Starting phenix.real_space_refine (version: 1.21rc1) on Thu Aug 31 16:29:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h4n_0137/08_2023/6h4n_0137_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h4n_0137/08_2023/6h4n_0137.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h4n_0137/08_2023/6h4n_0137.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h4n_0137/08_2023/6h4n_0137.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h4n_0137/08_2023/6h4n_0137_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h4n_0137/08_2023/6h4n_0137_neut.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.018 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: 5 Type Number sf(0) Gaussians P 4636 5.49 5 S 154 5.16 5 C 74269 2.51 5 N 27457 2.21 5 O 40766 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b ARG 107": "NH1" <-> "NH2" Residue "b ARG 224": "NH1" <-> "NH2" Residue "c ARG 106": "NH1" <-> "NH2" Residue "c ARG 130": "NH1" <-> "NH2" Residue "e ARG 156": "NH1" <-> "NH2" Residue "f TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 123": "NH1" <-> "NH2" Residue "l ARG 55": "NH1" <-> "NH2" Residue "p ARG 28": "NH1" <-> "NH2" Residue "p PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 111": "NH1" <-> "NH2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "G ARG 2": "NH1" <-> "NH2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 162": "NH1" <-> "NH2" Residue "G ARG 169": "NH1" <-> "NH2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 59": "NH1" <-> "NH2" Residue "M TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 71": "NH1" <-> "NH2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "O PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P ARG 61": "NH1" <-> "NH2" Residue "P ARG 88": "NH1" <-> "NH2" Residue "P TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 100": "NH1" <-> "NH2" Residue "P ARG 108": "NH1" <-> "NH2" Residue "Q ARG 2": "NH1" <-> "NH2" Residue "Q ARG 5": "NH1" <-> "NH2" Residue "Q ARG 12": "NH1" <-> "NH2" Residue "Q ARG 32": "NH1" <-> "NH2" Residue "Q ARG 47": "NH1" <-> "NH2" Residue "Q ARG 69": "NH1" <-> "NH2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T ARG 73": "NH1" <-> "NH2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 81": "NH1" <-> "NH2" Residue "U ARG 85": "NH1" <-> "NH2" Residue "U ARG 93": "NH1" <-> "NH2" Residue "V TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 10": "NH1" <-> "NH2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "0 ARG 9": "NH1" <-> "NH2" Residue "0 ARG 15": "NH1" <-> "NH2" Residue "0 ARG 39": "NH1" <-> "NH2" Residue "0 ARG 51": "NH1" <-> "NH2" Residue "1 ARG 43": "NH1" <-> "NH2" Residue "1 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 3": "NH1" <-> "NH2" Residue "2 ARG 12": "NH1" <-> "NH2" Residue "2 ARG 14": "NH1" <-> "NH2" Residue "2 ARG 19": "NH1" <-> "NH2" Residue "2 ARG 21": "NH1" <-> "NH2" Residue "2 ARG 33": "NH1" <-> "NH2" Residue "2 ARG 41": "NH1" <-> "NH2" Residue "3 ARG 12": "NH1" <-> "NH2" Residue "3 ARG 29": "NH1" <-> "NH2" Residue "3 ARG 39": "NH1" <-> "NH2" Residue "3 ARG 41": "NH1" <-> "NH2" Residue "4 ARG 12": "NH1" <-> "NH2" Residue "4 ARG 24": "NH1" <-> "NH2" Residue "6 ARG 49": "NH1" <-> "NH2" Residue "6 ARG 56": "NH1" <-> "NH2" Residue "y ASP 73": "OD1" <-> "OD2" Residue "y GLU 76": "OE1" <-> "OE2" Residue "y ARG 273": "NH1" <-> "NH2" Residue "y ARG 283": "NH1" <-> "NH2" Residue "y TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 340": "NH1" <-> "NH2" Residue "x ARG 17": "NH1" <-> "NH2" Residue "x TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 147282 Number of models: 1 Model: "" Number of chains: 57 Chain: "a" Number of atoms: 32916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1534, 32916 Classifications: {'RNA': 1534} Modifications used: {'p5*END': 1, 'rna2p_pur': 110, 'rna2p_pyr': 68, 'rna3p_pur': 764, 'rna3p_pyr': 592} Link IDs: {'rna2p': 178, 'rna3p': 1355} Chain: "b" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1704 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "c" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 198} Chain: "d" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "e" Number of atoms: 1141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1141 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 151} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "f" 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: "g" Number of atoms: 1266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1266 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 5, 'TRANS': 155} Chain: "h" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "i" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "j" 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: "k" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 869 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "l" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "m" 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: "n" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 799 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "o" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "p" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "q" 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: "r" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 504 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "s" 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: "t" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "u" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 495 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "A" Number of atoms: 62261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2900, 62261 Classifications: {'RNA': 2900} Modifications used: {'p5*END': 1, 'rna2p_pur': 248, 'rna2p_pyr': 121, 'rna3p_pur': 1426, 'rna3p_pyr': 1105} Link IDs: {'rna2p': 369, 'rna3p': 2530} Chain breaks: 1 Chain: "B" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2572 Classifications: {'RNA': 120} Modifications used: {'p5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 5, 'rna3p_pur': 57, 'rna3p_pyr': 50} Link IDs: {'rna2p': 13, 'rna3p': 106} Chain: "C" 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: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "E" 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: "F" 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: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "H" 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: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" 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: "L" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "N" 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: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" 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: "T" 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: "U" 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: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "0" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "1" 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: "2" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "3" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "4" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "6" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "w" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1642 Classifications: {'RNA': 77} Modifications used: {'p5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 6, 'rna3p_pur': 30, 'rna3p_pyr': 32} Link IDs: {'rna2p': 14, 'rna3p': 62} Chain breaks: 1 Chain: "v" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 453 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "y" Number of atoms: 2180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2180 Classifications: {'peptide': 351} Incomplete info: {'truncation_to_alanine': 159} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 340} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 575 Unresolved non-hydrogen angles: 733 Unresolved non-hydrogen dihedrals: 468 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 3, 'ASP:plan': 12, 'PHE:plan': 6, 'GLU:plan': 21, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 318 Chain: "x" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 754 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 94} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 4, 'rna3p_pyr': 1} Link IDs: {'rna2p': 3, 'rna3p': 1} Time building chain proxies: 52.78, per 1000 atoms: 0.36 Number of scatterers: 147282 At special positions: 0 Unit cell: (267.748, 277.504, 231.976, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 154 16.00 P 4636 15.00 O 40766 8.00 N 27457 7.00 C 74269 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 6 18 " - pdb=" SG CYS 6 40 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 55.64 Conformation dependent library (CDL) restraints added in 5.8 seconds 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11368 Finding SS restraints... Secondary structure from input PDB file: 179 helices and 77 sheets defined 33.4% alpha, 16.9% beta 1555 base pairs and 2549 stacking pairs defined. Time for finding SS restraints: 56.98 Creating SS restraints... Processing helix chain 'b' and resid 23 through 27 removed outlier: 3.583A pdb=" N LYS b 27 " --> pdb=" O PRO b 24 " (cutoff:3.500A) Processing helix chain 'b' and resid 41 through 61 removed outlier: 3.874A pdb=" N VAL b 46 " --> pdb=" O LEU b 42 " (cutoff:3.500A) Proline residue: b 47 - end of helix removed outlier: 3.739A pdb=" N GLU b 55 " --> pdb=" O GLU b 51 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS b 58 " --> pdb=" O ALA b 54 " (cutoff:3.500A) Processing helix chain 'b' and resid 75 through 85 removed outlier: 3.760A pdb=" N VAL b 79 " --> pdb=" O ALA b 75 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS b 80 " --> pdb=" O SER b 76 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER b 85 " --> pdb=" O ASP b 81 " (cutoff:3.500A) Processing helix chain 'b' and resid 102 through 122 removed outlier: 4.675A pdb=" N GLN b 108 " --> pdb=" O LYS b 104 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER b 109 " --> pdb=" O THR b 105 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN b 119 " --> pdb=" O ASP b 115 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ASP b 122 " --> pdb=" O THR b 118 " (cutoff:3.500A) Processing helix chain 'b' and resid 129 through 148 removed outlier: 3.779A pdb=" N ARG b 138 " --> pdb=" O LEU b 134 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASN b 145 " --> pdb=" O GLU b 141 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER b 146 " --> pdb=" O LYS b 142 " (cutoff:3.500A) Processing helix chain 'b' and resid 168 through 178 removed outlier: 3.971A pdb=" N LEU b 178 " --> pdb=" O GLU b 174 " (cutoff:3.500A) Processing helix chain 'b' and resid 205 through 224 removed outlier: 4.200A pdb=" N LEU b 213 " --> pdb=" O VAL b 209 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 46 removed outlier: 4.011A pdb=" N ASP c 35 " --> pdb=" O ASN c 31 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG c 39 " --> pdb=" O ASP c 35 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 77 removed outlier: 3.707A pdb=" N VAL c 75 " --> pdb=" O ARG c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 94 removed outlier: 3.995A pdb=" N GLU c 84 " --> pdb=" O GLY c 80 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL c 89 " --> pdb=" O LYS c 85 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE c 93 " --> pdb=" O VAL c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 125 Processing helix chain 'c' and resid 128 through 142 removed outlier: 3.881A pdb=" N VAL c 137 " --> pdb=" O MET c 133 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 15 Processing helix chain 'd' and resid 48 through 65 removed outlier: 3.751A pdb=" N GLN d 53 " --> pdb=" O ASP d 49 " (cutoff:3.500A) Processing helix chain 'd' and resid 67 through 81 Processing helix chain 'd' and resid 84 through 94 Processing helix chain 'd' and resid 96 through 105 Processing helix chain 'd' and resid 109 through 119 Processing helix chain 'd' and resid 152 through 161 Processing helix chain 'd' and resid 162 through 164 No H-bonds generated for 'chain 'd' and resid 162 through 164' Processing helix chain 'd' and resid 186 through 190 Processing helix chain 'd' and resid 195 through 205 removed outlier: 4.047A pdb=" N ILE d 199 " --> pdb=" O ASN d 195 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 68 removed outlier: 3.986A pdb=" N ARG e 68 " --> pdb=" O GLU e 64 " (cutoff:3.500A) Processing helix chain 'e' and resid 110 through 118 Processing helix chain 'e' and resid 131 through 146 Processing helix chain 'e' and resid 148 through 156 Processing helix chain 'e' and resid 159 through 164 Processing helix chain 'f' and resid 12 through 16 removed outlier: 5.454A pdb=" N GLU f 16 " --> pdb=" O ASP f 13 " (cutoff:3.500A) Processing helix chain 'f' and resid 17 through 31 Processing helix chain 'f' and resid 67 through 80 Processing helix chain 'g' and resid 20 through 30 removed outlier: 3.570A pdb=" N LEU g 29 " --> pdb=" O PHE g 25 " (cutoff:3.500A) Processing helix chain 'g' and resid 31 through 33 No H-bonds generated for 'chain 'g' and resid 31 through 33' Processing helix chain 'g' and resid 34 through 52 removed outlier: 3.999A pdb=" N ALA g 38 " --> pdb=" O LYS g 34 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR g 48 " --> pdb=" O SER g 44 " (cutoff:3.500A) Processing helix chain 'g' and resid 56 through 66 Processing helix chain 'g' and resid 91 through 109 removed outlier: 4.456A pdb=" N ASN g 96 " --> pdb=" O PRO g 92 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA g 97 " --> pdb=" O VAL g 93 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TRP g 102 " --> pdb=" O LEU g 98 " (cutoff:3.500A) Processing helix chain 'g' and resid 114 through 128 Processing helix chain 'g' and resid 132 through 147 Processing helix chain 'h' and resid 4 through 20 removed outlier: 3.628A pdb=" N ARG h 12 " --> pdb=" O ASP h 8 " (cutoff:3.500A) Processing helix chain 'h' and resid 29 through 43 Processing helix chain 'h' and resid 112 through 119 removed outlier: 3.594A pdb=" N GLN h 117 " --> pdb=" O ARG h 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 44 through 49 removed outlier: 4.148A pdb=" N ARG i 48 " --> pdb=" O ARG i 44 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 54 removed outlier: 3.938A pdb=" N LEU i 53 " --> pdb=" O GLN i 49 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL i 54 " --> pdb=" O PRO i 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 49 through 54' Processing helix chain 'i' and resid 70 through 86 removed outlier: 3.667A pdb=" N THR i 83 " --> pdb=" O ARG i 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 90 through 95 Processing helix chain 'j' and resid 14 through 32 removed outlier: 4.614A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA j 23 " --> pdb=" O ASP j 19 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU j 27 " --> pdb=" O ALA j 23 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N THR j 28 " --> pdb=" O GLU j 24 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 88 removed outlier: 3.771A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) Processing helix chain 'k' and resid 52 through 57 Processing helix chain 'k' and resid 58 through 71 removed outlier: 3.667A pdb=" N ALA k 62 " --> pdb=" O THR k 58 " (cutoff:3.500A) Processing helix chain 'k' and resid 73 through 77 Processing helix chain 'k' and resid 93 through 101 removed outlier: 3.537A pdb=" N LEU k 99 " --> pdb=" O THR k 95 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 9 Processing helix chain 'l' and resid 114 through 118 removed outlier: 4.490A pdb=" N VAL l 118 " --> pdb=" O LYS l 115 " (cutoff:3.500A) Processing helix chain 'm' and resid 13 through 18 Processing helix chain 'm' and resid 19 through 21 No H-bonds generated for 'chain 'm' and resid 19 through 21' Processing helix chain 'm' and resid 27 through 37 removed outlier: 3.557A pdb=" N LEU m 33 " --> pdb=" O SER m 29 " (cutoff:3.500A) Processing helix chain 'm' and resid 48 through 60 removed outlier: 4.539A pdb=" N THR m 54 " --> pdb=" O GLY m 50 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP m 57 " --> pdb=" O ASP m 53 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU m 58 " --> pdb=" O THR m 54 " (cutoff:3.500A) Processing helix chain 'm' and resid 64 through 83 Processing helix chain 'm' and resid 84 through 91 Processing helix chain 'm' and resid 105 through 110 Processing helix chain 'n' and resid 2 through 19 Processing helix chain 'n' and resid 24 through 29 Processing helix chain 'n' and resid 38 through 48 removed outlier: 3.656A pdb=" N TRP n 42 " --> pdb=" O ASP n 38 " (cutoff:3.500A) Processing helix chain 'n' and resid 52 through 60 removed outlier: 3.687A pdb=" N SER n 56 " --> pdb=" O ARG n 53 " (cutoff:3.500A) Proline residue: n 57 - end of helix removed outlier: 3.751A pdb=" N GLN n 60 " --> pdb=" O PRO n 57 " (cutoff:3.500A) Processing helix chain 'n' and resid 82 through 91 Processing helix chain 'o' and resid 3 through 15 Processing helix chain 'o' and resid 23 through 42 removed outlier: 4.473A pdb=" N GLY o 40 " --> pdb=" O ASN o 36 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N HIS o 41 " --> pdb=" O HIS o 37 " (cutoff:3.500A) Processing helix chain 'o' and resid 48 through 73 removed outlier: 4.076A pdb=" N GLY o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) Processing helix chain 'o' and resid 73 through 85 Processing helix chain 'p' and resid 53 through 64 Processing helix chain 'p' and resid 68 through 78 removed outlier: 3.555A pdb=" N LYS p 76 " --> pdb=" O ALA p 72 " (cutoff:3.500A) Processing helix chain 'r' and resid 11 through 16 Processing helix chain 'r' and resid 24 through 29 Processing helix chain 'r' and resid 40 through 45 Processing helix chain 'r' and resid 47 through 64 Processing helix chain 's' and resid 11 through 24 removed outlier: 4.425A pdb=" N LYS s 17 " --> pdb=" O HIS s 13 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLU s 23 " --> pdb=" O GLU s 19 " (cutoff:3.500A) Processing helix chain 's' and resid 40 through 44 removed outlier: 3.569A pdb=" N ILE s 44 " --> pdb=" O PRO s 41 " (cutoff:3.500A) Processing helix chain 's' and resid 62 through 66 removed outlier: 3.904A pdb=" N VAL s 66 " --> pdb=" O ASP s 63 " (cutoff:3.500A) Processing helix chain 's' and resid 69 through 74 removed outlier: 3.561A pdb=" N PHE s 73 " --> pdb=" O LEU s 70 " (cutoff:3.500A) Processing helix chain 't' and resid 7 through 28 removed outlier: 3.640A pdb=" N ILE t 11 " --> pdb=" O LYS t 7 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU t 14 " --> pdb=" O ALA t 10 " (cutoff:3.500A) Processing helix chain 't' and resid 29 through 41 removed outlier: 3.721A pdb=" N VAL t 34 " --> pdb=" O PHE t 30 " (cutoff:3.500A) Processing helix chain 't' and resid 42 through 63 Proline residue: t 55 - end of helix Processing helix chain 't' and resid 68 through 86 removed outlier: 3.712A pdb=" N LYS t 84 " --> pdb=" O ALA t 80 " (cutoff:3.500A) Processing helix chain 'u' and resid 13 through 32 Processing helix chain 'u' and resid 40 through 61 Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 196 through 202 removed outlier: 4.124A pdb=" N MET C 200 " --> pdb=" O ALA C 197 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG C 202 " --> pdb=" O HIS C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 214 removed outlier: 4.007A pdb=" N ALA C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 61 through 72 Processing helix chain 'D' and resid 97 through 102 Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 40 removed outlier: 3.879A pdb=" N ARG E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 115 Processing helix chain 'E' and resid 130 through 141 removed outlier: 3.899A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 162 removed outlier: 3.751A pdb=" N ALA E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 Processing helix chain 'E' and resid 190 through 201 Processing helix chain 'F' and resid 2 through 10 Processing helix chain 'F' and resid 10 through 20 Processing helix chain 'F' and resid 23 through 27 Processing helix chain 'F' and resid 47 through 60 removed outlier: 3.933A pdb=" N ASN F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA F 57 " --> pdb=" O ALA F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 106 Processing helix chain 'F' and resid 161 through 172 removed outlier: 3.675A pdb=" N GLY F 165 " --> pdb=" O SER F 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 80 Processing helix chain 'G' and resid 136 through 151 removed outlier: 4.068A pdb=" N ARG G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 29 Processing helix chain 'H' and resid 42 through 48 Processing helix chain 'H' and resid 53 through 59 removed outlier: 3.861A pdb=" N LYS H 57 " --> pdb=" O GLU H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 71 removed outlier: 4.475A pdb=" N ALA H 64 " --> pdb=" O GLU H 60 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA H 69 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 106 Processing helix chain 'J' and resid 24 through 38 removed outlier: 4.043A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 62 removed outlier: 3.644A pdb=" N LYS J 61 " --> pdb=" O ASN J 58 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL J 62 " --> pdb=" O ALA J 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 58 through 62' Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 89 through 96 Processing helix chain 'J' and resid 98 through 107 Processing helix chain 'J' and resid 112 through 119 Processing helix chain 'J' and resid 132 through 136 Processing helix chain 'K' and resid 104 through 108 Processing helix chain 'K' and resid 112 through 118 Processing helix chain 'L' and resid 37 through 41 Processing helix chain 'L' and resid 56 through 61 removed outlier: 3.602A pdb=" N LEU L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 138 Processing helix chain 'M' and resid 43 through 57 removed outlier: 3.548A pdb=" N ALA M 52 " --> pdb=" O ALA M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 122 Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.591A pdb=" N GLY N 26 " --> pdb=" O ARG N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 55 removed outlier: 4.385A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU N 49 " --> pdb=" O ARG N 45 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 59 through 69 Processing helix chain 'N' and resid 74 through 82 removed outlier: 4.825A pdb=" N PHE N 80 " --> pdb=" O VAL N 76 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 22 removed outlier: 4.800A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 60 Processing helix chain 'O' and resid 67 through 86 removed outlier: 3.937A pdb=" N LEU O 83 " --> pdb=" O ALA O 79 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 113 Processing helix chain 'P' and resid 2 through 10 removed outlier: 3.532A pdb=" N GLN P 6 " --> pdb=" O ASN P 2 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 102 removed outlier: 3.643A pdb=" N ARG P 100 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG P 102 " --> pdb=" O LEU P 99 " (cutoff:3.500A) Processing helix chain 'P' and resid 103 through 107 removed outlier: 3.647A pdb=" N ALA P 106 " --> pdb=" O THR P 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 20 removed outlier: 3.838A pdb=" N ALA Q 9 " --> pdb=" O ARG Q 5 " (cutoff:3.500A) Processing helix chain 'Q' and resid 24 through 28 Processing helix chain 'Q' and resid 30 through 71 removed outlier: 4.372A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 85 Processing helix chain 'Q' and resid 90 through 101 Processing helix chain 'Q' and resid 101 through 117 Processing helix chain 'S' and resid 13 through 22 removed outlier: 4.302A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 37 Processing helix chain 'S' and resid 42 through 62 removed outlier: 3.872A pdb=" N VAL S 50 " --> pdb=" O LEU S 46 " (cutoff:3.500A) Processing helix chain 'S' and resid 88 through 92 removed outlier: 3.680A pdb=" N GLY S 91 " --> pdb=" O ARG S 88 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 8 removed outlier: 3.554A pdb=" N LEU T 8 " --> pdb=" O GLU T 4 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 27 Processing helix chain 'T' and resid 39 through 52 Processing helix chain 'V' and resid 14 through 23 Processing helix chain 'V' and resid 44 through 51 Processing helix chain 'V' and resid 52 through 57 removed outlier: 6.101A pdb=" N GLU V 55 " --> pdb=" O ALA V 52 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR V 57 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 61 Processing helix chain 'X' and resid 62 through 71 Processing helix chain 'Y' and resid 9 through 23 Processing helix chain 'Y' and resid 24 through 35 Processing helix chain 'Y' and resid 41 through 61 removed outlier: 3.537A pdb=" N GLN Y 45 " --> pdb=" O HIS Y 41 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 50 Processing helix chain '0' and resid 8 through 16 Processing helix chain '2' and resid 8 through 17 Processing helix chain '2' and resid 17 through 23 Processing helix chain '2' and resid 24 through 38 removed outlier: 3.517A pdb=" N ARG 2 28 " --> pdb=" O THR 2 24 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN 2 29 " --> pdb=" O LYS 2 25 " (cutoff:3.500A) Processing helix chain '3' and resid 6 through 13 Processing helix chain '3' and resid 36 through 42 Processing helix chain '3' and resid 54 through 61 Processing helix chain '4' and resid 30 through 33 Processing helix chain '6' and resid 56 through 61 Processing helix chain 'v' and resid 11 through 22 Processing helix chain 'v' and resid 33 through 53 removed outlier: 4.763A pdb=" N GLN v 39 " --> pdb=" O ASN v 35 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA v 49 " --> pdb=" O ARG v 45 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP v 50 " --> pdb=" O GLU v 46 " (cutoff:3.500A) Processing helix chain 'y' and resid 4 through 16 Processing helix chain 'y' and resid 84 through 104 removed outlier: 3.964A pdb=" N LYS y 88 " --> pdb=" O LEU y 84 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA y 89 " --> pdb=" O SER y 85 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS y 90 " --> pdb=" O ARG y 86 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG y 91 " --> pdb=" O GLU y 87 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS y 92 " --> pdb=" O LYS y 88 " (cutoff:3.500A) Processing helix chain 'y' and resid 317 through 322 removed outlier: 3.877A pdb=" N VAL y 321 " --> pdb=" O HIS y 317 " (cutoff:3.500A) Processing helix chain 'y' and resid 350 through 361 removed outlier: 3.563A pdb=" N TRP y 354 " --> pdb=" O LYS y 350 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS y 361 " --> pdb=" O PHE y 357 " (cutoff:3.500A) Processing helix chain 'y' and resid 405 through 410 removed outlier: 3.897A pdb=" N TYR y 409 " --> pdb=" O ALA y 405 " (cutoff:3.500A) Processing helix chain 'y' and resid 425 through 428 removed outlier: 4.164A pdb=" N ARG y 428 " --> pdb=" O GLU y 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 425 through 428' Processing helix chain 'x' and resid 13 through 32 removed outlier: 3.703A pdb=" N ASP x 32 " --> pdb=" O GLU x 28 " (cutoff:3.500A) Processing helix chain 'x' and resid 70 through 92 Processing sheet with id=AA1, first strand: chain 'b' and resid 89 through 91 removed outlier: 6.133A pdb=" N ILE b 66 " --> pdb=" O PHE b 89 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N VAL b 91 " --> pdb=" O ILE b 66 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N PHE b 68 " --> pdb=" O VAL b 91 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LEU b 160 " --> pdb=" O PHE b 183 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE b 185 " --> pdb=" O LEU b 160 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL b 162 " --> pdb=" O ILE b 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'c' and resid 51 through 57 removed outlier: 6.624A pdb=" N HIS c 68 " --> pdb=" O SER c 52 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE c 54 " --> pdb=" O THR c 66 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N THR c 66 " --> pdb=" O ILE c 54 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE c 56 " --> pdb=" O ARG c 64 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ARG c 64 " --> pdb=" O ILE c 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'c' and resid 163 through 166 Processing sheet with id=AA4, first strand: chain 'c' and resid 163 through 166 removed outlier: 4.862A pdb=" N VAL c 194 " --> pdb=" O THR c 190 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR c 190 " --> pdb=" O VAL c 194 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLY c 196 " --> pdb=" O ALA c 188 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ALA c 188 " --> pdb=" O GLY c 196 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LYS c 198 " --> pdb=" O SER c 186 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N SER c 186 " --> pdb=" O LYS c 198 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N TRP c 200 " --> pdb=" O ASN c 184 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ASN c 184 " --> pdb=" O TRP c 200 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N PHE c 202 " --> pdb=" O ASP c 182 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASP c 182 " --> pdb=" O PHE c 202 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY c 204 " --> pdb=" O ASP c 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'd' and resid 127 through 128 removed outlier: 3.705A pdb=" N ASP d 140 " --> pdb=" O PHE d 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'e' and resid 13 through 14 Processing sheet with id=AA7, first strand: chain 'e' and resid 18 through 21 Processing sheet with id=AA8, first strand: chain 'e' and resid 93 through 96 removed outlier: 5.915A pdb=" N GLY e 103 " --> pdb=" O VAL e 122 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ALA e 124 " --> pdb=" O GLY e 103 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE e 105 " --> pdb=" O ALA e 124 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ALA e 126 " --> pdb=" O ILE e 105 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'f' and resid 41 through 45 removed outlier: 4.652A pdb=" N ASP f 41 " --> pdb=" O LEU f 61 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU f 61 " --> pdb=" O ASP f 41 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY f 43 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET f 9 " --> pdb=" O ILE f 85 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'g' and resid 72 through 76 Processing sheet with id=AB2, first strand: chain 'h' and resid 23 through 27 removed outlier: 5.053A pdb=" N ASP h 47 " --> pdb=" O THR h 61 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'h' and resid 74 through 76 removed outlier: 5.346A pdb=" N ILE h 124 " --> pdb=" O SER h 104 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N SER h 104 " --> pdb=" O ILE h 124 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'i' and resid 5 through 7 removed outlier: 6.182A pdb=" N VAL i 28 " --> pdb=" O ILE i 64 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'j' and resid 40 through 45 removed outlier: 4.604A pdb=" N LEU j 71 " --> pdb=" O LEU j 42 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR j 44 " --> pdb=" O THR j 69 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N THR j 69 " --> pdb=" O THR j 44 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'j' and resid 48 through 52 Processing sheet with id=AB7, first strand: chain 'k' and resid 40 through 45 removed outlier: 7.091A pdb=" N ALA k 40 " --> pdb=" O ASP k 35 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ASP k 35 " --> pdb=" O ALA k 40 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU k 81 " --> pdb=" O ASN k 108 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N THR k 110 " --> pdb=" O LEU k 81 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL k 83 " --> pdb=" O THR k 110 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'l' and resid 29 through 31 removed outlier: 4.236A pdb=" N TYR l 94 " --> pdb=" O THR l 63 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'p' and resid 50 through 52 removed outlier: 5.791A pdb=" N ARG p 35 " --> pdb=" O VAL p 21 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL p 21 " --> pdb=" O ARG p 35 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL p 2 " --> pdb=" O THR p 66 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'q' and resid 6 through 7 removed outlier: 5.625A pdb=" N ILE q 60 " --> pdb=" O ARG q 76 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ARG q 76 " --> pdb=" O ILE q 60 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N GLU q 62 " --> pdb=" O LEU q 74 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N LEU q 74 " --> pdb=" O GLU q 62 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ARG q 64 " --> pdb=" O TRP q 72 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N TRP q 72 " --> pdb=" O ARG q 64 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LYS q 70 " --> pdb=" O LEU q 66 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N HIS q 44 " --> pdb=" O LYS q 70 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TRP q 72 " --> pdb=" O HIS q 44 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL q 21 " --> pdb=" O VAL q 12 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'q' and resid 25 through 29 Processing sheet with id=AC3, first strand: chain 's' and resid 30 through 32 removed outlier: 6.241A pdb=" N LEU s 30 " --> pdb=" O ALA s 49 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N HIS s 51 " --> pdb=" O LEU s 30 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N THR s 32 " --> pdb=" O HIS s 51 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AC5, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AC6, first strand: chain 'C' and resid 100 through 104 removed outlier: 6.776A pdb=" N ILE C 90 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LEU C 80 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU C 92 " --> pdb=" O GLU C 78 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 128 through 130 removed outlier: 3.528A pdb=" N ALA C 189 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR C 172 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ARG C 166 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N TYR C 170 " --> pdb=" O ARG C 166 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N MET C 180 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 4 through 15 removed outlier: 5.756A pdb=" N LYS D 8 " --> pdb=" O GLU D 28 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLU D 28 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N GLY D 10 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL D 26 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LYS D 190 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL D 177 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N VAL D 107 " --> pdb=" O SER D 174 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 77 through 83 removed outlier: 5.312A pdb=" N GLY D 78 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N THR D 52 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA D 47 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N VAL D 37 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 117 through 119 Processing sheet with id=AD2, first strand: chain 'E' and resid 2 through 4 removed outlier: 3.647A pdb=" N LEU E 12 " --> pdb=" O LEU E 3 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 118 through 121 removed outlier: 6.521A pdb=" N ILE E 119 " --> pdb=" O MET E 188 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL E 146 " --> pdb=" O ASP E 168 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ARG E 170 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE E 148 " --> pdb=" O ARG E 170 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 65 through 68 Processing sheet with id=AD5, first strand: chain 'G' and resid 8 through 9 Processing sheet with id=AD6, first strand: chain 'G' and resid 22 through 26 Processing sheet with id=AD7, first strand: chain 'G' and resid 121 through 123 Processing sheet with id=AD8, first strand: chain 'G' and resid 94 through 98 removed outlier: 3.556A pdb=" N VAL G 101 " --> pdb=" O LYS G 98 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 18 through 20 Processing sheet with id=AE1, first strand: chain 'H' and resid 77 through 80 removed outlier: 3.584A pdb=" N VAL H 142 " --> pdb=" O VAL H 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 122 through 124 removed outlier: 6.398A pdb=" N TRP J 15 " --> pdb=" O GLN J 138 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 73 through 77 Processing sheet with id=AE4, first strand: chain 'K' and resid 6 through 10 removed outlier: 3.899A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL K 10 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ARG K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLU K 45 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL K 19 " --> pdb=" O ILE K 43 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE K 43 " --> pdb=" O VAL K 19 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N CYS K 21 " --> pdb=" O ILE K 41 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE K 41 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LYS K 23 " --> pdb=" O ILE K 39 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ILE K 39 " --> pdb=" O LYS K 23 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N CYS K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASN K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N LEU K 86 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 69 through 70 removed outlier: 3.542A pdb=" N VAL K 69 " --> pdb=" O ILE K 77 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL K 76 " --> pdb=" O VAL P 72 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA P 57 " --> pdb=" O ILE P 49 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ILE P 49 " --> pdb=" O ALA P 57 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR P 59 " --> pdb=" O ILE P 47 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ILE P 63 " --> pdb=" O GLU P 43 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N GLU P 43 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLU P 26 " --> pdb=" O VAL P 85 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N VAL P 85 " --> pdb=" O GLU P 26 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LYS P 28 " --> pdb=" O ILE P 83 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ILE P 83 " --> pdb=" O LYS P 28 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N TRP P 30 " --> pdb=" O ASP P 81 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASP P 81 " --> pdb=" O TRP P 30 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 89 through 90 removed outlier: 5.771A pdb=" N VAL L 90 " --> pdb=" O ARG L 123 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU L 143 " --> pdb=" O VAL L 122 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 109 through 110 Processing sheet with id=AE8, first strand: chain 'M' and resid 62 through 65 removed outlier: 3.505A pdb=" N LYS M 100 " --> pdb=" O ALA M 35 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU M 104 " --> pdb=" O PHE M 31 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N PHE M 31 " --> pdb=" O GLU M 104 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 39 through 42 removed outlier: 3.721A pdb=" N ASN M 88 " --> pdb=" O GLU M 75 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE M 73 " --> pdb=" O GLU M 90 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 33 through 37 removed outlier: 4.642A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'O' and resid 47 through 49 removed outlier: 6.396A pdb=" N VAL O 39 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL O 28 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'R' and resid 11 through 14 removed outlier: 6.192A pdb=" N VAL R 4 " --> pdb=" O LEU R 39 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'R' and resid 19 through 22 removed outlier: 7.381A pdb=" N VAL R 96 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N VAL R 64 " --> pdb=" O VAL R 96 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ILE R 98 " --> pdb=" O GLU R 62 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU R 62 " --> pdb=" O ILE R 98 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'R' and resid 72 through 78 removed outlier: 4.131A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'S' and resid 4 through 10 removed outlier: 5.419A pdb=" N ILE S 4 " --> pdb=" O VAL S 107 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL S 107 " --> pdb=" O ILE S 4 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LYS S 6 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL S 105 " --> pdb=" O LYS S 6 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ARG S 8 " --> pdb=" O ILE S 103 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE S 103 " --> pdb=" O ARG S 8 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'S' and resid 82 through 85 Processing sheet with id=AF8, first strand: chain 'T' and resid 11 through 14 removed outlier: 4.180A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL T 57 " --> pdb=" O THR T 86 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'T' and resid 67 through 70 removed outlier: 3.769A pdb=" N ARG T 73 " --> pdb=" O HIS T 70 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'U' and resid 64 through 65 removed outlier: 6.443A pdb=" N LYS U 32 " --> pdb=" O VAL U 27 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N VAL U 27 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'U' and resid 42 through 44 Processing sheet with id=AG3, first strand: chain 'U' and resid 82 through 86 Processing sheet with id=AG4, first strand: chain 'V' and resid 2 through 8 removed outlier: 7.813A pdb=" N ASN V 5 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASP V 43 " --> pdb=" O ASN V 5 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N LYS V 25 " --> pdb=" O GLN V 87 " (cutoff:3.500A) removed outlier: 9.669A pdb=" N ILE V 89 " --> pdb=" O LYS V 25 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N PHE V 91 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ILE V 29 " --> pdb=" O PHE V 91 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ARG V 93 " --> pdb=" O ILE V 29 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TYR V 31 " --> pdb=" O ARG V 93 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLN V 78 " --> pdb=" O GLN V 87 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE V 89 " --> pdb=" O ASP V 76 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASP V 76 " --> pdb=" O ILE V 89 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE V 91 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ALA V 74 " --> pdb=" O PHE V 91 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ARG V 93 " --> pdb=" O VAL V 72 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL V 72 " --> pdb=" O ARG V 93 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'W' and resid 18 through 19 removed outlier: 6.667A pdb=" N LEU W 55 " --> pdb=" O ILE W 33 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'W' and resid 26 through 27 removed outlier: 3.526A pdb=" N LYS W 62 " --> pdb=" O GLU W 79 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N HIS W 42 " --> pdb=" O ILE W 76 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N ILE W 78 " --> pdb=" O HIS W 42 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'X' and resid 12 through 15 Processing sheet with id=AG8, first strand: chain 'X' and resid 32 through 39 Processing sheet with id=AG9, first strand: chain 'Z' and resid 34 through 38 Processing sheet with id=AH1, first strand: chain '0' and resid 28 through 29 Processing sheet with id=AH2, first strand: chain '1' and resid 19 through 23 removed outlier: 3.596A pdb=" N GLN 1 44 " --> pdb=" O ASP 1 39 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain '3' and resid 14 through 15 Processing sheet with id=AH4, first strand: chain '4' and resid 2 through 3 removed outlier: 6.979A pdb=" N LYS 4 2 " --> pdb=" O ARG 4 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain '4' and resid 14 through 19 Processing sheet with id=AH6, first strand: chain '6' and resid 22 through 26 removed outlier: 3.518A pdb=" N LEU 6 32 " --> pdb=" O THR 6 13 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'y' and resid 26 through 27 removed outlier: 3.914A pdb=" N GLY y 26 " --> pdb=" O VAL y 68 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL y 68 " --> pdb=" O GLY y 26 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'y' and resid 30 through 32 removed outlier: 3.727A pdb=" N ALA y 30 " --> pdb=" O LEU y 37 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'y' and resid 121 through 124 Processing sheet with id=AI1, first strand: chain 'y' and resid 156 through 159 Processing sheet with id=AI2, first strand: chain 'y' and resid 282 through 283 Processing sheet with id=AI3, first strand: chain 'y' and resid 370 through 371 Processing sheet with id=AI4, first strand: chain 'y' and resid 423 through 424 removed outlier: 3.722A pdb=" N ILE y 429 " --> pdb=" O ALA y 424 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'x' and resid 2 through 8 removed outlier: 3.703A pdb=" N GLN x 2 " --> pdb=" O ASN x 35 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN x 36 " --> pdb=" O HIS x 55 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N HIS x 48 " --> pdb=" O GLY x 67 " (cutoff:3.500A) 1833 hydrogen bonds defined for protein. 5151 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3924 hydrogen bonds 6224 hydrogen bond angles 0 basepair planarities 1555 basepair parallelities 2549 stacking parallelities Total time for adding SS restraints: 237.97 Time building geometry restraints manager: 60.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.70 - 0.93: 1 0.93 - 1.15: 0 1.15 - 1.37: 50530 1.37 - 1.59: 104371 1.59 - 1.82: 4948 Bond restraints: 159850 Sorted by residual: bond pdb=" C GLN x 2 " pdb=" N LEU x 3 " ideal model delta sigma weight residual 1.328 0.704 0.624 1.42e-02 4.96e+03 1.93e+03 bond pdb=" N SER y 169 " pdb=" CA SER y 169 " ideal model delta sigma weight residual 1.457 1.608 -0.151 1.29e-02 6.01e+03 1.37e+02 bond pdb=" N LYS y 88 " pdb=" CA LYS y 88 " ideal model delta sigma weight residual 1.457 1.547 -0.090 1.29e-02 6.01e+03 4.85e+01 bond pdb=" C VAL y 168 " pdb=" N SER y 169 " ideal model delta sigma weight residual 1.332 1.422 -0.090 1.40e-02 5.10e+03 4.14e+01 bond pdb=" CA LYS y 88 " pdb=" C LYS y 88 " ideal model delta sigma weight residual 1.523 1.602 -0.079 1.34e-02 5.57e+03 3.46e+01 ... (remaining 159845 not shown) Histogram of bond angle deviations from ideal: 84.94 - 98.70: 12 98.70 - 112.47: 112440 112.47 - 126.24: 111277 126.24 - 140.00: 15092 140.00 - 153.77: 3 Bond angle restraints: 238824 Sorted by residual: angle pdb=" O LEU x 3 " pdb=" C LEU x 3 " pdb=" N ASN x 4 " ideal model delta sigma weight residual 123.03 84.94 38.09 1.13e+00 7.83e-01 1.14e+03 angle pdb=" CA LEU x 3 " pdb=" C LEU x 3 " pdb=" N ASN x 4 " ideal model delta sigma weight residual 115.23 153.77 -38.54 1.30e+00 5.92e-01 8.79e+02 angle pdb=" C LYS y 88 " pdb=" N ALA y 89 " pdb=" CA ALA y 89 " ideal model delta sigma weight residual 120.38 143.60 -23.22 1.37e+00 5.33e-01 2.87e+02 angle pdb=" C LEU x 3 " pdb=" N ASN x 4 " pdb=" CA ASN x 4 " ideal model delta sigma weight residual 121.33 144.38 -23.05 1.40e+00 5.10e-01 2.71e+02 angle pdb=" N VAL y 332 " pdb=" CA VAL y 332 " pdb=" C VAL y 332 " ideal model delta sigma weight residual 110.62 124.63 -14.01 1.02e+00 9.61e-01 1.89e+02 ... (remaining 238819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 82494 35.96 - 71.92: 2806 71.92 - 107.88: 212 107.88 - 143.84: 15 143.84 - 179.80: 34 Dihedral angle restraints: 85561 sinusoidal: 67941 harmonic: 17620 Sorted by residual: dihedral pdb=" CA HIS b 17 " pdb=" C HIS b 17 " pdb=" N GLN b 18 " pdb=" CA GLN b 18 " ideal model delta harmonic sigma weight residual -180.00 -114.10 -65.90 0 5.00e+00 4.00e-02 1.74e+02 dihedral pdb=" CA HIS g 152 " pdb=" C HIS g 152 " pdb=" N TYR g 153 " pdb=" CA TYR g 153 " ideal model delta harmonic sigma weight residual -180.00 -122.34 -57.66 0 5.00e+00 4.00e-02 1.33e+02 dihedral pdb=" CA ALA l 22 " pdb=" C ALA l 22 " pdb=" N LEU l 23 " pdb=" CA LEU l 23 " ideal model delta harmonic sigma weight residual -180.00 -128.46 -51.54 0 5.00e+00 4.00e-02 1.06e+02 ... (remaining 85558 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 30199 0.160 - 0.319: 271 0.319 - 0.479: 22 0.479 - 0.639: 4 0.639 - 0.799: 2 Chirality restraints: 30498 Sorted by residual: chirality pdb=" C3' U I1537 " pdb=" C4' U I1537 " pdb=" O3' U I1537 " pdb=" C2' U I1537 " both_signs ideal model delta sigma weight residual False -2.74 -1.95 -0.80 2.00e-01 2.50e+01 1.59e+01 chirality pdb=" CA HIS y 305 " pdb=" N HIS y 305 " pdb=" C HIS y 305 " pdb=" CB HIS y 305 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CA SER y 169 " pdb=" N SER y 169 " pdb=" C SER y 169 " pdb=" CB SER y 169 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.23e+00 ... (remaining 30495 not shown) Planarity restraints: 13064 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U I1537 " 0.057 2.00e-02 2.50e+03 3.15e-02 2.23e+01 pdb=" N1 U I1537 " -0.049 2.00e-02 2.50e+03 pdb=" C2 U I1537 " -0.033 2.00e-02 2.50e+03 pdb=" O2 U I1537 " 0.002 2.00e-02 2.50e+03 pdb=" N3 U I1537 " 0.007 2.00e-02 2.50e+03 pdb=" C4 U I1537 " 0.040 2.00e-02 2.50e+03 pdb=" O4 U I1537 " -0.001 2.00e-02 2.50e+03 pdb=" C5 U I1537 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U I1537 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A2137 " -0.051 2.00e-02 2.50e+03 2.59e-02 1.51e+01 pdb=" N1 U A2137 " 0.053 2.00e-02 2.50e+03 pdb=" C2 U A2137 " 0.004 2.00e-02 2.50e+03 pdb=" O2 U A2137 " 0.006 2.00e-02 2.50e+03 pdb=" N3 U A2137 " 0.003 2.00e-02 2.50e+03 pdb=" C4 U A2137 " -0.012 2.00e-02 2.50e+03 pdb=" O4 U A2137 " -0.015 2.00e-02 2.50e+03 pdb=" C5 U A2137 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U A2137 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE m 8 " 0.063 5.00e-02 4.00e+02 9.58e-02 1.47e+01 pdb=" N PRO m 9 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO m 9 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO m 9 " 0.053 5.00e-02 4.00e+02 ... (remaining 13061 not shown) Histogram of nonbonded interaction distances: 0.42 - 1.31: 5 1.31 - 2.21: 50 2.21 - 3.11: 95205 3.11 - 4.00: 478352 4.00 - 4.90: 775672 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1349284 Sorted by model distance: nonbonded pdb=" CD2 HIS b 17 " pdb=" CE LYS y 43 " model vdw 0.418 3.660 nonbonded pdb=" O ALA y 358 " pdb=" CB ASN y 362 " model vdw 0.920 3.440 nonbonded pdb=" N ARG y 163 " pdb=" CG GLU y 298 " model vdw 1.135 3.520 nonbonded pdb=" NH1 ARG b 34 " pdb=" NH2 ARG y 19 " model vdw 1.210 3.200 nonbonded pdb=" OP1 C a1533 " pdb=" NZ LYS v 26 " model vdw 1.305 2.520 ... (remaining 1349279 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.800 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: 0.090 Extract box with map and model: 20.300 Check model and map are aligned: 1.600 Set scattering table: 1.020 Process input model: 502.580 Find NCS groups from input model: 3.030 Set up NCS constraints: 0.340 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:11.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 542.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.624 159850 Z= 0.446 Angle : 0.960 38.537 238824 Z= 0.502 Chirality : 0.050 0.799 30498 Planarity : 0.007 0.096 13064 Dihedral : 14.510 179.802 74190 Min Nonbonded Distance : 0.418 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.54 % Allowed : 10.10 % Favored : 89.36 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 1.55 % Twisted General : 0.50 % 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: -4.18 (0.09), residues: 6082 helix: -3.02 (0.08), residues: 1855 sheet: -2.05 (0.14), residues: 1132 loop : -2.90 (0.09), residues: 3095 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2509 residues out of total 5071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 2473 time to evaluate : 6.489 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 outliers start: 36 outliers final: 11 residues processed: 2489 average time/residue: 2.2111 time to fit residues: 7848.6821 Evaluate side-chains 1866 residues out of total 5071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1855 time to evaluate : 6.528 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 5 average time/residue: 1.0497 time to fit residues: 16.9660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 892 optimal weight: 0.8980 chunk 801 optimal weight: 1.9990 chunk 444 optimal weight: 10.0000 chunk 273 optimal weight: 5.9990 chunk 540 optimal weight: 10.0000 chunk 428 optimal weight: 7.9990 chunk 828 optimal weight: 0.9990 chunk 320 optimal weight: 0.7980 chunk 503 optimal weight: 10.0000 chunk 616 optimal weight: 8.9990 chunk 959 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 41 ASN ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 ASN c 138 GLN c 189 HIS d 53 GLN d 58 GLN d 70 GLN d 99 ASN e 76 ASN e 88 HIS e 131 ASN f 3 HIS ** g 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 4 GLN i 30 ASN i 109 GLN i 125 GLN j 70 HIS k 28 ASN l 4 ASN l 28 GLN m 51 GLN n 3 GLN o 45 HIS o 79 GLN p 18 GLN p 79 ASN ** q 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 30 HIS r 51 GLN s 55 GLN t 20 ASN t 51 ASN ** t 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN D 130 GLN D 136 ASN D 150 GLN D 164 GLN F 134 GLN G 103 ASN H 11 ASN H 73 ASN H 135 HIS H 145 ASN J 40 HIS K 5 GLN K 29 HIS L 4 ASN L 35 HIS M 22 GLN N 9 GLN N 81 ASN N 107 ASN O 38 GLN P 40 GLN Q 19 GLN Q 36 GLN Q 43 GLN Q 55 GLN Q 71 ASN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 HIS S 61 ASN U 65 GLN ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 8 ASN Y 45 GLN Y 58 ASN Z 8 GLN ** Z 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 29 GLN 4 35 GLN 4 37 GLN v 14 GLN v 18 GLN x 8 ASN x 36 GLN x 55 HIS ** x 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 95 HIS Total number of N/Q/H flips: 76 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.121 159850 Z= 0.165 Angle : 0.603 15.046 238824 Z= 0.315 Chirality : 0.035 0.395 30498 Planarity : 0.005 0.067 13064 Dihedral : 14.350 179.256 62455 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.52 % Favored : 91.20 % Rotamer Outliers : 6.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 1.03 % Twisted General : 0.25 % 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: -2.87 (0.10), residues: 6082 helix: -1.13 (0.11), residues: 1875 sheet: -1.62 (0.14), residues: 1148 loop : -2.54 (0.10), residues: 3059 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2308 residues out of total 5071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 295 poor density : 2013 time to evaluate : 6.596 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 outliers start: 295 outliers final: 116 residues processed: 2108 average time/residue: 2.1505 time to fit residues: 6612.4725 Evaluate side-chains 1948 residues out of total 5071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 1832 time to evaluate : 6.642 Switching outliers to nearest non-outliers outliers start: 116 outliers final: 43 residues processed: 78 average time/residue: 1.2722 time to fit residues: 185.3746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 533 optimal weight: 20.0000 chunk 297 optimal weight: 1.9990 chunk 798 optimal weight: 40.0000 chunk 653 optimal weight: 10.0000 chunk 264 optimal weight: 9.9990 chunk 961 optimal weight: 10.0000 chunk 1038 optimal weight: 2.9990 chunk 856 optimal weight: 3.9990 chunk 953 optimal weight: 2.9990 chunk 327 optimal weight: 7.9990 chunk 771 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 57 ASN c 122 GLN c 138 GLN c 139 ASN d 58 GLN d 70 GLN ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 131 ASN ** g 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 85 GLN ** g 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 141 HIS i 4 GLN i 30 ASN i 109 GLN i 125 GLN l 4 ASN l 111 GLN n 3 GLN n 43 ASN n 60 GLN o 39 GLN p 63 GLN ** q 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 20 ASN t 47 GLN C 52 HIS C 116 GLN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN D 130 GLN D 136 ASN E 41 GLN E 163 ASN F 51 ASN F 134 GLN G 63 GLN G 103 ASN H 133 GLN J 128 ASN K 5 GLN K 29 HIS L 4 ASN L 38 GLN L 99 ASN N 9 GLN N 23 ASN N 107 ASN O 38 GLN P 2 ASN ** P 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN Q 51 GLN ** Q 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 71 ASN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN U 65 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 ASN Y 58 ASN ** Z 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 29 GLN 4 35 GLN x 36 GLN Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 159850 Z= 0.259 Angle : 0.595 12.339 238824 Z= 0.310 Chirality : 0.036 0.370 30498 Planarity : 0.005 0.067 13064 Dihedral : 14.183 179.854 62455 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.26 % Favored : 90.56 % Rotamer Outliers : 7.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 1.03 % 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: -2.16 (0.10), residues: 6082 helix: -0.16 (0.12), residues: 1886 sheet: -1.37 (0.15), residues: 1144 loop : -2.33 (0.10), residues: 3052 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2331 residues out of total 5071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 383 poor density : 1948 time to evaluate : 6.726 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 outliers start: 383 outliers final: 173 residues processed: 2090 average time/residue: 2.1187 time to fit residues: 6480.2091 Evaluate side-chains 1993 residues out of total 5071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 1820 time to evaluate : 5.864 Switching outliers to nearest non-outliers outliers start: 173 outliers final: 71 residues processed: 109 average time/residue: 1.0682 time to fit residues: 220.1678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 950 optimal weight: 4.9990 chunk 722 optimal weight: 10.0000 chunk 499 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 458 optimal weight: 8.9990 chunk 645 optimal weight: 10.0000 chunk 965 optimal weight: 4.9990 chunk 1021 optimal weight: 40.0000 chunk 504 optimal weight: 10.0000 chunk 914 optimal weight: 9.9990 chunk 275 optimal weight: 8.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 23 ASN c 7 ASN c 138 GLN c 139 ASN d 70 GLN d 151 GLN e 60 GLN ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 96 GLN f 68 GLN f 94 HIS g 85 GLN g 141 HIS g 152 HIS i 4 GLN i 30 ASN i 109 GLN i 125 GLN k 118 ASN l 111 GLN n 3 GLN ** n 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 63 GLN ** q 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 20 ASN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN D 130 GLN D 136 ASN E 41 GLN E 62 GLN F 51 ASN F 134 GLN G 29 ASN G 44 HIS G 103 ASN J 80 HIS ** K 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN N 9 GLN N 23 ASN N 107 ASN O 38 GLN P 2 ASN P 11 GLN ** P 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN Q 51 GLN Q 71 ASN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN S 61 ASN T 48 GLN T 70 HIS U 65 GLN W 46 ASN Y 58 ASN 2 26 ASN 2 29 GLN 4 35 GLN v 18 GLN v 32 GLN Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.083 159850 Z= 0.525 Angle : 0.721 12.064 238824 Z= 0.371 Chirality : 0.043 0.426 30498 Planarity : 0.006 0.103 13064 Dihedral : 14.356 178.670 62455 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.87 % Favored : 89.94 % Rotamer Outliers : 9.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 1.03 % Twisted General : 0.20 % 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: -2.00 (0.10), residues: 6082 helix: 0.05 (0.12), residues: 1882 sheet: -1.34 (0.15), residues: 1164 loop : -2.25 (0.10), residues: 3036 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2348 residues out of total 5071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 472 poor density : 1876 time to evaluate : 10.642 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 outliers start: 472 outliers final: 262 residues processed: 2069 average time/residue: 2.1160 time to fit residues: 6430.0986 Evaluate side-chains 2076 residues out of total 5071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 1814 time to evaluate : 6.557 Switching outliers to nearest non-outliers outliers start: 262 outliers final: 106 residues processed: 161 average time/residue: 1.2457 time to fit residues: 367.5776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 850 optimal weight: 4.9990 chunk 579 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 760 optimal weight: 2.9990 chunk 421 optimal weight: 7.9990 chunk 871 optimal weight: 4.9990 chunk 706 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 521 optimal weight: 10.0000 chunk 917 optimal weight: 5.9990 chunk 257 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 108 GLN c 138 GLN c 139 ASN d 53 GLN e 60 GLN ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 96 GLN f 68 GLN g 85 GLN g 141 HIS h 17 GLN i 4 GLN i 30 ASN i 109 GLN i 125 GLN j 64 GLN l 111 GLN n 3 GLN n 43 ASN o 61 GLN p 63 GLN ** q 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 46 HIS s 55 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 ASN E 195 GLN F 51 ASN G 103 ASN K 29 HIS K 89 ASN L 4 ASN M 22 GLN N 9 GLN N 23 ASN N 107 ASN O 38 GLN ** P 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN Q 71 ASN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN U 65 GLN U 98 ASN ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 GLN Y 58 ASN Z 19 HIS 4 35 GLN v 32 GLN ** v 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.107 159850 Z= 0.270 Angle : 0.609 13.856 238824 Z= 0.317 Chirality : 0.037 0.384 30498 Planarity : 0.005 0.095 13064 Dihedral : 14.200 179.967 62455 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.34 % Favored : 90.51 % Rotamer Outliers : 7.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 1.03 % 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: -1.72 (0.10), residues: 6082 helix: 0.36 (0.12), residues: 1883 sheet: -1.16 (0.15), residues: 1130 loop : -2.15 (0.10), residues: 3069 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2251 residues out of total 5071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 371 poor density : 1880 time to evaluate : 6.547 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 outliers start: 371 outliers final: 230 residues processed: 2036 average time/residue: 2.0629 time to fit residues: 6152.7174 Evaluate side-chains 2032 residues out of total 5071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 1802 time to evaluate : 6.649 Switching outliers to nearest non-outliers outliers start: 230 outliers final: 117 residues processed: 121 average time/residue: 1.3109 time to fit residues: 283.1888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 343 optimal weight: 1.9990 chunk 920 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 chunk 599 optimal weight: 40.0000 chunk 252 optimal weight: 7.9990 chunk 1022 optimal weight: 20.0000 chunk 848 optimal weight: 3.9990 chunk 473 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 338 optimal weight: 9.9990 chunk 536 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 41 ASN c 138 GLN c 139 ASN d 70 GLN ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 96 GLN f 68 GLN g 85 GLN g 141 HIS h 17 GLN i 4 GLN i 30 ASN i 109 GLN i 125 GLN l 111 GLN n 3 GLN n 43 ASN n 60 GLN o 61 GLN p 29 ASN p 63 GLN ** q 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 51 HIS t 47 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN D 136 ASN E 195 GLN F 51 ASN G 44 HIS G 103 ASN K 29 HIS N 9 GLN N 18 GLN N 23 ASN N 107 ASN O 38 GLN ** P 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN S 61 ASN T 15 HIS ** T 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 GLN U 65 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 58 ASN 4 35 GLN 6 33 ASN v 32 GLN v 36 GLN ** v 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.105 159850 Z= 0.323 Angle : 0.624 17.943 238824 Z= 0.324 Chirality : 0.038 0.396 30498 Planarity : 0.005 0.093 13064 Dihedral : 14.157 178.999 62455 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.85 % Favored : 89.99 % Rotamer Outliers : 7.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 1.03 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.10), residues: 6082 helix: 0.46 (0.12), residues: 1892 sheet: -1.09 (0.15), residues: 1113 loop : -2.13 (0.10), residues: 3077 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2226 residues out of total 5071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 376 poor density : 1850 time to evaluate : 6.633 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 outliers start: 376 outliers final: 243 residues processed: 2014 average time/residue: 2.0463 time to fit residues: 6049.6547 Evaluate side-chains 2060 residues out of total 5071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 1817 time to evaluate : 6.538 Switching outliers to nearest non-outliers outliers start: 243 outliers final: 124 residues processed: 125 average time/residue: 1.2963 time to fit residues: 291.9060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 986 optimal weight: 0.9990 chunk 115 optimal weight: 10.0000 chunk 582 optimal weight: 7.9990 chunk 746 optimal weight: 3.9990 chunk 578 optimal weight: 10.0000 chunk 860 optimal weight: 4.9990 chunk 571 optimal weight: 10.0000 chunk 1018 optimal weight: 10.0000 chunk 637 optimal weight: 7.9990 chunk 621 optimal weight: 10.0000 chunk 470 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 176 ASN c 7 ASN c 138 GLN c 139 ASN e 60 GLN e 72 ASN ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 96 GLN f 68 GLN g 85 GLN g 141 HIS h 17 GLN i 4 GLN i 30 ASN i 109 GLN i 125 GLN l 111 GLN n 3 GLN n 43 ASN n 60 GLN o 39 GLN p 63 GLN ** q 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 19 HIS ** t 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN D 136 ASN E 195 GLN F 51 ASN G 44 HIS G 103 ASN K 29 HIS N 9 GLN N 18 GLN N 23 ASN N 107 ASN O 38 GLN ** P 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 9 HIS S 57 ASN T 48 GLN U 65 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 35 GLN 6 33 ASN v 32 GLN ** v 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 7 GLN x 62 HIS Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.105 159850 Z= 0.371 Angle : 0.651 18.493 238824 Z= 0.336 Chirality : 0.039 0.408 30498 Planarity : 0.005 0.093 13064 Dihedral : 14.172 178.943 62455 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.88 % Favored : 89.95 % Rotamer Outliers : 7.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 1.03 % 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: -1.60 (0.10), residues: 6082 helix: 0.48 (0.12), residues: 1898 sheet: -1.03 (0.15), residues: 1121 loop : -2.14 (0.10), residues: 3063 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2190 residues out of total 5071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 348 poor density : 1842 time to evaluate : 6.633 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 outliers start: 348 outliers final: 228 residues processed: 2010 average time/residue: 2.1347 time to fit residues: 6336.8282 Evaluate side-chains 2031 residues out of total 5071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 1803 time to evaluate : 6.624 Switching outliers to nearest non-outliers outliers start: 228 outliers final: 124 residues processed: 111 average time/residue: 1.2597 time to fit residues: 253.6262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 630 optimal weight: 10.0000 chunk 406 optimal weight: 10.0000 chunk 608 optimal weight: 10.0000 chunk 306 optimal weight: 0.9990 chunk 200 optimal weight: 4.9990 chunk 197 optimal weight: 5.9990 chunk 647 optimal weight: 10.0000 chunk 694 optimal weight: 4.9990 chunk 503 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 800 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 7 ASN c 138 GLN c 139 ASN ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 96 GLN f 68 GLN g 85 GLN g 141 HIS h 17 GLN i 4 GLN i 30 ASN i 31 GLN i 109 GLN i 125 GLN l 111 GLN n 3 GLN n 43 ASN n 66 GLN p 63 GLN ** q 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 55 GLN s 56 HIS t 19 HIS t 47 GLN ** t 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN E 195 GLN F 51 ASN G 44 HIS G 103 ASN ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS K 29 HIS ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 9 GLN N 23 ASN N 107 ASN O 38 GLN P 9 GLN ** P 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 28 ASN T 48 GLN V 49 ASN ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 35 GLN 6 33 ASN v 32 GLN ** v 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 7 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.104 159850 Z= 0.311 Angle : 0.634 20.197 238824 Z= 0.327 Chirality : 0.037 0.395 30498 Planarity : 0.005 0.089 13064 Dihedral : 14.131 179.433 62455 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.91 % Favored : 89.94 % Rotamer Outliers : 6.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 1.03 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.11), residues: 6082 helix: 0.56 (0.12), residues: 1896 sheet: -1.05 (0.15), residues: 1116 loop : -2.07 (0.11), residues: 3070 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2164 residues out of total 5071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 310 poor density : 1854 time to evaluate : 6.676 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 outliers start: 310 outliers final: 212 residues processed: 2015 average time/residue: 2.0685 time to fit residues: 6090.0553 Evaluate side-chains 2018 residues out of total 5071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1806 time to evaluate : 6.656 Switching outliers to nearest non-outliers outliers start: 212 outliers final: 129 residues processed: 91 average time/residue: 1.3459 time to fit residues: 219.2449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 926 optimal weight: 7.9990 chunk 976 optimal weight: 6.9990 chunk 890 optimal weight: 2.9990 chunk 949 optimal weight: 0.9990 chunk 975 optimal weight: 8.9990 chunk 571 optimal weight: 10.0000 chunk 413 optimal weight: 10.0000 chunk 745 optimal weight: 3.9990 chunk 291 optimal weight: 10.0000 chunk 857 optimal weight: 2.9990 chunk 897 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 145 ASN ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 7 ASN c 138 GLN c 139 ASN e 60 GLN ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 96 GLN ** g 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 141 HIS h 17 GLN i 4 GLN i 24 ASN i 30 ASN i 109 GLN i 125 GLN l 111 GLN n 3 GLN n 43 ASN n 60 GLN n 66 GLN p 63 GLN ** t 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN D 130 GLN D 136 ASN E 195 GLN ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 ASN ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 2 GLN H 66 ASN J 80 HIS K 29 HIS ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 9 GLN N 23 ASN O 38 GLN Q 19 GLN ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 GLN T 92 ASN U 65 GLN ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 35 GLN v 32 GLN ** v 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.106 159850 Z= 0.265 Angle : 0.621 19.582 238824 Z= 0.320 Chirality : 0.036 0.428 30498 Planarity : 0.005 0.087 13064 Dihedral : 14.069 179.794 62455 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.68 % Favored : 90.17 % Rotamer Outliers : 5.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 1.03 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.11), residues: 6082 helix: 0.63 (0.12), residues: 1897 sheet: -0.91 (0.15), residues: 1108 loop : -2.07 (0.11), residues: 3077 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2089 residues out of total 5071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 1832 time to evaluate : 6.605 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 outliers start: 257 outliers final: 197 residues processed: 1979 average time/residue: 2.1134 time to fit residues: 6125.1439 Evaluate side-chains 1977 residues out of total 5071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 1780 time to evaluate : 6.598 Switching outliers to nearest non-outliers outliers start: 197 outliers final: 128 residues processed: 78 average time/residue: 1.3528 time to fit residues: 188.8687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 946 optimal weight: 0.9990 chunk 623 optimal weight: 10.0000 chunk 1003 optimal weight: 30.0000 chunk 612 optimal weight: 10.0000 chunk 476 optimal weight: 10.0000 chunk 697 optimal weight: 0.7980 chunk 1053 optimal weight: 3.9990 chunk 969 optimal weight: 1.9990 chunk 838 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 647 optimal weight: 10.0000 overall best weight: 3.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 145 ASN ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 7 ASN c 138 GLN c 139 ASN ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN g 85 GLN g 141 HIS h 17 GLN i 4 GLN i 30 ASN i 109 GLN i 125 GLN l 111 GLN n 3 GLN n 43 ASN n 60 GLN p 63 GLN ** t 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN D 130 GLN D 136 ASN E 195 GLN ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 ASN J 80 HIS K 29 HIS ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 9 GLN N 13 ASN N 23 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN ** P 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN T 28 ASN T 48 GLN U 65 GLN V 49 ASN ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 33 ASN v 32 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.105 159850 Z= 0.274 Angle : 0.628 19.530 238824 Z= 0.323 Chirality : 0.036 0.380 30498 Planarity : 0.005 0.087 13064 Dihedral : 14.031 179.596 62455 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.67 % Favored : 90.20 % Rotamer Outliers : 3.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 1.03 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.11), residues: 6082 helix: 0.67 (0.12), residues: 1896 sheet: -0.86 (0.15), residues: 1099 loop : -2.06 (0.10), residues: 3087 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2017 residues out of total 5071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 1824 time to evaluate : 6.543 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 outliers start: 193 outliers final: 157 residues processed: 1955 average time/residue: 2.0017 time to fit residues: 5766.1418 Evaluate side-chains 1951 residues out of total 5071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1794 time to evaluate : 5.517 Switching outliers to nearest non-outliers outliers start: 157 outliers final: 125 residues processed: 43 average time/residue: 1.1397 time to fit residues: 91.4318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 514 optimal weight: 10.0000 chunk 666 optimal weight: 10.0000 chunk 893 optimal weight: 1.9990 chunk 256 optimal weight: 0.8980 chunk 773 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 233 optimal weight: 10.0000 chunk 839 optimal weight: 8.9990 chunk 351 optimal weight: 9.9990 chunk 862 optimal weight: 8.9990 chunk 106 optimal weight: 10.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -build -allalt -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: