Starting phenix.real_space_refine (version: 1.21rc1) on Fri Sep 1 00:56:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qgh_13955/08_2023/7qgh_13955.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qgh_13955/08_2023/7qgh_13955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qgh_13955/08_2023/7qgh_13955.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qgh_13955/08_2023/7qgh_13955.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qgh_13955/08_2023/7qgh_13955.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qgh_13955/08_2023/7qgh_13955.pdb" } resolution = 4.48 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= -0.008 sd= 0.144 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: 7 Type Number sf(0) Gaussians K 1 8.98 5 P 4717 5.49 5 Mg 2 5.21 5 S 152 5.16 5 C 74424 2.51 5 N 27554 2.21 5 O 41123 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P ARG 52": "NH1" <-> "NH2" Residue "P ARG 63": "NH1" <-> "NH2" Residue "P ARG 80": "NH1" <-> "NH2" Residue "P ARG 133": "NH1" <-> "NH2" Residue "P ARG 167": "NH1" <-> "NH2" Residue "P ARG 177": "NH1" <-> "NH2" Residue "P ARG 182": "NH1" <-> "NH2" Residue "P ARG 189": "NH1" <-> "NH2" Residue "P ARG 203": "NH1" <-> "NH2" Residue "P ARG 212": "NH1" <-> "NH2" Residue "Q ARG 13": "NH1" <-> "NH2" Residue "Q ARG 33": "NH1" <-> "NH2" Residue "Q ARG 59": "NH1" <-> "NH2" Residue "Q ARG 77": "NH1" <-> "NH2" Residue "Q ARG 83": "NH1" <-> "NH2" Residue "Q ARG 169": "NH1" <-> "NH2" Residue "Q ARG 184": "NH1" <-> "NH2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R ARG 44": "NH1" <-> "NH2" Residue "R ARG 49": "NH1" <-> "NH2" Residue "R ARG 88": "NH1" <-> "NH2" Residue "R ARG 102": "NH1" <-> "NH2" Residue "R ARG 162": "NH1" <-> "NH2" Residue "R ARG 170": "NH1" <-> "NH2" Residue "S ARG 71": "NH1" <-> "NH2" Residue "S ARG 80": "NH1" <-> "NH2" Residue "S ARG 92": "NH1" <-> "NH2" Residue "S ARG 102": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "S ARG 112": "NH1" <-> "NH2" Residue "S ARG 115": "NH1" <-> "NH2" Residue "S ARG 133": "NH1" <-> "NH2" Residue "T ARG 3": "NH1" <-> "NH2" Residue "T ARG 153": "NH1" <-> "NH2" Residue "T ARG 163": "NH1" <-> "NH2" Residue "T ARG 170": "NH1" <-> "NH2" Residue "V TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 13": "NH1" <-> "NH2" Residue "W ARG 37": "NH1" <-> "NH2" Residue "W TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 96": "NH1" <-> "NH2" Residue "W ARG 120": "NH1" <-> "NH2" Residue "Y ARG 21": "NH1" <-> "NH2" Residue "Y ARG 33": "NH1" <-> "NH2" Residue "Y ARG 41": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 60": "NH1" <-> "NH2" Residue "Y ARG 78": "NH1" <-> "NH2" Residue "Y ARG 126": "NH1" <-> "NH2" Residue "Z ARG 10": "NH1" <-> "NH2" Residue "Z ARG 18": "NH1" <-> "NH2" Residue "Z ARG 40": "NH1" <-> "NH2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "Z ARG 50": "NH1" <-> "NH2" Residue "Z ARG 55": "NH1" <-> "NH2" Residue "Z ARG 59": "NH1" <-> "NH2" Residue "Z ARG 114": "NH1" <-> "NH2" Residue "Z PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 8": "NH1" <-> "NH2" Residue "a ARG 12": "NH1" <-> "NH2" Residue "a ARG 17": "NH1" <-> "NH2" Residue "a ARG 22": "NH1" <-> "NH2" Residue "a ARG 46": "NH1" <-> "NH2" Residue "a ARG 63": "NH1" <-> "NH2" Residue "a ARG 64": "NH1" <-> "NH2" Residue "a ARG 69": "NH1" <-> "NH2" Residue "a ARG 71": "NH1" <-> "NH2" Residue "a ARG 96": "NH1" <-> "NH2" Residue "a ARG 118": "NH1" <-> "NH2" Residue "b ARG 10": "NH1" <-> "NH2" Residue "b ARG 16": "NH1" <-> "NH2" Residue "b ARG 25": "NH1" <-> "NH2" Residue "b ARG 81": "NH1" <-> "NH2" Residue "b ARG 94": "NH1" <-> "NH2" Residue "b ARG 102": "NH1" <-> "NH2" Residue "b ARG 111": "NH1" <-> "NH2" Residue "c ARG 21": "NH1" <-> "NH2" Residue "c ARG 39": "NH1" <-> "NH2" Residue "c ARG 62": "NH1" <-> "NH2" Residue "c ARG 89": "NH1" <-> "NH2" Residue "c TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 101": "NH1" <-> "NH2" Residue "c ARG 109": "NH1" <-> "NH2" Residue "d ARG 3": "NH1" <-> "NH2" Residue "d ARG 6": "NH1" <-> "NH2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "d ARG 48": "NH1" <-> "NH2" Residue "d ARG 70": "NH1" <-> "NH2" Residue "e TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 21": "NH1" <-> "NH2" Residue "e ARG 68": "NH1" <-> "NH2" Residue "e ARG 78": "NH1" <-> "NH2" Residue "e ARG 79": "NH1" <-> "NH2" Residue "e ARG 84": "NH1" <-> "NH2" Residue "e PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 84": "NH1" <-> "NH2" Residue "f ARG 88": "NH1" <-> "NH2" Residue "f ARG 92": "NH1" <-> "NH2" Residue "f ARG 110": "NH1" <-> "NH2" Residue "g ARG 73": "NH1" <-> "NH2" Residue "h ARG 6": "NH1" <-> "NH2" Residue "h ARG 7": "NH1" <-> "NH2" Residue "h ARG 82": "NH1" <-> "NH2" Residue "h ARG 86": "NH1" <-> "NH2" Residue "h ARG 94": "NH1" <-> "NH2" Residue "j PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 3": "NH1" <-> "NH2" Residue "k ARG 11": "NH1" <-> "NH2" Residue "k ARG 18": "NH1" <-> "NH2" Residue "k ARG 37": "NH1" <-> "NH2" Residue "k ARG 50": "NH1" <-> "NH2" Residue "k ARG 57": "NH1" <-> "NH2" Residue "k ARG 74": "NH1" <-> "NH2" Residue "l ARG 29": "NH1" <-> "NH2" Residue "l ARG 47": "NH1" <-> "NH2" Residue "l ARG 52": "NH1" <-> "NH2" Residue "m ARG 11": "NH1" <-> "NH2" Residue "m ARG 30": "NH1" <-> "NH2" Residue "m ARG 45": "NH1" <-> "NH2" Residue "m PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 10": "NH1" <-> "NH2" Residue "n ARG 16": "NH1" <-> "NH2" Residue "n ARG 52": "NH1" <-> "NH2" Residue "o ARG 44": "NH1" <-> "NH2" Residue "p ARG 3": "NH1" <-> "NH2" Residue "p ARG 12": "NH1" <-> "NH2" Residue "p ARG 14": "NH1" <-> "NH2" Residue "p ARG 19": "NH1" <-> "NH2" Residue "p ARG 21": "NH1" <-> "NH2" Residue "p ARG 33": "NH1" <-> "NH2" Residue "p ARG 41": "NH1" <-> "NH2" Residue "q ARG 13": "NH1" <-> "NH2" Residue "q ARG 30": "NH1" <-> "NH2" Residue "q ARG 40": "NH1" <-> "NH2" Residue "q ARG 42": "NH1" <-> "NH2" Residue "r ARG 24": "NH1" <-> "NH2" Residue "L ARG 49": "NH1" <-> "NH2" Residue "C ARG 7": "NH1" <-> "NH2" Residue "C ARG 12": "NH1" <-> "NH2" Residue "C ARG 162": "NH1" <-> "NH2" Residue "U GLU 45": "OE1" <-> "OE2" Residue "U GLU 53": "OE1" <-> "OE2" Residue "U GLU 127": "OE1" <-> "OE2" Residue "2 PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 131": "NH1" <-> "NH2" Residue "8 PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 124": "NH1" <-> "NH2" Residue "B ARG 56": "NH1" <-> "NH2" Residue "G PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 28": "NH1" <-> "NH2" Residue "G PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 147973 Number of models: 1 Model: "" Number of chains: 58 Chain: "O" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2529 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 4, 'rna3p_pur': 62, 'rna3p_pyr': 50} Link IDs: {'rna2p': 6, 'rna3p': 111} Chain: "P" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "Q" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1564 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "R" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "S" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "T" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1322 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "V" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1031 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "W" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1128 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "X" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "Y" Number of atoms: 1044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1044 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "Z" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1073 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "a" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "b" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 891 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "c" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 915 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 946 Classifications: {'peptide': 117} Link IDs: {'TRANS': 116} Chain: "e" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 815 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "f" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "g" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "h" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "i" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 752 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "j" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 568 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} 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: "k" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 624 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "l" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 508 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "m" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 448 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "n" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 443 Classifications: {'peptide': 56} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 53} Chain: "o" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "p" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 376 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "q" Number of atoms: 503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 503 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "r" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 301 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "N" Number of atoms: 62215 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2897, 62195 Classifications: {'RNA': 2897} Modifications used: {'rna2p_pur': 213, 'rna2p_pyr': 118, 'rna3p_pur': 1459, 'rna3p_pyr': 1107} Link IDs: {'rna2p': 331, 'rna3p': 2565} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 2897, 62195 Classifications: {'RNA': 2897} Modifications used: {'rna2p_pur': 213, 'rna2p_pyr': 117, 'rna3p_pur': 1459, 'rna3p_pyr': 1108} Link IDs: {'rna2p': 330, 'rna3p': 2566} Chain breaks: 1 bond proxies already assigned to first conformer: 69636 Chain: "L" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 404 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "C" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1027 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 1 Chain: "U" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "M" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1594 Classifications: {'RNA': 75} Modifications used: {'p5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p_pur': 32, 'rna3p_pyr': 36} Link IDs: {'rna2p': 6, 'rna3p': 68} Chain: "x" Number of atoms: 294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 294 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 5, 'rna3p_pur': 3, 'rna3p_pyr': 3} Link IDs: {'rna2p': 8, 'rna3p': 5} Chain: "0" Number of atoms: 33015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33015 Classifications: {'RNA': 1539} Modifications used: {'rna2p_pur': 87, 'rna2p_pyr': 60, 'rna3p_pur': 787, 'rna3p_pyr': 605} Link IDs: {'rna2p': 147, 'rna3p': 1391} Chain: "1" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1704 Classifications: {'peptide': 218} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 208} Chain: "2" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "3" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1642 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "4" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1105 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "5" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 817 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "6" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "7" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 978 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "8" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1021 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "9" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "A" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 876 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "B" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 954 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "D" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "E" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 773 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Chain: "F" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 709 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 87} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 648 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "H" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "I" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 455 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "J" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "K" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 664 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "s" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "t" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 704 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 120} Link IDs: {'PTRANS': 3, 'TRANS': 139} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 412 Unresolved non-hydrogen angles: 526 Unresolved non-hydrogen dihedrals: 323 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 4, 'GLU:plan': 16, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 215 Chain: "u" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1573 Unusual residues: {' K': 1, ' MG': 2} Classifications: {'RNA': 73, 'undetermined': 3, 'water': 9} Modifications used: {'p5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 5, 'rna3p_pur': 29, 'rna3p_pyr': 30} Link IDs: {'rna2p': 13, 'rna3p': 59, None: 12} Not linked: pdbres=" A u 73 " pdbres=" MG u 101 " Not linked: pdbres=" MG u 101 " pdbres=" MG u 102 " Not linked: pdbres=" MG u 102 " pdbres=" K u 103 " Not linked: pdbres=" K u 103 " pdbres="HOH u 201 " Not linked: pdbres="HOH u 201 " pdbres="HOH u 202 " ... (remaining 7 not shown) Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" P A U N2506 " occ=0.50 ... (38 atoms not shown) pdb=" C6 B U N2506 " occ=0.50 residue: pdb=" N GLN t 52 " occ=0.58 ... (3 atoms not shown) pdb=" CB GLN t 52 " occ=0.58 residue: pdb=" O HOH u 203 " occ=0.00 Time building chain proxies: 73.37, per 1000 atoms: 0.50 Number of scatterers: 147973 At special positions: 0 Unit cell: (236.53, 250.7, 298.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 1 19.00 S 152 16.00 P 4717 15.00 Mg 2 11.99 O 41123 8.00 N 27554 7.00 C 74424 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS r 11 " - pdb=" SG CYS r 14 " distance=2.17 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 Atom "ATOM 93926 O4' G x 451 .*. O " rejected from bonding due to valence issues. Atom "ATOM 67697 O4' A N1876 .*. O " rejected from bonding due to valence issues. Atom "ATOM 93425 O4' C M 55 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 58.15 Conformation dependent library (CDL) restraints added in 5.6 seconds 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11110 Finding SS restraints... Secondary structure from input PDB file: 182 helices and 79 sheets defined 33.2% alpha, 18.2% beta 1619 base pairs and 2611 stacking pairs defined. Time for finding SS restraints: 60.76 Creating SS restraints... Processing helix chain 'P' and resid 30 through 32 No H-bonds generated for 'chain 'P' and resid 30 through 32' Processing helix chain 'P' and resid 197 through 203 removed outlier: 3.616A pdb=" N ARG P 203 " --> pdb=" O HIS P 200 " (cutoff:3.500A) Processing helix chain 'P' and resid 207 through 213 removed outlier: 3.998A pdb=" N ALA P 211 " --> pdb=" O LYS P 207 " (cutoff:3.500A) Processing helix chain 'P' and resid 221 through 225 Processing helix chain 'Q' and resid 61 through 72 Processing helix chain 'Q' and resid 97 through 102 Processing helix chain 'Q' and resid 120 through 125 Processing helix chain 'R' and resid 15 through 20 Processing helix chain 'R' and resid 24 through 39 Processing helix chain 'R' and resid 97 through 115 Processing helix chain 'R' and resid 130 through 141 Processing helix chain 'R' and resid 154 through 161 Processing helix chain 'R' and resid 176 through 183 removed outlier: 3.560A pdb=" N LEU R 180 " --> pdb=" O ASP R 176 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 200 Processing helix chain 'S' and resid 3 through 20 removed outlier: 5.074A pdb=" N VAL S 13 " --> pdb=" O LYS S 9 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 45 removed outlier: 3.763A pdb=" N ILE S 44 " --> pdb=" O GLY S 41 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA S 45 " --> pdb=" O GLU S 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 41 through 45' Processing helix chain 'S' and resid 47 through 61 Processing helix chain 'S' and resid 93 through 106 removed outlier: 3.643A pdb=" N TRP S 97 " --> pdb=" O GLY S 93 " (cutoff:3.500A) Processing helix chain 'S' and resid 142 through 146 removed outlier: 3.903A pdb=" N VAL S 146 " --> pdb=" O TYR S 143 " (cutoff:3.500A) Processing helix chain 'S' and resid 162 through 172 Processing helix chain 'T' and resid 60 through 81 Processing helix chain 'T' and resid 137 through 152 removed outlier: 4.303A pdb=" N ARG T 152 " --> pdb=" O LEU T 148 " (cutoff:3.500A) Processing helix chain 'V' and resid 24 through 29 Processing helix chain 'V' and resid 35 through 39 removed outlier: 3.677A pdb=" N PHE V 38 " --> pdb=" O ILE V 35 " (cutoff:3.500A) Processing helix chain 'V' and resid 40 through 45 Processing helix chain 'V' and resid 103 through 113 Processing helix chain 'V' and resid 125 through 136 removed outlier: 3.952A pdb=" N ILE V 129 " --> pdb=" O MET V 125 " (cutoff:3.500A) Processing helix chain 'W' and resid 24 through 38 Processing helix chain 'W' and resid 58 through 62 removed outlier: 3.747A pdb=" N VAL W 62 " --> pdb=" O ALA W 59 " (cutoff:3.500A) Processing helix chain 'W' and resid 67 through 72 removed outlier: 3.543A pdb=" N LYS W 72 " --> pdb=" O LYS W 68 " (cutoff:3.500A) Processing helix chain 'W' and resid 89 through 96 Processing helix chain 'W' and resid 97 through 109 Processing helix chain 'W' and resid 112 through 120 Processing helix chain 'X' and resid 104 through 108 removed outlier: 3.505A pdb=" N ARG X 108 " --> pdb=" O ARG X 105 " (cutoff:3.500A) Processing helix chain 'X' and resid 112 through 118 removed outlier: 3.560A pdb=" N LEU X 118 " --> pdb=" O LYS X 114 " (cutoff:3.500A) Processing helix chain 'Y' and resid 56 through 61 removed outlier: 3.702A pdb=" N LEU Y 61 " --> pdb=" O LEU Y 57 " (cutoff:3.500A) Processing helix chain 'Y' and resid 128 through 138 Processing helix chain 'Z' and resid 43 through 57 Processing helix chain 'Z' and resid 109 through 121 Processing helix chain 'a' and resid 13 through 32 Processing helix chain 'a' and resid 38 through 56 removed outlier: 4.299A pdb=" N ARG a 46 " --> pdb=" O LYS a 42 " (cutoff:3.500A) Proline residue: a 50 - end of helix Processing helix chain 'a' and resid 59 through 69 removed outlier: 3.595A pdb=" N ARG a 69 " --> pdb=" O LEU a 65 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 82 removed outlier: 4.883A pdb=" N PHE a 80 " --> pdb=" O VAL a 76 " (cutoff:3.500A) Processing helix chain 'a' and resid 82 through 88 Processing helix chain 'b' and resid 3 through 22 removed outlier: 4.991A pdb=" N ARG b 13 " --> pdb=" O ARG b 9 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ALA b 14 " --> pdb=" O ARG b 10 " (cutoff:3.500A) Processing helix chain 'b' and resid 55 through 60 Processing helix chain 'b' and resid 67 through 85 Processing helix chain 'b' and resid 101 through 113 Processing helix chain 'c' and resid 3 through 10 Processing helix chain 'c' and resid 53 through 56 removed outlier: 3.514A pdb=" N HIS c 56 " --> pdb=" O ARG c 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 53 through 56' Processing helix chain 'c' and resid 97 through 103 removed outlier: 3.525A pdb=" N ARG c 103 " --> pdb=" O LEU c 100 " (cutoff:3.500A) Processing helix chain 'd' and resid 6 through 20 removed outlier: 3.563A pdb=" N ALA d 10 " --> pdb=" O ARG d 6 " (cutoff:3.500A) Processing helix chain 'd' and resid 25 through 30 Processing helix chain 'd' and resid 31 through 72 removed outlier: 4.482A pdb=" N GLN d 37 " --> pdb=" O ARG d 33 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS d 54 " --> pdb=" O ARG d 50 " (cutoff:3.500A) Processing helix chain 'd' and resid 75 through 86 Processing helix chain 'd' and resid 91 through 102 Processing helix chain 'd' and resid 102 through 118 Processing helix chain 'f' and resid 13 through 25 removed outlier: 4.465A pdb=" N VAL f 20 " --> pdb=" O LYS f 16 " (cutoff:3.500A) Processing helix chain 'f' and resid 28 through 38 removed outlier: 3.985A pdb=" N TYR f 38 " --> pdb=" O ASP f 34 " (cutoff:3.500A) Processing helix chain 'f' and resid 42 through 62 removed outlier: 3.643A pdb=" N LEU f 46 " --> pdb=" O LYS f 42 " (cutoff:3.500A) Processing helix chain 'f' and resid 65 through 69 Processing helix chain 'f' and resid 89 through 91 No H-bonds generated for 'chain 'f' and resid 89 through 91' Processing helix chain 'g' and resid 3 through 10 removed outlier: 3.933A pdb=" N LYS g 9 " --> pdb=" O GLU g 5 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL g 10 " --> pdb=" O ARG g 6 " (cutoff:3.500A) Processing helix chain 'g' and resid 17 through 28 removed outlier: 3.643A pdb=" N ASN g 28 " --> pdb=" O MET g 24 " (cutoff:3.500A) Processing helix chain 'g' and resid 39 through 51 Processing helix chain 'i' and resid 13 through 23 removed outlier: 3.619A pdb=" N ALA i 23 " --> pdb=" O ARG i 19 " (cutoff:3.500A) Processing helix chain 'i' and resid 44 through 52 Processing helix chain 'k' and resid 54 through 63 Processing helix chain 'k' and resid 63 through 74 Processing helix chain 'l' and resid 9 through 23 Processing helix chain 'l' and resid 24 through 33 Processing helix chain 'l' and resid 40 through 61 removed outlier: 4.158A pdb=" N LYS l 44 " --> pdb=" O SER l 40 " (cutoff:3.500A) Processing helix chain 'm' and resid 17 through 28 Processing helix chain 'm' and resid 41 through 51 Processing helix chain 'n' and resid 10 through 17 Processing helix chain 'n' and resid 18 through 20 No H-bonds generated for 'chain 'n' and resid 18 through 20' Processing helix chain 'p' and resid 8 through 17 Processing helix chain 'p' and resid 17 through 22 Processing helix chain 'p' and resid 24 through 38 Processing helix chain 'q' and resid 7 through 12 removed outlier: 3.641A pdb=" N LYS q 12 " --> pdb=" O ARG q 8 " (cutoff:3.500A) Processing helix chain 'q' and resid 37 through 45 Processing helix chain 'q' and resid 54 through 62 Processing helix chain 'r' and resid 30 through 33 Processing helix chain 'L' and resid 43 through 52 Processing helix chain 'C' and resid 5 through 13 Processing helix chain 'C' and resid 22 through 30 removed outlier: 5.030A pdb=" N ALA C 28 " --> pdb=" O ASN C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 58 Processing helix chain 'C' and resid 181 through 197 removed outlier: 4.061A pdb=" N ASN C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA C 195 " --> pdb=" O ALA C 191 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS C 197 " --> pdb=" O LEU C 193 " (cutoff:3.500A) Processing helix chain 'U' and resid 22 through 28 Processing helix chain 'U' and resid 40 through 49 Processing helix chain 'U' and resid 54 through 71 removed outlier: 3.625A pdb=" N LEU U 58 " --> pdb=" O LEU U 54 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA U 59 " --> pdb=" O GLU U 55 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU U 60 " --> pdb=" O ALA U 56 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL U 61 " --> pdb=" O LYS U 57 " (cutoff:3.500A) Processing helix chain 'U' and resid 95 through 103 removed outlier: 3.759A pdb=" N ILE U 99 " --> pdb=" O GLY U 95 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP U 101 " --> pdb=" O ARG U 97 " (cutoff:3.500A) Processing helix chain 'U' and resid 111 through 113 No H-bonds generated for 'chain 'U' and resid 111 through 113' Processing helix chain '1' and resid 24 through 31 Proline residue: 1 29 - end of helix Processing helix chain '1' and resid 34 through 38 removed outlier: 4.415A pdb=" N LYS 1 37 " --> pdb=" O ALA 1 34 " (cutoff:3.500A) Processing helix chain '1' and resid 42 through 62 Proline residue: 1 48 - end of helix Processing helix chain '1' and resid 78 through 87 Processing helix chain '1' and resid 103 through 123 removed outlier: 3.829A pdb=" N VAL 1 107 " --> pdb=" O ASN 1 103 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP 1 123 " --> pdb=" O THR 1 119 " (cutoff:3.500A) Processing helix chain '1' and resid 131 through 148 Processing helix chain '1' and resid 149 through 154 removed outlier: 3.740A pdb=" N LYS 1 152 " --> pdb=" O GLY 1 149 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP 1 153 " --> pdb=" O GLY 1 150 " (cutoff:3.500A) Processing helix chain '1' and resid 169 through 180 Processing helix chain '1' and resid 206 through 222 removed outlier: 3.624A pdb=" N ARG 1 222 " --> pdb=" O ALA 1 218 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 12 removed outlier: 3.711A pdb=" N LEU 2 12 " --> pdb=" O GLY 2 9 " (cutoff:3.500A) Processing helix chain '2' and resid 28 through 46 Processing helix chain '2' and resid 72 through 78 removed outlier: 3.592A pdb=" N VAL 2 76 " --> pdb=" O ARG 2 72 " (cutoff:3.500A) Processing helix chain '2' and resid 81 through 96 Processing helix chain '2' and resid 108 through 111 Processing helix chain '2' and resid 112 through 125 Processing helix chain '2' and resid 129 through 144 removed outlier: 4.029A pdb=" N LEU 2 144 " --> pdb=" O ASN 2 140 " (cutoff:3.500A) Processing helix chain '3' and resid 7 through 15 removed outlier: 3.987A pdb=" N LEU 3 11 " --> pdb=" O PRO 3 7 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU 3 15 " --> pdb=" O LEU 3 11 " (cutoff:3.500A) Processing helix chain '3' and resid 49 through 66 Processing helix chain '3' and resid 68 through 82 Processing helix chain '3' and resid 85 through 96 Processing helix chain '3' and resid 97 through 105 Processing helix chain '3' and resid 110 through 120 Processing helix chain '3' and resid 152 through 161 removed outlier: 3.712A pdb=" N LYS 3 156 " --> pdb=" O GLN 3 152 " (cutoff:3.500A) Processing helix chain '3' and resid 187 through 191 Processing helix chain '3' and resid 196 through 205 removed outlier: 3.897A pdb=" N ILE 3 200 " --> pdb=" O ASN 3 196 " (cutoff:3.500A) Processing helix chain '4' and resid 55 through 69 removed outlier: 4.040A pdb=" N ARG 4 69 " --> pdb=" O GLU 4 65 " (cutoff:3.500A) Processing helix chain '4' and resid 111 through 118 Processing helix chain '4' and resid 132 through 137 removed outlier: 3.817A pdb=" N VAL 4 137 " --> pdb=" O PRO 4 133 " (cutoff:3.500A) Processing helix chain '4' and resid 140 through 145 Processing helix chain '4' and resid 149 through 157 removed outlier: 3.536A pdb=" N ALA 4 155 " --> pdb=" O GLU 4 151 " (cutoff:3.500A) Processing helix chain '5' and resid 12 through 16 removed outlier: 5.361A pdb=" N GLU 5 16 " --> pdb=" O ASP 5 13 " (cutoff:3.500A) Processing helix chain '5' and resid 17 through 31 Processing helix chain '5' and resid 67 through 81 removed outlier: 3.645A pdb=" N ILE 5 71 " --> pdb=" O PRO 5 67 " (cutoff:3.500A) Processing helix chain '6' and resid 20 through 31 Processing helix chain '6' and resid 35 through 55 removed outlier: 3.666A pdb=" N ALA 6 39 " --> pdb=" O LYS 6 35 " (cutoff:3.500A) Processing helix chain '6' and resid 58 through 68 Processing helix chain '6' and resid 92 through 111 Processing helix chain '6' and resid 115 through 129 removed outlier: 3.802A pdb=" N GLU 6 129 " --> pdb=" O SER 6 125 " (cutoff:3.500A) Processing helix chain '6' and resid 133 through 148 Processing helix chain '7' and resid 5 through 19 Processing helix chain '7' and resid 30 through 43 Processing helix chain '7' and resid 95 through 99 Processing helix chain '7' and resid 112 through 119 Processing helix chain '8' and resid 34 through 39 removed outlier: 3.617A pdb=" N PHE 8 39 " --> pdb=" O LEU 8 35 " (cutoff:3.500A) Processing helix chain '8' and resid 45 through 53 removed outlier: 3.679A pdb=" N VAL 8 48 " --> pdb=" O ARG 8 45 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN 8 50 " --> pdb=" O VAL 8 47 " (cutoff:3.500A) Proline residue: 8 51 - end of helix Processing helix chain '8' and resid 72 through 86 Processing helix chain '8' and resid 93 through 101 removed outlier: 4.093A pdb=" N GLU 8 97 " --> pdb=" O SER 8 93 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG 8 99 " --> pdb=" O ARG 8 95 " (cutoff:3.500A) Processing helix chain '9' and resid 14 through 33 Processing helix chain '9' and resid 80 through 86 Processing helix chain 'A' and resid 59 through 72 Processing helix chain 'A' and resid 74 through 78 removed outlier: 3.641A pdb=" N GLY A 78 " --> pdb=" O LYS A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 101 Processing helix chain 'B' and resid 3 through 10 Processing helix chain 'B' and resid 23 through 27 removed outlier: 3.849A pdb=" N CYS B 27 " --> pdb=" O LEU B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 118 removed outlier: 3.526A pdb=" N LYS B 116 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY B 118 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 19 Processing helix chain 'D' and resid 20 through 22 No H-bonds generated for 'chain 'D' and resid 20 through 22' Processing helix chain 'D' and resid 27 through 37 Processing helix chain 'D' and resid 49 through 61 Processing helix chain 'D' and resid 65 through 84 Processing helix chain 'D' and resid 85 through 94 removed outlier: 3.586A pdb=" N GLY D 94 " --> pdb=" O ARG D 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 20 removed outlier: 3.713A pdb=" N LYS E 7 " --> pdb=" O LYS E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 31 removed outlier: 4.342A pdb=" N LYS E 28 " --> pdb=" O ARG E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 48 Processing helix chain 'E' and resid 56 through 60 removed outlier: 3.947A pdb=" N GLN E 60 " --> pdb=" O PRO E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 91 Processing helix chain 'F' and resid 4 through 16 Processing helix chain 'F' and resid 24 through 45 removed outlier: 4.091A pdb=" N GLU F 45 " --> pdb=" O GLY F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 72 Processing helix chain 'F' and resid 74 through 86 Processing helix chain 'G' and resid 53 through 64 Processing helix chain 'G' and resid 68 through 76 Processing helix chain 'H' and resid 49 through 52 removed outlier: 4.553A pdb=" N GLU H 52 " --> pdb=" O GLU H 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 49 through 52' Processing helix chain 'I' and resid 25 through 32 Processing helix chain 'I' and resid 41 through 46 Processing helix chain 'I' and resid 48 through 65 Processing helix chain 'J' and resid 12 through 25 Processing helix chain 'J' and resid 41 through 45 removed outlier: 3.575A pdb=" N ILE J 45 " --> pdb=" O PRO J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 67 removed outlier: 3.956A pdb=" N VAL J 67 " --> pdb=" O ASP J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 75 Processing helix chain 'K' and resid 6 through 39 removed outlier: 3.656A pdb=" N ARG K 10 " --> pdb=" O SER K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 65 removed outlier: 3.708A pdb=" N ALA K 47 " --> pdb=" O ASP K 43 " (cutoff:3.500A) Proline residue: K 56 - end of helix removed outlier: 3.517A pdb=" N GLY K 65 " --> pdb=" O GLN K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 87 Processing helix chain 's' and resid 27 through 32 removed outlier: 3.769A pdb=" N VAL s 32 " --> pdb=" O VAL s 28 " (cutoff:3.500A) Processing helix chain 's' and resid 39 through 52 Processing helix chain 't' and resid 49 through 53 Processing helix chain 't' and resid 94 through 97 Processing helix chain 't' and resid 98 through 103 Processing helix chain 't' and resid 172 through 177 Processing sheet with id=AA1, first strand: chain 'P' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'P' and resid 34 through 36 Processing sheet with id=AA3, first strand: chain 'P' and resid 101 through 105 removed outlier: 6.203A pdb=" N LEU P 95 " --> pdb=" O VAL P 78 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N VAL P 78 " --> pdb=" O LEU P 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 129 through 131 removed outlier: 6.195A pdb=" N THR P 173 " --> pdb=" O VAL P 165 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N MET P 181 " --> pdb=" O VAL P 268 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 144 through 145 removed outlier: 5.979A pdb=" N VAL P 144 " --> pdb=" O GLN P 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Q' and resid 4 through 5 removed outlier: 6.566A pdb=" N VAL Q 109 " --> pdb=" O GLN Q 173 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N GLN Q 173 " --> pdb=" O VAL Q 109 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLY Q 111 " --> pdb=" O THR Q 171 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N THR Q 171 " --> pdb=" O GLY Q 111 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Q' and resid 8 through 15 removed outlier: 5.804A pdb=" N LYS Q 8 " --> pdb=" O GLU Q 28 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLU Q 28 " --> pdb=" O LYS Q 8 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY Q 10 " --> pdb=" O VAL Q 26 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU Q 186 " --> pdb=" O VAL Q 180 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL Q 180 " --> pdb=" O LEU Q 186 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU Q 188 " --> pdb=" O VAL Q 178 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Q' and resid 79 through 83 removed outlier: 6.593A pdb=" N ALA Q 47 " --> pdb=" O VAL Q 37 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL Q 37 " --> pdb=" O ALA Q 47 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLN Q 49 " --> pdb=" O THR Q 35 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Q' and resid 117 through 119 Processing sheet with id=AB1, first strand: chain 'R' and resid 2 through 4 Processing sheet with id=AB2, first strand: chain 'R' and resid 118 through 121 Processing sheet with id=AB3, first strand: chain 'S' and resid 66 through 69 Processing sheet with id=AB4, first strand: chain 'T' and resid 16 through 20 Processing sheet with id=AB5, first strand: chain 'T' and resid 41 through 44 Processing sheet with id=AB6, first strand: chain 'T' and resid 122 through 124 Processing sheet with id=AB7, first strand: chain 'T' and resid 95 through 99 Processing sheet with id=AB8, first strand: chain 'V' and resid 99 through 102 removed outlier: 6.726A pdb=" N GLY V 99 " --> pdb=" O VAL V 139 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N GLU V 141 " --> pdb=" O GLY V 99 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE V 101 " --> pdb=" O GLU V 141 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'W' and resid 122 through 124 removed outlier: 6.425A pdb=" N ILE W 54 " --> pdb=" O LYS W 123 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N TYR W 16 " --> pdb=" O ILE W 55 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N LEU W 57 " --> pdb=" O TYR W 16 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL W 18 " --> pdb=" O LEU W 57 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'W' and resid 73 through 77 Processing sheet with id=AC2, first strand: chain 'X' and resid 7 through 10 removed outlier: 3.994A pdb=" N VAL X 10 " --> pdb=" O ARG X 17 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ARG X 17 " --> pdb=" O VAL X 10 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA X 16 " --> pdb=" O ALA X 46 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ALA X 46 " --> pdb=" O ALA X 16 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG X 18 " --> pdb=" O LYS X 44 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYS X 40 " --> pdb=" O ILE X 22 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N VAL X 24 " --> pdb=" O ILE X 38 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ILE X 38 " --> pdb=" O VAL X 24 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N VAL X 62 " --> pdb=" O VAL X 85 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL X 85 " --> pdb=" O VAL X 62 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N CYS X 84 " --> pdb=" O MET X 7 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASN X 9 " --> pdb=" O CYS X 84 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'X' and resid 69 through 70 removed outlier: 3.571A pdb=" N VAL X 76 " --> pdb=" O VAL c 73 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALA c 58 " --> pdb=" O ILE c 50 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ILE c 50 " --> pdb=" O ALA c 58 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N THR c 60 " --> pdb=" O ILE c 48 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE c 64 " --> pdb=" O GLU c 44 " (cutoff:3.500A) removed outlier: 9.055A pdb=" N GLU c 44 " --> pdb=" O ILE c 64 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLU c 27 " --> pdb=" O VAL c 86 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N VAL c 86 " --> pdb=" O GLU c 27 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N LYS c 29 " --> pdb=" O ILE c 84 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ILE c 84 " --> pdb=" O LYS c 29 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N TRP c 31 " --> pdb=" O ASP c 82 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ASP c 82 " --> pdb=" O TRP c 31 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Y' and resid 89 through 90 removed outlier: 5.825A pdb=" N VAL Y 90 " --> pdb=" O ARG Y 123 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Z' and resid 62 through 65 removed outlier: 6.460A pdb=" N LEU Z 33 " --> pdb=" O LEU Z 102 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLU Z 104 " --> pdb=" O PHE Z 31 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N PHE Z 31 " --> pdb=" O GLU Z 104 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Z' and resid 40 through 42 removed outlier: 5.498A pdb=" N VAL Z 89 " --> pdb=" O GLU Z 75 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLU Z 75 " --> pdb=" O VAL Z 89 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR Z 91 " --> pdb=" O ILE Z 73 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'a' and resid 33 through 37 removed outlier: 5.888A pdb=" N MET a 110 " --> pdb=" O CYS a 100 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'b' and resid 47 through 52 removed outlier: 6.595A pdb=" N VAL b 39 " --> pdb=" O LEU b 48 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA b 50 " --> pdb=" O ALA b 37 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ALA b 37 " --> pdb=" O ALA b 50 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N SER b 52 " --> pdb=" O ILE b 35 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE b 35 " --> pdb=" O SER b 52 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'c' and resid 90 through 91 removed outlier: 4.218A pdb=" N LYS c 111 " --> pdb=" O ALA c 91 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'e' and resid 11 through 14 removed outlier: 6.711A pdb=" N TYR e 2 " --> pdb=" O ILE e 41 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE e 41 " --> pdb=" O TYR e 2 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VAL e 4 " --> pdb=" O LEU e 39 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'e' and resid 19 through 23 removed outlier: 6.670A pdb=" N PHE e 93 " --> pdb=" O HIS e 66 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N HIS e 66 " --> pdb=" O PHE e 93 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ASP e 95 " --> pdb=" O VAL e 64 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LYS e 60 " --> pdb=" O THR e 99 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ILE e 101 " --> pdb=" O VAL e 58 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL e 58 " --> pdb=" O ILE e 101 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'e' and resid 72 through 78 removed outlier: 4.302A pdb=" N TYR e 83 " --> pdb=" O ARG e 78 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'f' and resid 3 through 10 removed outlier: 5.732A pdb=" N SER f 101 " --> pdb=" O HIS f 9 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N HIS f 102 " --> pdb=" O VAL f 76 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL f 76 " --> pdb=" O HIS f 102 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR f 104 " --> pdb=" O ILE f 74 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE f 74 " --> pdb=" O THR f 104 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL f 106 " --> pdb=" O THR f 72 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'f' and resid 82 through 87 Processing sheet with id=AD6, first strand: chain 'g' and resid 11 through 14 removed outlier: 6.688A pdb=" N LYS g 33 " --> pdb=" O ARG g 12 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N VAL g 31 " --> pdb=" O PRO g 14 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LYS g 81 " --> pdb=" O VAL g 34 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'g' and resid 67 through 70 Processing sheet with id=AD8, first strand: chain 'h' and resid 65 through 66 Processing sheet with id=AD9, first strand: chain 'h' and resid 41 through 45 Processing sheet with id=AE1, first strand: chain 'h' and resid 83 through 88 Processing sheet with id=AE2, first strand: chain 'i' and resid 3 through 8 removed outlier: 7.797A pdb=" N ASN i 5 " --> pdb=" O ASP i 43 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASP i 43 " --> pdb=" O ASN i 5 " (cutoff:3.500A) removed outlier: 8.930A pdb=" N LYS i 25 " --> pdb=" O GLN i 87 " (cutoff:3.500A) removed outlier: 9.664A pdb=" N ILE i 89 " --> pdb=" O LYS i 25 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N PHE i 91 " --> pdb=" O PRO i 27 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE i 29 " --> pdb=" O PHE i 91 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ARG i 93 " --> pdb=" O ILE i 29 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N TYR i 31 " --> pdb=" O ARG i 93 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLN i 78 " --> pdb=" O GLN i 87 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ILE i 89 " --> pdb=" O ASP i 76 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASP i 76 " --> pdb=" O ILE i 89 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE i 91 " --> pdb=" O ALA i 74 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA i 74 " --> pdb=" O PHE i 91 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG i 93 " --> pdb=" O VAL i 72 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL i 72 " --> pdb=" O ARG i 93 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'j' and resid 22 through 23 removed outlier: 6.799A pdb=" N LEU j 59 " --> pdb=" O ILE j 37 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'j' and resid 30 through 31 Processing sheet with id=AE5, first strand: chain 'k' and resid 13 through 17 Processing sheet with id=AE6, first strand: chain 'k' and resid 34 through 40 Processing sheet with id=AE7, first strand: chain 'm' and resid 36 through 38 Processing sheet with id=AE8, first strand: chain 'n' and resid 29 through 30 Processing sheet with id=AE9, first strand: chain 'n' and resid 48 through 49 Processing sheet with id=AF1, first strand: chain 'o' and resid 20 through 25 Processing sheet with id=AF2, first strand: chain 'q' and resid 14 through 16 Processing sheet with id=AF3, first strand: chain 'r' and resid 2 through 3 removed outlier: 6.531A pdb=" N LYS r 2 " --> pdb=" O ARG r 36 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N GLY r 38 " --> pdb=" O LYS r 2 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE r 23 " --> pdb=" O GLN r 37 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 21 through 25 removed outlier: 9.297A pdb=" N LEU L 32 " --> pdb=" O GLU L 11 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N THR L 13 " --> pdb=" O LEU L 32 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 20 through 21 removed outlier: 7.917A pdb=" N TYR C 21 " --> pdb=" O GLY C 221 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA C 223 " --> pdb=" O TYR C 21 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL C 212 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS C 211 " --> pdb=" O ASN C 47 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N VAL C 42 " --> pdb=" O ILE C 175 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE C 175 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR C 173 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL C 46 " --> pdb=" O ILE C 171 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 60 through 63 Processing sheet with id=AF7, first strand: chain 'U' and resid 4 through 5 Processing sheet with id=AF8, first strand: chain 'U' and resid 77 through 82 removed outlier: 7.207A pdb=" N VAL U 78 " --> pdb=" O ASN U 145 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL U 147 " --> pdb=" O VAL U 78 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE U 80 " --> pdb=" O VAL U 147 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL U 142 " --> pdb=" O VAL U 130 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL U 130 " --> pdb=" O VAL U 142 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER U 131 " --> pdb=" O ARG U 116 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain '1' and resid 91 through 92 removed outlier: 6.641A pdb=" N PHE 1 69 " --> pdb=" O VAL 1 92 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU 1 161 " --> pdb=" O PHE 1 184 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ILE 1 186 " --> pdb=" O LEU 1 161 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL 1 163 " --> pdb=" O ILE 1 186 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL 1 183 " --> pdb=" O PHE 1 198 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ILE 1 200 " --> pdb=" O VAL 1 183 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA 1 185 " --> pdb=" O ILE 1 200 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain '2' and resid 52 through 56 removed outlier: 6.731A pdb=" N HIS 2 69 " --> pdb=" O SER 2 53 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE 2 55 " --> pdb=" O THR 2 67 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N THR 2 67 " --> pdb=" O ILE 2 55 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain '2' and resid 167 through 171 Processing sheet with id=AG3, first strand: chain '3' and resid 128 through 129 Processing sheet with id=AG4, first strand: chain '4' and resid 13 through 15 Processing sheet with id=AG5, first strand: chain '4' and resid 19 through 22 Processing sheet with id=AG6, first strand: chain '4' and resid 85 through 89 Processing sheet with id=AG7, first strand: chain '5' and resid 40 through 45 removed outlier: 5.326A pdb=" N ASP 5 41 " --> pdb=" O LEU 5 61 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LEU 5 61 " --> pdb=" O ASP 5 41 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY 5 43 " --> pdb=" O TYR 5 59 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain '5' and resid 40 through 45 removed outlier: 5.326A pdb=" N ASP 5 41 " --> pdb=" O LEU 5 61 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LEU 5 61 " --> pdb=" O ASP 5 41 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY 5 43 " --> pdb=" O TYR 5 59 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ARG 5 86 " --> pdb=" O MET 5 9 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain '6' and resid 73 through 77 Processing sheet with id=AH1, first strand: chain '7' and resid 24 through 28 removed outlier: 6.221A pdb=" N GLU 7 58 " --> pdb=" O VAL 7 51 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL 7 51 " --> pdb=" O GLU 7 58 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLU 7 60 " --> pdb=" O PHE 7 49 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE 7 49 " --> pdb=" O GLU 7 60 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR 7 62 " --> pdb=" O GLU 7 47 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain '7' and resid 75 through 77 Processing sheet with id=AH3, first strand: chain '7' and resid 75 through 77 removed outlier: 6.559A pdb=" N VAL 7 103 " --> pdb=" O ILE 7 126 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain '8' and resid 6 through 8 removed outlier: 5.990A pdb=" N VAL 8 29 " --> pdb=" O ILE 8 65 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N VAL 8 67 " --> pdb=" O VAL 8 29 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain '9' and resid 45 through 52 Processing sheet with id=AH6, first strand: chain '9' and resid 45 through 52 Processing sheet with id=AH7, first strand: chain 'A' and resid 41 through 46 removed outlier: 6.716A pdb=" N ALA A 41 " --> pdb=" O ASP A 36 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ASP A 36 " --> pdb=" O ALA A 41 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU A 82 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASN A 109 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'B' and resid 30 through 32 Processing sheet with id=AH9, first strand: chain 'B' and resid 36 through 40 removed outlier: 4.279A pdb=" N TYR B 95 " --> pdb=" O THR B 64 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'E' and resid 73 through 74 removed outlier: 3.566A pdb=" N LEU E 79 " --> pdb=" O LEU E 74 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'G' and resid 34 through 35 Processing sheet with id=AI3, first strand: chain 'G' and resid 37 through 39 removed outlier: 3.731A pdb=" N ARG G 51 " --> pdb=" O PHE G 38 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'H' and resid 8 through 14 removed outlier: 7.813A pdb=" N GLN H 9 " --> pdb=" O GLU H 26 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N GLU H 26 " --> pdb=" O GLN H 9 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL H 22 " --> pdb=" O VAL H 13 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TRP H 73 " --> pdb=" O HIS H 45 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLU H 60 " --> pdb=" O VAL H 76 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N VAL H 78 " --> pdb=" O VAL H 58 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL H 58 " --> pdb=" O VAL H 78 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'J' and resid 31 through 33 Processing sheet with id=AI6, first strand: chain 't' and resid 46 through 48 removed outlier: 3.887A pdb=" N ALA t 30 " --> pdb=" O LEU t 37 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASP t 39 " --> pdb=" O VAL t 28 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL t 28 " --> pdb=" O ASP t 39 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 't' and resid 112 through 115 removed outlier: 6.963A pdb=" N THR t 121 " --> pdb=" O ASN t 113 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LYS t 115 " --> pdb=" O GLY t 119 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLY t 119 " --> pdb=" O LYS t 115 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL t 122 " --> pdb=" O ALA t 129 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ARG t 128 " --> pdb=" O VAL t 166 " (cutoff:3.500A) 1856 hydrogen bonds defined for protein. 5142 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4070 hydrogen bonds 6370 hydrogen bond angles 0 basepair planarities 1619 basepair parallelities 2611 stacking parallelities Total time for adding SS restraints: 242.16 Time building geometry restraints manager: 63.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.25: 10392 1.25 - 1.41: 57921 1.41 - 1.57: 84211 1.57 - 1.74: 7913 1.74 - 1.90: 272 Bond restraints: 160709 Sorted by residual: bond pdb=" P G N2502 " pdb=" OP2 G N2502 " ideal model delta sigma weight residual 1.485 1.768 -0.283 2.00e-02 2.50e+03 2.00e+02 bond pdb=" P A N1156 " pdb=" OP2 A N1156 " ideal model delta sigma weight residual 1.485 1.743 -0.258 2.00e-02 2.50e+03 1.66e+02 bond pdb=" P G N1333 " pdb=" OP2 G N1333 " ideal model delta sigma weight residual 1.485 1.703 -0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" P A N 783 " pdb=" OP2 A N 783 " ideal model delta sigma weight residual 1.485 1.701 -0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C ALA 4 127 " pdb=" O ALA 4 127 " ideal model delta sigma weight residual 1.234 1.105 0.129 1.22e-02 6.72e+03 1.11e+02 ... (remaining 160704 not shown) Histogram of bond angle deviations from ideal: 80.76 - 93.23: 9 93.23 - 105.70: 27854 105.70 - 118.18: 126168 118.18 - 130.65: 84642 130.65 - 143.12: 1675 Bond angle restraints: 240348 Sorted by residual: angle pdb=" O3' C M 73 " pdb=" P C M 74 " pdb=" O5' C M 74 " ideal model delta sigma weight residual 104.00 131.33 -27.33 1.50e+00 4.44e-01 3.32e+02 angle pdb=" O3'A U N2506 " pdb=" P C N2507 " pdb=" O5' C N2507 " ideal model delta sigma weight residual 104.00 80.76 23.24 1.50e+00 4.44e-01 2.40e+02 angle pdb=" C THR Q 151 " pdb=" N PRO Q 152 " pdb=" CA PRO Q 152 " ideal model delta sigma weight residual 119.47 134.22 -14.75 1.16e+00 7.43e-01 1.62e+02 angle pdb=" O3'A U N2506 " pdb=" P C N2507 " pdb=" OP1 C N2507 " ideal model delta sigma weight residual 108.00 142.87 -34.87 3.00e+00 1.11e-01 1.35e+02 angle pdb=" C4' A N1936 " pdb=" C3' A N1936 " pdb=" O3' A N1936 " ideal model delta sigma weight residual 113.00 96.43 16.57 1.50e+00 4.44e-01 1.22e+02 ... (remaining 240343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 82696 35.88 - 71.75: 2959 71.75 - 107.63: 223 107.63 - 143.50: 27 143.50 - 179.38: 35 Dihedral angle restraints: 85940 sinusoidal: 68725 harmonic: 17215 Sorted by residual: dihedral pdb=" CA THR Q 151 " pdb=" C THR Q 151 " pdb=" N PRO Q 152 " pdb=" CA PRO Q 152 " ideal model delta harmonic sigma weight residual -180.00 -48.31 -131.69 0 5.00e+00 4.00e-02 6.94e+02 dihedral pdb=" CA ASN 5 52 " pdb=" C ASN 5 52 " pdb=" N LYS 5 53 " pdb=" CA LYS 5 53 " ideal model delta harmonic sigma weight residual -180.00 -115.17 -64.83 0 5.00e+00 4.00e-02 1.68e+02 dihedral pdb=" CA LYS A 125 " pdb=" C LYS A 125 " pdb=" N LYS A 126 " pdb=" CA LYS A 126 " ideal model delta harmonic sigma weight residual -180.00 -115.38 -64.62 0 5.00e+00 4.00e-02 1.67e+02 ... (remaining 85937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.215: 29213 0.215 - 0.430: 1440 0.430 - 0.645: 93 0.645 - 0.860: 11 0.860 - 1.075: 5 Chirality restraints: 30762 Sorted by residual: chirality pdb=" CA ARG j 41 " pdb=" N ARG j 41 " pdb=" C ARG j 41 " pdb=" CB ARG j 41 " both_signs ideal model delta sigma weight residual False 2.51 1.44 1.08 2.00e-01 2.50e+01 2.89e+01 chirality pdb=" C3' G 01347 " pdb=" C4' G 01347 " pdb=" O3' G 01347 " pdb=" C2' G 01347 " both_signs ideal model delta sigma weight residual False -2.74 -1.85 -0.89 2.00e-01 2.50e+01 2.00e+01 chirality pdb=" CA VAL P 204 " pdb=" N VAL P 204 " pdb=" C VAL P 204 " pdb=" CB VAL P 204 " both_signs ideal model delta sigma weight residual False 2.44 1.56 0.88 2.00e-01 2.50e+01 1.94e+01 ... (remaining 30759 not shown) Planarity restraints: 12915 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A N2765 " 0.012 2.00e-02 2.50e+03 8.69e-02 2.08e+02 pdb=" N9 A N2765 " -0.010 2.00e-02 2.50e+03 pdb=" C8 A N2765 " 0.062 2.00e-02 2.50e+03 pdb=" N7 A N2765 " 0.045 2.00e-02 2.50e+03 pdb=" C5 A N2765 " -0.058 2.00e-02 2.50e+03 pdb=" C6 A N2765 " -0.083 2.00e-02 2.50e+03 pdb=" N6 A N2765 " -0.070 2.00e-02 2.50e+03 pdb=" N1 A N2765 " 0.235 2.00e-02 2.50e+03 pdb=" C2 A N2765 " -0.026 2.00e-02 2.50e+03 pdb=" N3 A N2765 " -0.057 2.00e-02 2.50e+03 pdb=" C4 A N2765 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A N1802 " -0.111 2.00e-02 2.50e+03 7.16e-02 1.41e+02 pdb=" N9 A N1802 " 0.022 2.00e-02 2.50e+03 pdb=" C8 A N1802 " -0.039 2.00e-02 2.50e+03 pdb=" N7 A N1802 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A N1802 " 0.068 2.00e-02 2.50e+03 pdb=" C6 A N1802 " 0.001 2.00e-02 2.50e+03 pdb=" N6 A N1802 " -0.024 2.00e-02 2.50e+03 pdb=" N1 A N1802 " -0.079 2.00e-02 2.50e+03 pdb=" C2 A N1802 " -0.062 2.00e-02 2.50e+03 pdb=" N3 A N1802 " 0.091 2.00e-02 2.50e+03 pdb=" C4 A N1802 " 0.135 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U N2522 " -0.021 2.00e-02 2.50e+03 7.72e-02 1.34e+02 pdb=" N1 U N2522 " 0.046 2.00e-02 2.50e+03 pdb=" C2 U N2522 " 0.038 2.00e-02 2.50e+03 pdb=" O2 U N2522 " 0.055 2.00e-02 2.50e+03 pdb=" N3 U N2522 " -0.188 2.00e-02 2.50e+03 pdb=" C4 U N2522 " 0.023 2.00e-02 2.50e+03 pdb=" O4 U N2522 " 0.092 2.00e-02 2.50e+03 pdb=" C5 U N2522 " -0.048 2.00e-02 2.50e+03 pdb=" C6 U N2522 " 0.002 2.00e-02 2.50e+03 ... (remaining 12912 not shown) Histogram of nonbonded interaction distances: 0.20 - 1.19: 17 1.19 - 2.17: 108 2.17 - 3.16: 110627 3.16 - 4.15: 571223 4.15 - 5.14: 939569 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1621544 Sorted by model distance: nonbonded pdb=" O2' U N1923 " pdb=" O2' C M 12 " model vdw 0.197 2.440 nonbonded pdb=" CD2 HIS 1 18 " pdb=" CB LYS t 43 " model vdw 0.223 3.660 nonbonded pdb=" CG ASP S 113 " pdb=" NH1 ARG D 71 " model vdw 0.295 3.350 nonbonded pdb=" OD1 ASP S 113 " pdb=" CZ ARG D 71 " model vdw 0.638 3.270 nonbonded pdb=" NE2 HIS 1 18 " pdb=" CA LYS t 43 " model vdw 0.697 3.550 ... (remaining 1621539 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 9.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 48.710 Check model and map are aligned: 1.620 Set scattering table: 0.990 Process input model: 539.310 Find NCS groups from input model: 3.010 Set up NCS constraints: 0.390 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:2.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 605.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3860 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 : 0.016 0.283 160709 Z= 0.978 Angle : 1.619 34.873 240348 Z= 0.965 Chirality : 0.112 1.075 30762 Planarity : 0.015 0.113 12915 Dihedral : 15.098 179.379 74827 Min Nonbonded Distance : 0.197 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 1.01 % Allowed : 8.79 % Favored : 90.20 % Rotamer Outliers : 1.41 % Cbeta Deviations : 1.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 1.01 % Twisted General : 0.55 % 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: -4.05 (0.09), residues: 5936 helix: -2.92 (0.08), residues: 1857 sheet: -2.32 (0.13), residues: 1110 loop : -2.63 (0.09), residues: 2969 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 892 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 824 time to evaluate : 6.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 6 residues processed: 883 average time/residue: 1.4614 time to fit residues: 2160.8660 Evaluate side-chains 406 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 400 time to evaluate : 6.321 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 1.6245 time to fit residues: 22.5015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 887 optimal weight: 10.0000 chunk 796 optimal weight: 20.0000 chunk 442 optimal weight: 5.9990 chunk 272 optimal weight: 7.9990 chunk 537 optimal weight: 50.0000 chunk 425 optimal weight: 50.0000 chunk 823 optimal weight: 7.9990 chunk 318 optimal weight: 8.9990 chunk 500 optimal weight: 6.9990 chunk 613 optimal weight: 5.9990 chunk 954 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 86 ASN P 134 ASN P 153 GLN ** P 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 243 HIS Q 32 ASN ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 173 GLN ** R 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 165 HIS T 22 GLN T 88 GLN T 143 GLN V 12 GLN V 43 ASN W 40 HIS X 3 GLN ** a 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 18 GLN ** a 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 29 HIS b 38 GLN b 98 GLN c 12 GLN d 37 GLN d 44 GLN f 15 GLN i 49 ASN i 87 GLN l 27 ASN l 58 ASN m 20 HIS n 19 HIS o 19 HIS L 20 ASN L 41 HIS C 172 HIS ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 2 GLN U 28 ASN U 43 ASN ** U 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 19 GLN 1 94 HIS 1 170 HIS ** 3 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 28 ASN 6 122 ASN ** 6 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 32 GLN 8 81 HIS ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 ASN E 49 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN H 31 HIS I 52 GLN J 57 HIS ** K 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 ASN K 75 HIS Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4163 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.227 160709 Z= 0.225 Angle : 0.717 14.207 240348 Z= 0.366 Chirality : 0.039 0.472 30762 Planarity : 0.006 0.135 12915 Dihedral : 14.673 178.704 63245 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.11 % Favored : 92.67 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 1.01 % Twisted General : 0.38 % 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: -2.64 (0.10), residues: 5936 helix: -1.02 (0.11), residues: 1871 sheet: -1.95 (0.14), residues: 1112 loop : -2.13 (0.10), residues: 2953 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 550 time to evaluate : 5.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 3 residues processed: 560 average time/residue: 1.4188 time to fit residues: 1348.8230 Evaluate side-chains 370 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 367 time to evaluate : 6.335 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 1.0398 time to fit residues: 12.8510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 530 optimal weight: 50.0000 chunk 296 optimal weight: 0.2980 chunk 794 optimal weight: 30.0000 chunk 649 optimal weight: 50.0000 chunk 263 optimal weight: 30.0000 chunk 956 optimal weight: 30.0000 chunk 1032 optimal weight: 50.0000 chunk 851 optimal weight: 9.9990 chunk 948 optimal weight: 10.0000 chunk 325 optimal weight: 40.0000 chunk 767 optimal weight: 20.0000 overall best weight: 14.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 15 HIS ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 70 ASN ** P 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 200 HIS ** P 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 260 ASN ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 73 ASN T 128 GLN W 58 ASN W 80 HIS ** X 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 62 ASN a 81 ASN ** b 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 15 HIS ** g 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 45 HIS h 53 ASN ** h 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 74 ASN ** i 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 25 GLN l 58 ASN n 6 ASN n 42 HIS ** o 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 28 ASN L 20 ASN C 57 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 39 HIS 1 51 ASN 1 94 HIS ** 1 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 69 HIS ** 2 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 74 ASN ** 3 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 28 ASN 7 16 ASN ** 9 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 ASN D 8 ASN D 105 ASN E 60 GLN ** E 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 GLN ** F 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 57 HIS ** K 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4817 moved from start: 0.7286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.186 160709 Z= 0.393 Angle : 1.026 17.410 240348 Z= 0.513 Chirality : 0.049 0.666 30762 Planarity : 0.009 0.104 12915 Dihedral : 17.090 177.626 63245 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 50.95 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.03 % Favored : 90.73 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 1.01 % Twisted General : 0.40 % 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: -2.82 (0.10), residues: 5936 helix: -1.22 (0.11), residues: 1883 sheet: -1.93 (0.15), residues: 1046 loop : -2.26 (0.10), residues: 3007 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 511 time to evaluate : 6.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 3 residues processed: 530 average time/residue: 1.4141 time to fit residues: 1292.3901 Evaluate side-chains 374 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 371 time to evaluate : 6.639 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 1.0703 time to fit residues: 13.1814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 944 optimal weight: 8.9990 chunk 718 optimal weight: 30.0000 chunk 496 optimal weight: 40.0000 chunk 105 optimal weight: 40.0000 chunk 456 optimal weight: 20.0000 chunk 642 optimal weight: 50.0000 chunk 959 optimal weight: 20.0000 chunk 1015 optimal weight: 7.9990 chunk 501 optimal weight: 30.0000 chunk 909 optimal weight: 2.9990 chunk 273 optimal weight: 50.0000 overall best weight: 11.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 200 HIS ** P 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 260 ASN Q 36 GLN ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 73 ASN T 104 ASN ** T 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 107 ASN ** b 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 72 ASN e 86 GLN ** g 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 46 GLN ** h 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 58 ASN ** n 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 119 ASN U 133 GLN 1 19 GLN 1 94 HIS ** 1 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 190 HIS 3 41 HIS 3 120 HIS ** 3 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 GLN E 62 ASN ** F 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 29 ASN ** G 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 ASN ** K 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 75 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4816 moved from start: 0.8330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.186 160709 Z= 0.278 Angle : 0.781 16.396 240348 Z= 0.400 Chirality : 0.041 0.479 30762 Planarity : 0.006 0.122 12915 Dihedral : 17.237 179.159 63245 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 37.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.31 % Favored : 91.56 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.51 % Twisted General : 0.24 % 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: -2.48 (0.10), residues: 5936 helix: -0.81 (0.11), residues: 1887 sheet: -1.71 (0.15), residues: 1031 loop : -2.17 (0.10), residues: 3018 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 464 time to evaluate : 6.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 466 average time/residue: 1.3466 time to fit residues: 1090.6371 Evaluate side-chains 351 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 351 time to evaluate : 6.453 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.6570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 846 optimal weight: 5.9990 chunk 576 optimal weight: 40.0000 chunk 14 optimal weight: 0.3980 chunk 756 optimal weight: 40.0000 chunk 419 optimal weight: 40.0000 chunk 866 optimal weight: 7.9990 chunk 702 optimal weight: 30.0000 chunk 1 optimal weight: 50.0000 chunk 518 optimal weight: 40.0000 chunk 911 optimal weight: 8.9990 chunk 256 optimal weight: 20.0000 overall best weight: 8.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 200 HIS ** P 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 173 GLN ** T 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 128 GLN V 19 ASN ** X 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 44 GLN ** e 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 46 GLN h 74 ASN ** i 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 119 ASN 1 94 HIS ** 1 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 152 GLN ** 3 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 38 ASN 8 31 ASN ** 9 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 29 ASN J 69 HIS ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4842 moved from start: 0.9301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.129 160709 Z= 0.235 Angle : 0.721 15.275 240348 Z= 0.367 Chirality : 0.039 0.331 30762 Planarity : 0.006 0.195 12915 Dihedral : 17.122 179.924 63245 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 36.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.13 % Favored : 90.80 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.51 % Twisted General : 0.19 % 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: -2.23 (0.10), residues: 5936 helix: -0.44 (0.12), residues: 1895 sheet: -1.71 (0.15), residues: 1032 loop : -2.09 (0.10), residues: 3009 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 461 time to evaluate : 6.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 463 average time/residue: 1.3810 time to fit residues: 1116.5165 Evaluate side-chains 338 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 338 time to evaluate : 6.352 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.8401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 341 optimal weight: 30.0000 chunk 914 optimal weight: 9.9990 chunk 200 optimal weight: 7.9990 chunk 596 optimal weight: 30.0000 chunk 250 optimal weight: 8.9990 chunk 1016 optimal weight: 9.9990 chunk 844 optimal weight: 20.0000 chunk 470 optimal weight: 40.0000 chunk 84 optimal weight: 50.0000 chunk 336 optimal weight: 50.0000 chunk 533 optimal weight: 50.0000 overall best weight: 11.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 HIS ** P 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 35 HIS ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 34 HIS ** b 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 71 GLN ** e 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 74 ASN ** i 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN ** U 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 119 ASN 1 94 HIS ** 1 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 70 ASN ** 5 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 38 ASN ** 9 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN J 69 HIS ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4991 moved from start: 1.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.126 160709 Z= 0.287 Angle : 0.805 19.965 240348 Z= 0.408 Chirality : 0.042 0.329 30762 Planarity : 0.006 0.122 12915 Dihedral : 17.775 177.531 63245 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 46.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.60 % Favored : 90.33 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.51 % Twisted General : 0.24 % 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: -2.30 (0.10), residues: 5936 helix: -0.54 (0.11), residues: 1872 sheet: -1.85 (0.16), residues: 1001 loop : -2.05 (0.10), residues: 3063 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 443 time to evaluate : 6.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 444 average time/residue: 1.3248 time to fit residues: 1035.4095 Evaluate side-chains 333 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 333 time to evaluate : 8.461 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.7126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 980 optimal weight: 9.9990 chunk 114 optimal weight: 0.0470 chunk 579 optimal weight: 30.0000 chunk 742 optimal weight: 30.0000 chunk 575 optimal weight: 50.0000 chunk 856 optimal weight: 2.9990 chunk 567 optimal weight: 40.0000 chunk 1012 optimal weight: 30.0000 chunk 633 optimal weight: 10.0000 chunk 617 optimal weight: 10.0000 chunk 467 optimal weight: 50.0000 overall best weight: 6.6090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 30 ASN ** X 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 54 GLN b 34 HIS ** b 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 59 ASN h 46 GLN h 74 ASN i 49 ASN ** i 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 15 ASN ** n 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 16 HIS ** p 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 119 ASN ** 1 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 58 ASN ** 9 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 GLN G 29 ASN H 45 HIS J 69 HIS K 52 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4884 moved from start: 1.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 160709 Z= 0.192 Angle : 0.676 14.590 240348 Z= 0.345 Chirality : 0.037 0.399 30762 Planarity : 0.005 0.103 12915 Dihedral : 17.345 179.053 63245 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 34.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.66 % Favored : 91.26 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.51 % Twisted General : 0.21 % 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: -2.09 (0.10), residues: 5936 helix: -0.17 (0.12), residues: 1871 sheet: -1.80 (0.15), residues: 1019 loop : -2.03 (0.11), residues: 3046 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 457 time to evaluate : 6.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 458 average time/residue: 1.3594 time to fit residues: 1082.1059 Evaluate side-chains 339 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 6.272 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.6632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 626 optimal weight: 0.0020 chunk 404 optimal weight: 40.0000 chunk 605 optimal weight: 50.0000 chunk 305 optimal weight: 8.9990 chunk 199 optimal weight: 20.0000 chunk 196 optimal weight: 7.9990 chunk 644 optimal weight: 50.0000 chunk 690 optimal weight: 30.0000 chunk 500 optimal weight: 50.0000 chunk 94 optimal weight: 10.0000 chunk 796 optimal weight: 30.0000 overall best weight: 9.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 19 ASN W 58 ASN W 128 ASN ** X 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 3 ASN c 77 HIS ** e 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 46 GLN h 74 ASN ** i 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 25 GLN l 27 ASN ** n 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 ASN ** U 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 119 ASN ** 1 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN G 29 ASN G 79 ASN J 69 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4988 moved from start: 1.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.103 160709 Z= 0.238 Angle : 0.733 14.251 240348 Z= 0.371 Chirality : 0.039 0.325 30762 Planarity : 0.006 0.156 12915 Dihedral : 17.589 178.414 63245 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 42.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.87 % Favored : 90.06 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.51 % Twisted General : 0.17 % 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: -2.14 (0.10), residues: 5936 helix: -0.31 (0.11), residues: 1892 sheet: -1.77 (0.16), residues: 991 loop : -2.03 (0.11), residues: 3053 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 427 time to evaluate : 6.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 428 average time/residue: 1.3346 time to fit residues: 1011.3949 Evaluate side-chains 333 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 332 time to evaluate : 6.348 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.2317 time to fit residues: 8.9883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 921 optimal weight: 7.9990 chunk 970 optimal weight: 20.0000 chunk 885 optimal weight: 7.9990 chunk 943 optimal weight: 0.1980 chunk 568 optimal weight: 40.0000 chunk 411 optimal weight: 50.0000 chunk 741 optimal weight: 40.0000 chunk 289 optimal weight: 8.9990 chunk 853 optimal weight: 7.9990 chunk 892 optimal weight: 20.0000 chunk 940 optimal weight: 2.9990 overall best weight: 5.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 GLN ** Q 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 67 ASN a 3 HIS b 34 HIS ** b 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 74 ASN ** i 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 6 ASN ** p 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 66 ASN U 119 ASN 1 94 HIS ** 1 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 38 GLN ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 29 ASN J 69 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4877 moved from start: 1.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.091 160709 Z= 0.172 Angle : 0.647 13.128 240348 Z= 0.331 Chirality : 0.036 0.358 30762 Planarity : 0.005 0.130 12915 Dihedral : 17.220 178.473 63245 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 32.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.59 % Favored : 91.32 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.51 % Twisted General : 0.16 % 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: -2.02 (0.10), residues: 5936 helix: -0.17 (0.12), residues: 1895 sheet: -1.67 (0.16), residues: 1005 loop : -2.00 (0.11), residues: 3036 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 428 time to evaluate : 6.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 428 average time/residue: 1.3541 time to fit residues: 1019.9130 Evaluate side-chains 332 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 5.758 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.1401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 619 optimal weight: 8.9990 chunk 998 optimal weight: 8.9990 chunk 609 optimal weight: 50.0000 chunk 473 optimal weight: 40.0000 chunk 693 optimal weight: 40.0000 chunk 1047 optimal weight: 50.0000 chunk 963 optimal weight: 6.9990 chunk 833 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 chunk 644 optimal weight: 50.0000 chunk 511 optimal weight: 50.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 165 HIS V 19 ASN ** X 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 34 HIS ** b 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 52 ASN c 77 HIS ** e 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 74 ASN ** i 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 66 ASN U 119 ASN 1 94 HIS ** 1 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 176 HIS ** 2 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 29 ASN J 69 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4973 moved from start: 1.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.099 160709 Z= 0.218 Angle : 0.692 12.623 240348 Z= 0.351 Chirality : 0.037 0.449 30762 Planarity : 0.005 0.106 12915 Dihedral : 17.439 179.322 63245 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 40.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.64 % Favored : 90.30 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.51 % Twisted General : 0.17 % 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: -2.08 (0.10), residues: 5936 helix: -0.24 (0.12), residues: 1888 sheet: -1.77 (0.16), residues: 1002 loop : -2.00 (0.11), residues: 3046 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 420 time to evaluate : 6.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 420 average time/residue: 1.3368 time to fit residues: 991.2023 Evaluate side-chains 323 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 323 time to evaluate : 5.700 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.0567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 662 optimal weight: 40.0000 chunk 888 optimal weight: 50.0000 chunk 255 optimal weight: 7.9990 chunk 768 optimal weight: 30.0000 chunk 123 optimal weight: 50.0000 chunk 231 optimal weight: 5.9990 chunk 835 optimal weight: 20.0000 chunk 349 optimal weight: 50.0000 chunk 857 optimal weight: 0.9980 chunk 105 optimal weight: 50.0000 chunk 153 optimal weight: 30.0000 overall best weight: 12.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 200 HIS ** P 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 130 GLN Q 167 ASN ** S 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 30 ASN ** V 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 3 GLN X 5 GLN ** X 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 31 HIS b 34 HIS ** b 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 14 HIS ** d 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 74 ASN ** i 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 66 ASN ** U 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 39 HIS ** 1 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 94 HIS ** 1 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 140 ASN ** 3 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 HIS ** I 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 14 HIS ** K 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.053170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.038621 restraints weight = 2723392.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.038834 restraints weight = 2357081.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.038828 restraints weight = 2029464.858| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 1.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.154 160709 Z= 0.329 Angle : 0.900 14.551 240348 Z= 0.454 Chirality : 0.046 0.432 30762 Planarity : 0.008 0.233 12915 Dihedral : 18.729 177.757 63245 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 59.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.40 % Favored : 88.46 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.51 % Twisted General : 0.22 % 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: -2.68 (0.10), residues: 5936 helix: -0.88 (0.11), residues: 1860 sheet: -1.91 (0.16), residues: 945 loop : -2.33 (0.10), residues: 3131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24572.14 seconds wall clock time: 442 minutes 46.52 seconds (26566.52 seconds total)