: 0 Unit cell: (216.988, 210.543, 238.472, 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 43 15.00 Mg 1 11.99 O 12024 8.00 N 11093 7.00 C 43276 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=2.04 Simple disulfide: pdb=" SG CYS V 95 " - pdb=" SG CYS V 115 " distance=2.07 Simple disulfide: pdb=" SG CYS d 113 " - pdb=" SG CYS d 125 " distance=2.03 Simple disulfide: pdb=" SG CYS h 33 " - pdb=" SG CYS h 66 " distance=2.03 Simple disulfide: pdb=" SG CYS h 43 " - pdb=" SG CYS h 56 " distance=2.03 Simple disulfide: pdb=" SG CYS u 88 " - pdb=" SG CYS u 100 " distance=2.03 Simple disulfide: pdb=" SG CYS v 69 " - pdb=" SG CYS v 80 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.82 Conformation dependent library (CDL) restraints added in 9.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 92 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 64 " pdb=" FES O 301 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 140 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 180 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 135 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb=" SF4 A 501 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " 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=" SF4 B 301 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 116 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " pdb=" SF4 B 302 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 152 " 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="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " pdb="FE3 SF4 C 301 " - pdb=" NE2 HIS Q 223 " pdb=" SF4 M 801 " pdb="FE3 SF4 M 801 " - pdb=" NE2 HIS M 124 " pdb="FE4 SF4 M 801 " - pdb=" SG CYS M 137 " pdb="FE1 SF4 M 801 " - pdb=" SG CYS M 131 " pdb="FE2 SF4 M 801 " - pdb=" SG CYS M 128 " pdb=" SF4 M 802 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " pdb="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " 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 150 " pdb="ZN ZN T 150 " - pdb=" SG CYS T 86 " pdb="ZN ZN T 150 " - pdb=" SG CYS T 111 " pdb="ZN ZN T 150 " - 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: 345 helices and 29 sheets defined 53.0% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.82 Creating SS restraints... Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 73 through 82 Processing helix chain 'A' and resid 95 through 103 removed outlier: 3.520A 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 264 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 400 Processing helix chain 'A' and resid 406 through 419 removed outlier: 4.101A 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 removed outlier: 3.571A pdb=" N PHE B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) 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: 5.921A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LEU B 210 " --> pdb=" O GLN B 206 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N TYR B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 60 Processing helix chain 'C' and resid 71 through 79 Processing helix chain 'C' and resid 86 through 89 Processing helix chain 'C' and resid 111 through 122 Proline residue: C 115 - end of helix Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 141 through 143 No H-bonds generated for 'chain 'C' and resid 141 through 143' Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 189 through 195 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: 4.113A 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: 4.394A pdb=" N PHE E 106 " --> pdb=" O HIS E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 124 Processing helix chain 'F' and resid 28 through 47 removed outlier: 4.929A pdb=" N GLY F 32 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TYR F 41 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 5.457A 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 137 removed outlier: 5.250A pdb=" N LYS G 137 " --> pdb=" O ILE G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'H' and resid 20 through 37 removed outlier: 3.923A 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 65 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: 4.069A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N MET J 76 " --> pdb=" O HIS J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 97 removed outlier: 4.688A pdb=" N HIS J 93 " --> pdb=" O TYR J 89 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N LEU J 94 " --> pdb=" O ASP J 90 " (cutoff:3.500A) removed outlier: 4.073A 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 214 through 218 Processing helix chain 'J' and resid 242 through 254 Processing helix chain 'J' and resid 273 through 283 Processing helix chain 'J' and resid 317 through 322 Processing helix chain 'J' and resid 335 through 338 Processing helix chain 'J' and resid 345 through 355 removed outlier: 4.671A pdb=" N ILE J 350 " --> pdb=" O GLU J 346 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLU J 351 " --> pdb=" O LEU J 347 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ARG J 355 " --> pdb=" O GLU J 351 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 80 removed outlier: 3.937A pdb=" N GLU K 80 " --> pdb=" O GLN K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 96 removed outlier: 4.534A pdb=" N LYS K 95 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N PHE K 96 " --> pdb=" O GLU K 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 65 No H-bonds generated for 'chain 'L' and resid 62 through 65' Processing helix chain 'L' and resid 69 through 71 No H-bonds generated for 'chain 'L' and resid 69 through 71' Processing helix chain 'L' and resid 120 through 123 removed outlier: 4.490A pdb=" N ASN L 123 " --> pdb=" O PRO L 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 120 through 123' Processing helix chain 'L' and resid 131 through 141 Processing helix chain 'L' and resid 161 through 163 No H-bonds generated for 'chain 'L' and resid 161 through 163' Processing helix chain 'M' and resid 49 through 56 Processing helix chain 'M' and resid 107 through 122 Processing helix chain 'M' and resid 138 through 146 Processing helix chain 'M' and resid 173 through 175 No H-bonds generated for 'chain 'M' and resid 173 through 175' Processing helix chain 'M' and resid 181 through 188 Processing helix chain 'M' and resid 201 through 203 No H-bonds generated for 'chain 'M' and resid 201 through 203' Processing helix chain 'M' and resid 219 through 225 removed outlier: 3.834A pdb=" N ILE M 225 " --> pdb=" O ILE M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 298 removed outlier: 5.064A pdb=" N TYR M 294 " --> pdb=" O THR M 290 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ASP M 295 " --> pdb=" O ARG M 291 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N GLY M 296 " --> pdb=" O PHE M 292 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU M 297 " --> pdb=" O ALA M 293 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LYS M 298 " --> pdb=" O TYR M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 319 through 332 removed outlier: 3.654A 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 361 removed outlier: 3.716A pdb=" N VAL M 361 " --> pdb=" O LEU M 357 " (cutoff:3.500A) Processing helix chain 'M' and resid 382 through 385 Processing helix chain 'M' and resid 390 through 395 removed outlier: 3.615A pdb=" N VAL M 394 " --> pdb=" O THR M 390 " (cutoff:3.500A) removed outlier: 4.654A 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 425 Processing helix chain 'M' and resid 449 through 457 Processing helix chain 'M' and resid 461 through 467 Processing helix chain 'M' and resid 478 through 481 Processing helix chain 'M' and resid 486 through 503 Processing helix chain 'M' and resid 522 through 528 Processing helix chain 'M' and resid 535 through 539 Processing helix chain 'M' and resid 619 through 629 Processing helix chain 'M' and resid 639 through 649 Processing helix chain 'M' and resid 651 through 653 No H-bonds generated for 'chain 'M' and resid 651 through 653' Processing helix chain 'M' and resid 665 through 672 Processing helix chain 'M' and resid 691 through 693 No H-bonds generated for 'chain 'M' and resid 691 through 693' Processing helix chain 'M' and resid 699 through 702 No H-bonds generated for 'chain 'M' and resid 699 through 702' Processing helix chain 'M' and resid 705 through 715 Processing helix chain 'N' and resid 3 through 17 removed outlier: 4.000A 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: 4.745A pdb=" N LEU O 80 " --> pdb=" O ALA O 77 " (cutoff:3.500A) Proline residue: O 81 - end of helix Processing helix chain 'O' and resid 95 through 105 Processing helix chain 'O' and resid 109 through 118 Processing helix chain 'O' and resid 138 through 143 removed outlier: 3.816A pdb=" N ARG O 143 " --> pdb=" O PRO O 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 146 through 156 Processing helix chain 'O' and resid 180 through 182 No H-bonds generated for 'chain 'O' and resid 180 through 182' Processing helix chain 'O' and resid 198 through 210 Processing helix chain 'P' and resid 52 through 68 Processing helix chain 'P' and resid 90 through 102 removed outlier: 4.943A 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: 3.908A pdb=" N TRP P 165 " --> pdb=" O ALA P 162 " (cutoff:3.500A) removed outlier: 4.100A 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: 4.068A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE Q 47 " --> pdb=" O TRP Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 57 through 60 removed outlier: 4.323A pdb=" N HIS Q 60 " --> pdb=" O GLU Q 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 57 through 60' Processing helix chain 'Q' and resid 120 through 126 removed outlier: 3.688A pdb=" N GLU Q 125 " --> pdb=" O GLU Q 121 " (cutoff:3.500A) removed outlier: 4.128A 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: 4.117A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.691A 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: 4.213A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 240 through 248 Processing helix chain 'Q' and resid 251 through 262 Processing helix chain 'Q' and resid 266 through 272 Processing helix chain 'Q' and resid 280 through 285 Processing helix chain 'Q' and resid 290 through 296 removed outlier: 4.037A 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: 4.437A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N LYS Q 437 " --> pdb=" O ALA Q 433 " (cutoff:3.500A) Processing helix chain 'Q' and resid 444 through 454 removed outlier: 4.345A 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 43 through 55 Processing helix chain 'S' and resid 66 through 68 No H-bonds generated for 'chain 'S' and resid 66 through 68' Processing helix chain 'T' and resid 50 through 55 Processing helix chain 'T' and resid 67 through 72 Processing helix chain 'T' and resid 91 through 93 No H-bonds generated for 'chain 'T' and resid 91 through 93' Processing helix chain 'U' and resid 3 through 13 Processing helix chain 'U' and resid 17 through 34 Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 39 through 47 Processing helix chain 'U' and resid 79 through 83 Processing helix chain 'V' and resid 4 through 11 Processing helix chain 'V' and resid 18 through 43 Processing helix chain 'V' and resid 49 through 81 Processing helix chain 'V' and resid 87 through 105 Processing helix chain 'V' and resid 108 through 131 removed outlier: 3.656A pdb=" N THR V 121 " --> pdb=" O TYR V 117 " (cutoff:3.500A) Processing helix chain 'W' and resid 32 through 100 Proline residue: W 73 - end of helix removed outlier: 3.790A pdb=" N LYS W 99 " --> pdb=" O ALA W 95 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ASP W 100 " --> pdb=" O ILE W 96 " (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: 6.282A pdb=" N PHE W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ILE W 141 " --> pdb=" O THR W 137 " (cutoff:3.500A) Processing helix chain 'X' and resid 76 through 88 Processing helix chain 'X' and resid 112 through 126 Processing helix chain 'X' and resid 132 through 137 removed outlier: 4.544A pdb=" N LYS X 137 " --> pdb=" O ILE X 133 " (cutoff:3.500A) Processing helix chain 'X' and resid 141 through 152 Processing helix chain 'Y' and resid 52 through 75 Processing helix chain 'Y' and resid 78 through 81 No H-bonds generated for 'chain 'Y' and resid 78 through 81' Processing helix chain '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 29 through 37 Processing helix chain 'Z' and resid 46 through 53 removed outlier: 3.651A pdb=" N GLU Z 49 " --> pdb=" O GLY Z 46 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TRP Z 51 " --> pdb=" O ASN Z 48 " (cutoff:3.500A) Processing helix chain 'Z' and resid 56 through 58 No H-bonds generated for 'chain 'Z' and resid 56 through 58' Processing helix chain 'Z' and resid 63 through 67 Processing helix chain 'Z' and resid 71 through 89 Processing helix chain 'a' and resid 62 through 92 Proline residue: a 81 - end of helix Processing helix chain 'a' and resid 109 through 112 removed outlier: 4.026A pdb=" N TYR a 112 " --> pdb=" O HIS a 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 109 through 112' Processing helix chain 'a' and resid 116 through 125 Processing helix chain 'a' and resid 129 through 163 Processing helix chain 'a' and resid 176 through 178 No H-bonds generated for 'chain 'a' and resid 176 through 178' Processing helix chain 'b' and resid 6 through 26 Processing helix chain 'b' and resid 65 through 73 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 109 through 111 No H-bonds generated for 'chain 'c' and resid 109 through 111' Processing helix chain 'c' and resid 126 through 149 Processing helix chain 'd' and resid 29 through 58 removed outlier: 4.664A 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 116 Processing helix chain 'd' and resid 121 through 124 No H-bonds generated for 'chain 'd' and resid 121 through 124' Processing helix chain 'd' and resid 126 through 143 Processing helix chain 'd' and resid 152 through 174 Processing helix chain 'e' and resid 66 through 69 No H-bonds generated for 'chain 'e' and resid 66 through 69' Processing helix chain 'e' and resid 80 through 94 Processing helix chain 'e' and resid 98 through 107 Processing helix chain 'e' and resid 115 through 131 Processing helix chain 'e' and resid 144 through 146 No H-bonds generated for 'chain 'e' and resid 144 through 146' Processing helix chain 'f' and resid 41 through 73 Processing helix chain 'g' and resid 4 through 6 No H-bonds generated for 'chain 'g' and resid 4 through 6' Processing helix chain 'g' and resid 18 through 22 Processing helix chain 'g' and resid 31 through 50 Processing helix chain 'g' and resid 60 through 98 Processing helix chain 'g' and resid 111 through 113 No H-bonds generated for 'chain 'g' and resid 111 through 113' Processing helix chain 'h' and resid 6 through 10 Processing helix chain 'h' and resid 16 through 18 No H-bonds generated for 'chain 'h' and resid 16 through 18' Processing helix chain 'h' and resid 26 through 28 No H-bonds generated for 'chain 'h' and resid 26 through 28' Processing helix chain 'h' and resid 34 through 44 Processing helix chain 'h' and resid 49 through 55 Processing helix chain 'h' and resid 57 through 68 Processing helix chain 'h' and resid 70 through 89 Processing helix chain 'h' and resid 97 through 99 No H-bonds generated for 'chain 'h' and resid 97 through 99' Processing helix chain 'i' and resid 3 through 22 Processing helix chain 'i' and resid 26 through 44 removed outlier: 3.587A 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 94 through 106 Processing helix chain 'i' and resid 113 through 121 removed outlier: 4.386A pdb=" N GLU i 117 " --> pdb=" O PHE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 144 removed outlier: 3.836A pdb=" N GLN i 134 " --> pdb=" O LEU i 130 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LYS i 135 " --> pdb=" O LEU i 131 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU i 136 " --> pdb=" O THR i 132 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ALA i 137 " --> pdb=" O TRP i 133 " (cutoff:3.500A) Proline residue: i 138 - end of helix Processing helix chain 'i' and resid 146 through 148 No H-bonds generated for 'chain 'i' and resid 146 through 148' Processing helix chain 'i' and resid 151 through 171 removed outlier: 3.809A pdb=" N LEU i 170 " --> pdb=" O GLY i 166 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ASN i 171 " --> pdb=" O TRP i 167 " (cutoff:3.500A) Processing helix chain 'i' and resid 175 through 191 Processing helix chain 'i' and resid 198 through 221 Processing helix chain 'i' and resid 227 through 235 removed outlier: 4.022A pdb=" N THR i 233 " --> pdb=" O SER i 229 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N TRP i 234 " --> pdb=" O LEU i 230 " (cutoff:3.500A) removed outlier: 5.633A 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: 4.421A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) Processing helix chain 'i' and resid 310 through 316 Processing helix chain 'i' and resid 326 through 334 Processing helix chain 'i' and resid 340 through 345 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: 5.833A 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: 3.847A 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: 4.268A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR l 16 " --> pdb=" O LEU l 12 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE l 17 " --> pdb=" O THR l 13 " (cutoff:3.500A) Proline residue: l 18 - end of helix removed outlier: 4.855A pdb=" N ASN l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) Processing helix chain 'l' and resid 26 through 28 No H-bonds generated for 'chain 'l' and resid 26 through 28' Processing helix chain 'l' and resid 32 through 57 removed outlier: 4.294A 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: 3.796A pdb=" N TRP l 106 " --> pdb=" O GLU l 102 " (cutoff:3.500A) Processing helix chain 'l' and resid 114 through 133 Processing helix chain 'l' and resid 137 through 157 removed outlier: 3.559A pdb=" N GLY l 148 " --> pdb=" O TRP l 144 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TRP l 157 " --> pdb=" O LEU l 153 " (cutoff:3.500A) Processing helix chain 'l' and resid 162 through 192 removed outlier: 3.948A 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: 4.193A pdb=" N MET l 237 " --> pdb=" O LEU l 233 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N GLU l 238 " --> pdb=" O PRO l 234 " (cutoff:3.500A) Processing helix chain 'l' and resid 241 through 250 removed outlier: 3.764A pdb=" N HIS l 248 " --> pdb=" O SER l 244 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N SER l 249 " --> pdb=" O ALA l 245 " (cutoff:3.500A) removed outlier: 3.974A 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 267 No H-bonds generated for 'chain 'l' and resid 264 through 267' Processing helix chain 'l' and resid 271 through 294 removed outlier: 4.567A 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: 3.726A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) Processing helix chain 'l' and resid 356 through 358 No H-bonds generated for 'chain 'l' and resid 356 through 358' Processing helix chain 'l' and resid 367 through 380 Processing helix chain 'l' and resid 389 through 400 removed outlier: 4.766A 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: 3.723A pdb=" N LEU l 457 " --> pdb=" O SER l 453 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.046A 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: 3.803A pdb=" N THR l 507 " --> pdb=" O GLU l 503 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N THR l 508 " --> pdb=" O LEU l 504 " (cutoff:3.500A) removed outlier: 4.833A 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 534 Proline residue: l 530 - end of helix removed outlier: 4.344A pdb=" N MET l 533 " --> pdb=" O PRO l 530 " (cutoff:3.500A) Processing helix chain 'l' and resid 536 through 547 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: 3.882A pdb=" N LEU m 61 " --> pdb=" O PHE m 57 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU m 65 " --> pdb=" O LEU m 61 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N VAL m 66 " --> pdb=" O GLY m 62 " (cutoff:3.500A) Processing helix chain 'm' and resid 138 through 146 removed outlier: 4.259A pdb=" N LEU m 146 " --> pdb=" O GLY m 142 " (cutoff:3.500A) Processing helix chain 'm' and resid 151 through 173 Processing helix chain 'n' and resid 8 through 34 removed outlier: 6.422A pdb=" N VAL n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N HIS n 14 " --> pdb=" O ASP n 10 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ILE n 15 " --> pdb=" O HIS n 11 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU n 16 " --> pdb=" O TRP n 12 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL n 17 " --> pdb=" O VAL n 13 " (cutoff:3.500A) Proline residue: n 18 - end of helix removed outlier: 3.628A pdb=" N LYS n 34 " --> pdb=" O ARG n 30 " (cutoff:3.500A) 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 49 Processing helix chain 'p' and resid 57 through 62 Processing helix chain 'p' and resid 66 through 73 Processing helix chain 'p' and resid 95 through 97 No H-bonds generated for 'chain 'p' and resid 95 through 97' Processing helix chain 'p' and resid 101 through 106 Processing helix chain 'p' and resid 109 through 113 Processing helix chain 'p' and resid 116 through 143 removed outlier: 3.773A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 3.934A 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: 4.197A 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: 4.278A pdb=" N SER r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU r 42 " --> pdb=" O SER r 38 " (cutoff:3.500A) Processing helix chain 'r' and resid 62 through 83 removed outlier: 3.867A pdb=" N LEU r 73 " --> pdb=" O THR r 69 " (cutoff:3.500A) Proline residue: r 74 - end of helix removed outlier: 4.475A pdb=" N SER r 82 " --> pdb=" O MET r 78 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N HIS r 83 " --> pdb=" O ALA r 79 " (cutoff:3.500A) Processing helix chain 'r' and resid 89 through 111 removed outlier: 3.654A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 115 through 135 removed outlier: 4.552A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL r 127 " --> pdb=" O GLU r 123 " (cutoff:3.500A) Proline residue: r 128 - end of helix Processing helix chain 'r' and resid 140 through 170 removed outlier: 4.009A pdb=" N LEU r 143 " --> pdb=" O THR r 140 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N TYR r 152 " --> pdb=" O PHE r 149 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LEU r 158 " --> pdb=" O ALA r 155 " (cutoff:3.500A) Proline residue: r 159 - end of helix Processing helix chain 'r' and resid 176 through 181 Processing helix chain 'r' and resid 190 through 204 removed outlier: 4.211A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 222 removed outlier: 4.060A pdb=" N LYS r 218 " --> pdb=" O LEU r 214 " (cutoff:3.500A) Processing helix chain 'r' and resid 225 through 233 Processing helix chain 'r' and resid 237 through 249 removed outlier: 4.779A pdb=" N THR r 248 " --> pdb=" O MET r 244 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ILE r 249 " --> pdb=" O ARG r 245 " (cutoff:3.500A) Processing helix chain 'r' and resid 253 through 257 removed outlier: 3.664A pdb=" N MET r 257 " --> pdb=" O THR r 254 " (cutoff:3.500A) Processing helix chain 'r' and resid 259 through 266 removed outlier: 3.530A pdb=" N LEU r 264 " --> pdb=" O PRO r 260 " (cutoff:3.500A) Processing helix chain 'r' and resid 268 through 277 removed outlier: 3.564A 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: 3.653A 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: 3.710A 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: 4.381A pdb=" N LEU r 449 " --> pdb=" O LEU r 445 " (cutoff:3.500A) Processing helix chain 'r' and resid 451 through 453 No H-bonds generated for 'chain 'r' and resid 451 through 453' Processing helix chain 's' and resid 2 through 32 Proline residue: s 12 - end of helix removed outlier: 3.749A pdb=" N THR s 21 " --> pdb=" O VAL s 17 " (cutoff:3.500A) removed outlier: 4.055A 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 88 Proline residue: s 75 - end of helix removed outlier: 4.269A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL s 87 " --> pdb=" O LEU s 83 " (cutoff:3.500A) Proline residue: s 88 - end of helix Processing helix chain 's' and resid 101 through 123 removed outlier: 4.246A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 156 removed outlier: 3.880A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 168 removed outlier: 3.654A pdb=" N THR s 168 " --> pdb=" O LEU s 165 " (cutoff:3.500A) Processing helix chain 's' and resid 174 through 177 No H-bonds generated for 'chain 's' and resid 174 through 177' Processing helix chain 's' and resid 179 through 192 Processing helix chain 's' and resid 218 through 242 Processing helix chain 's' and resid 252 through 276 Processing helix chain 's' and resid 282 through 311 removed outlier: 5.073A pdb=" N LEU s 294 " --> pdb=" O TRP s 290 " (cutoff:3.500A) Proline residue: s 295 - end of helix Proline residue: s 308 - end of helix Processing helix chain 'u' and resid 22 through 27 Processing helix chain 'u' and resid 29 through 35 Processing helix chain 'u' and resid 37 through 50 Processing helix chain 'u' and resid 53 through 55 No H-bonds generated for 'chain 'u' and resid 53 through 55' Processing helix chain 'u' and resid 57 through 77 Processing helix chain 'u' and resid 79 through 91 Processing helix chain 'u' and resid 101 through 114 Processing helix chain 'v' and resid 3 through 10 Processing helix chain 'v' and resid 13 through 15 No H-bonds generated for 'chain 'v' and resid 13 through 15' Processing helix chain 'v' and resid 19 through 21 No H-bonds generated for 'chain 'v' and resid 19 through 21' 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 48 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 69 through 81 removed outlier: 3.601A pdb=" N LEU w 81 " --> pdb=" O ALA w 78 " (cutoff:3.500A) 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: 5.054A pdb=" N GLU w 197 " --> pdb=" O VAL w 193 " (cutoff:3.500A) Processing helix chain 'w' and resid 211 through 221 Processing helix chain 'w' and resid 226 through 228 No H-bonds generated for 'chain 'w' and resid 226 through 228' Processing helix chain 'w' and resid 231 through 243 Processing helix chain 'w' and resid 245 through 251 removed outlier: 3.770A pdb=" N GLU w 251 " --> pdb=" O PRO w 247 " (cutoff:3.500A) 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 309 removed outlier: 5.181A pdb=" N TYR w 307 " --> pdb=" O GLU w 303 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N THR w 308 " --> pdb=" O VAL w 304 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N THR w 309 " --> pdb=" O LEU w 305 " (cutoff:3.500A) Processing helix chain 'w' and resid 321 through 332 Processing helix chain 'w' and resid 352 through 354 No H-bonds generated for 'chain 'w' and resid 352 through 354' Processing sheet with id= A, first strand: chain 'A' and resid 239 through 244 removed outlier: 3.608A pdb=" N THR A 241 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA A 153 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N VAL A 115 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TYR A 155 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ALA A 117 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TYR A 157 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ASP A 194 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE A 156 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N PHE A 196 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ILE A 158 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL A 198 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 286 through 291 Processing sheet with id= C, first strand: chain 'B' and resid 101 through 103 Processing sheet with id= D, first strand: chain 'B' and resid 128 through 134 removed outlier: 5.952A pdb=" N GLU B 133 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 5.291A 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: 6.354A pdb=" N VAL C 102 " --> pdb=" O MET C 65 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N PHE C 67 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE C 104 " --> pdb=" O PHE C 67 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N TYR C 129 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N VAL C 105 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL C 131 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.432A 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: 7.035A pdb=" N ARG F 68 " --> pdb=" O ARG F 17 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE F 19 " --> pdb=" O TRP F 66 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP F 66 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ILE F 21 " --> pdb=" O LYS F 64 " (cutoff:3.500A) removed outlier: 6.707A 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: 6.712A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE J 167 " --> pdb=" O ASN J 128 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLN J 79 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL J 58 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE J 81 " --> pdb=" O VAL J 58 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'L' and resid 144 through 147 Processing sheet with id= I, first strand: chain 'L' and resid 106 through 108 Processing sheet with id= J, first strand: chain 'M' and resid 32 through 36 Processing sheet with id= K, first strand: chain 'M' and resid 79 through 81 Processing sheet with id= L, first strand: chain 'M' and resid 169 through 171 Processing sheet with id= M, first strand: chain 'M' and resid 196 through 198 Processing sheet with id= N, first strand: chain 'M' and resid 246 through 251 Processing sheet with id= O, first strand: chain 'M' and resid 306 through 308 Processing sheet with id= P, first strand: chain 'M' and resid 366 through 368 removed outlier: 8.665A pdb=" N CYS M 367 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ALA M 340 " --> pdb=" O CYS M 367 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL M 544 " --> pdb=" O ALA M 339 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N ILE M 341 " --> pdb=" O VAL M 544 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE M 546 " --> pdb=" O ILE M 341 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N PHE M 565 " --> pdb=" O LEU M 545 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU M 547 " --> pdb=" O PHE M 565 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE M 567 " --> pdb=" O LEU M 547 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL M 582 " --> pdb=" O TYR M 568 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N GLY M 570 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU M 584 " --> pdb=" O GLY M 570 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'M' and resid 513 through 516 removed outlier: 6.238A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS M 428 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N LEU M 402 " --> pdb=" O LYS M 428 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA M 430 " --> pdb=" O LEU M 402 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASP M 443 " --> pdb=" O LEU M 431 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'M' and resid 595 through 597 Processing sheet with id= S, first strand: chain 'N' and resid 60 through 63 removed outlier: 6.387A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N LEU N 38 " --> pdb=" O GLU N 50 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'O' and resid 169 through 174 removed outlier: 6.486A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N VAL O 134 " --> pdb=" O VAL O 174 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N CYS O 135 " --> pdb=" O MET O 185 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N MET O 185 " --> pdb=" O CYS O 135 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'P' and resid 110 through 118 removed outlier: 6.815A pdb=" N ASN P 131 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU P 114 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL P 129 " --> pdb=" O LEU P 114 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA P 116 " --> pdb=" O GLU P 127 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLU P 127 " --> pdb=" O ALA P 116 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LEU P 84 " --> pdb=" O ARG P 140 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N TYR P 146 " --> pdb=" O ILE P 88 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'P' and resid 208 through 213 Processing sheet with id= W, first strand: chain 'Q' and resid 80 through 84 removed outlier: 3.629A pdb=" N ARG Q 96 " --> pdb=" O HIS Q 112 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N VAL Q 106 " --> pdb=" O SER Q 102 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'Q' and resid 394 through 402 Processing sheet with id= Y, first strand: chain 'T' and resid 83 through 86 Processing sheet with id= Z, first strand: chain 'l' and resid 69 through 71 Processing sheet with id= AA, first strand: chain 'l' and resid 62 through 67 removed outlier: 6.423A 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: 6.709A pdb=" N VAL w 203 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ASP w 63 " --> pdb=" O VAL w 203 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL w 205 " --> pdb=" O ASP w 63 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N GLU w 254 " --> pdb=" O VAL w 204 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N TYR w 206 " --> pdb=" O GLU w 254 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU w 256 " --> pdb=" O TYR w 206 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASP w 208 " --> pdb=" O LEU w 256 " (cutoff:3.500A) removed outlier: 6.634A 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 2918 hydrogen bonds defined for protein. 8142 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: 22.08 Time building geometry restraints manager: 23.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 27314 1.40 - 1.62: 40364 1.62 - 1.85: 823 1.85 - 2.07: 4 2.07 - 2.29: 80 Bond restraints: 68585 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 1.287 0.241 2.00e-02 2.50e+03 1.45e+02 bond pdb=" C1B NAI A 503 " pdb=" O4B NAI A 503 " ideal model delta sigma weight residual 1.397 1.630 -0.233 2.00e-02 2.50e+03 1.35e+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 1.298 0.226 2.00e-02 2.50e+03 1.27e+02 ... (remaining 68580 not shown) Histogram of bond angle deviations from ideal: 73.54 - 85.94: 76 85.94 - 98.33: 4 98.33 - 110.73: 23176 110.73 - 123.12: 66160 123.12 - 135.51: 3320 Bond angle restraints: 92736 Sorted by residual: angle pdb=" N GLY A 120 " pdb=" CA GLY A 120 " pdb=" C GLY A 120 " ideal model delta sigma weight residual 112.73 122.45 -9.72 1.20e+00 6.94e-01 6.57e+01 angle pdb=" C VAL s 87 " pdb=" N PRO s 88 " pdb=" CA PRO s 88 " ideal model delta sigma weight residual 118.85 127.65 -8.80 1.09e+00 8.42e-01 6.52e+01 angle pdb=" C11 CDL l 712 " pdb=" CA5 CDL l 712 " pdb=" OA6 CDL l 712 " ideal model delta sigma weight residual 111.33 121.99 -10.66 1.32e+00 5.72e-01 6.50e+01 angle pdb=" PA NDP J 401 " pdb=" O3 NDP J 401 " pdb=" PN NDP J 401 " ideal model delta sigma weight residual 107.74 123.06 -15.32 1.95e+00 2.62e-01 6.15e+01 angle pdb=" C11 CDL n 102 " pdb=" CA5 CDL n 102 " pdb=" OA6 CDL n 102 " ideal model delta sigma weight residual 111.33 121.00 -9.67 1.32e+00 5.72e-01 5.35e+01 ... (remaining 92731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 40403 35.92 - 71.83: 1212 71.83 - 107.75: 96 107.75 - 143.66: 31 143.66 - 179.58: 18 Dihedral angle restraints: 41760 sinusoidal: 18058 harmonic: 23702 Sorted by residual: dihedral pdb=" CB CYS V 95 " pdb=" SG CYS V 95 " pdb=" SG CYS V 115 " pdb=" CB CYS V 115 " ideal model delta sinusoidal sigma weight residual -86.00 -5.19 -80.81 1 1.00e+01 1.00e-02 8.07e+01 dihedral pdb=" C10 FMN A 502 " pdb=" C1' FMN A 502 " pdb=" N10 FMN A 502 " pdb=" C2' FMN A 502 " ideal model delta sinusoidal sigma weight residual -102.41 74.28 -176.69 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP w 401 " pdb=" O5' ADP w 401 " pdb=" PA ADP w 401 " pdb=" O2A ADP w 401 " ideal model delta sinusoidal sigma weight residual -60.00 98.97 -158.97 1 2.00e+01 2.50e-03 4.64e+01 ... (remaining 41757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 9037 0.074 - 0.149: 947 0.149 - 0.223: 45 0.223 - 0.297: 9 0.297 - 0.372: 3 Chirality restraints: 10041 Sorted by residual: chirality pdb=" CA MET Q 222 " pdb=" N MET Q 222 " pdb=" C MET Q 222 " pdb=" CB MET Q 222 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" C3D NDP J 401 " pdb=" C2D NDP J 401 " pdb=" C4D NDP J 401 " pdb=" O3D NDP J 401 " both_signs ideal model delta sigma weight residual False -2.71 -2.36 -0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CA VAL Q 217 " pdb=" N VAL Q 217 " pdb=" C VAL Q 217 " pdb=" CB VAL Q 217 " both_signs ideal model delta sigma weight residual False 2.44 2.12 0.32 2.00e-01 2.50e+01 2.62e+00 ... (remaining 10038 not shown) Planarity restraints: 11573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 UQ s 403 " -0.345 2.00e-02 2.50e+03 4.91e-01 3.01e+03 pdb=" C11 UQ s 403 " -0.225 2.00e-02 2.50e+03 pdb=" C7 UQ s 403 " -0.578 2.00e-02 2.50e+03 pdb=" C8 UQ s 403 " 0.716 2.00e-02 2.50e+03 pdb=" C9 UQ s 403 " 0.432 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 UQ s 403 " -0.246 2.00e-02 2.50e+03 2.52e-01 7.96e+02 pdb=" C18 UQ s 403 " 0.202 2.00e-02 2.50e+03 pdb=" C19 UQ s 403 " 0.359 2.00e-02 2.50e+03 pdb=" C20 UQ s 403 " -0.020 2.00e-02 2.50e+03 pdb=" C21 UQ s 403 " -0.295 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ s 403 " 0.167 2.00e-02 2.50e+03 2.08e-01 5.38e+02 pdb=" C13 UQ s 403 " -0.100 2.00e-02 2.50e+03 pdb=" C14 UQ s 403 " -0.346 2.00e-02 2.50e+03 pdb=" C15 UQ s 403 " 0.045 2.00e-02 2.50e+03 pdb=" C16 UQ s 403 " 0.235 2.00e-02 2.50e+03 ... (remaining 11570 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 214 2.40 - 3.02: 39403 3.02 - 3.65: 100903 3.65 - 4.27: 160239 4.27 - 4.90: 267897 Nonbonded interactions: 568656 Sorted by model distance: nonbonded pdb=" O GLY w 69 " pdb=" N GLY w 71 " model vdw 1.772 2.520 nonbonded pdb=" OE2 GLU a 95 " pdb=" O1 CDL a 201 " model vdw 1.795 2.440 nonbonded pdb=" OE1 GLN w 235 " pdb=" OE2 GLU w 238 " model vdw 1.869 3.040 nonbonded pdb=" OE1 GLU s 24 " pdb=" OH TYR s 228 " model vdw 1.946 2.440 nonbonded pdb=" O GLU C 126 " pdb=" OH TYR J 89 " model vdw 2.056 2.440 ... (remaining 568651 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 96 or (resid 97 through 98 and (name N or name \ CA or name C or name O or name CB )) or resid 99 through 101 or (resid 102 and ( \ name N or name CA or name C or name O or name CB )) or resid 103 through 156 or \ resid 201)) selection = (chain 'X' and (resid 69 through 149 or (resid 150 through 153 and (name N or na \ me CA or name C or name O or name CB )) or resid 154 through 156 or resid 201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.310 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: 8.740 Check model and map are aligned: 0.720 Set scattering table: 0.450 Process input model: 158.470 Find NCS groups from input model: 2.100 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: 0.020 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 174.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 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 : 0.008 0.312 68585 Z= 0.495 Angle : 0.854 17.355 92736 Z= 0.439 Chirality : 0.046 0.372 10041 Planarity : 0.008 0.491 11573 Dihedral : 17.351 179.580 26453 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.19 % Favored : 95.70 % Rotamer: Outliers : 0.06 % Allowed : 0.61 % Favored : 99.33 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 2.85 % 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: 0.58 (0.09), residues: 8027 helix: 1.21 (0.08), residues: 4241 sheet: -0.02 (0.25), residues: 409 loop : -0.56 (0.11), residues: 3377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP w 353 HIS 0.007 0.001 HIS J 37 PHE 0.033 0.002 PHE i 292 TYR 0.041 0.002 TYR C 142 ARG 0.008 0.001 ARG K 109 *********************** 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 1314 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1310 time to evaluate : 5.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 THR cc_start: 0.8799 (OUTLIER) cc_final: 0.8479 (m) REVERT: E 80 ASP cc_start: 0.8160 (p0) cc_final: 0.7937 (p0) REVERT: H 83 GLN cc_start: 0.7925 (tp40) cc_final: 0.7640 (tp-100) REVERT: L 69 GLU cc_start: 0.7644 (tt0) cc_final: 0.7334 (tt0) REVERT: M 188 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7577 (mt-10) REVERT: N 9 ARG cc_start: 0.8096 (mtm-85) cc_final: 0.7757 (mtm-85) REVERT: V 35 ILE cc_start: 0.8647 (mt) cc_final: 0.8347 (mt) REVERT: W 98 MET cc_start: 0.8324 (mmm) cc_final: 0.7510 (mmm) REVERT: k 9 ILE cc_start: 0.9209 (mm) cc_final: 0.8996 (mm) REVERT: k 14 ILE cc_start: 0.8555 (mt) cc_final: 0.8259 (mt) REVERT: l 573 MET cc_start: 0.8604 (mmm) cc_final: 0.8388 (mmm) REVERT: m 157 THR cc_start: 0.9032 (m) cc_final: 0.8811 (m) REVERT: p 73 TYR cc_start: 0.8399 (t80) cc_final: 0.8195 (t80) REVERT: s 286 MET cc_start: 0.8791 (mmm) cc_final: 0.8534 (mmp) REVERT: w 246 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8419 (mt) REVERT: w 303 GLU cc_start: 0.7285 (tt0) cc_final: 0.6969 (tt0) REVERT: w 332 THR cc_start: 0.8860 (m) cc_final: 0.8634 (m) outliers start: 4 outliers final: 1 residues processed: 1313 average time/residue: 0.6720 time to fit residues: 1487.9441 Evaluate side-chains 1189 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1186 time to evaluate : 5.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain w residue 246 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 669 optimal weight: 3.9990 chunk 601 optimal weight: 0.9980 chunk 333 optimal weight: 5.9990 chunk 205 optimal weight: 1.9990 chunk 405 optimal weight: 5.9990 chunk 321 optimal weight: 3.9990 chunk 621 optimal weight: 2.9990 chunk 240 optimal weight: 1.9990 chunk 377 optimal weight: 0.9990 chunk 462 optimal weight: 2.9990 chunk 720 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 GLN H 37 GLN H 71 GLN K 79 HIS M 260 ASN M 460 HIS M 604 GLN O 153 GLN O 187 GLN P 63 GLN P 75 GLN P 77 GLN ** Q 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 44 GLN V 79 GLN ** Y 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 59 ASN ** i 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 470 ASN l 580 GLN ** o 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 192 ASN s 235 ASN ** v 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.0626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 68585 Z= 0.212 Angle : 0.558 10.813 92736 Z= 0.281 Chirality : 0.042 0.193 10041 Planarity : 0.005 0.078 11573 Dihedral : 15.676 179.760 10456 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.24 % Favored : 95.70 % Rotamer: Outliers : 0.89 % Allowed : 6.16 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.09), residues: 8027 helix: 1.41 (0.08), residues: 4262 sheet: 0.06 (0.25), residues: 408 loop : -0.53 (0.11), residues: 3357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.011 0.001 HIS Y 83 PHE 0.030 0.001 PHE i 292 TYR 0.025 0.001 TYR l 422 ARG 0.005 0.000 ARG K 109 *********************** 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 1331 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 1268 time to evaluate : 6.106 Fit side-chains revert: symmetry clash REVERT: C 93 PHE cc_start: 0.7168 (t80) cc_final: 0.6945 (t80) REVERT: C 98 ARG cc_start: 0.7143 (ttp80) cc_final: 0.6828 (ttm170) REVERT: E 80 ASP cc_start: 0.8127 (p0) cc_final: 0.7925 (p0) REVERT: H 70 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6846 (mp0) REVERT: H 85 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7603 (mp0) REVERT: K 77 GLN cc_start: 0.7393 (mm110) cc_final: 0.6850 (mm110) REVERT: L 69 GLU cc_start: 0.7613 (tt0) cc_final: 0.7332 (tt0) REVERT: L 86 ASN cc_start: 0.9044 (OUTLIER) cc_final: 0.8529 (m110) REVERT: M 188 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7611 (mt-10) REVERT: N 67 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7518 (tm-30) REVERT: Q 371 MET cc_start: 0.9078 (tmm) cc_final: 0.8807 (tmm) REVERT: V 35 ILE cc_start: 0.8620 (mt) cc_final: 0.8354 (mt) REVERT: W 98 MET cc_start: 0.8341 (mmm) cc_final: 0.8138 (mmm) REVERT: Z 39 ARG cc_start: 0.8036 (ttm-80) cc_final: 0.7736 (ttm-80) REVERT: i 89 MET cc_start: 0.8599 (tpt) cc_final: 0.7966 (tpt) REVERT: k 9 ILE cc_start: 0.9160 (mm) cc_final: 0.8902 (mm) REVERT: k 14 ILE cc_start: 0.8582 (mt) cc_final: 0.8231 (mt) REVERT: l 486 MET cc_start: 0.8029 (ttm) cc_final: 0.7767 (ttm) REVERT: p 55 LYS cc_start: 0.7231 (mmtt) cc_final: 0.6922 (tttm) REVERT: p 73 TYR cc_start: 0.8382 (t80) cc_final: 0.8145 (t80) REVERT: s 142 TYR cc_start: 0.9092 (m-80) cc_final: 0.8743 (m-80) REVERT: s 286 MET cc_start: 0.8847 (mmm) cc_final: 0.8606 (mmp) outliers start: 63 outliers final: 48 residues processed: 1294 average time/residue: 0.6722 time to fit residues: 1464.0629 Evaluate side-chains 1228 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 1177 time to evaluate : 5.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain H residue 70 GLU Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 144 SER Chi-restraints excluded: chain M residue 398 ASP Chi-restraints excluded: chain M residue 509 ASP Chi-restraints excluded: chain M residue 513 MET Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain P residue 109 LYS Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain V residue 40 SER Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 75 CYS Chi-restraints excluded: chain V residue 121 THR Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 129 THR Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain Z residue 31 THR Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 69 ILE Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 96 ASP Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 550 SER Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain p residue 57 MET Chi-restraints excluded: chain r residue 15 THR Chi-restraints excluded: chain r residue 343 ILE Chi-restraints excluded: chain u residue 22 SER Chi-restraints excluded: chain w residue 66 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 400 optimal weight: 5.9990 chunk 223 optimal weight: 7.9990 chunk 599 optimal weight: 9.9990 chunk 490 optimal weight: 5.9990 chunk 198 optimal weight: 9.9990 chunk 721 optimal weight: 3.9990 chunk 779 optimal weight: 10.0000 chunk 642 optimal weight: 6.9990 chunk 715 optimal weight: 4.9990 chunk 245 optimal weight: 8.9990 chunk 578 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 GLN E 51 GLN H 71 GLN ** I 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 278 GLN K 79 HIS ** K 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 ASN M 202 ASN M 460 HIS O 153 GLN Q 160 ASN Q 270 ASN ** Q 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 68 ASN ** V 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 149 HIS h 45 HIS ** i 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 63 GLN ** l 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 446 ASN ** o 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 124 ASN s 194 ASN s 235 ASN ** v 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 127 ASN w 235 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.097 68585 Z= 0.515 Angle : 0.708 15.578 92736 Z= 0.357 Chirality : 0.049 0.211 10041 Planarity : 0.006 0.075 11573 Dihedral : 15.229 177.860 10452 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.90 % Favored : 94.99 % Rotamer: Outliers : 1.73 % Allowed : 9.24 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.09), residues: 8027 helix: 1.00 (0.08), residues: 4288 sheet: -0.15 (0.25), residues: 399 loop : -0.72 (0.11), residues: 3340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP M 422 HIS 0.011 0.002 HIS Y 83 PHE 0.035 0.002 PHE i 292 TYR 0.030 0.002 TYR s 277 ARG 0.010 0.001 ARG l 176 *********************** 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 1307 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 1185 time to evaluate : 5.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 99 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7493 (pm20) REVERT: E 80 ASP cc_start: 0.8140 (p0) cc_final: 0.7932 (p0) REVERT: G 115 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7593 (tt0) REVERT: G 119 ILE cc_start: 0.8686 (mm) cc_final: 0.8459 (mt) REVERT: H 83 GLN cc_start: 0.7905 (tp-100) cc_final: 0.7483 (tp-100) REVERT: L 69 GLU cc_start: 0.7726 (tt0) cc_final: 0.7462 (tt0) REVERT: M 158 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8110 (ptt90) REVERT: M 188 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7748 (mt-10) REVERT: N 67 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7556 (tm-30) REVERT: O 80 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9023 (mp) REVERT: V 35 ILE cc_start: 0.8672 (mt) cc_final: 0.8367 (mt) REVERT: Z 39 ARG cc_start: 0.7975 (ttm-80) cc_final: 0.7746 (ttm-80) REVERT: Z 72 LYS cc_start: 0.7996 (mptt) cc_final: 0.7453 (mppt) REVERT: c 161 TYR cc_start: 0.8566 (m-80) cc_final: 0.7982 (m-80) REVERT: k 9 ILE cc_start: 0.9265 (mm) cc_final: 0.9039 (mm) REVERT: k 14 ILE cc_start: 0.8632 (mt) cc_final: 0.8208 (mt) REVERT: l 486 MET cc_start: 0.8065 (ttm) cc_final: 0.7841 (ttm) REVERT: l 573 MET cc_start: 0.8739 (mmm) cc_final: 0.8528 (mmm) REVERT: o 123 GLN cc_start: 0.7691 (mt0) cc_final: 0.7422 (mp10) REVERT: p 55 LYS cc_start: 0.7317 (mmtt) cc_final: 0.6898 (tttt) REVERT: r 302 MET cc_start: 0.8658 (mmp) cc_final: 0.8275 (mmt) REVERT: s 70 MET cc_start: 0.7410 (mtt) cc_final: 0.7193 (mtt) REVERT: s 277 TYR cc_start: 0.9011 (m-10) cc_final: 0.8739 (m-10) REVERT: s 286 MET cc_start: 0.8914 (mmm) cc_final: 0.8654 (mmp) outliers start: 122 outliers final: 90 residues processed: 1249 average time/residue: 0.6551 time to fit residues: 1378.4310 Evaluate side-chains 1226 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 1132 time to evaluate : 5.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain H residue 70 GLU Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 144 SER Chi-restraints excluded: chain M residue 158 ARG Chi-restraints excluded: chain M residue 398 ASP Chi-restraints excluded: chain M residue 509 ASP Chi-restraints excluded: chain M residue 513 MET Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 654 VAL Chi-restraints excluded: chain M residue 689 LEU Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain O residue 50 ASP Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain P residue 109 LYS Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 75 CYS Chi-restraints excluded: chain V residue 121 THR Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 129 THR Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain Z residue 31 THR Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 69 ILE Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain j residue 8 LEU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 58 MET Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain l residue 62 ILE Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 293 ILE Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 401 MET Chi-restraints excluded: chain l residue 417 SER Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 472 ILE Chi-restraints excluded: chain l residue 476 THR Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 132 ASP Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 15 ILE Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain p residue 57 MET Chi-restraints excluded: chain p residue 151 THR Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 129 THR Chi-restraints excluded: chain r residue 187 SER Chi-restraints excluded: chain r residue 343 ILE Chi-restraints excluded: chain s residue 73 ILE Chi-restraints excluded: chain s residue 201 THR Chi-restraints excluded: chain s residue 311 THR Chi-restraints excluded: chain u residue 22 SER Chi-restraints excluded: chain v residue 31 PHE Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 63 ASP Chi-restraints excluded: chain w residue 66 ILE Chi-restraints excluded: chain w residue 163 ILE Chi-restraints excluded: chain w residue 332 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 712 optimal weight: 0.9980 chunk 542 optimal weight: 0.9990 chunk 374 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 344 optimal weight: 3.9990 chunk 484 optimal weight: 2.9990 chunk 724 optimal weight: 0.8980 chunk 766 optimal weight: 8.9990 chunk 378 optimal weight: 0.9980 chunk 686 optimal weight: 0.8980 chunk 206 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 GLN H 71 GLN ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 HIS L 86 ASN M 304 GLN ** M 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 153 GLN ** Q 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 44 GLN ** V 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 59 ASN a 189 ASN d 149 HIS i 49 ASN j 83 ASN l 170 GLN l 446 ASN ** o 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 188 ASN r 304 GLN s 124 ASN s 194 ASN ** v 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 68585 Z= 0.164 Angle : 0.529 10.590 92736 Z= 0.268 Chirality : 0.040 0.169 10041 Planarity : 0.005 0.067 11573 Dihedral : 14.192 179.958 10452 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.87 % Favored : 96.06 % Rotamer: Outliers : 1.29 % Allowed : 11.14 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.10), residues: 8027 helix: 1.45 (0.08), residues: 4262 sheet: 0.02 (0.26), residues: 402 loop : -0.54 (0.11), residues: 3363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.011 0.001 HIS Y 83 PHE 0.027 0.001 PHE i 292 TYR 0.024 0.001 TYR l 422 ARG 0.006 0.000 ARG J 221 *********************** 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 1328 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 1237 time to evaluate : 5.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 THR cc_start: 0.8662 (OUTLIER) cc_final: 0.8436 (m) REVERT: G 115 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7581 (tm130) REVERT: L 69 GLU cc_start: 0.7771 (tt0) cc_final: 0.7499 (tt0) REVERT: M 58 MET cc_start: 0.7638 (ttt) cc_final: 0.7366 (ttt) REVERT: M 173 MET cc_start: 0.9256 (mmm) cc_final: 0.9011 (mmm) REVERT: M 188 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7599 (mt-10) REVERT: N 7 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7699 (mm) REVERT: N 8 ARG cc_start: 0.7021 (mtm-85) cc_final: 0.6790 (mtp85) REVERT: N 67 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7588 (tm-30) REVERT: V 35 ILE cc_start: 0.8575 (mt) cc_final: 0.8316 (mt) REVERT: W 98 MET cc_start: 0.8368 (mmm) cc_final: 0.7584 (mmm) REVERT: X 92 LYS cc_start: 0.8413 (ttmt) cc_final: 0.8157 (mttt) REVERT: Z 72 LYS cc_start: 0.8019 (mptt) cc_final: 0.7443 (mppt) REVERT: a 185 THR cc_start: 0.8154 (p) cc_final: 0.7854 (p) REVERT: b 25 ASP cc_start: 0.8455 (m-30) cc_final: 0.8199 (m-30) REVERT: e 83 ASP cc_start: 0.8156 (OUTLIER) cc_final: 0.7536 (t70) REVERT: i 157 MET cc_start: 0.8586 (mtm) cc_final: 0.8313 (mtt) REVERT: k 14 ILE cc_start: 0.8588 (mt) cc_final: 0.8149 (mt) REVERT: l 486 MET cc_start: 0.8071 (ttm) cc_final: 0.7823 (ttm) REVERT: o 121 LEU cc_start: 0.7301 (tp) cc_final: 0.6916 (tp) REVERT: o 123 GLN cc_start: 0.7629 (mt0) cc_final: 0.7365 (mp10) REVERT: p 55 LYS cc_start: 0.7291 (mmtt) cc_final: 0.6810 (tttm) REVERT: p 73 TYR cc_start: 0.8369 (t80) cc_final: 0.8136 (t80) REVERT: s 134 ARG cc_start: 0.8689 (mtp85) cc_final: 0.8313 (mtp85) REVERT: s 286 MET cc_start: 0.8868 (mmm) cc_final: 0.8663 (mmp) REVERT: w 160 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.6883 (mp0) REVERT: w 249 MET cc_start: 0.8131 (mmp) cc_final: 0.7871 (mmt) outliers start: 91 outliers final: 56 residues processed: 1287 average time/residue: 0.6635 time to fit residues: 1436.4622 Evaluate side-chains 1238 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 1177 time to evaluate : 5.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 334 THR 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 123 GLN Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 70 GLU Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 338 VAL Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 398 ASP Chi-restraints excluded: chain M residue 509 ASP Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 39 VAL Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 312 ASP Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain V residue 75 CYS Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 129 THR Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain Z residue 31 THR Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 374 ILE Chi-restraints excluded: chain l residue 404 THR Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain p residue 151 THR Chi-restraints excluded: chain p residue 171 VAL Chi-restraints excluded: chain r residue 375 LEU Chi-restraints excluded: chain s residue 143 GLU Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 199 ASP Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 63 ASP Chi-restraints excluded: chain w residue 66 ILE Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 160 GLU Chi-restraints excluded: chain w residue 204 VAL 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: 4.9990 chunk 11 optimal weight: 10.0000 chunk 570 optimal weight: 7.9990 chunk 316 optimal weight: 10.0000 chunk 654 optimal weight: 0.0070 chunk 529 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 391 optimal weight: 0.0070 chunk 688 optimal weight: 10.0000 chunk 193 optimal weight: 8.9990 overall best weight: 3.6022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN H 71 GLN ** I 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 GLN K 79 HIS M 74 ASN ** M 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 153 GLN O 187 GLN ** Q 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 59 ASN d 149 HIS ** l 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 170 GLN ** o 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 124 ASN s 194 ASN ** v 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 68585 Z= 0.374 Angle : 0.618 12.396 92736 Z= 0.311 Chirality : 0.045 0.196 10041 Planarity : 0.005 0.069 11573 Dihedral : 14.029 177.954 10452 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.67 % Favored : 95.27 % Rotamer: Outliers : 2.14 % Allowed : 11.69 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.85 % 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: 0.63 (0.09), residues: 8027 helix: 1.31 (0.08), residues: 4273 sheet: -0.08 (0.26), residues: 399 loop : -0.63 (0.11), residues: 3355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP u 86 HIS 0.012 0.001 HIS Y 83 PHE 0.033 0.002 PHE i 292 TYR 0.027 0.002 TYR b 88 ARG 0.006 0.000 ARG K 109 *********************** 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 1323 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 1172 time to evaluate : 5.920 Fit side-chains revert: symmetry clash REVERT: A 119 GLU cc_start: 0.7572 (tp30) cc_final: 0.7363 (tp30) REVERT: G 115 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7693 (tm130) REVERT: H 70 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6641 (mp0) REVERT: L 69 GLU cc_start: 0.7776 (tt0) cc_final: 0.7545 (tt0) REVERT: M 158 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8095 (ptt90) REVERT: M 188 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7649 (mt-10) REVERT: M 671 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8704 (mt) REVERT: N 7 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7687 (mm) REVERT: N 8 ARG cc_start: 0.7095 (mtm-85) cc_final: 0.6893 (mtp85) REVERT: N 67 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7471 (tm-30) REVERT: V 35 ILE cc_start: 0.8646 (mt) cc_final: 0.8393 (mt) REVERT: W 105 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7959 (ttmm) REVERT: X 92 LYS cc_start: 0.8460 (ttmt) cc_final: 0.8184 (mttt) REVERT: Z 72 LYS cc_start: 0.7993 (mptt) cc_final: 0.7462 (mppt) REVERT: b 25 ASP cc_start: 0.8646 (m-30) cc_final: 0.8360 (m-30) REVERT: d 85 MET cc_start: 0.8666 (mtp) cc_final: 0.8380 (mtp) REVERT: d 164 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8121 (mp) REVERT: e 83 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.7730 (t70) REVERT: e 134 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.7002 (mt) REVERT: k 14 ILE cc_start: 0.8619 (mt) cc_final: 0.8118 (mt) REVERT: l 486 MET cc_start: 0.8072 (ttm) cc_final: 0.7857 (ttm) REVERT: o 121 LEU cc_start: 0.7293 (tp) cc_final: 0.6948 (tp) REVERT: o 123 GLN cc_start: 0.7646 (mt0) cc_final: 0.7369 (mp10) REVERT: p 55 LYS cc_start: 0.7340 (mmtt) cc_final: 0.6788 (tttt) REVERT: s 134 ARG cc_start: 0.8764 (mtp85) cc_final: 0.8366 (mtp85) REVERT: s 277 TYR cc_start: 0.8985 (m-80) cc_final: 0.8760 (m-10) REVERT: s 286 MET cc_start: 0.8904 (mmm) cc_final: 0.8682 (mmp) REVERT: w 160 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.6987 (mp0) outliers start: 151 outliers final: 112 residues processed: 1254 average time/residue: 0.6864 time to fit residues: 1459.2397 Evaluate side-chains 1268 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 1146 time to evaluate : 5.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 70 GLU Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 144 SER Chi-restraints excluded: chain M residue 158 ARG Chi-restraints excluded: chain M residue 204 MET Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 338 VAL Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 398 ASP Chi-restraints excluded: chain M residue 509 ASP Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 671 LEU Chi-restraints excluded: chain M residue 689 LEU Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 68 MET Chi-restraints excluded: chain O residue 50 ASP Chi-restraints excluded: chain O residue 51 THR Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain P residue 109 LYS Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain Q residue 145 MET Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain T residue 59 GLN Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 75 CYS Chi-restraints excluded: chain V residue 121 THR Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 105 LYS Chi-restraints excluded: chain W residue 129 THR Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 29 SER Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain e residue 134 LEU Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain j residue 8 LEU Chi-restraints excluded: chain j residue 82 ASN Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain l residue 62 ILE Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 197 ASP Chi-restraints excluded: chain l residue 293 ILE Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 374 ILE Chi-restraints excluded: chain l residue 401 MET Chi-restraints excluded: chain l residue 417 SER Chi-restraints excluded: chain l residue 476 THR Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 132 ASP Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 15 ILE Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain p residue 57 MET Chi-restraints excluded: chain p residue 114 MET Chi-restraints excluded: chain p residue 151 THR Chi-restraints excluded: chain p residue 171 VAL Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 123 GLU Chi-restraints excluded: chain r residue 129 THR Chi-restraints excluded: chain r residue 187 SER Chi-restraints excluded: chain r residue 343 ILE Chi-restraints excluded: chain r residue 375 LEU Chi-restraints excluded: chain r residue 400 MET Chi-restraints excluded: chain s residue 111 LEU Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 199 ASP Chi-restraints excluded: chain s residue 201 THR Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain u residue 22 SER Chi-restraints excluded: chain v residue 31 PHE Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 63 ASP Chi-restraints excluded: chain w residue 66 ILE Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 160 GLU Chi-restraints excluded: chain w residue 163 ILE Chi-restraints excluded: chain w residue 204 VAL Chi-restraints excluded: chain w residue 332 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 257 optimal weight: 5.9990 chunk 690 optimal weight: 4.9990 chunk 151 optimal weight: 10.0000 chunk 450 optimal weight: 10.0000 chunk 189 optimal weight: 1.9990 chunk 767 optimal weight: 1.9990 chunk 636 optimal weight: 9.9990 chunk 355 optimal weight: 6.9990 chunk 63 optimal weight: 0.6980 chunk 253 optimal weight: 0.9980 chunk 402 optimal weight: 8.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 GLN F 62 GLN H 71 GLN ** I 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 278 GLN K 79 HIS L 86 ASN M 74 ASN ** M 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 153 GLN O 187 GLN ** Q 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 44 GLN ** V 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 21 GLN Z 59 ASN l 170 GLN ** o 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 304 GLN s 124 ASN s 194 ASN ** v 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 142 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 68585 Z= 0.246 Angle : 0.557 10.781 92736 Z= 0.281 Chirality : 0.042 0.180 10041 Planarity : 0.005 0.069 11573 Dihedral : 13.650 179.264 10452 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.36 % Favored : 95.58 % Rotamer: Outliers : 1.97 % Allowed : 12.56 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.09), residues: 8027 helix: 1.42 (0.08), residues: 4264 sheet: -0.02 (0.26), residues: 399 loop : -0.58 (0.11), residues: 3364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP u 86 HIS 0.014 0.001 HIS Y 83 PHE 0.030 0.001 PHE i 292 TYR 0.025 0.001 TYR b 88 ARG 0.008 0.000 ARG K 109 *********************** 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 1331 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 1192 time to evaluate : 5.819 Fit side-chains revert: symmetry clash REVERT: G 115 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7647 (tm130) REVERT: H 70 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6574 (mp0) REVERT: H 83 GLN cc_start: 0.7889 (tp40) cc_final: 0.7372 (tp-100) REVERT: I 30 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8196 (pm20) REVERT: L 69 GLU cc_start: 0.7806 (tt0) cc_final: 0.7570 (tt0) REVERT: M 188 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7648 (mt-10) REVERT: M 671 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8679 (mt) REVERT: N 7 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7749 (mm) REVERT: N 67 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7488 (tm-30) REVERT: O 80 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9104 (mp) REVERT: V 35 ILE cc_start: 0.8598 (mt) cc_final: 0.8356 (mt) REVERT: V 118 MET cc_start: 0.8079 (mtt) cc_final: 0.7761 (mtp) REVERT: W 98 MET cc_start: 0.8400 (mmm) cc_final: 0.7832 (mmm) REVERT: W 105 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7935 (ttmm) REVERT: X 92 LYS cc_start: 0.8468 (ttmt) cc_final: 0.8180 (mttt) REVERT: Z 72 LYS cc_start: 0.8023 (mptt) cc_final: 0.7478 (mppt) REVERT: b 25 ASP cc_start: 0.8615 (m-30) cc_final: 0.8268 (m-30) REVERT: d 164 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8196 (mp) REVERT: e 83 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7598 (t70) REVERT: h 102 GLU cc_start: 0.7593 (pm20) cc_final: 0.7350 (pm20) REVERT: k 14 ILE cc_start: 0.8620 (mt) cc_final: 0.8174 (mt) REVERT: l 486 MET cc_start: 0.8067 (ttm) cc_final: 0.7843 (ttm) REVERT: o 121 LEU cc_start: 0.7354 (tp) cc_final: 0.7052 (tp) REVERT: o 123 GLN cc_start: 0.7612 (mt0) cc_final: 0.7339 (mp10) REVERT: p 55 LYS cc_start: 0.7241 (mmtt) cc_final: 0.6653 (tttm) REVERT: p 115 TYR cc_start: 0.8608 (m-80) cc_final: 0.8020 (m-80) REVERT: s 134 ARG cc_start: 0.8738 (mtp85) cc_final: 0.8348 (mtp85) REVERT: s 142 TYR cc_start: 0.9057 (m-80) cc_final: 0.8717 (m-80) REVERT: s 183 MET cc_start: 0.7811 (mtp) cc_final: 0.7450 (mtm) REVERT: s 277 TYR cc_start: 0.8911 (m-80) cc_final: 0.8680 (m-10) REVERT: w 160 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.6907 (mp0) outliers start: 139 outliers final: 103 residues processed: 1273 average time/residue: 0.6817 time to fit residues: 1472.1768 Evaluate side-chains 1282 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1169 time to evaluate : 5.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 351 THR 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 71 CYS Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 70 GLU Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 30 GLU Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 144 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 204 MET Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 338 VAL Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 398 ASP Chi-restraints excluded: chain M residue 509 ASP Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 671 LEU Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 68 MET Chi-restraints excluded: chain O residue 51 THR Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain P residue 109 LYS Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain Q residue 145 MET Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 46 ASP Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain T residue 59 GLN Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 75 CYS Chi-restraints excluded: chain V residue 121 THR Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 105 LYS Chi-restraints excluded: chain W residue 129 THR Chi-restraints excluded: chain X residue 155 TYR Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain Z residue 21 GLN Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain b residue 29 SER Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain j residue 8 LEU Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 293 ILE Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 401 MET Chi-restraints excluded: chain l residue 476 THR Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain p residue 57 MET Chi-restraints excluded: chain p residue 151 THR Chi-restraints excluded: chain p residue 171 VAL Chi-restraints excluded: chain r residue 375 LEU Chi-restraints excluded: chain s residue 59 GLU Chi-restraints excluded: chain s residue 111 LEU Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 199 ASP Chi-restraints excluded: chain s residue 201 THR Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain u residue 22 SER Chi-restraints excluded: chain v residue 31 PHE Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 63 ASP Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 160 GLU Chi-restraints excluded: chain w residue 163 ILE Chi-restraints excluded: chain w residue 204 VAL Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 332 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 739 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 437 optimal weight: 7.9990 chunk 560 optimal weight: 0.9990 chunk 434 optimal weight: 3.9990 chunk 645 optimal weight: 0.1980 chunk 428 optimal weight: 0.5980 chunk 764 optimal weight: 6.9990 chunk 478 optimal weight: 7.9990 chunk 465 optimal weight: 0.9980 chunk 352 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 GLN ** I 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 HIS ** M 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 153 GLN O 187 GLN ** P 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 59 ASN l 170 GLN ** o 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 124 ASN s 194 ASN ** v 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 68585 Z= 0.190 Angle : 0.534 10.612 92736 Z= 0.270 Chirality : 0.041 0.175 10041 Planarity : 0.005 0.066 11573 Dihedral : 13.311 179.963 10452 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.34 % Favored : 95.60 % Rotamer: Outliers : 1.88 % Allowed : 13.05 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.10), residues: 8027 helix: 1.53 (0.08), residues: 4264 sheet: 0.03 (0.25), residues: 403 loop : -0.53 (0.11), residues: 3360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP u 86 HIS 0.013 0.001 HIS Y 83 PHE 0.030 0.001 PHE i 292 TYR 0.031 0.001 TYR b 88 ARG 0.007 0.000 ARG K 109 *********************** 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 1336 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 1203 time to evaluate : 5.808 Fit side-chains revert: symmetry clash REVERT: G 115 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7600 (tm130) REVERT: H 70 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6580 (mp0) REVERT: H 83 GLN cc_start: 0.7886 (tp40) cc_final: 0.7411 (tp-100) REVERT: I 30 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8217 (pm20) REVERT: L 69 GLU cc_start: 0.7817 (tt0) cc_final: 0.7573 (tt0) REVERT: M 173 MET cc_start: 0.9270 (mmm) cc_final: 0.9009 (mmm) REVERT: M 188 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7611 (mt-10) REVERT: M 671 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8728 (mt) REVERT: N 7 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7526 (mm) REVERT: N 67 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7468 (tm-30) REVERT: O 80 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9124 (mp) REVERT: S 44 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8702 (pm20) REVERT: V 35 ILE cc_start: 0.8581 (mt) cc_final: 0.8336 (mt) REVERT: V 118 MET cc_start: 0.8128 (mtt) cc_final: 0.7813 (mtp) REVERT: W 98 MET cc_start: 0.8373 (mmm) cc_final: 0.7844 (mmm) REVERT: W 105 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7918 (ttmm) REVERT: X 92 LYS cc_start: 0.8452 (ttmt) cc_final: 0.8175 (mttt) REVERT: X 139 MET cc_start: 0.8101 (mmt) cc_final: 0.7887 (mmp) REVERT: Z 72 LYS cc_start: 0.8007 (mptt) cc_final: 0.7463 (mppt) REVERT: b 25 ASP cc_start: 0.8584 (m-30) cc_final: 0.8253 (m-30) REVERT: c 161 TYR cc_start: 0.8442 (m-80) cc_final: 0.7852 (m-80) REVERT: e 83 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7556 (t70) REVERT: h 102 GLU cc_start: 0.7570 (pm20) cc_final: 0.7285 (pm20) REVERT: i 157 MET cc_start: 0.8601 (mtm) cc_final: 0.8338 (mtt) REVERT: i 334 THR cc_start: 0.9067 (m) cc_final: 0.8809 (m) REVERT: k 14 ILE cc_start: 0.8611 (mt) cc_final: 0.8132 (mt) REVERT: l 486 MET cc_start: 0.8026 (ttm) cc_final: 0.7820 (ttm) REVERT: o 121 LEU cc_start: 0.7399 (tp) cc_final: 0.7183 (tp) REVERT: p 115 TYR cc_start: 0.8576 (m-80) cc_final: 0.8038 (m-80) REVERT: s 142 TYR cc_start: 0.9036 (m-80) cc_final: 0.8680 (m-80) REVERT: s 277 TYR cc_start: 0.8872 (m-80) cc_final: 0.8642 (m-10) REVERT: w 160 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.6913 (mp0) outliers start: 133 outliers final: 102 residues processed: 1280 average time/residue: 0.6504 time to fit residues: 1410.0353 Evaluate side-chains 1288 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1176 time to evaluate : 5.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 351 THR 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 71 CYS Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 26 ARG Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 70 GLU Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 30 GLU Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 144 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 204 MET Chi-restraints excluded: chain M residue 338 VAL Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 398 ASP Chi-restraints excluded: chain M residue 509 ASP Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 671 LEU Chi-restraints excluded: chain M residue 689 LEU Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 68 MET Chi-restraints excluded: chain O residue 51 THR Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain P residue 109 LYS Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain Q residue 145 MET Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain T residue 46 ASP Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain T residue 59 GLN Chi-restraints excluded: chain V residue 75 CYS Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain V residue 121 THR Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 105 LYS Chi-restraints excluded: chain W residue 129 THR Chi-restraints excluded: chain X residue 155 TYR Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 29 SER Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain j residue 8 LEU Chi-restraints excluded: chain j residue 82 ASN Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 293 ILE Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 401 MET Chi-restraints excluded: chain l residue 476 THR Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain p residue 57 MET Chi-restraints excluded: chain p residue 114 MET Chi-restraints excluded: chain p residue 151 THR Chi-restraints excluded: chain p residue 171 VAL Chi-restraints excluded: chain r residue 129 THR Chi-restraints excluded: chain r residue 187 SER Chi-restraints excluded: chain r residue 375 LEU Chi-restraints excluded: chain s residue 59 GLU Chi-restraints excluded: chain s residue 111 LEU Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 199 ASP Chi-restraints excluded: chain s residue 201 THR Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain u residue 22 SER Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 63 ASP Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 160 GLU Chi-restraints excluded: chain w residue 163 ILE Chi-restraints excluded: chain w residue 204 VAL Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 332 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 472 optimal weight: 0.0980 chunk 305 optimal weight: 1.9990 chunk 456 optimal weight: 5.9990 chunk 230 optimal weight: 8.9990 chunk 150 optimal weight: 4.9990 chunk 148 optimal weight: 9.9990 chunk 485 optimal weight: 8.9990 chunk 520 optimal weight: 6.9990 chunk 377 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 600 optimal weight: 6.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 GLN ** I 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 HIS L 86 ASN ** M 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 153 GLN O 187 GLN ** P 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 147 ASN ** Q 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 44 GLN ** V 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 59 ASN l 170 GLN s 124 ASN s 194 ASN ** v 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 68585 Z= 0.305 Angle : 0.585 11.105 92736 Z= 0.295 Chirality : 0.043 0.188 10041 Planarity : 0.005 0.068 11573 Dihedral : 13.282 178.919 10452 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.51 % Favored : 95.43 % Rotamer: Outliers : 2.10 % Allowed : 13.38 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.09), residues: 8027 helix: 1.42 (0.08), residues: 4260 sheet: -0.01 (0.26), residues: 397 loop : -0.59 (0.11), residues: 3370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP u 86 HIS 0.013 0.001 HIS Y 83 PHE 0.032 0.002 PHE i 292 TYR 0.045 0.002 TYR b 88 ARG 0.008 0.000 ARG K 109 *********************** 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 1320 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1172 time to evaluate : 5.895 Fit side-chains revert: symmetry clash REVERT: G 115 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7584 (tm130) REVERT: H 70 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.6633 (mp0) REVERT: I 30 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8254 (pm20) REVERT: L 69 GLU cc_start: 0.7780 (tt0) cc_final: 0.7554 (tt0) REVERT: M 158 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8077 (ptt90) REVERT: M 188 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7647 (mt-10) REVERT: M 671 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8711 (mt) REVERT: N 7 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7454 (mm) REVERT: N 67 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7421 (tm-30) REVERT: O 80 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9091 (mp) REVERT: V 35 ILE cc_start: 0.8608 (mt) cc_final: 0.8362 (mt) REVERT: V 118 MET cc_start: 0.8053 (mtt) cc_final: 0.7732 (mtp) REVERT: X 92 LYS cc_start: 0.8478 (ttmt) cc_final: 0.8209 (mttt) REVERT: X 139 MET cc_start: 0.8123 (mmt) cc_final: 0.7902 (mmp) REVERT: Z 72 LYS cc_start: 0.8028 (mptt) cc_final: 0.7485 (mppt) REVERT: b 25 ASP cc_start: 0.8616 (m-30) cc_final: 0.8252 (m-30) REVERT: d 64 TYR cc_start: 0.8705 (m-80) cc_final: 0.8394 (m-80) REVERT: e 83 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.7655 (t70) REVERT: h 102 GLU cc_start: 0.7581 (pm20) cc_final: 0.7271 (pm20) REVERT: i 157 MET cc_start: 0.8591 (mtm) cc_final: 0.8320 (mtt) REVERT: j 22 PHE cc_start: 0.8042 (t80) cc_final: 0.7816 (t80) REVERT: k 14 ILE cc_start: 0.8558 (mt) cc_final: 0.8089 (mt) REVERT: l 486 MET cc_start: 0.8006 (ttm) cc_final: 0.7777 (ttm) REVERT: o 123 GLN cc_start: 0.7994 (mt0) cc_final: 0.7600 (mp10) REVERT: p 55 LYS cc_start: 0.7367 (mmtt) cc_final: 0.6754 (tttt) REVERT: p 59 LYS cc_start: 0.7570 (tmmt) cc_final: 0.7293 (tttp) REVERT: p 115 TYR cc_start: 0.8606 (m-80) cc_final: 0.8101 (m-80) REVERT: s 134 ARG cc_start: 0.8729 (mtp85) cc_final: 0.8363 (mtp85) REVERT: s 142 TYR cc_start: 0.9078 (m-80) cc_final: 0.8735 (m-80) REVERT: s 277 TYR cc_start: 0.8935 (m-80) cc_final: 0.8732 (m-10) REVERT: w 160 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7004 (mp0) outliers start: 148 outliers final: 123 residues processed: 1257 average time/residue: 0.6754 time to fit residues: 1433.4398 Evaluate side-chains 1289 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 1157 time to evaluate : 5.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 351 THR 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 71 CYS Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 70 GLU Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 30 GLU Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 144 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 158 ARG Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 204 MET Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 338 VAL Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 398 ASP Chi-restraints excluded: chain M residue 509 ASP Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 671 LEU Chi-restraints excluded: chain M residue 689 LEU Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 39 VAL Chi-restraints excluded: chain N residue 68 MET Chi-restraints excluded: chain O residue 50 ASP Chi-restraints excluded: chain O residue 51 THR Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain P residue 109 LYS Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain Q residue 145 MET Chi-restraints excluded: chain Q residue 147 ASN Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 312 ASP Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain T residue 59 GLN Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 75 CYS Chi-restraints excluded: chain V residue 121 THR Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 129 THR Chi-restraints excluded: chain X residue 155 TYR Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 29 SER Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain j residue 8 LEU Chi-restraints excluded: chain j residue 82 ASN Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 293 ILE Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 401 MET Chi-restraints excluded: chain l residue 476 THR Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain p residue 57 MET Chi-restraints excluded: chain p residue 114 MET Chi-restraints excluded: chain p residue 151 THR Chi-restraints excluded: chain p residue 171 VAL Chi-restraints excluded: chain r residue 88 THR Chi-restraints excluded: chain r residue 123 GLU Chi-restraints excluded: chain r residue 129 THR Chi-restraints excluded: chain r residue 187 SER Chi-restraints excluded: chain r residue 375 LEU Chi-restraints excluded: chain r residue 400 MET Chi-restraints excluded: chain s residue 59 GLU Chi-restraints excluded: chain s residue 73 ILE Chi-restraints excluded: chain s residue 111 LEU Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 199 ASP Chi-restraints excluded: chain s residue 201 THR Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain u residue 22 SER Chi-restraints excluded: chain v residue 31 PHE Chi-restraints excluded: chain v residue 52 MET Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 63 ASP Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 160 GLU Chi-restraints excluded: chain w residue 163 ILE Chi-restraints excluded: chain w residue 204 VAL Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 332 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 695 optimal weight: 4.9990 chunk 732 optimal weight: 8.9990 chunk 668 optimal weight: 2.9990 chunk 712 optimal weight: 0.9990 chunk 428 optimal weight: 0.9990 chunk 310 optimal weight: 1.9990 chunk 559 optimal weight: 3.9990 chunk 218 optimal weight: 0.8980 chunk 643 optimal weight: 8.9990 chunk 673 optimal weight: 0.8980 chunk 709 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN H 71 GLN ** I 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 278 GLN K 79 HIS L 86 ASN ** M 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 153 GLN O 187 GLN ** P 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 124 ASN ** Q 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 59 ASN l 170 GLN s 124 ASN s 194 ASN ** v 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 68585 Z= 0.167 Angle : 0.529 10.587 92736 Z= 0.267 Chirality : 0.040 0.173 10041 Planarity : 0.004 0.067 11573 Dihedral : 12.844 179.338 10452 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.04 % Favored : 95.91 % Rotamer: Outliers : 1.60 % Allowed : 14.00 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.85 % 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 (0.10), residues: 8027 helix: 1.60 (0.08), residues: 4264 sheet: 0.01 (0.25), residues: 412 loop : -0.47 (0.11), residues: 3351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.013 0.001 HIS Y 83 PHE 0.030 0.001 PHE F 36 TYR 0.037 0.001 TYR b 88 ARG 0.008 0.000 ARG K 109 *********************** 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 1313 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1200 time to evaluate : 5.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 85 TYR cc_start: 0.5399 (t80) cc_final: 0.4943 (t80) REVERT: G 88 LYS cc_start: 0.6476 (pptt) cc_final: 0.6091 (pptt) REVERT: G 115 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7658 (tm130) REVERT: H 70 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6616 (mp0) REVERT: H 82 LEU cc_start: 0.8905 (tp) cc_final: 0.8688 (tp) REVERT: J 327 MET cc_start: 0.7431 (ptp) cc_final: 0.7212 (ptp) REVERT: L 69 GLU cc_start: 0.7813 (tt0) cc_final: 0.7565 (tt0) REVERT: M 173 MET cc_start: 0.9257 (mmm) cc_final: 0.9027 (mmm) REVERT: M 188 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7584 (mt-10) REVERT: M 671 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8678 (mt) REVERT: N 7 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7371 (mm) REVERT: N 67 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7378 (tm-30) REVERT: W 98 MET cc_start: 0.8343 (mmm) cc_final: 0.7884 (mmm) REVERT: X 92 LYS cc_start: 0.8438 (ttmt) cc_final: 0.8171 (mttt) REVERT: X 139 MET cc_start: 0.8108 (mmt) cc_final: 0.7794 (mmp) REVERT: Z 72 LYS cc_start: 0.8021 (mptt) cc_final: 0.7458 (mppt) REVERT: b 25 ASP cc_start: 0.8549 (m-30) cc_final: 0.8199 (m-30) REVERT: c 160 GLN cc_start: 0.8217 (mt0) cc_final: 0.7873 (mt0) REVERT: c 161 TYR cc_start: 0.8384 (m-80) cc_final: 0.7793 (m-80) REVERT: d 64 TYR cc_start: 0.8699 (m-80) cc_final: 0.8414 (m-80) REVERT: e 83 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7566 (t70) REVERT: i 157 MET cc_start: 0.8594 (mtm) cc_final: 0.8333 (mtt) REVERT: i 334 THR cc_start: 0.9045 (m) cc_final: 0.8793 (m) REVERT: j 22 PHE cc_start: 0.8027 (t80) cc_final: 0.7823 (t80) REVERT: k 14 ILE cc_start: 0.8606 (mt) cc_final: 0.8142 (mt) REVERT: k 82 SER cc_start: 0.8850 (m) cc_final: 0.8639 (m) REVERT: l 486 MET cc_start: 0.7997 (ttm) cc_final: 0.7766 (ttm) REVERT: o 123 GLN cc_start: 0.7909 (mt0) cc_final: 0.7544 (mp10) REVERT: p 59 LYS cc_start: 0.7563 (tmmt) cc_final: 0.7294 (tttp) REVERT: p 115 TYR cc_start: 0.8546 (m-80) cc_final: 0.8037 (m-80) REVERT: s 142 TYR cc_start: 0.9038 (m-80) cc_final: 0.8693 (m-80) REVERT: w 160 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.6854 (mp0) outliers start: 113 outliers final: 88 residues processed: 1270 average time/residue: 0.6778 time to fit residues: 1454.6842 Evaluate side-chains 1273 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 1179 time to evaluate : 5.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 70 GLU Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 338 VAL Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 398 ASP Chi-restraints excluded: chain M residue 509 ASP Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 671 LEU Chi-restraints excluded: chain M residue 689 LEU Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 39 VAL Chi-restraints excluded: chain N residue 68 MET Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain P residue 109 LYS Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 312 ASP Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain V residue 75 CYS Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 129 THR Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain X residue 155 TYR Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain b residue 29 SER Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain j residue 8 LEU Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 293 ILE Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain m residue 20 PHE Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain p residue 57 MET Chi-restraints excluded: chain p residue 151 THR Chi-restraints excluded: chain p residue 171 VAL Chi-restraints excluded: chain r residue 187 SER Chi-restraints excluded: chain r residue 375 LEU Chi-restraints excluded: chain s residue 59 GLU Chi-restraints excluded: chain s residue 73 ILE Chi-restraints excluded: chain s residue 113 VAL Chi-restraints excluded: chain s residue 144 VAL Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 199 ASP Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain u residue 22 SER Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 63 ASP Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 160 GLU Chi-restraints excluded: chain w residue 163 ILE Chi-restraints excluded: chain w residue 204 VAL Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 332 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 467 optimal weight: 0.9990 chunk 753 optimal weight: 9.9990 chunk 459 optimal weight: 5.9990 chunk 357 optimal weight: 1.9990 chunk 523 optimal weight: 1.9990 chunk 790 optimal weight: 6.9990 chunk 727 optimal weight: 5.9990 chunk 629 optimal weight: 0.0040 chunk 65 optimal weight: 0.0970 chunk 485 optimal weight: 9.9990 chunk 385 optimal weight: 9.9990 overall best weight: 1.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 GLN ** I 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 278 GLN K 79 HIS L 86 ASN M 74 ASN ** M 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 153 GLN O 187 GLN ** P 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 147 ASN ** Q 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 44 GLN ** V 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 21 GLN Z 33 GLN Z 59 ASN l 170 GLN l 580 GLN s 124 ASN s 194 ASN ** v 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 124 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 68585 Z= 0.170 Angle : 0.530 11.662 92736 Z= 0.266 Chirality : 0.040 0.404 10041 Planarity : 0.004 0.064 11573 Dihedral : 12.544 178.787 10452 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.11 % Favored : 95.84 % Rotamer: Outliers : 1.49 % Allowed : 14.34 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.85 % 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 (0.10), residues: 8027 helix: 1.66 (0.08), residues: 4268 sheet: 0.02 (0.25), residues: 413 loop : -0.42 (0.11), residues: 3346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.014 0.001 HIS Y 83 PHE 0.030 0.001 PHE i 292 TYR 0.034 0.001 TYR b 88 ARG 0.008 0.000 ARG K 109 ********************** 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 1319 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1214 time to evaluate : 5.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.8672 (tpt) cc_final: 0.8335 (tpt) REVERT: G 85 TYR cc_start: 0.5438 (t80) cc_final: 0.5008 (t80) REVERT: G 88 LYS cc_start: 0.6401 (pptt) cc_final: 0.6084 (pptt) REVERT: G 115 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7625 (tm130) REVERT: H 70 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.6565 (mp0) REVERT: J 327 MET cc_start: 0.7418 (ptp) cc_final: 0.7205 (ptp) REVERT: L 69 GLU cc_start: 0.7808 (tt0) cc_final: 0.7562 (tt0) REVERT: M 188 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7567 (mt-10) REVERT: N 7 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7253 (mm) REVERT: W 98 MET cc_start: 0.8350 (mmm) cc_final: 0.7897 (mmm) REVERT: X 92 LYS cc_start: 0.8421 (ttmt) cc_final: 0.8176 (mttt) REVERT: X 139 MET cc_start: 0.8080 (mmt) cc_final: 0.7758 (mmp) REVERT: Z 72 LYS cc_start: 0.7920 (mptt) cc_final: 0.7415 (mppt) REVERT: b 25 ASP cc_start: 0.8551 (m-30) cc_final: 0.8177 (m-30) REVERT: c 160 GLN cc_start: 0.8198 (mt0) cc_final: 0.7845 (mt0) REVERT: c 161 TYR cc_start: 0.8349 (m-80) cc_final: 0.7754 (m-80) REVERT: d 64 TYR cc_start: 0.8687 (m-80) cc_final: 0.8431 (m-80) REVERT: e 83 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7591 (t70) REVERT: i 89 MET cc_start: 0.8680 (tpt) cc_final: 0.8042 (tpt) REVERT: i 157 MET cc_start: 0.8577 (mtm) cc_final: 0.8321 (mtt) REVERT: i 334 THR cc_start: 0.9028 (m) cc_final: 0.8768 (m) REVERT: j 22 PHE cc_start: 0.8052 (t80) cc_final: 0.7844 (t80) REVERT: k 14 ILE cc_start: 0.8583 (mt) cc_final: 0.8108 (mt) REVERT: l 486 MET cc_start: 0.7987 (ttm) cc_final: 0.7747 (ttm) REVERT: n 28 ASP cc_start: 0.7687 (m-30) cc_final: 0.7464 (m-30) REVERT: o 123 GLN cc_start: 0.7940 (mt0) cc_final: 0.7561 (mp10) REVERT: p 59 LYS cc_start: 0.7567 (tmmt) cc_final: 0.7301 (tttp) REVERT: p 115 TYR cc_start: 0.8542 (m-80) cc_final: 0.8021 (m-80) REVERT: w 160 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.6844 (mp0) outliers start: 105 outliers final: 91 residues processed: 1284 average time/residue: 0.6772 time to fit residues: 1464.4624 Evaluate side-chains 1285 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 1189 time to evaluate : 5.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 70 GLU Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 338 VAL Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 398 ASP Chi-restraints excluded: chain M residue 509 ASP Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 689 LEU Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 39 VAL Chi-restraints excluded: chain N residue 68 MET Chi-restraints excluded: chain O residue 51 THR Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain P residue 109 LYS Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain Q residue 147 ASN Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 312 ASP Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain V residue 75 CYS Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 129 THR Chi-restraints excluded: chain X residue 155 TYR Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain Z residue 21 GLN Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain a residue 78 THR Chi-restraints excluded: chain b residue 29 SER Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain j residue 8 LEU Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 293 ILE Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain p residue 57 MET Chi-restraints excluded: chain p residue 151 THR Chi-restraints excluded: chain p residue 171 VAL Chi-restraints excluded: chain r residue 187 SER Chi-restraints excluded: chain r residue 375 LEU Chi-restraints excluded: chain s residue 59 GLU Chi-restraints excluded: chain s residue 73 ILE Chi-restraints excluded: chain s residue 111 LEU Chi-restraints excluded: chain s residue 113 VAL Chi-restraints excluded: chain s residue 144 VAL Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 199 ASP Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain u residue 22 SER Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 63 ASP Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 160 GLU Chi-restraints excluded: chain w residue 163 ILE Chi-restraints excluded: chain w residue 204 VAL Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 332 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 499 optimal weight: 3.9990 chunk 670 optimal weight: 5.9990 chunk 192 optimal weight: 0.1980 chunk 580 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 174 optimal weight: 6.9990 chunk 630 optimal weight: 7.9990 chunk 263 optimal weight: 2.9990 chunk 647 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 116 optimal weight: 0.0060 overall best weight: 1.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 GLN ** I 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 HIS ** M 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 153 GLN O 187 GLN ** P 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 44 GLN ** V 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 21 GLN s 124 ASN s 194 ASN ** v 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.122447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.097624 restraints weight = 96678.418| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.50 r_work: 0.2859 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.119 68585 Z= 0.196 Angle : 0.541 11.972 92736 Z= 0.271 Chirality : 0.041 0.310 10041 Planarity : 0.004 0.066 11573 Dihedral : 12.445 178.917 10452 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.14 % Favored : 95.81 % Rotamer: Outliers : 1.59 % Allowed : 14.27 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.85 % 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 (0.10), residues: 8027 helix: 1.67 (0.08), residues: 4262 sheet: 0.03 (0.25), residues: 413 loop : -0.43 (0.11), residues: 3352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP u 86 HIS 0.013 0.001 HIS Y 83 PHE 0.031 0.001 PHE i 292 TYR 0.033 0.001 TYR b 88 ARG 0.008 0.000 ARG J 221 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21080.01 seconds wall clock time: 368 minutes 26.19 seconds (22106.19 seconds total)