Starting phenix.real_space_refine on Fri Mar 1 03:51:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dnc_7970/03_2024/6dnc_7970_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dnc_7970/03_2024/6dnc_7970.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dnc_7970/03_2024/6dnc_7970.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dnc_7970/03_2024/6dnc_7970.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dnc_7970/03_2024/6dnc_7970_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dnc_7970/03_2024/6dnc_7970_neut.pdb" } resolution = 3.7 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= -0.215 sd= 1.283 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 4729 5.49 5 S 176 5.16 5 C 77119 2.51 5 N 28394 2.21 5 O 42020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 13": "NH1" <-> "NH2" Residue "G ARG 33": "NH1" <-> "NH2" Residue "G ARG 59": "NH1" <-> "NH2" Residue "G ARG 77": "NH1" <-> "NH2" Residue "G ARG 83": "NH1" <-> "NH2" Residue "G ARG 169": "NH1" <-> "NH2" Residue "G ARG 184": "NH1" <-> "NH2" Residue "H ARG 21": "NH1" <-> "NH2" Residue "H ARG 44": "NH1" <-> "NH2" Residue "H ARG 49": "NH1" <-> "NH2" Residue "H ARG 61": "NH1" <-> "NH2" Residue "H ARG 88": "NH1" <-> "NH2" Residue "H ARG 102": "NH1" <-> "NH2" Residue "H ARG 162": "NH1" <-> "NH2" Residue "H ARG 170": "NH1" <-> "NH2" Residue "I ARG 70": "NH1" <-> "NH2" Residue "I ARG 79": "NH1" <-> "NH2" Residue "I ARG 91": "NH1" <-> "NH2" Residue "I ARG 101": "NH1" <-> "NH2" Residue "I ARG 109": "NH1" <-> "NH2" Residue "I ARG 111": "NH1" <-> "NH2" Residue "I ARG 114": "NH1" <-> "NH2" Residue "I ARG 132": "NH1" <-> "NH2" Residue "J ARG 2": "NH1" <-> "NH2" Residue "J ARG 152": "NH1" <-> "NH2" Residue "J ARG 162": "NH1" <-> "NH2" Residue "J ARG 169": "NH1" <-> "NH2" Residue "N ARG 13": "NH1" <-> "NH2" Residue "N ARG 37": "NH1" <-> "NH2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N ARG 120": "NH1" <-> "NH2" Residue "O TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 21": "NH1" <-> "NH2" Residue "P ARG 33": "NH1" <-> "NH2" Residue "P ARG 41": "NH1" <-> "NH2" Residue "P ARG 47": "NH1" <-> "NH2" Residue "P ARG 60": "NH1" <-> "NH2" Residue "P ARG 78": "NH1" <-> "NH2" Residue "P ARG 126": "NH1" <-> "NH2" Residue "Q ARG 10": "NH1" <-> "NH2" Residue "Q ARG 18": "NH1" <-> "NH2" Residue "Q ARG 40": "NH1" <-> "NH2" Residue "Q ARG 44": "NH1" <-> "NH2" Residue "Q ARG 50": "NH1" <-> "NH2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "Q ARG 59": "NH1" <-> "NH2" Residue "Q ARG 114": "NH1" <-> "NH2" Residue "R ARG 8": "NH1" <-> "NH2" Residue "R ARG 12": "NH1" <-> "NH2" Residue "R ARG 17": "NH1" <-> "NH2" Residue "R ARG 22": "NH1" <-> "NH2" Residue "R ARG 46": "NH1" <-> "NH2" Residue "R ARG 63": "NH1" <-> "NH2" Residue "R ARG 64": "NH1" <-> "NH2" Residue "R ARG 69": "NH1" <-> "NH2" Residue "R ARG 71": "NH1" <-> "NH2" Residue "R ARG 96": "NH1" <-> "NH2" Residue "R ARG 118": "NH1" <-> "NH2" Residue "S ARG 10": "NH1" <-> "NH2" Residue "S ARG 16": "NH1" <-> "NH2" Residue "S ARG 25": "NH1" <-> "NH2" Residue "S ARG 81": "NH1" <-> "NH2" Residue "S ARG 94": "NH1" <-> "NH2" Residue "S ARG 102": "NH1" <-> "NH2" Residue "S ARG 111": "NH1" <-> "NH2" Residue "S PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 20": "NH1" <-> "NH2" Residue "T ARG 38": "NH1" <-> "NH2" Residue "T ARG 61": "NH1" <-> "NH2" Residue "T ARG 88": "NH1" <-> "NH2" Residue "T TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 100": "NH1" <-> "NH2" Residue "T ARG 108": "NH1" <-> "NH2" Residue "U ARG 2": "NH1" <-> "NH2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "U ARG 12": "NH1" <-> "NH2" Residue "U ARG 32": "NH1" <-> "NH2" Residue "U ARG 47": "NH1" <-> "NH2" Residue "U ARG 69": "NH1" <-> "NH2" Residue "V ARG 21": "NH1" <-> "NH2" Residue "V ARG 68": "NH1" <-> "NH2" Residue "V ARG 78": "NH1" <-> "NH2" Residue "V ARG 79": "NH1" <-> "NH2" Residue "V ARG 84": "NH1" <-> "NH2" Residue "W ARG 84": "NH1" <-> "NH2" Residue "W ARG 88": "NH1" <-> "NH2" Residue "W ARG 95": "NH1" <-> "NH2" Residue "W ARG 110": "NH1" <-> "NH2" Residue "X ARG 73": "NH1" <-> "NH2" Residue "Y ARG 5": "NH1" <-> "NH2" Residue "Y ARG 6": "NH1" <-> "NH2" Residue "Y ARG 81": "NH1" <-> "NH2" Residue "Y ARG 85": "NH1" <-> "NH2" Residue "Y ARG 93": "NH1" <-> "NH2" Residue "Z TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA ARG 29": "NH1" <-> "NH2" Residue "CA ARG 47": "NH1" <-> "NH2" Residue "CA ARG 52": "NH1" <-> "NH2" Residue "DA ARG 10": "NH1" <-> "NH2" Residue "DA ARG 29": "NH1" <-> "NH2" Residue "DA ARG 44": "NH1" <-> "NH2" Residue "EA PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EA ARG 49": "NH1" <-> "NH2" Residue "EA ARG 56": "NH1" <-> "NH2" Residue "FA ARG 9": "NH1" <-> "NH2" Residue "FA ARG 15": "NH1" <-> "NH2" Residue "FA ARG 39": "NH1" <-> "NH2" Residue "FA ARG 51": "NH1" <-> "NH2" Residue "GA ARG 43": "NH1" <-> "NH2" Residue "HA ARG 3": "NH1" <-> "NH2" Residue "HA ARG 12": "NH1" <-> "NH2" Residue "HA ARG 14": "NH1" <-> "NH2" Residue "HA ARG 19": "NH1" <-> "NH2" Residue "HA ARG 21": "NH1" <-> "NH2" Residue "HA ARG 33": "NH1" <-> "NH2" Residue "HA ARG 41": "NH1" <-> "NH2" Residue "IA ARG 12": "NH1" <-> "NH2" Residue "IA ARG 29": "NH1" <-> "NH2" Residue "IA ARG 39": "NH1" <-> "NH2" Residue "IA ARG 41": "NH1" <-> "NH2" Residue "JA ARG 12": "NH1" <-> "NH2" Residue "JA ARG 24": "NH1" <-> "NH2" Residue "MA ARG 15": "NH1" <-> "NH2" Residue "MA ARG 36": "NH1" <-> "NH2" Residue "MA ARG 50": "NH1" <-> "NH2" Residue "MA ARG 75": "NH1" <-> "NH2" Residue "MA ARG 83": "NH1" <-> "NH2" Residue "OA PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "OA ARG 224": "NH1" <-> "NH2" Residue "PA ARG 106": "NH1" <-> "NH2" Residue "PA ARG 130": "NH1" <-> "NH2" Residue "RA ARG 156": "NH1" <-> "NH2" Residue "TA TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "UA PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "VA PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "VA ARG 123": "NH1" <-> "NH2" Residue "YA ARG 55": "NH1" <-> "NH2" Residue "CB ARG 28": "NH1" <-> "NH2" Residue "EB ARG 11": "NH1" <-> "NH2" Residue "HB ARG 66": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 152438 Number of models: 1 Model: "" Number of chains: 59 Chain: "A" Number of atoms: 33012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33012 Classifications: {'RNA': 1539} Modifications used: {'5*END': 1, 'rna2p_pur': 95, 'rna2p_pyr': 54, 'rna3p_pur': 779, 'rna3p_pyr': 611} Link IDs: {'rna2p': 149, 'rna3p': 1389} Chain: "B" Number of atoms: 62318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62318 Classifications: {'RNA': 2903} Modifications used: {'5*END': 1, 'rna2p_pur': 217, 'rna2p_pyr': 99, 'rna3p_pur': 1457, 'rna3p_pyr': 1130} Link IDs: {'rna2p': 316, 'rna3p': 2586} Chain: "C" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2568 Classifications: {'RNA': 120} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 61, 'rna3p_pyr': 53} Link IDs: {'rna2p': 6, 'rna3p': 113} Chain: "D" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 3, 'rna3p_pur': 34, 'rna3p_pyr': 35} Link IDs: {'rna2p': 8, 'rna3p': 68} Chain: "E" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1637 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 7, 'TRANS': 212} Chain: "F" 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: "G" 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: "H" 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: "I" 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: "J" 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: "K" 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: "L" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 988 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "M" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: "S" 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: "T" 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: "U" 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: "V" 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: "W" 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: "X" 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: "Y" 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: "Z" 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: "AA" 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: "BA" 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: "CA" 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: "DA" 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: "EA" 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: "FA" 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: "GA" 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: "HA" 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: "IA" 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: "JA" 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: "KA" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 412 Classifications: {'RNA': 19} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 13, 'rna3p_pyr': 3} Link IDs: {'rna2p': 2, 'rna3p': 16} Chain: "LA" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 34, 'rna3p_pyr': 33} Link IDs: {'rna2p': 10, 'rna3p': 66} Chain: "MA" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2714 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 9, 'TRANS': 334} Chain breaks: 1 Chain: "OA" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1756 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "PA" 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: "QA" 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: "RA" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1156 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "SA" 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: "TA" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "UA" 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: "VA" 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: "WA" 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: "XA" 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: "YA" 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: "ZA" 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: "AB" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 810 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "BB" 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: "CB" 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: "DB" 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: "EB" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "FB" 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: "GB" 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: "HB" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 544 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Time building chain proxies: 57.50, per 1000 atoms: 0.38 Number of scatterers: 152438 At special positions: 0 Unit cell: (273.465, 262.341, 243.801, 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 176 16.00 P 4729 15.00 O 42020 8.00 N 28394 7.00 C 77119 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 62.98 Conformation dependent library (CDL) restraints added in 7.3 seconds 12824 Ramachandran restraints generated. 6412 Oldfield, 0 Emsley, 6412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11990 Finding SS restraints... Secondary structure from input PDB file: 211 helices and 80 sheets defined 36.1% alpha, 16.2% beta 1377 base pairs and 2417 stacking pairs defined. Time for finding SS restraints: 48.92 Creating SS restraints... Processing helix chain 'E' and resid 7 through 15 removed outlier: 4.018A pdb=" N ILE E 11 " --> pdb=" O ARG E 7 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU E 13 " --> pdb=" O ARG E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 31 removed outlier: 4.105A pdb=" N ILE E 27 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU E 29 " --> pdb=" O GLU E 25 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS E 31 " --> pdb=" O ILE E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 86 Processing helix chain 'E' and resid 100 through 104 removed outlier: 4.140A pdb=" N GLN E 103 " --> pdb=" O LEU E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 121 removed outlier: 3.899A pdb=" N MET E 121 " --> pdb=" O PRO E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 153 removed outlier: 3.594A pdb=" N ALA E 152 " --> pdb=" O ASN E 148 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL E 153 " --> pdb=" O VAL E 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 148 through 153' Processing helix chain 'E' and resid 184 through 199 removed outlier: 3.660A pdb=" N VAL E 194 " --> pdb=" O GLU E 190 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA E 195 " --> pdb=" O ALA E 191 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LEU E 196 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS E 197 " --> pdb=" O LEU E 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 33 Processing helix chain 'F' and resid 196 through 202 removed outlier: 3.921A pdb=" N MET F 200 " --> pdb=" O ALA F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 212 Processing helix chain 'F' and resid 220 through 224 Processing helix chain 'G' and resid 61 through 70 Processing helix chain 'G' and resid 98 through 102 Processing helix chain 'G' and resid 120 through 126 Processing helix chain 'H' and resid 15 through 20 Processing helix chain 'H' and resid 24 through 40 Processing helix chain 'H' and resid 97 through 113 Processing helix chain 'H' and resid 130 through 141 Processing helix chain 'H' and resid 154 through 161 removed outlier: 3.598A pdb=" N ALA H 160 " --> pdb=" O ASN H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 183 Processing helix chain 'H' and resid 190 through 201 Processing helix chain 'I' and resid 2 through 9 Processing helix chain 'I' and resid 9 through 20 removed outlier: 3.770A pdb=" N THR I 17 " --> pdb=" O LYS I 13 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU I 18 " --> pdb=" O LYS I 14 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 60 removed outlier: 4.052A pdb=" N LEU I 49 " --> pdb=" O ASP I 45 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP I 50 " --> pdb=" O LYS I 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 104 Processing helix chain 'I' and resid 106 through 110 Processing helix chain 'I' and resid 161 through 171 removed outlier: 5.375A pdb=" N ALA I 167 " --> pdb=" O GLU I 163 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU I 168 " --> pdb=" O GLU I 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 48 removed outlier: 3.656A pdb=" N ASN J 47 " --> pdb=" O HIS J 44 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR J 48 " --> pdb=" O ALA J 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 44 through 48' Processing helix chain 'J' and resid 59 through 80 Processing helix chain 'J' and resid 136 through 151 removed outlier: 4.373A pdb=" N ARG J 151 " --> pdb=" O LEU J 147 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 29 removed outlier: 3.582A pdb=" N PHE K 29 " --> pdb=" O TYR K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 49 removed outlier: 4.251A pdb=" N ALA K 49 " --> pdb=" O GLU K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 71 Processing helix chain 'K' and resid 96 through 105 Processing helix chain 'K' and resid 111 through 113 No H-bonds generated for 'chain 'K' and resid 111 through 113' Processing helix chain 'L' and resid 3 through 21 removed outlier: 3.861A pdb=" N LYS L 20 " --> pdb=" O SER L 16 " (cutoff:3.500A) Processing helix chain 'L' and resid 33 through 48 removed outlier: 4.358A pdb=" N ARG L 42 " --> pdb=" O MET L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 67 removed outlier: 3.702A pdb=" N THR L 67 " --> pdb=" O ALA L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 78 removed outlier: 4.642A pdb=" N PHE L 76 " --> pdb=" O LYS L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 106 removed outlier: 3.554A pdb=" N PHE L 99 " --> pdb=" O LEU L 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 19 through 28 Proline residue: M 25 - end of helix Processing helix chain 'M' and resid 33 through 46 Processing helix chain 'M' and resid 74 through 83 Processing helix chain 'M' and resid 102 through 116 Processing helix chain 'M' and resid 120 through 136 Processing helix chain 'N' and resid 24 through 38 Processing helix chain 'N' and resid 58 through 62 Processing helix chain 'N' and resid 89 through 94 Processing helix chain 'N' and resid 96 through 107 removed outlier: 4.011A pdb=" N VAL N 100 " --> pdb=" O ARG N 96 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE N 101 " --> pdb=" O PRO N 97 " (cutoff:3.500A) Processing helix chain 'N' and resid 112 through 121 removed outlier: 3.825A pdb=" N LYS N 121 " --> pdb=" O ALA N 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 132 through 136 Processing helix chain 'O' and resid 104 through 108 Processing helix chain 'O' and resid 112 through 117 Processing helix chain 'P' and resid 22 through 26 removed outlier: 3.583A pdb=" N SER P 25 " --> pdb=" O GLY P 22 " (cutoff:3.500A) Processing helix chain 'P' and resid 56 through 61 removed outlier: 3.588A pdb=" N LEU P 61 " --> pdb=" O LEU P 57 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 72 Processing helix chain 'P' and resid 78 through 82 Processing helix chain 'P' and resid 93 through 98 Processing helix chain 'P' and resid 128 through 137 Processing helix chain 'Q' and resid 43 through 58 Processing helix chain 'Q' and resid 109 through 123 removed outlier: 3.759A pdb=" N LYS Q 118 " --> pdb=" O ARG Q 114 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU Q 119 " --> pdb=" O GLU Q 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 32 Processing helix chain 'R' and resid 38 through 55 removed outlier: 4.412A pdb=" N ARG R 46 " --> pdb=" O LYS R 42 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL R 47 " --> pdb=" O GLU R 43 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU R 49 " --> pdb=" O ARG R 45 " (cutoff:3.500A) Proline residue: R 50 - end of helix Processing helix chain 'R' and resid 60 through 69 Processing helix chain 'R' and resid 74 through 79 Processing helix chain 'R' and resid 82 through 88 Processing helix chain 'S' and resid 3 through 22 removed outlier: 5.505A pdb=" N ARG S 13 " --> pdb=" O ARG S 9 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ALA S 14 " --> pdb=" O ARG S 10 " (cutoff:3.500A) Processing helix chain 'S' and resid 55 through 60 Processing helix chain 'S' and resid 67 through 86 Processing helix chain 'S' and resid 101 through 113 Processing helix chain 'T' and resid 2 through 10 Processing helix chain 'T' and resid 52 through 55 Processing helix chain 'T' and resid 96 through 101 removed outlier: 3.589A pdb=" N GLU T 101 " --> pdb=" O TYR T 98 " (cutoff:3.500A) Processing helix chain 'T' and resid 103 through 108 Processing helix chain 'U' and resid 6 through 18 Processing helix chain 'U' and resid 24 through 29 removed outlier: 4.061A pdb=" N SER U 28 " --> pdb=" O GLY U 25 " (cutoff:3.500A) Processing helix chain 'U' and resid 30 through 71 removed outlier: 4.205A pdb=" N GLN U 36 " --> pdb=" O ARG U 32 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG U 50 " --> pdb=" O TYR U 46 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LYS U 53 " --> pdb=" O ARG U 49 " (cutoff:3.500A) Processing helix chain 'U' and resid 74 through 85 Processing helix chain 'U' and resid 90 through 98 removed outlier: 3.664A pdb=" N ASP U 96 " --> pdb=" O LYS U 92 " (cutoff:3.500A) Processing helix chain 'U' and resid 101 through 117 Processing helix chain 'W' and resid 13 through 22 removed outlier: 4.160A pdb=" N VAL W 17 " --> pdb=" O SER W 13 " (cutoff:3.500A) Processing helix chain 'W' and resid 28 through 38 removed outlier: 3.923A pdb=" N TYR W 38 " --> pdb=" O ASP W 34 " (cutoff:3.500A) Processing helix chain 'W' and resid 41 through 62 removed outlier: 3.640A pdb=" N VAL W 50 " --> pdb=" O LEU W 46 " (cutoff:3.500A) Processing helix chain 'W' and resid 89 through 91 No H-bonds generated for 'chain 'W' and resid 89 through 91' Processing helix chain 'X' and resid 2 through 8 Processing helix chain 'X' and resid 17 through 28 Processing helix chain 'X' and resid 39 through 51 Processing helix chain 'Z' and resid 13 through 22 Processing helix chain 'Z' and resid 44 through 49 Processing helix chain 'Z' and resid 53 through 58 removed outlier: 3.816A pdb=" N SER Z 58 " --> pdb=" O GLU Z 55 " (cutoff:3.500A) Processing helix chain 'BA' and resid 52 through 62 Processing helix chain 'BA' and resid 62 through 73 Processing helix chain 'CA' and resid 2 through 6 removed outlier: 3.573A pdb=" N LEUCA 6 " --> pdb=" O LYSCA 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'CA' and resid 2 through 6' Processing helix chain 'CA' and resid 9 through 22 Processing helix chain 'CA' and resid 23 through 34 removed outlier: 3.724A pdb=" N ASNCA 27 " --> pdb=" O ARGCA 23 " (cutoff:3.500A) Processing helix chain 'CA' and resid 40 through 61 Processing helix chain 'DA' and resid 16 through 27 Processing helix chain 'DA' and resid 40 through 48 Processing helix chain 'EA' and resid 45 through 51 Processing helix chain 'EA' and resid 55 through 65 removed outlier: 3.746A pdb=" N ARGEA 63 " --> pdb=" O ARGEA 59 " (cutoff:3.500A) Processing helix chain 'FA' and resid 8 through 16 Processing helix chain 'FA' and resid 17 through 19 No H-bonds generated for 'chain 'FA' and resid 17 through 19' Processing helix chain 'HA' and resid 8 through 16 Processing helix chain 'HA' and resid 17 through 23 Processing helix chain 'HA' and resid 24 through 38 Processing helix chain 'IA' and resid 8 through 12 Processing helix chain 'IA' and resid 36 through 43 Processing helix chain 'IA' and resid 50 through 61 removed outlier: 4.439A pdb=" N GLYIA 55 " --> pdb=" O LYSIA 51 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEUIA 56 " --> pdb=" O GLYIA 52 " (cutoff:3.500A) Processing helix chain 'JA' and resid 18 through 22 Processing helix chain 'MA' and resid 7 through 23 Processing helix chain 'MA' and resid 27 through 30 Processing helix chain 'MA' and resid 31 through 65 removed outlier: 3.865A pdb=" N ASPMA 47 " --> pdb=" O ALAMA 43 " (cutoff:3.500A) Processing helix chain 'MA' and resid 71 through 98 Processing helix chain 'MA' and resid 120 through 141 removed outlier: 3.522A pdb=" N ALAMA 124 " --> pdb=" O GLYMA 120 " (cutoff:3.500A) Processing helix chain 'MA' and resid 171 through 176 Processing helix chain 'MA' and resid 177 through 179 No H-bonds generated for 'chain 'MA' and resid 177 through 179' Processing helix chain 'MA' and resid 234 through 239 removed outlier: 3.554A pdb=" N ASNMA 238 " --> pdb=" O GLYMA 234 " (cutoff:3.500A) Processing helix chain 'MA' and resid 262 through 296 Processing helix chain 'MA' and resid 329 through 334 Processing helix chain 'MA' and resid 337 through 354 Proline residue: MA 343 - end of helix removed outlier: 3.891A pdb=" N ALAMA 354 " --> pdb=" O ALAMA 350 " (cutoff:3.500A) Processing helix chain 'OA' and resid 4 through 12 removed outlier: 3.598A pdb=" N METOA 8 " --> pdb=" O SEROA 4 " (cutoff:3.500A) Processing helix chain 'OA' and resid 23 through 30 Proline residue: OA 28 - end of helix Processing helix chain 'OA' and resid 41 through 44 Processing helix chain 'OA' and resid 45 through 62 Processing helix chain 'OA' and resid 72 through 85 removed outlier: 4.608A pdb=" N GLUOA 77 " --> pdb=" O ARGOA 73 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ALAOA 78 " --> pdb=" O ALAOA 74 " (cutoff:3.500A) Processing helix chain 'OA' and resid 102 through 123 removed outlier: 4.803A pdb=" N GLNOA 108 " --> pdb=" O LYSOA 104 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLNOA 121 " --> pdb=" O GLUOA 117 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASPOA 122 " --> pdb=" O THROA 118 " (cutoff:3.500A) Processing helix chain 'OA' and resid 124 through 128 Processing helix chain 'OA' and resid 129 through 148 Processing helix chain 'OA' and resid 149 through 151 No H-bonds generated for 'chain 'OA' and resid 149 through 151' Processing helix chain 'OA' and resid 168 through 176 Processing helix chain 'OA' and resid 205 through 224 Processing helix chain 'PA' and resid 7 through 11 Processing helix chain 'PA' and resid 27 through 46 Processing helix chain 'PA' and resid 47 through 49 No H-bonds generated for 'chain 'PA' and resid 47 through 49' Processing helix chain 'PA' and resid 71 through 77 Processing helix chain 'PA' and resid 80 through 94 Processing helix chain 'PA' and resid 107 through 110 Processing helix chain 'PA' and resid 111 through 125 removed outlier: 3.619A pdb=" N ARGPA 125 " --> pdb=" O SERPA 121 " (cutoff:3.500A) Processing helix chain 'PA' and resid 128 through 144 Processing helix chain 'QA' and resid 6 through 14 removed outlier: 4.008A pdb=" N LEUQA 10 " --> pdb=" O PROQA 6 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SERQA 11 " --> pdb=" O LYSQA 7 " (cutoff:3.500A) Processing helix chain 'QA' and resid 48 through 65 Processing helix chain 'QA' and resid 67 through 80 Processing helix chain 'QA' and resid 84 through 95 removed outlier: 4.100A pdb=" N LEUQA 90 " --> pdb=" O GLYQA 86 " (cutoff:3.500A) Processing helix chain 'QA' and resid 96 through 105 Processing helix chain 'QA' and resid 109 through 118 Processing helix chain 'QA' and resid 146 through 149 Processing helix chain 'QA' and resid 152 through 162 Processing helix chain 'QA' and resid 186 through 190 Processing helix chain 'QA' and resid 196 through 205 Processing helix chain 'RA' and resid 54 through 69 removed outlier: 3.616A pdb=" N GLURA 64 " --> pdb=" O GLNRA 60 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYSRA 65 " --> pdb=" O LYSRA 61 " (cutoff:3.500A) Processing helix chain 'RA' and resid 109 through 118 Processing helix chain 'RA' and resid 131 through 145 Processing helix chain 'RA' and resid 148 through 153 Processing helix chain 'RA' and resid 159 through 165 Processing helix chain 'SA' and resid 11 through 17 removed outlier: 3.520A pdb=" N GLNSA 17 " --> pdb=" O ASPSA 13 " (cutoff:3.500A) Processing helix chain 'SA' and resid 17 through 32 removed outlier: 4.056A pdb=" N METSA 21 " --> pdb=" O GLNSA 17 " (cutoff:3.500A) Processing helix chain 'SA' and resid 67 through 80 removed outlier: 3.928A pdb=" N PHESA 78 " --> pdb=" O LEUSA 74 " (cutoff:3.500A) Processing helix chain 'TA' and resid 19 through 30 removed outlier: 3.716A pdb=" N LEUTA 29 " --> pdb=" O PHETA 25 " (cutoff:3.500A) Processing helix chain 'TA' and resid 34 through 54 Processing helix chain 'TA' and resid 57 through 63 Processing helix chain 'TA' and resid 91 through 108 removed outlier: 3.989A pdb=" N ALATA 97 " --> pdb=" O VALTA 93 " (cutoff:3.500A) Processing helix chain 'TA' and resid 114 through 127 Processing helix chain 'TA' and resid 131 through 146 Processing helix chain 'UA' and resid 4 through 19 Processing helix chain 'UA' and resid 29 through 43 Processing helix chain 'UA' and resid 79 through 83 removed outlier: 4.074A pdb=" N ARGUA 83 " --> pdb=" O PROUA 80 " (cutoff:3.500A) Processing helix chain 'UA' and resid 87 through 91 Processing helix chain 'UA' and resid 93 through 98 removed outlier: 3.637A pdb=" N ALAUA 96 " --> pdb=" O LYSUA 93 " (cutoff:3.500A) Processing helix chain 'UA' and resid 112 through 119 removed outlier: 3.935A pdb=" N GLNUA 117 " --> pdb=" O ARGUA 113 " (cutoff:3.500A) Processing helix chain 'VA' and resid 10 through 14 removed outlier: 4.021A pdb=" N SERVA 13 " --> pdb=" O ARGVA 10 " (cutoff:3.500A) Processing helix chain 'VA' and resid 34 through 38 removed outlier: 3.702A pdb=" N PHEVA 38 " --> pdb=" O LEUVA 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'VA' and resid 34 through 38' Processing helix chain 'VA' and resid 49 through 54 removed outlier: 3.573A pdb=" N VALVA 54 " --> pdb=" O LEUVA 51 " (cutoff:3.500A) Processing helix chain 'VA' and resid 70 through 86 Processing helix chain 'VA' and resid 89 through 99 removed outlier: 4.783A pdb=" N GLUVA 96 " --> pdb=" O SERVA 92 " (cutoff:3.500A) Processing helix chain 'WA' and resid 14 through 31 removed outlier: 4.878A pdb=" N GLNWA 20 " --> pdb=" O ARGWA 16 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALAWA 29 " --> pdb=" O ILEWA 25 " (cutoff:3.500A) Processing helix chain 'WA' and resid 80 through 88 removed outlier: 3.671A pdb=" N METWA 88 " --> pdb=" O VALWA 84 " (cutoff:3.500A) Processing helix chain 'XA' and resid 46 through 50 Processing helix chain 'XA' and resid 54 through 57 Processing helix chain 'XA' and resid 58 through 71 Processing helix chain 'XA' and resid 93 through 102 removed outlier: 4.224A pdb=" N ARGXA 97 " --> pdb=" O GLUXA 93 " (cutoff:3.500A) Processing helix chain 'YA' and resid 2 through 9 Processing helix chain 'YA' and resid 114 through 118 removed outlier: 3.852A pdb=" N GLYYA 117 " --> pdb=" O SERYA 114 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VALYA 118 " --> pdb=" O LYSYA 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'YA' and resid 114 through 118' Processing helix chain 'ZA' and resid 13 through 20 Processing helix chain 'ZA' and resid 25 through 36 Processing helix chain 'ZA' and resid 48 through 60 removed outlier: 4.747A pdb=" N THRZA 54 " --> pdb=" O GLYZA 50 " (cutoff:3.500A) Processing helix chain 'ZA' and resid 64 through 83 Processing helix chain 'ZA' and resid 84 through 93 Processing helix chain 'ZA' and resid 105 through 110 Processing helix chain 'AB' and resid 2 through 17 Processing helix chain 'AB' and resid 37 through 51 removed outlier: 4.240A pdb=" N GLNAB 49 " --> pdb=" O VALAB 45 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THRAB 50 " --> pdb=" O LEUAB 46 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEUAB 51 " --> pdb=" O LYSAB 47 " (cutoff:3.500A) Processing helix chain 'AB' and resid 55 through 59 removed outlier: 3.602A pdb=" N SERAB 58 " --> pdb=" O SERAB 55 " (cutoff:3.500A) Processing helix chain 'AB' and resid 81 through 89 Processing helix chain 'BB' and resid 3 through 15 Processing helix chain 'BB' and resid 23 through 40 removed outlier: 4.378A pdb=" N GLYBB 40 " --> pdb=" O ASNBB 36 " (cutoff:3.500A) Processing helix chain 'BB' and resid 40 through 45 removed outlier: 3.564A pdb=" N GLUBB 44 " --> pdb=" O GLYBB 40 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HISBB 45 " --> pdb=" O HISBB 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'BB' and resid 40 through 45' Processing helix chain 'BB' and resid 48 through 85 removed outlier: 8.830A pdb=" N ALABB 75 " --> pdb=" O ARGBB 71 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ARGBB 76 " --> pdb=" O LYSBB 72 " (cutoff:3.500A) Processing helix chain 'CB' and resid 53 through 62 Processing helix chain 'CB' and resid 68 through 78 Processing helix chain 'EB' and resid 24 through 30 removed outlier: 3.842A pdb=" N ASNEB 30 " --> pdb=" O ALAEB 26 " (cutoff:3.500A) Processing helix chain 'EB' and resid 40 through 45 Processing helix chain 'EB' and resid 47 through 64 Processing helix chain 'FB' and resid 11 through 24 Processing helix chain 'FB' and resid 40 through 44 Processing helix chain 'FB' and resid 69 through 74 Processing helix chain 'GB' and resid 4 through 6 No H-bonds generated for 'chain 'GB' and resid 4 through 6' Processing helix chain 'GB' and resid 7 through 41 removed outlier: 3.956A pdb=" N ILEGB 11 " --> pdb=" O LYSGB 7 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N HISGB 19 " --> pdb=" O LYSGB 15 " (cutoff:3.500A) Processing helix chain 'GB' and resid 42 through 52 Processing helix chain 'GB' and resid 53 through 62 Processing helix chain 'GB' and resid 67 through 86 Processing helix chain 'HB' and resid 27 through 32 Processing helix chain 'HB' and resid 38 through 60 Processing sheet with id=AA1, first strand: chain 'E' and resid 43 through 46 Processing sheet with id=AA2, first strand: chain 'E' and resid 60 through 64 removed outlier: 3.641A pdb=" N GLY E 61 " --> pdb=" O TYR E 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 94 through 96 Processing sheet with id=AA4, first strand: chain 'F' and resid 2 through 4 Processing sheet with id=AA5, first strand: chain 'F' and resid 99 through 104 removed outlier: 4.134A pdb=" N GLU F 99 " --> pdb=" O TYR F 95 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE F 90 " --> pdb=" O LEU F 80 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N LEU F 80 " --> pdb=" O ILE F 90 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU F 92 " --> pdb=" O GLU F 78 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE F 73 " --> pdb=" O SER F 117 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N SER F 117 " --> pdb=" O ILE F 73 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 128 through 130 Processing sheet with id=AA7, first strand: chain 'F' and resid 170 through 172 removed outlier: 6.928A pdb=" N LYS F 182 " --> pdb=" O ILE F 266 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE F 266 " --> pdb=" O LYS F 182 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 4 through 15 removed outlier: 4.126A pdb=" N VAL G 26 " --> pdb=" O VAL G 9 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N MET G 11 " --> pdb=" O VAL G 24 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL G 24 " --> pdb=" O MET G 11 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ARG G 13 " --> pdb=" O ILE G 22 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE G 22 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU G 186 " --> pdb=" O VAL G 180 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N VAL G 180 " --> pdb=" O LEU G 186 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU G 188 " --> pdb=" O VAL G 178 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ASP G 176 " --> pdb=" O LYS G 190 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N THR G 171 " --> pdb=" O GLY G 111 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N GLY G 111 " --> pdb=" O THR G 171 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN G 173 " --> pdb=" O VAL G 109 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL G 109 " --> pdb=" O GLN G 173 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR G 112 " --> pdb=" O ASP G 200 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASP G 200 " --> pdb=" O THR G 112 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 83 removed outlier: 5.634A pdb=" N GLY G 78 " --> pdb=" O THR G 52 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N THR G 52 " --> pdb=" O GLY G 78 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA G 47 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL G 37 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLN G 49 " --> pdb=" O THR G 35 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 117 through 119 Processing sheet with id=AB2, first strand: chain 'H' and resid 118 through 121 Processing sheet with id=AB3, first strand: chain 'H' and resid 146 through 150 removed outlier: 6.945A pdb=" N VAL H 146 " --> pdb=" O ASP H 168 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N ARG H 170 " --> pdb=" O VAL H 146 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE H 148 " --> pdb=" O ARG H 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'I' and resid 65 through 68 removed outlier: 3.873A pdb=" N GLY I 85 " --> pdb=" O THR I 67 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS I 32 " --> pdb=" O THR I 156 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 15 through 19 Processing sheet with id=AB6, first strand: chain 'J' and resid 40 through 43 Processing sheet with id=AB7, first strand: chain 'J' and resid 122 through 123 Processing sheet with id=AB8, first strand: chain 'J' and resid 94 through 98 Processing sheet with id=AB9, first strand: chain 'K' and resid 3 through 5 Processing sheet with id=AC1, first strand: chain 'K' and resid 77 through 81 removed outlier: 6.667A pdb=" N VAL K 78 " --> pdb=" O ASN K 145 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N VAL K 147 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE K 80 " --> pdb=" O VAL K 147 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 8 through 10 Processing sheet with id=AC3, first strand: chain 'M' and resid 99 through 101 removed outlier: 5.186A pdb=" N ILE M 100 " --> pdb=" O GLU M 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'N' and resid 122 through 124 removed outlier: 6.579A pdb=" N ILE N 54 " --> pdb=" O LYS N 123 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TYR N 16 " --> pdb=" O ILE N 55 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LEU N 57 " --> pdb=" O TYR N 16 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL N 18 " --> pdb=" O LEU N 57 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 73 through 77 Processing sheet with id=AC6, first strand: chain 'O' and resid 6 through 10 removed outlier: 3.880A pdb=" N THR O 6 " --> pdb=" O CYS O 21 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ARG O 17 " --> pdb=" O VAL O 10 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLU O 45 " --> pdb=" O ARG O 17 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL O 19 " --> pdb=" O ILE O 43 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ILE O 43 " --> pdb=" O VAL O 19 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N CYS O 21 " --> pdb=" O ILE O 41 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE O 41 " --> pdb=" O CYS O 21 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LYS O 23 " --> pdb=" O ILE O 39 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE O 39 " --> pdb=" O LYS O 23 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL O 62 " --> pdb=" O VAL O 85 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL O 85 " --> pdb=" O VAL O 62 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N CYS O 84 " --> pdb=" O MET O 7 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ASN O 9 " --> pdb=" O CYS O 84 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N LEU O 86 " --> pdb=" O ASN O 9 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'O' and resid 69 through 70 removed outlier: 3.528A pdb=" N VAL O 69 " --> pdb=" O ILE O 77 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'P' and resid 74 through 75 Processing sheet with id=AC9, first strand: chain 'P' and resid 89 through 90 Processing sheet with id=AD1, first strand: chain 'Q' and resid 64 through 65 removed outlier: 6.656A pdb=" N LEU Q 33 " --> pdb=" O LEU Q 102 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU Q 104 " --> pdb=" O PHE Q 31 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE Q 31 " --> pdb=" O GLU Q 104 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Q' and resid 39 through 42 removed outlier: 5.726A pdb=" N VAL Q 89 " --> pdb=" O GLU Q 75 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLU Q 75 " --> pdb=" O VAL Q 89 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'R' and resid 33 through 37 removed outlier: 6.933A pdb=" N MET R 110 " --> pdb=" O CYS R 100 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'S' and resid 30 through 31 removed outlier: 4.011A pdb=" N HIS S 34 " --> pdb=" O THR S 31 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL S 49 " --> pdb=" O VAL S 39 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'S' and resid 30 through 31 removed outlier: 4.011A pdb=" N HIS S 34 " --> pdb=" O THR S 31 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'T' and resid 37 through 42 removed outlier: 7.525A pdb=" N THR T 24 " --> pdb=" O VAL T 85 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N VAL T 85 " --> pdb=" O THR T 24 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N GLU T 26 " --> pdb=" O ILE T 83 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE T 83 " --> pdb=" O GLU T 26 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LYS T 28 " --> pdb=" O ASP T 81 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'T' and resid 45 through 50 removed outlier: 5.526A pdb=" N VAL T 46 " --> pdb=" O ARG T 61 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ARG T 61 " --> pdb=" O VAL T 46 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA T 48 " --> pdb=" O THR T 59 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'V' and resid 11 through 14 removed outlier: 3.507A pdb=" N PHE V 5 " --> pdb=" O HIS V 12 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL V 4 " --> pdb=" O LEU V 39 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'V' and resid 19 through 23 removed outlier: 6.547A pdb=" N PHE V 93 " --> pdb=" O HIS V 66 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N HIS V 66 " --> pdb=" O PHE V 93 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ASP V 95 " --> pdb=" O VAL V 64 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LYS V 60 " --> pdb=" O THR V 99 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'V' and resid 72 through 77 Processing sheet with id=AE2, first strand: chain 'W' and resid 7 through 10 removed outlier: 3.839A pdb=" N HIS W 9 " --> pdb=" O SER W 101 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N SER W 101 " --> pdb=" O HIS W 9 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ARG W 92 " --> pdb=" O MET W 86 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N MET W 86 " --> pdb=" O ARG W 92 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASP W 94 " --> pdb=" O ARG W 84 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ARG W 84 " --> pdb=" O ASP W 94 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE W 96 " --> pdb=" O MET W 82 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N MET W 82 " --> pdb=" O ILE W 96 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LYS W 98 " --> pdb=" O PRO W 80 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N THR W 100 " --> pdb=" O GLU W 78 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N GLU W 78 " --> pdb=" O THR W 100 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N HIS W 102 " --> pdb=" O VAL W 76 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL W 76 " --> pdb=" O HIS W 102 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR W 104 " --> pdb=" O ILE W 74 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ILE W 74 " --> pdb=" O THR W 104 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL W 106 " --> pdb=" O THR W 72 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'X' and resid 11 through 14 removed outlier: 6.565A pdb=" N LYS X 33 " --> pdb=" O ARG X 12 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N VAL X 31 " --> pdb=" O PRO X 14 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS X 81 " --> pdb=" O VAL X 34 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'X' and resid 69 through 70 Processing sheet with id=AE5, first strand: chain 'Y' and resid 64 through 65 removed outlier: 6.768A pdb=" N LYS Y 32 " --> pdb=" O VAL Y 27 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N VAL Y 27 " --> pdb=" O LYS Y 32 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE Y 34 " --> pdb=" O LYS Y 25 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LYS Y 23 " --> pdb=" O GLU Y 36 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Y' and resid 40 through 44 Processing sheet with id=AE7, first strand: chain 'Y' and resid 82 through 86 Processing sheet with id=AE8, first strand: chain 'Z' and resid 3 through 8 removed outlier: 7.699A pdb=" N ASN Z 5 " --> pdb=" O ASP Z 43 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASP Z 43 " --> pdb=" O ASN Z 5 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N LYS Z 25 " --> pdb=" O GLN Z 87 " (cutoff:3.500A) removed outlier: 10.176A pdb=" N ILE Z 89 " --> pdb=" O LYS Z 25 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N PHE Z 91 " --> pdb=" O PRO Z 27 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE Z 29 " --> pdb=" O PHE Z 91 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG Z 93 " --> pdb=" O ILE Z 29 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR Z 31 " --> pdb=" O ARG Z 93 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N VAL Z 92 " --> pdb=" O ALA Z 74 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ALA Z 74 " --> pdb=" O VAL Z 92 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE Z 4 " --> pdb=" O VAL Z 64 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'AA' and resid 18 through 19 removed outlier: 6.935A pdb=" N LEUAA 55 " --> pdb=" O ILEAA 33 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'AA' and resid 26 through 27 Processing sheet with id=AF2, first strand: chain 'BA' and resid 12 through 15 Processing sheet with id=AF3, first strand: chain 'BA' and resid 32 through 39 Processing sheet with id=AF4, first strand: chain 'DA' and resid 34 through 38 removed outlier: 4.109A pdb=" N LYSDA 5 " --> pdb=" O GLUDA 57 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'EA' and resid 22 through 26 removed outlier: 8.770A pdb=" N LEUEA 32 " --> pdb=" O GLUEA 11 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N THREA 13 " --> pdb=" O LEUEA 32 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEUEA 34 " --> pdb=" O THREA 13 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N SEREA 15 " --> pdb=" O LEUEA 34 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'FA' and resid 28 through 29 Processing sheet with id=AF7, first strand: chain 'GA' and resid 22 through 24 removed outlier: 3.528A pdb=" N LEUGA 35 " --> pdb=" O TYRGA 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'IA' and resid 14 through 15 Processing sheet with id=AF9, first strand: chain 'JA' and resid 14 through 17 Processing sheet with id=AG1, first strand: chain 'MA' and resid 147 through 152 removed outlier: 6.856A pdb=" N ILEMA 163 " --> pdb=" O METMA 149 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALAMA 151 " --> pdb=" O GLUMA 161 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLUMA 161 " --> pdb=" O ALAMA 151 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N GLYMA 181 " --> pdb=" O ARGMA 308 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N TYRMA 310 " --> pdb=" O GLYMA 181 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ARGMA 183 " --> pdb=" O TYRMA 310 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'MA' and resid 222 through 227 removed outlier: 3.739A pdb=" N ILEMA 253 " --> pdb=" O HISMA 248 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'OA' and resid 16 through 18 removed outlier: 3.892A pdb=" N HISOA 17 " --> pdb=" O HISOA 38 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HISOA 38 " --> pdb=" O HISOA 17 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'OA' and resid 89 through 91 removed outlier: 6.725A pdb=" N VALOA 182 " --> pdb=" O PHEOA 197 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ILEOA 199 " --> pdb=" O VALOA 182 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALAOA 184 " --> pdb=" O ILEOA 199 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'PA' and resid 19 through 20 removed outlier: 6.878A pdb=" N HISPA 68 " --> pdb=" O SERPA 52 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILEPA 54 " --> pdb=" O THRPA 66 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N THRPA 66 " --> pdb=" O ILEPA 54 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILEPA 56 " --> pdb=" O ARGPA 64 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ARGPA 64 " --> pdb=" O ILEPA 56 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'PA' and resid 165 through 170 removed outlier: 6.374A pdb=" N ASPPA 180 " --> pdb=" O LYSPA 203 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'QA' and resid 127 through 128 Processing sheet with id=AG8, first strand: chain 'RA' and resid 12 through 14 Processing sheet with id=AG9, first strand: chain 'RA' and resid 18 through 20 Processing sheet with id=AH1, first strand: chain 'RA' and resid 84 through 85 Processing sheet with id=AH2, first strand: chain 'SA' and resid 2 through 4 Processing sheet with id=AH3, first strand: chain 'SA' and resid 41 through 46 removed outlier: 5.052A pdb=" N ASPSA 41 " --> pdb=" O LEUSA 61 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEUSA 61 " --> pdb=" O ASPSA 41 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ARGSA 86 " --> pdb=" O METSA 9 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'TA' and resid 72 through 75 Processing sheet with id=AH5, first strand: chain 'UA' and resid 23 through 27 removed outlier: 4.151A pdb=" N THRUA 61 " --> pdb=" O ASPUA 47 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ASPUA 47 " --> pdb=" O THRUA 61 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'UA' and resid 73 through 76 removed outlier: 6.050A pdb=" N ILEUA 124 " --> pdb=" O SERUA 104 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N SERUA 104 " --> pdb=" O ILEUA 124 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'VA' and resid 5 through 7 removed outlier: 6.127A pdb=" N VALVA 28 " --> pdb=" O ILEVA 64 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VALVA 66 " --> pdb=" O VALVA 28 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'WA' and resid 40 through 41 removed outlier: 3.624A pdb=" N GLUWA 47 " --> pdb=" O ILEWA 67 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'WA' and resid 40 through 41 Processing sheet with id=AI1, first strand: chain 'XA' and resid 40 through 44 removed outlier: 4.036A pdb=" N GLYXA 42 " --> pdb=" O ILEXA 33 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VALXA 83 " --> pdb=" O THRXA 107 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILEXA 109 " --> pdb=" O VALXA 83 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N VALXA 85 " --> pdb=" O ILEXA 109 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASPXA 111 " --> pdb=" O VALXA 85 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'YA' and resid 28 through 31 Processing sheet with id=AI3, first strand: chain 'YA' and resid 34 through 39 removed outlier: 4.671A pdb=" N ARGYA 35 " --> pdb=" O ARGYA 53 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'CB' and resid 34 through 35 removed outlier: 6.392A pdb=" N VALCB 2 " --> pdb=" O THRCB 66 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'CB' and resid 10 through 11 Processing sheet with id=AI6, first strand: chain 'CB' and resid 38 through 39 Processing sheet with id=AI7, first strand: chain 'DB' and resid 10 through 13 removed outlier: 6.731A pdb=" N VALDB 21 " --> pdb=" O VALDB 12 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N LYSDB 70 " --> pdb=" O LYSDB 42 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N HISDB 44 " --> pdb=" O LYSDB 70 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N TRPDB 72 " --> pdb=" O HISDB 44 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N SERDB 71 " --> pdb=" O CYSDB 63 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLUDB 59 " --> pdb=" O VALDB 75 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'FB' and resid 31 through 32 2035 hydrogen bonds defined for protein. 5601 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3388 hydrogen bonds 5538 hydrogen bond angles 0 basepair planarities 1377 basepair parallelities 2417 stacking parallelities Total time for adding SS restraints: 224.05 Time building geometry restraints manager: 68.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.36: 40181 1.36 - 1.53: 101044 1.53 - 1.70: 23764 1.70 - 1.87: 307 1.87 - 2.04: 8 Bond restraints: 165304 Sorted by residual: bond pdb=" C PHEOA 31 " pdb=" O PHEOA 31 " ideal model delta sigma weight residual 1.230 1.370 -0.140 1.15e-02 7.56e+03 1.48e+02 bond pdb=" SD METMA 77 " pdb=" CE METMA 77 " ideal model delta sigma weight residual 1.791 2.044 -0.253 2.50e-02 1.60e+03 1.02e+02 bond pdb=" CA ARGAB 63 " pdb=" C ARGAB 63 " ideal model delta sigma weight residual 1.524 1.654 -0.130 1.31e-02 5.83e+03 9.79e+01 bond pdb=" CA HISAB 71 " pdb=" C HISAB 71 " ideal model delta sigma weight residual 1.520 1.622 -0.102 1.16e-02 7.43e+03 7.70e+01 bond pdb=" SD METMA 67 " pdb=" CE METMA 67 " ideal model delta sigma weight residual 1.791 2.006 -0.215 2.50e-02 1.60e+03 7.41e+01 ... (remaining 165299 not shown) Histogram of bond angle deviations from ideal: 89.22 - 100.48: 115 100.48 - 111.74: 107718 111.74 - 123.00: 110627 123.00 - 134.26: 28157 134.26 - 145.52: 7 Bond angle restraints: 246624 Sorted by residual: angle pdb=" N GLYOA 32 " pdb=" CA GLYOA 32 " pdb=" C GLYOA 32 " ideal model delta sigma weight residual 111.63 145.52 -33.89 1.15e+00 7.56e-01 8.69e+02 angle pdb=" C GLUMA 342 " pdb=" N PROMA 343 " pdb=" CA PROMA 343 " ideal model delta sigma weight residual 119.28 101.59 17.69 1.10e+00 8.26e-01 2.59e+02 angle pdb=" N ALAYA 22 " pdb=" CA ALAYA 22 " pdb=" C ALAYA 22 " ideal model delta sigma weight residual 111.03 97.25 13.78 1.11e+00 8.12e-01 1.54e+02 angle pdb=" C PHEOA 31 " pdb=" N GLYOA 32 " pdb=" CA GLYOA 32 " ideal model delta sigma weight residual 122.92 102.70 20.22 1.66e+00 3.63e-01 1.48e+02 angle pdb=" N PRO L 119 " pdb=" CA PRO L 119 " pdb=" C PRO L 119 " ideal model delta sigma weight residual 112.47 89.22 23.25 2.06e+00 2.36e-01 1.27e+02 ... (remaining 246619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 94284 35.78 - 71.55: 10281 71.55 - 107.33: 1243 107.33 - 143.10: 11 143.10 - 178.88: 27 Dihedral angle restraints: 105846 sinusoidal: 87267 harmonic: 18579 Sorted by residual: dihedral pdb=" O4' U B1917 " pdb=" C1' U B1917 " pdb=" N1 U B1917 " pdb=" C2 U B1917 " ideal model delta sinusoidal sigma weight residual 200.00 22.23 177.77 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U B2076 " pdb=" C1' U B2076 " pdb=" N1 U B2076 " pdb=" C2 U B2076 " ideal model delta sinusoidal sigma weight residual 200.00 26.45 173.55 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' U B 955 " pdb=" C1' U B 955 " pdb=" N1 U B 955 " pdb=" C2 U B 955 " ideal model delta sinusoidal sigma weight residual -160.00 8.93 -168.93 1 1.50e+01 4.44e-03 8.45e+01 ... (remaining 105843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.150: 28900 0.150 - 0.299: 2409 0.299 - 0.449: 115 0.449 - 0.598: 8 0.598 - 0.748: 3 Chirality restraints: 31435 Sorted by residual: chirality pdb=" C3' G A1297 " pdb=" C4' G A1297 " pdb=" O3' G A1297 " pdb=" C2' G A1297 " both_signs ideal model delta sigma weight residual False -2.74 -2.00 -0.75 2.00e-01 2.50e+01 1.40e+01 chirality pdb=" C3' U B1130 " pdb=" C4' U B1130 " pdb=" O3' U B1130 " pdb=" C2' U B1130 " both_signs ideal model delta sigma weight residual False -2.74 -2.09 -0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" CA VALPA 96 " pdb=" N VALPA 96 " pdb=" C VALPA 96 " pdb=" CB VALPA 96 " both_signs ideal model delta sigma weight residual False 2.44 3.05 -0.61 2.00e-01 2.50e+01 9.40e+00 ... (remaining 31432 not shown) Planarity restraints: 13698 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A B1937 " -0.215 2.00e-02 2.50e+03 9.67e-02 2.57e+02 pdb=" N9 A B1937 " 0.004 2.00e-02 2.50e+03 pdb=" C8 A B1937 " 0.081 2.00e-02 2.50e+03 pdb=" N7 A B1937 " 0.086 2.00e-02 2.50e+03 pdb=" C5 A B1937 " 0.055 2.00e-02 2.50e+03 pdb=" C6 A B1937 " -0.028 2.00e-02 2.50e+03 pdb=" N6 A B1937 " -0.163 2.00e-02 2.50e+03 pdb=" N1 A B1937 " -0.008 2.00e-02 2.50e+03 pdb=" C2 A B1937 " 0.044 2.00e-02 2.50e+03 pdb=" N3 A B1937 " 0.074 2.00e-02 2.50e+03 pdb=" C4 A B1937 " 0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B1993 " 0.172 2.00e-02 2.50e+03 9.53e-02 2.04e+02 pdb=" N1 U B1993 " -0.003 2.00e-02 2.50e+03 pdb=" C2 U B1993 " -0.032 2.00e-02 2.50e+03 pdb=" O2 U B1993 " -0.070 2.00e-02 2.50e+03 pdb=" N3 U B1993 " -0.027 2.00e-02 2.50e+03 pdb=" C4 U B1993 " -0.030 2.00e-02 2.50e+03 pdb=" O4 U B1993 " 0.169 2.00e-02 2.50e+03 pdb=" C5 U B1993 " -0.097 2.00e-02 2.50e+03 pdb=" C6 U B1993 " -0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B1171 " -0.189 2.00e-02 2.50e+03 7.98e-02 1.91e+02 pdb=" N9 G B1171 " 0.009 2.00e-02 2.50e+03 pdb=" C8 G B1171 " 0.090 2.00e-02 2.50e+03 pdb=" N7 G B1171 " 0.085 2.00e-02 2.50e+03 pdb=" C5 G B1171 " 0.035 2.00e-02 2.50e+03 pdb=" C6 G B1171 " -0.039 2.00e-02 2.50e+03 pdb=" O6 G B1171 " -0.120 2.00e-02 2.50e+03 pdb=" N1 G B1171 " -0.033 2.00e-02 2.50e+03 pdb=" C2 G B1171 " 0.018 2.00e-02 2.50e+03 pdb=" N2 G B1171 " 0.054 2.00e-02 2.50e+03 pdb=" N3 G B1171 " 0.043 2.00e-02 2.50e+03 pdb=" C4 G B1171 " 0.047 2.00e-02 2.50e+03 ... (remaining 13695 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 99 2.39 - 3.02: 76259 3.02 - 3.65: 267629 3.65 - 4.27: 413681 4.27 - 4.90: 566128 Nonbonded interactions: 1323796 Sorted by model distance: nonbonded pdb=" O LEUAB 79 " pdb=" O SERAB 80 " model vdw 1.764 3.040 nonbonded pdb=" O VALOA 13 " pdb=" O HISOA 14 " model vdw 1.911 3.040 nonbonded pdb=" O GLN M 11 " pdb=" O ILE M 54 " model vdw 1.945 3.040 nonbonded pdb=" O SERAB 55 " pdb=" C SERAB 56 " model vdw 2.056 3.270 nonbonded pdb=" N PRO L 119 " pdb=" N ALA L 120 " model vdw 2.061 2.560 ... (remaining 1323791 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'LA' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 27.290 Check model and map are aligned: 1.630 Set scattering table: 1.030 Process input model: 494.430 Find NCS groups from input model: 3.060 Set up NCS constraints: 0.400 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: 0.030 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 538.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.253 165304 Z= 0.464 Angle : 1.136 33.891 246624 Z= 0.733 Chirality : 0.088 0.748 31435 Planarity : 0.012 0.117 13698 Dihedral : 22.181 178.878 93856 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 1.98 % Allowed : 13.54 % Favored : 84.48 % Rotamer: Outliers : 1.11 % Allowed : 4.99 % Favored : 93.90 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.52 (0.09), residues: 6412 helix: -2.82 (0.08), residues: 2041 sheet: -2.64 (0.14), residues: 1133 loop : -3.28 (0.09), residues: 3238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.009 TRP H 78 HIS 0.014 0.001 HISOA 17 PHE 0.120 0.008 PHEOA 15 TYR 0.077 0.009 TYR W 38 ARG 0.027 0.001 ARGAB 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12824 Ramachandran restraints generated. 6412 Oldfield, 0 Emsley, 6412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12824 Ramachandran restraints generated. 6412 Oldfield, 0 Emsley, 6412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1624 residues out of total 5312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 1565 time to evaluate : 6.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 218 MET cc_start: 0.3857 (mtm) cc_final: 0.2688 (mtt) REVERT: J 74 MET cc_start: 0.8939 (mtm) cc_final: 0.8730 (ttm) REVERT: K 131 SER cc_start: 0.9561 (m) cc_final: 0.8723 (p) REVERT: K 132 PHE cc_start: 0.9218 (m-80) cc_final: 0.8416 (m-80) REVERT: K 135 HIS cc_start: 0.9241 (t-170) cc_final: 0.8343 (t-90) REVERT: L 1 MET cc_start: 0.3975 (ttm) cc_final: 0.2752 (tmm) REVERT: L 33 VAL cc_start: 0.8547 (OUTLIER) cc_final: 0.7573 (p) REVERT: M 61 TYR cc_start: 0.8290 (m-10) cc_final: 0.7659 (m-10) REVERT: O 32 TYR cc_start: 0.7102 (p90) cc_final: 0.6875 (p90) REVERT: Q 126 ILE cc_start: 0.8182 (pt) cc_final: 0.7930 (mt) REVERT: R 21 PHE cc_start: 0.8247 (m-80) cc_final: 0.7765 (m-10) REVERT: W 100 THR cc_start: 0.7547 (p) cc_final: 0.7328 (p) REVERT: X 1 MET cc_start: 0.4385 (ptp) cc_final: 0.4075 (ttt) REVERT: X 7 LEU cc_start: 0.9297 (mt) cc_final: 0.8815 (mm) REVERT: JA 23 ILE cc_start: 0.8502 (mp) cc_final: 0.8222 (mp) REVERT: MA 55 TRP cc_start: 0.3180 (t-100) cc_final: 0.2954 (t-100) REVERT: MA 144 TRP cc_start: 0.8084 (m-10) cc_final: 0.7711 (m-10) REVERT: MA 323 ASN cc_start: 0.7794 (t0) cc_final: 0.7475 (t0) REVERT: OA 5 MET cc_start: 0.9065 (ttm) cc_final: 0.8501 (mmm) REVERT: OA 119 GLN cc_start: 0.9688 (mt0) cc_final: 0.9422 (tt0) REVERT: QA 189 ASP cc_start: 0.8058 (m-30) cc_final: 0.7652 (t0) REVERT: RA 80 LEU cc_start: 0.7432 (mp) cc_final: 0.6950 (mp) REVERT: WA 83 THR cc_start: 0.9441 (m) cc_final: 0.9173 (m) REVERT: XA 76 TYR cc_start: 0.8328 (m-80) cc_final: 0.7818 (m-10) outliers start: 59 outliers final: 12 residues processed: 1612 average time/residue: 1.3696 time to fit residues: 3735.2642 Evaluate side-chains 824 residues out of total 5312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 811 time to evaluate : 6.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain M residue 94 LYS Chi-restraints excluded: chain P residue 89 VAL Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain W residue 62 ASP Chi-restraints excluded: chain Y residue 27 VAL Chi-restraints excluded: chain MA residue 115 VAL Chi-restraints excluded: chain RA residue 17 VAL Chi-restraints excluded: chain RA residue 145 ASN Chi-restraints excluded: chain XA residue 30 ILE Chi-restraints excluded: chain HB residue 13 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1099 random chunks: chunk 928 optimal weight: 9.9990 chunk 832 optimal weight: 30.0000 chunk 462 optimal weight: 7.9990 chunk 284 optimal weight: 20.0000 chunk 561 optimal weight: 8.9990 chunk 445 optimal weight: 20.0000 chunk 861 optimal weight: 6.9990 chunk 333 optimal weight: 20.0000 chunk 523 optimal weight: 8.9990 chunk 641 optimal weight: 8.9990 chunk 998 optimal weight: 40.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 58 ASN E 155 ASN E 172 HIS ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN F 20 ASN F 24 HIS F 36 ASN F 196 ASN ** F 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 HIS H 24 ASN H 30 GLN H 92 HIS H 163 ASN H 165 HIS I 126 ASN J 29 ASN ** J 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 HIS ** K 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 30 GLN ** M 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 82 ASN R 11 ASN R 23 ASN R 81 ASN S 38 GLN S 100 HIS ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 82 HIS ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 9 HIS ** Y 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 42 HIS AA 72 ASN ** BA 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EA 41 HIS FA 4 GLN ** HA 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** MA 44 GLN MA 79 GLN ** MA 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** MA 156 HIS MA 236 HIS ** MA 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** MA 320 HIS OA 38 HIS OA 93 HIS ** PA 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** PA 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** QA 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** QA 139 ASN RA 131 ASN RA 145 ASN ** SA 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SA 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TA 121 ASN UA 15 ASN VA 31 GLN ** XA 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BB 19 ASN BB 34 GLN CB 18 GLN CB 40 ASN ** CB 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 30 HIS EB 51 GLN ** GB 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GB 19 HIS GB 60 GLN ** HB 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 165304 Z= 0.285 Angle : 0.735 12.475 246624 Z= 0.374 Chirality : 0.037 0.305 31435 Planarity : 0.006 0.206 13698 Dihedral : 23.529 179.637 81126 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.33 % Favored : 90.36 % Rotamer: Outliers : 4.20 % Allowed : 14.76 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.05 % 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: -2.94 (0.10), residues: 6412 helix: -0.90 (0.11), residues: 2091 sheet: -1.93 (0.15), residues: 1140 loop : -2.72 (0.10), residues: 3181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP Q 92 HIS 0.011 0.002 HIS N 80 PHE 0.052 0.002 PHEHB 36 TYR 0.035 0.002 TYREA 9 ARG 0.030 0.001 ARGPA 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12824 Ramachandran restraints generated. 6412 Oldfield, 0 Emsley, 6412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12824 Ramachandran restraints generated. 6412 Oldfield, 0 Emsley, 6412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1126 residues out of total 5312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 903 time to evaluate : 6.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 218 MET cc_start: 0.4247 (mtm) cc_final: 0.3112 (mtt) REVERT: I 16 MET cc_start: 0.8167 (tpp) cc_final: 0.7730 (tpp) REVERT: J 74 MET cc_start: 0.8957 (mtm) cc_final: 0.8740 (mmm) REVERT: K 89 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8133 (tmtt) REVERT: K 94 ILE cc_start: 0.9646 (mm) cc_final: 0.9437 (tt) REVERT: K 123 ARG cc_start: 0.8690 (mtt180) cc_final: 0.8301 (mmm-85) REVERT: K 132 PHE cc_start: 0.9156 (m-80) cc_final: 0.8722 (m-80) REVERT: K 143 ILE cc_start: 0.9599 (mm) cc_final: 0.9277 (tp) REVERT: L 1 MET cc_start: 0.5396 (ttm) cc_final: 0.3018 (tpp) REVERT: L 38 MET cc_start: -0.0525 (mtt) cc_final: -0.0977 (mtt) REVERT: L 86 MET cc_start: 0.6719 (OUTLIER) cc_final: 0.6115 (ppp) REVERT: M 135 MET cc_start: 0.4134 (mmt) cc_final: 0.3851 (mmt) REVERT: N 19 ASP cc_start: 0.8185 (t0) cc_final: 0.7957 (t0) REVERT: O 89 ASN cc_start: 0.8280 (m-40) cc_final: 0.8068 (m-40) REVERT: W 69 LEU cc_start: 0.8606 (tp) cc_final: 0.8233 (mt) REVERT: X 37 ASP cc_start: 0.8810 (p0) cc_final: 0.8601 (p0) REVERT: BA 63 ILE cc_start: 0.9143 (tt) cc_final: 0.8935 (pt) REVERT: GA 26 LYS cc_start: 0.9204 (tptp) cc_final: 0.8775 (tptm) REVERT: MA 127 PHE cc_start: 0.8293 (t80) cc_final: 0.8037 (t80) REVERT: MA 323 ASN cc_start: 0.8039 (t0) cc_final: 0.7790 (t0) REVERT: OA 5 MET cc_start: 0.8860 (ttm) cc_final: 0.8386 (mmm) REVERT: OA 8 MET cc_start: 0.9580 (ptp) cc_final: 0.9277 (ptp) REVERT: RA 146 MET cc_start: 0.7789 (tmm) cc_final: 0.7574 (tmm) REVERT: TA 30 MET cc_start: 0.8273 (ttt) cc_final: 0.7977 (tmm) REVERT: TA 115 MET cc_start: 0.8423 (tpp) cc_final: 0.7973 (ttp) REVERT: UA 9 MET cc_start: 0.8293 (tmm) cc_final: 0.7993 (tmm) REVERT: WA 63 ASP cc_start: 0.6703 (p0) cc_final: 0.6472 (p0) REVERT: XA 76 TYR cc_start: 0.8319 (m-80) cc_final: 0.7337 (m-80) REVERT: FB 65 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8312 (ptp) outliers start: 223 outliers final: 102 residues processed: 1037 average time/residue: 1.4568 time to fit residues: 2620.6621 Evaluate side-chains 792 residues out of total 5312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 687 time to evaluate : 6.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 263 ASP Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain I residue 51 ASN Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain J residue 19 ASN Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain K residue 17 ASP Chi-restraints excluded: chain K residue 40 THR Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 89 LYS Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 141 LYS Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 52 MET Chi-restraints excluded: chain L residue 86 MET Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain O residue 5 GLN Chi-restraints excluded: chain O residue 56 ASP Chi-restraints excluded: chain O residue 58 LEU Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain O residue 110 GLU Chi-restraints excluded: chain P residue 77 ILE Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain T residue 15 ASP Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain V residue 40 MET Chi-restraints excluded: chain V residue 84 ARG Chi-restraints excluded: chain W residue 36 LEU Chi-restraints excluded: chain W residue 94 ASP Chi-restraints excluded: chain Y residue 27 VAL Chi-restraints excluded: chain Z residue 5 ASN Chi-restraints excluded: chain Z residue 43 ASP Chi-restraints excluded: chain Z residue 66 ASP Chi-restraints excluded: chain Z residue 89 ILE Chi-restraints excluded: chain Z residue 90 ASP Chi-restraints excluded: chain AA residue 78 ILE Chi-restraints excluded: chain BA residue 39 VAL Chi-restraints excluded: chain BA residue 58 ILE Chi-restraints excluded: chain EA residue 34 LEU Chi-restraints excluded: chain FA residue 8 THR Chi-restraints excluded: chain FA residue 22 THR Chi-restraints excluded: chain GA residue 47 ILE Chi-restraints excluded: chain HA residue 8 SER Chi-restraints excluded: chain HA residue 43 THR Chi-restraints excluded: chain IA residue 43 LEU Chi-restraints excluded: chain IA residue 50 SER Chi-restraints excluded: chain MA residue 176 LYS Chi-restraints excluded: chain MA residue 206 MET Chi-restraints excluded: chain OA residue 146 SER Chi-restraints excluded: chain PA residue 7 ASN Chi-restraints excluded: chain PA residue 30 ASP Chi-restraints excluded: chain PA residue 51 VAL Chi-restraints excluded: chain QA residue 159 GLU Chi-restraints excluded: chain QA residue 168 THR Chi-restraints excluded: chain RA residue 17 VAL Chi-restraints excluded: chain RA residue 59 ILE Chi-restraints excluded: chain RA residue 130 THR Chi-restraints excluded: chain RA residue 137 ARG Chi-restraints excluded: chain SA residue 22 ILE Chi-restraints excluded: chain UA residue 89 ASP Chi-restraints excluded: chain VA residue 26 LYS Chi-restraints excluded: chain WA residue 17 LEU Chi-restraints excluded: chain WA residue 30 LYS Chi-restraints excluded: chain WA residue 51 VAL Chi-restraints excluded: chain WA residue 88 MET Chi-restraints excluded: chain WA residue 100 ILE Chi-restraints excluded: chain XA residue 37 GLN Chi-restraints excluded: chain XA residue 45 THR Chi-restraints excluded: chain XA residue 67 GLU Chi-restraints excluded: chain XA residue 120 CYS Chi-restraints excluded: chain YA residue 2 THR Chi-restraints excluded: chain YA residue 40 THR Chi-restraints excluded: chain YA residue 72 ASN Chi-restraints excluded: chain YA residue 96 THR Chi-restraints excluded: chain ZA residue 8 ILE Chi-restraints excluded: chain AB residue 48 LEU Chi-restraints excluded: chain AB residue 62 ASN Chi-restraints excluded: chain AB residue 67 THR Chi-restraints excluded: chain BB residue 3 SER Chi-restraints excluded: chain BB residue 88 ARG Chi-restraints excluded: chain FB residue 5 LYS Chi-restraints excluded: chain FB residue 14 LEU Chi-restraints excluded: chain FB residue 42 ASN Chi-restraints excluded: chain FB residue 57 VAL Chi-restraints excluded: chain FB residue 65 MET Chi-restraints excluded: chain FB residue 78 THR Chi-restraints excluded: chain GB residue 11 ILE Chi-restraints excluded: chain HB residue 12 ASP Chi-restraints excluded: chain HB residue 13 VAL Chi-restraints excluded: chain HB residue 18 PHE Chi-restraints excluded: chain HB residue 36 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1099 random chunks: chunk 554 optimal weight: 20.0000 chunk 309 optimal weight: 20.0000 chunk 830 optimal weight: 30.0000 chunk 679 optimal weight: 7.9990 chunk 275 optimal weight: 20.0000 chunk 999 optimal weight: 10.0000 chunk 1080 optimal weight: 40.0000 chunk 890 optimal weight: 9.9990 chunk 991 optimal weight: 20.0000 chunk 340 optimal weight: 20.0000 chunk 802 optimal weight: 8.9990 overall best weight: 11.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 165 ASN ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 85 ASN F 116 GLN F 133 ASN F 225 ASN F 238 ASN G 49 GLN ** G 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN I 20 ASN ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 128 HIS ** M 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 43 GLN ** W 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 73 ASN Z 49 ASN ** Z 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FA 37 HIS ** HA 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HA 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MA 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** MA 197 HIS MA 266 ASN ** OA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** PA 7 ASN ** PA 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** PA 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** QA 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SA 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SA 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SA 63 ASN SA 68 GLN ** TA 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TA 27 ASN TA 67 ASN ** UA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** WA 56 HIS WA 70 HIS ** XA 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** YA 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BB 36 ASN ** CB 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 49 ASN ** FB 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** HB 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 165304 Z= 0.345 Angle : 0.725 15.617 246624 Z= 0.371 Chirality : 0.037 0.360 31435 Planarity : 0.006 0.084 13698 Dihedral : 24.093 179.763 81109 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 29.49 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.46 % Favored : 89.25 % Rotamer: Outliers : 4.89 % Allowed : 15.25 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.08 % 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: -2.41 (0.10), residues: 6412 helix: -0.47 (0.11), residues: 2146 sheet: -1.55 (0.15), residues: 1141 loop : -2.46 (0.10), residues: 3125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 61 HIS 0.011 0.002 HISPA 5 PHE 0.044 0.003 PHEHB 36 TYR 0.038 0.003 TYRAB 19 ARG 0.020 0.001 ARGUA 79 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12824 Ramachandran restraints generated. 6412 Oldfield, 0 Emsley, 6412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12824 Ramachandran restraints generated. 6412 Oldfield, 0 Emsley, 6412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1025 residues out of total 5312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 765 time to evaluate : 6.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 218 MET cc_start: 0.4853 (mtm) cc_final: 0.3711 (mtt) REVERT: J 74 MET cc_start: 0.9007 (mtm) cc_final: 0.8494 (ttm) REVERT: K 127 GLU cc_start: 0.9364 (OUTLIER) cc_final: 0.9161 (tp30) REVERT: K 132 PHE cc_start: 0.9069 (m-80) cc_final: 0.8728 (m-80) REVERT: K 135 HIS cc_start: 0.9276 (t-90) cc_final: 0.8912 (t-90) REVERT: K 143 ILE cc_start: 0.9606 (mm) cc_final: 0.9318 (tp) REVERT: L 1 MET cc_start: 0.5066 (ttm) cc_final: 0.3492 (tpp) REVERT: L 6 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8549 (tm-30) REVERT: L 31 ARG cc_start: 0.7754 (mmt-90) cc_final: 0.7361 (mmt-90) REVERT: L 38 MET cc_start: -0.0457 (mtt) cc_final: -0.1034 (mtt) REVERT: L 52 MET cc_start: 0.4649 (tpt) cc_final: 0.3937 (tpt) REVERT: M 20 SER cc_start: 0.7265 (t) cc_final: 0.6982 (m) REVERT: M 61 TYR cc_start: 0.7800 (m-10) cc_final: 0.7577 (m-10) REVERT: M 124 MET cc_start: 0.8870 (mmm) cc_final: 0.8633 (mmm) REVERT: R 1 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.7035 (mtp) REVERT: W 67 ASP cc_start: 0.8601 (p0) cc_final: 0.8322 (p0) REVERT: W 69 LEU cc_start: 0.8641 (tp) cc_final: 0.8138 (mt) REVERT: X 37 ASP cc_start: 0.8819 (p0) cc_final: 0.8546 (p0) REVERT: X 57 VAL cc_start: 0.8799 (OUTLIER) cc_final: 0.8598 (p) REVERT: EA 8 LYS cc_start: 0.8258 (pptt) cc_final: 0.7358 (pptt) REVERT: MA 110 ASN cc_start: 0.6985 (OUTLIER) cc_final: 0.6110 (t0) REVERT: MA 127 PHE cc_start: 0.8173 (t80) cc_final: 0.7939 (t80) REVERT: MA 323 ASN cc_start: 0.8422 (t0) cc_final: 0.8125 (t0) REVERT: OA 8 MET cc_start: 0.9591 (ptp) cc_final: 0.9358 (mpp) REVERT: TA 30 MET cc_start: 0.8342 (ttt) cc_final: 0.7895 (tmm) REVERT: WA 82 LYS cc_start: 0.9157 (pttm) cc_final: 0.8549 (pttt) REVERT: XA 86 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7816 (tmmt) REVERT: AB 58 SER cc_start: 0.8863 (OUTLIER) cc_final: 0.8585 (t) REVERT: DB 48 GLU cc_start: 0.7940 (tp30) cc_final: 0.7658 (tp30) REVERT: DB 49 ASN cc_start: 0.8375 (p0) cc_final: 0.7939 (p0) REVERT: FB 65 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8242 (ptp) outliers start: 260 outliers final: 143 residues processed: 932 average time/residue: 1.3543 time to fit residues: 2189.2428 Evaluate side-chains 779 residues out of total 5312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 628 time to evaluate : 6.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 82 TYR Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 263 ASP Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 19 ASN Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain K residue 17 ASP Chi-restraints excluded: chain K residue 40 THR Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 127 GLU Chi-restraints excluded: chain K residue 141 LYS Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain M residue 33 ASN Chi-restraints excluded: chain N residue 25 LEU Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain N residue 84 ILE Chi-restraints excluded: chain O residue 5 GLN Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 37 ASP Chi-restraints excluded: chain O residue 56 ASP Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 110 GLU Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain P residue 77 ILE Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 102 LEU Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 13 ASN Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 69 ASP Chi-restraints excluded: chain T residue 1 SER Chi-restraints excluded: chain T residue 15 ASP Chi-restraints excluded: chain T residue 83 ILE Chi-restraints excluded: chain T residue 103 THR Chi-restraints excluded: chain U residue 16 ILE Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain V residue 40 MET Chi-restraints excluded: chain V residue 46 GLU Chi-restraints excluded: chain V residue 60 LYS Chi-restraints excluded: chain V residue 98 ILE Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 22 ASP Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 76 ARG Chi-restraints excluded: chain Y residue 27 VAL Chi-restraints excluded: chain Y residue 48 VAL Chi-restraints excluded: chain Y residue 61 GLU Chi-restraints excluded: chain Z residue 43 ASP Chi-restraints excluded: chain Z residue 66 ASP Chi-restraints excluded: chain Z residue 77 VAL Chi-restraints excluded: chain Z residue 89 ILE Chi-restraints excluded: chain Z residue 90 ASP Chi-restraints excluded: chain AA residue 39 THR Chi-restraints excluded: chain AA residue 78 ILE Chi-restraints excluded: chain BA residue 39 VAL Chi-restraints excluded: chain BA residue 58 ILE Chi-restraints excluded: chain CA residue 59 GLU Chi-restraints excluded: chain DA residue 20 LYS Chi-restraints excluded: chain DA residue 31 ILE Chi-restraints excluded: chain DA residue 56 VAL Chi-restraints excluded: chain EA residue 4 ASP Chi-restraints excluded: chain EA residue 39 LYS Chi-restraints excluded: chain FA residue 22 THR Chi-restraints excluded: chain FA residue 52 LYS Chi-restraints excluded: chain GA residue 8 ILE Chi-restraints excluded: chain HA residue 8 SER Chi-restraints excluded: chain HA residue 43 THR Chi-restraints excluded: chain IA residue 53 ASP Chi-restraints excluded: chain JA residue 7 VAL Chi-restraints excluded: chain MA residue 110 ASN Chi-restraints excluded: chain MA residue 166 ILE Chi-restraints excluded: chain MA residue 206 MET Chi-restraints excluded: chain MA residue 255 VAL Chi-restraints excluded: chain PA residue 30 ASP Chi-restraints excluded: chain PA residue 51 VAL Chi-restraints excluded: chain PA residue 101 ASN Chi-restraints excluded: chain PA residue 106 ARG Chi-restraints excluded: chain RA residue 14 LEU Chi-restraints excluded: chain RA residue 17 VAL Chi-restraints excluded: chain RA residue 77 ASN Chi-restraints excluded: chain RA residue 105 ILE Chi-restraints excluded: chain RA residue 115 GLU Chi-restraints excluded: chain RA residue 130 THR Chi-restraints excluded: chain RA residue 151 MET Chi-restraints excluded: chain SA residue 16 GLU Chi-restraints excluded: chain TA residue 51 GLN Chi-restraints excluded: chain UA residue 66 GLN Chi-restraints excluded: chain UA residue 74 ILE Chi-restraints excluded: chain VA residue 26 LYS Chi-restraints excluded: chain VA residue 36 GLN Chi-restraints excluded: chain WA residue 17 LEU Chi-restraints excluded: chain WA residue 24 GLU Chi-restraints excluded: chain WA residue 30 LYS Chi-restraints excluded: chain WA residue 51 VAL Chi-restraints excluded: chain WA residue 52 LEU Chi-restraints excluded: chain WA residue 83 THR Chi-restraints excluded: chain WA residue 88 MET Chi-restraints excluded: chain XA residue 37 GLN Chi-restraints excluded: chain XA residue 45 THR Chi-restraints excluded: chain XA residue 73 VAL Chi-restraints excluded: chain XA residue 75 GLU Chi-restraints excluded: chain XA residue 80 ASN Chi-restraints excluded: chain XA residue 86 LYS Chi-restraints excluded: chain XA residue 120 CYS Chi-restraints excluded: chain YA residue 2 THR Chi-restraints excluded: chain YA residue 40 THR Chi-restraints excluded: chain YA residue 72 ASN Chi-restraints excluded: chain ZA residue 8 ILE Chi-restraints excluded: chain ZA residue 11 HIS Chi-restraints excluded: chain ZA residue 84 CYS Chi-restraints excluded: chain AB residue 33 VAL Chi-restraints excluded: chain AB residue 58 SER Chi-restraints excluded: chain AB residue 62 ASN Chi-restraints excluded: chain AB residue 67 THR Chi-restraints excluded: chain AB residue 74 LEU Chi-restraints excluded: chain BB residue 3 SER Chi-restraints excluded: chain BB residue 88 ARG Chi-restraints excluded: chain DB residue 54 ILE Chi-restraints excluded: chain DB residue 82 VAL Chi-restraints excluded: chain FB residue 5 LYS Chi-restraints excluded: chain FB residue 14 LEU Chi-restraints excluded: chain FB residue 65 MET Chi-restraints excluded: chain GB residue 11 ILE Chi-restraints excluded: chain HB residue 3 ILE Chi-restraints excluded: chain HB residue 12 ASP Chi-restraints excluded: chain HB residue 13 VAL Chi-restraints excluded: chain HB residue 18 PHE Chi-restraints excluded: chain HB residue 27 VAL Chi-restraints excluded: chain HB residue 36 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1099 random chunks: chunk 987 optimal weight: 10.0000 chunk 751 optimal weight: 8.9990 chunk 518 optimal weight: 10.0000 chunk 110 optimal weight: 30.0000 chunk 477 optimal weight: 0.0770 chunk 671 optimal weight: 9.9990 chunk 1003 optimal weight: 9.9990 chunk 1062 optimal weight: 30.0000 chunk 524 optimal weight: 50.0000 chunk 950 optimal weight: 7.9990 chunk 286 optimal weight: 20.0000 overall best weight: 7.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 133 ASN G 49 GLN G 94 GLN G 130 GLN ** G 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 GLN ** H 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 29 ASN J 114 HIS ** K 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 ASN M 33 ASN M 42 ASN ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 58 ASN N 136 GLN N 138 GLN ** Q 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 72 GLN ** Y 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 12 GLN EA 20 ASN ** HA 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HA 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** MA 94 GLN ** MA 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** OA 167 HIS PA 138 GLN ** QA 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SA 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** TA 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** UA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** VA 31 GLN ** XA 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** YA 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 79 ASN FB 51 HIS GB 12 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.4943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 165304 Z= 0.233 Angle : 0.613 11.919 246624 Z= 0.313 Chirality : 0.033 0.373 31435 Planarity : 0.005 0.083 13698 Dihedral : 24.071 179.621 81109 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 22.59 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.78 % Favored : 91.03 % Rotamer: Outliers : 3.88 % Allowed : 17.58 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.08 % 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: -1.92 (0.10), residues: 6412 helix: 0.05 (0.11), residues: 2139 sheet: -1.35 (0.15), residues: 1132 loop : -2.22 (0.11), residues: 3141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRPMA 55 HIS 0.016 0.001 HISPA 5 PHE 0.046 0.002 PHEHB 36 TYR 0.031 0.002 TYRHB 37 ARG 0.015 0.001 ARGRA 53 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12824 Ramachandran restraints generated. 6412 Oldfield, 0 Emsley, 6412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12824 Ramachandran restraints generated. 6412 Oldfield, 0 Emsley, 6412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 918 residues out of total 5312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 712 time to evaluate : 6.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 97 MET cc_start: 0.2661 (mpp) cc_final: 0.2397 (mpp) REVERT: E 218 MET cc_start: 0.4829 (mtm) cc_final: 0.3681 (mtt) REVERT: K 15 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8347 (mp) REVERT: K 66 ASN cc_start: 0.9038 (m-40) cc_final: 0.8478 (m-40) REVERT: K 101 ASP cc_start: 0.9495 (p0) cc_final: 0.9142 (p0) REVERT: K 123 ARG cc_start: 0.8820 (mtt180) cc_final: 0.8491 (mmm-85) REVERT: K 132 PHE cc_start: 0.9033 (m-80) cc_final: 0.8778 (m-80) REVERT: K 135 HIS cc_start: 0.9133 (t-90) cc_final: 0.8826 (t70) REVERT: K 143 ILE cc_start: 0.9597 (mm) cc_final: 0.9343 (tp) REVERT: L 1 MET cc_start: 0.5129 (ttm) cc_final: 0.2193 (tpp) REVERT: L 31 ARG cc_start: 0.7599 (mmt-90) cc_final: 0.7159 (mmt-90) REVERT: L 38 MET cc_start: -0.0463 (mtt) cc_final: -0.1034 (mtt) REVERT: L 52 MET cc_start: 0.4848 (tpt) cc_final: 0.4357 (tpt) REVERT: M 20 SER cc_start: 0.7208 (t) cc_final: 0.6927 (m) REVERT: M 124 MET cc_start: 0.8924 (mmm) cc_final: 0.8590 (mmm) REVERT: V 60 LYS cc_start: 0.9140 (pttm) cc_final: 0.8893 (pttm) REVERT: W 69 LEU cc_start: 0.8532 (tp) cc_final: 0.8063 (mt) REVERT: X 37 ASP cc_start: 0.8699 (p0) cc_final: 0.8440 (p0) REVERT: MA 112 PHE cc_start: 0.8095 (m-80) cc_final: 0.7847 (m-80) REVERT: MA 127 PHE cc_start: 0.8145 (t80) cc_final: 0.7893 (t80) REVERT: MA 323 ASN cc_start: 0.8524 (t0) cc_final: 0.8234 (t0) REVERT: OA 119 GLN cc_start: 0.9677 (mt0) cc_final: 0.9353 (tt0) REVERT: TA 30 MET cc_start: 0.8438 (ttt) cc_final: 0.8110 (tmm) REVERT: UA 72 GLU cc_start: 0.8875 (mp0) cc_final: 0.8363 (pm20) REVERT: ZA 80 MET cc_start: 0.8660 (mmp) cc_final: 0.8285 (mmp) REVERT: DB 16 MET cc_start: 0.7786 (mmt) cc_final: 0.7414 (mmp) REVERT: DB 49 ASN cc_start: 0.8344 (p0) cc_final: 0.7816 (p0) REVERT: DB 79 GLU cc_start: 0.8276 (pm20) cc_final: 0.8066 (tm-30) REVERT: FB 65 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8203 (ptp) outliers start: 206 outliers final: 123 residues processed: 844 average time/residue: 1.3249 time to fit residues: 1943.3093 Evaluate side-chains 744 residues out of total 5312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 619 time to evaluate : 6.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain H residue 30 GLN Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain J residue 19 ASN Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 17 ASP Chi-restraints excluded: chain K residue 40 THR Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 141 LYS Chi-restraints excluded: chain L residue 86 MET Chi-restraints excluded: chain N residue 25 LEU Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain O residue 5 GLN Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 37 ASP Chi-restraints excluded: chain O residue 56 ASP Chi-restraints excluded: chain O residue 110 GLU Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain P residue 77 ILE Chi-restraints excluded: chain Q residue 73 ILE Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 102 LEU Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 13 ASN Chi-restraints excluded: chain R residue 43 GLU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 69 ASP Chi-restraints excluded: chain T residue 1 SER Chi-restraints excluded: chain T residue 15 ASP Chi-restraints excluded: chain T residue 83 ILE Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain V residue 40 MET Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain Y residue 27 VAL Chi-restraints excluded: chain Z residue 5 ASN Chi-restraints excluded: chain Z residue 43 ASP Chi-restraints excluded: chain Z residue 61 LEU Chi-restraints excluded: chain Z residue 66 ASP Chi-restraints excluded: chain Z residue 77 VAL Chi-restraints excluded: chain Z residue 86 LEU Chi-restraints excluded: chain AA residue 78 ILE Chi-restraints excluded: chain BA residue 39 VAL Chi-restraints excluded: chain BA residue 58 ILE Chi-restraints excluded: chain CA residue 7 ARG Chi-restraints excluded: chain DA residue 20 LYS Chi-restraints excluded: chain DA residue 56 VAL Chi-restraints excluded: chain EA residue 34 LEU Chi-restraints excluded: chain FA residue 22 THR Chi-restraints excluded: chain GA residue 47 ILE Chi-restraints excluded: chain HA residue 8 SER Chi-restraints excluded: chain HA residue 43 THR Chi-restraints excluded: chain IA residue 53 ASP Chi-restraints excluded: chain MA residue 59 GLN Chi-restraints excluded: chain MA residue 115 VAL Chi-restraints excluded: chain MA residue 166 ILE Chi-restraints excluded: chain MA residue 176 LYS Chi-restraints excluded: chain MA residue 206 MET Chi-restraints excluded: chain MA residue 255 VAL Chi-restraints excluded: chain OA residue 48 MET Chi-restraints excluded: chain PA residue 30 ASP Chi-restraints excluded: chain PA residue 51 VAL Chi-restraints excluded: chain PA residue 106 ARG Chi-restraints excluded: chain RA residue 17 VAL Chi-restraints excluded: chain RA residue 77 ASN Chi-restraints excluded: chain RA residue 115 GLU Chi-restraints excluded: chain RA residue 130 THR Chi-restraints excluded: chain SA residue 16 GLU Chi-restraints excluded: chain TA residue 51 GLN Chi-restraints excluded: chain TA residue 105 GLU Chi-restraints excluded: chain UA residue 74 ILE Chi-restraints excluded: chain UA residue 84 ILE Chi-restraints excluded: chain VA residue 26 LYS Chi-restraints excluded: chain WA residue 17 LEU Chi-restraints excluded: chain WA residue 30 LYS Chi-restraints excluded: chain WA residue 83 THR Chi-restraints excluded: chain WA residue 88 MET Chi-restraints excluded: chain WA residue 97 ASP Chi-restraints excluded: chain XA residue 30 ILE Chi-restraints excluded: chain XA residue 37 GLN Chi-restraints excluded: chain XA residue 45 THR Chi-restraints excluded: chain XA residue 120 CYS Chi-restraints excluded: chain YA residue 2 THR Chi-restraints excluded: chain YA residue 40 THR Chi-restraints excluded: chain ZA residue 8 ILE Chi-restraints excluded: chain ZA residue 11 HIS Chi-restraints excluded: chain ZA residue 84 CYS Chi-restraints excluded: chain AB residue 33 VAL Chi-restraints excluded: chain AB residue 58 SER Chi-restraints excluded: chain AB residue 67 THR Chi-restraints excluded: chain BB residue 3 SER Chi-restraints excluded: chain BB residue 88 ARG Chi-restraints excluded: chain DB residue 54 ILE Chi-restraints excluded: chain DB residue 82 VAL Chi-restraints excluded: chain FB residue 5 LYS Chi-restraints excluded: chain FB residue 14 LEU Chi-restraints excluded: chain FB residue 46 LEU Chi-restraints excluded: chain FB residue 57 VAL Chi-restraints excluded: chain FB residue 65 MET Chi-restraints excluded: chain FB residue 78 THR Chi-restraints excluded: chain GB residue 11 ILE Chi-restraints excluded: chain HB residue 12 ASP Chi-restraints excluded: chain HB residue 13 VAL Chi-restraints excluded: chain HB residue 18 PHE Chi-restraints excluded: chain HB residue 22 CYS Chi-restraints excluded: chain HB residue 27 VAL Chi-restraints excluded: chain HB residue 36 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1099 random chunks: chunk 884 optimal weight: 7.9990 chunk 603 optimal weight: 40.0000 chunk 15 optimal weight: 20.0000 chunk 790 optimal weight: 0.9980 chunk 438 optimal weight: 20.0000 chunk 906 optimal weight: 50.0000 chunk 734 optimal weight: 30.0000 chunk 1 optimal weight: 30.0000 chunk 542 optimal weight: 10.0000 chunk 953 optimal weight: 6.9990 chunk 268 optimal weight: 20.0000 overall best weight: 9.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 GLN H 30 GLN ** H 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 49 ASN ** CA 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HA 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** PA 40 GLN ** QA 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SA 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SA 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TA 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** UA 15 ASN ** UA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** UA 37 ASN VA 125 GLN ** WA 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** XA 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** YA 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GB 81 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.5580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 165304 Z= 0.281 Angle : 0.645 14.644 246624 Z= 0.328 Chirality : 0.034 0.286 31435 Planarity : 0.005 0.081 13698 Dihedral : 24.199 179.916 81109 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 27.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.81 % Favored : 90.02 % Rotamer: Outliers : 3.97 % Allowed : 18.32 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.08 % 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: -1.89 (0.10), residues: 6412 helix: -0.03 (0.11), residues: 2171 sheet: -1.31 (0.15), residues: 1127 loop : -2.15 (0.11), residues: 3114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP Q 92 HIS 0.011 0.002 HIS H 29 PHE 0.052 0.002 PHEHB 36 TYR 0.032 0.002 TYRHB 37 ARG 0.015 0.001 ARG Q 51 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12824 Ramachandran restraints generated. 6412 Oldfield, 0 Emsley, 6412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12824 Ramachandran restraints generated. 6412 Oldfield, 0 Emsley, 6412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 5312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 680 time to evaluate : 6.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 218 MET cc_start: 0.4555 (mtm) cc_final: 0.3365 (mtt) REVERT: H 19 PHE cc_start: 0.8533 (OUTLIER) cc_final: 0.8208 (t80) REVERT: K 66 ASN cc_start: 0.9012 (m-40) cc_final: 0.8427 (m-40) REVERT: K 132 PHE cc_start: 0.8972 (m-80) cc_final: 0.8692 (m-80) REVERT: K 135 HIS cc_start: 0.9035 (t-90) cc_final: 0.8662 (t70) REVERT: K 143 ILE cc_start: 0.9601 (mm) cc_final: 0.9210 (tp) REVERT: L 1 MET cc_start: 0.4522 (ttm) cc_final: 0.2126 (tpt) REVERT: L 31 ARG cc_start: 0.7680 (mmt-90) cc_final: 0.7190 (mmt-90) REVERT: L 36 ASP cc_start: 0.9004 (m-30) cc_final: 0.8460 (t0) REVERT: L 38 MET cc_start: -0.0457 (mtt) cc_final: -0.1024 (mtt) REVERT: L 52 MET cc_start: 0.4805 (tpt) cc_final: 0.4306 (tpt) REVERT: M 16 MET cc_start: 0.4428 (tmm) cc_final: 0.4130 (ppp) REVERT: M 20 SER cc_start: 0.7134 (t) cc_final: 0.6838 (m) REVERT: M 124 MET cc_start: 0.8814 (mmm) cc_final: 0.8406 (mmm) REVERT: O 4 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8258 (mm-30) REVERT: O 32 TYR cc_start: 0.7498 (OUTLIER) cc_final: 0.7061 (p90) REVERT: W 69 LEU cc_start: 0.8619 (tp) cc_final: 0.8063 (mt) REVERT: X 37 ASP cc_start: 0.8693 (p0) cc_final: 0.8392 (p0) REVERT: MA 127 PHE cc_start: 0.8215 (t80) cc_final: 0.7955 (t80) REVERT: MA 323 ASN cc_start: 0.8566 (t0) cc_final: 0.8346 (t0) REVERT: OA 119 GLN cc_start: 0.9630 (mt0) cc_final: 0.9295 (tt0) REVERT: SA 90 MET cc_start: 0.8182 (mmm) cc_final: 0.7816 (mmm) REVERT: TA 30 MET cc_start: 0.8463 (ttt) cc_final: 0.8160 (tmm) REVERT: UA 89 ASP cc_start: 0.8515 (OUTLIER) cc_final: 0.8287 (p0) REVERT: AB 58 SER cc_start: 0.8755 (OUTLIER) cc_final: 0.8421 (t) REVERT: CB 1 MET cc_start: 0.8136 (tmm) cc_final: 0.7893 (tmm) REVERT: DB 16 MET cc_start: 0.7847 (mmt) cc_final: 0.7464 (mmp) REVERT: DB 48 GLU cc_start: 0.7677 (tp30) cc_final: 0.7198 (tp30) REVERT: DB 49 ASN cc_start: 0.8405 (p0) cc_final: 0.7918 (p0) REVERT: DB 76 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8367 (ttp80) REVERT: FB 65 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8303 (ptp) outliers start: 211 outliers final: 145 residues processed: 812 average time/residue: 1.3096 time to fit residues: 1850.1789 Evaluate side-chains 752 residues out of total 5312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 601 time to evaluate : 6.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 82 TYR Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 263 ASP Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 19 ASN Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain K residue 17 ASP Chi-restraints excluded: chain K residue 40 THR Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 141 LYS Chi-restraints excluded: chain L residue 86 MET Chi-restraints excluded: chain M residue 33 ASN Chi-restraints excluded: chain M residue 85 ILE Chi-restraints excluded: chain N residue 25 LEU Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain N residue 84 ILE Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 32 TYR Chi-restraints excluded: chain O residue 37 ASP Chi-restraints excluded: chain O residue 52 VAL Chi-restraints excluded: chain O residue 56 ASP Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 84 CYS Chi-restraints excluded: chain O residue 110 GLU Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain P residue 77 ILE Chi-restraints excluded: chain Q residue 73 ILE Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 102 LEU Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 13 ASN Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 69 ASP Chi-restraints excluded: chain T residue 15 ASP Chi-restraints excluded: chain T residue 83 ILE Chi-restraints excluded: chain U residue 16 ILE Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain V residue 40 MET Chi-restraints excluded: chain V residue 46 GLU Chi-restraints excluded: chain V residue 60 LYS Chi-restraints excluded: chain V residue 98 ILE Chi-restraints excluded: chain W residue 22 ASP Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain W residue 51 LEU Chi-restraints excluded: chain W residue 109 ASP Chi-restraints excluded: chain Y residue 27 VAL Chi-restraints excluded: chain Y residue 48 VAL Chi-restraints excluded: chain Z residue 43 ASP Chi-restraints excluded: chain Z residue 56 PHE Chi-restraints excluded: chain Z residue 61 LEU Chi-restraints excluded: chain Z residue 66 ASP Chi-restraints excluded: chain Z residue 77 VAL Chi-restraints excluded: chain AA residue 39 THR Chi-restraints excluded: chain AA residue 52 ASP Chi-restraints excluded: chain AA residue 78 ILE Chi-restraints excluded: chain BA residue 39 VAL Chi-restraints excluded: chain BA residue 58 ILE Chi-restraints excluded: chain CA residue 7 ARG Chi-restraints excluded: chain CA residue 11 VAL Chi-restraints excluded: chain DA residue 20 LYS Chi-restraints excluded: chain DA residue 56 VAL Chi-restraints excluded: chain EA residue 39 LYS Chi-restraints excluded: chain FA residue 8 THR Chi-restraints excluded: chain FA residue 22 THR Chi-restraints excluded: chain GA residue 8 ILE Chi-restraints excluded: chain GA residue 47 ILE Chi-restraints excluded: chain HA residue 8 SER Chi-restraints excluded: chain HA residue 43 THR Chi-restraints excluded: chain IA residue 43 LEU Chi-restraints excluded: chain IA residue 53 ASP Chi-restraints excluded: chain MA residue 115 VAL Chi-restraints excluded: chain MA residue 166 ILE Chi-restraints excluded: chain MA residue 176 LYS Chi-restraints excluded: chain MA residue 255 VAL Chi-restraints excluded: chain OA residue 48 MET Chi-restraints excluded: chain PA residue 30 ASP Chi-restraints excluded: chain PA residue 40 GLN Chi-restraints excluded: chain PA residue 51 VAL Chi-restraints excluded: chain PA residue 101 ASN Chi-restraints excluded: chain PA residue 106 ARG Chi-restraints excluded: chain QA residue 19 PHE Chi-restraints excluded: chain QA residue 168 THR Chi-restraints excluded: chain RA residue 17 VAL Chi-restraints excluded: chain RA residue 77 ASN Chi-restraints excluded: chain RA residue 105 ILE Chi-restraints excluded: chain RA residue 130 THR Chi-restraints excluded: chain SA residue 16 GLU Chi-restraints excluded: chain SA residue 82 ASP Chi-restraints excluded: chain TA residue 105 GLU Chi-restraints excluded: chain UA residue 74 ILE Chi-restraints excluded: chain UA residue 89 ASP Chi-restraints excluded: chain VA residue 26 LYS Chi-restraints excluded: chain VA residue 36 GLN Chi-restraints excluded: chain WA residue 17 LEU Chi-restraints excluded: chain WA residue 30 LYS Chi-restraints excluded: chain WA residue 51 VAL Chi-restraints excluded: chain WA residue 83 THR Chi-restraints excluded: chain WA residue 88 MET Chi-restraints excluded: chain WA residue 97 ASP Chi-restraints excluded: chain XA residue 45 THR Chi-restraints excluded: chain XA residue 80 ASN Chi-restraints excluded: chain XA residue 120 CYS Chi-restraints excluded: chain YA residue 2 THR Chi-restraints excluded: chain YA residue 40 THR Chi-restraints excluded: chain YA residue 72 ASN Chi-restraints excluded: chain ZA residue 8 ILE Chi-restraints excluded: chain ZA residue 11 HIS Chi-restraints excluded: chain ZA residue 84 CYS Chi-restraints excluded: chain AB residue 33 VAL Chi-restraints excluded: chain AB residue 58 SER Chi-restraints excluded: chain AB residue 62 ASN Chi-restraints excluded: chain AB residue 64 CYS Chi-restraints excluded: chain AB residue 67 THR Chi-restraints excluded: chain BB residue 3 SER Chi-restraints excluded: chain BB residue 88 ARG Chi-restraints excluded: chain DB residue 76 ARG Chi-restraints excluded: chain EB residue 33 THR Chi-restraints excluded: chain FB residue 5 LYS Chi-restraints excluded: chain FB residue 14 LEU Chi-restraints excluded: chain FB residue 46 LEU Chi-restraints excluded: chain FB residue 65 MET Chi-restraints excluded: chain FB residue 78 THR Chi-restraints excluded: chain GB residue 11 ILE Chi-restraints excluded: chain GB residue 81 GLN Chi-restraints excluded: chain HB residue 12 ASP Chi-restraints excluded: chain HB residue 13 VAL Chi-restraints excluded: chain HB residue 18 PHE Chi-restraints excluded: chain HB residue 22 CYS Chi-restraints excluded: chain HB residue 36 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1099 random chunks: chunk 357 optimal weight: 20.0000 chunk 956 optimal weight: 0.4980 chunk 209 optimal weight: 20.0000 chunk 623 optimal weight: 10.0000 chunk 262 optimal weight: 40.0000 chunk 1063 optimal weight: 8.9990 chunk 882 optimal weight: 9.9990 chunk 492 optimal weight: 6.9990 chunk 88 optimal weight: 20.0000 chunk 351 optimal weight: 20.0000 chunk 558 optimal weight: 30.0000 overall best weight: 7.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 HIS ** G 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 58 ASN N 128 ASN ** N 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 59 ASN ** Y 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HA 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MA 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** PA 40 GLN ** QA 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SA 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SA 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TA 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** UA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** WA 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** XA 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** YA 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** YA 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 46 HIS ** DB 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GB 81 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.5751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 165304 Z= 0.226 Angle : 0.607 15.700 246624 Z= 0.307 Chirality : 0.033 0.257 31435 Planarity : 0.004 0.080 13698 Dihedral : 24.199 179.834 81109 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 24.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.86 % Favored : 90.97 % Rotamer: Outliers : 3.99 % Allowed : 19.71 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.08 % 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: -1.75 (0.10), residues: 6412 helix: 0.08 (0.11), residues: 2175 sheet: -1.11 (0.15), residues: 1132 loop : -2.11 (0.11), residues: 3105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Q 64 HIS 0.009 0.001 HISPA 5 PHE 0.047 0.002 PHEHB 36 TYR 0.029 0.002 TYRXA 76 ARG 0.011 0.001 ARGMA 145 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12824 Ramachandran restraints generated. 6412 Oldfield, 0 Emsley, 6412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12824 Ramachandran restraints generated. 6412 Oldfield, 0 Emsley, 6412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 871 residues out of total 5312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 659 time to evaluate : 6.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 97 MET cc_start: 0.2921 (mpp) cc_final: 0.2213 (mmt) REVERT: E 218 MET cc_start: 0.4514 (mtm) cc_final: 0.3234 (mtt) REVERT: I 98 PHE cc_start: 0.8779 (t80) cc_final: 0.8441 (t80) REVERT: J 25 ILE cc_start: 0.9497 (OUTLIER) cc_final: 0.9294 (mm) REVERT: J 74 MET cc_start: 0.9314 (mtt) cc_final: 0.8696 (ttm) REVERT: K 15 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.7839 (mt) REVERT: K 66 ASN cc_start: 0.9066 (m-40) cc_final: 0.8505 (m-40) REVERT: K 89 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8327 (tmtt) REVERT: K 123 ARG cc_start: 0.8927 (mtt180) cc_final: 0.8621 (mmm-85) REVERT: K 132 PHE cc_start: 0.9040 (m-80) cc_final: 0.8746 (m-80) REVERT: K 135 HIS cc_start: 0.8989 (t-90) cc_final: 0.8577 (t70) REVERT: K 143 ILE cc_start: 0.9585 (mm) cc_final: 0.9197 (tp) REVERT: L 1 MET cc_start: 0.4706 (ttm) cc_final: 0.2085 (tpp) REVERT: L 31 ARG cc_start: 0.7632 (mmt-90) cc_final: 0.7050 (mmt-90) REVERT: L 38 MET cc_start: -0.1019 (mtt) cc_final: -0.1612 (mtt) REVERT: L 52 MET cc_start: 0.4963 (tpt) cc_final: 0.4484 (tpt) REVERT: M 16 MET cc_start: 0.4084 (tmm) cc_final: 0.3802 (ppp) REVERT: M 20 SER cc_start: 0.6928 (t) cc_final: 0.6664 (m) REVERT: M 124 MET cc_start: 0.8883 (mmm) cc_final: 0.8470 (mmm) REVERT: O 32 TYR cc_start: 0.7520 (OUTLIER) cc_final: 0.7029 (p90) REVERT: W 69 LEU cc_start: 0.8622 (tp) cc_final: 0.8002 (mt) REVERT: X 37 ASP cc_start: 0.8514 (p0) cc_final: 0.8194 (p0) REVERT: MA 127 PHE cc_start: 0.8218 (t80) cc_final: 0.7863 (t80) REVERT: MA 162 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8798 (pt) REVERT: MA 323 ASN cc_start: 0.8622 (t0) cc_final: 0.8417 (t0) REVERT: MA 339 MET cc_start: 0.8621 (pmm) cc_final: 0.8412 (pmm) REVERT: OA 119 GLN cc_start: 0.9575 (mt0) cc_final: 0.9286 (tt0) REVERT: RA 13 LYS cc_start: 0.8109 (pttt) cc_final: 0.7115 (pttt) REVERT: RA 63 MET cc_start: 0.8682 (ppp) cc_final: 0.8476 (ppp) REVERT: TA 30 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8211 (tmm) REVERT: UA 89 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.8211 (p0) REVERT: YA 75 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7570 (tp30) REVERT: ZA 80 MET cc_start: 0.8665 (mmp) cc_final: 0.8258 (mmt) REVERT: CB 1 MET cc_start: 0.8036 (tmm) cc_final: 0.7836 (tmm) REVERT: DB 16 MET cc_start: 0.7677 (mmt) cc_final: 0.7439 (mmp) REVERT: DB 48 GLU cc_start: 0.7684 (tp30) cc_final: 0.7296 (tp30) REVERT: DB 49 ASN cc_start: 0.8434 (p0) cc_final: 0.7891 (p0) REVERT: DB 76 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8113 (ttp80) outliers start: 212 outliers final: 140 residues processed: 803 average time/residue: 1.3164 time to fit residues: 1851.1271 Evaluate side-chains 741 residues out of total 5312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 592 time to evaluate : 6.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 82 TYR Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 263 ASP Chi-restraints excluded: chain G residue 11 MET Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 19 ASN Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 17 ASP Chi-restraints excluded: chain K residue 40 THR Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 89 LYS Chi-restraints excluded: chain K residue 141 LYS Chi-restraints excluded: chain L residue 86 MET Chi-restraints excluded: chain M residue 85 ILE Chi-restraints excluded: chain N residue 25 LEU Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain O residue 32 TYR Chi-restraints excluded: chain O residue 37 ASP Chi-restraints excluded: chain O residue 52 VAL Chi-restraints excluded: chain O residue 56 ASP Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 110 GLU Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain P residue 77 ILE Chi-restraints excluded: chain Q residue 73 ILE Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 102 LEU Chi-restraints excluded: chain Q residue 134 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 13 ASN Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain S residue 69 ASP Chi-restraints excluded: chain T residue 15 ASP Chi-restraints excluded: chain T residue 83 ILE Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain V residue 40 MET Chi-restraints excluded: chain V residue 46 GLU Chi-restraints excluded: chain V residue 98 ILE Chi-restraints excluded: chain W residue 7 HIS Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain Y residue 7 ASP Chi-restraints excluded: chain Y residue 27 VAL Chi-restraints excluded: chain Z residue 43 ASP Chi-restraints excluded: chain Z residue 56 PHE Chi-restraints excluded: chain Z residue 61 LEU Chi-restraints excluded: chain Z residue 66 ASP Chi-restraints excluded: chain Z residue 77 VAL Chi-restraints excluded: chain Z residue 89 ILE Chi-restraints excluded: chain AA residue 52 ASP Chi-restraints excluded: chain AA residue 78 ILE Chi-restraints excluded: chain BA residue 39 VAL Chi-restraints excluded: chain CA residue 4 LYS Chi-restraints excluded: chain CA residue 7 ARG Chi-restraints excluded: chain DA residue 56 VAL Chi-restraints excluded: chain EA residue 39 LYS Chi-restraints excluded: chain FA residue 8 THR Chi-restraints excluded: chain FA residue 22 THR Chi-restraints excluded: chain GA residue 47 ILE Chi-restraints excluded: chain HA residue 8 SER Chi-restraints excluded: chain HA residue 43 THR Chi-restraints excluded: chain IA residue 43 LEU Chi-restraints excluded: chain IA residue 53 ASP Chi-restraints excluded: chain MA residue 12 LEU Chi-restraints excluded: chain MA residue 115 VAL Chi-restraints excluded: chain MA residue 162 ILE Chi-restraints excluded: chain MA residue 166 ILE Chi-restraints excluded: chain MA residue 176 LYS Chi-restraints excluded: chain MA residue 184 VAL Chi-restraints excluded: chain MA residue 255 VAL Chi-restraints excluded: chain OA residue 48 MET Chi-restraints excluded: chain OA residue 124 THR Chi-restraints excluded: chain PA residue 30 ASP Chi-restraints excluded: chain PA residue 51 VAL Chi-restraints excluded: chain PA residue 106 ARG Chi-restraints excluded: chain QA residue 19 PHE Chi-restraints excluded: chain RA residue 17 VAL Chi-restraints excluded: chain RA residue 77 ASN Chi-restraints excluded: chain RA residue 105 ILE Chi-restraints excluded: chain RA residue 130 THR Chi-restraints excluded: chain SA residue 16 GLU Chi-restraints excluded: chain SA residue 30 THR Chi-restraints excluded: chain SA residue 82 ASP Chi-restraints excluded: chain TA residue 30 MET Chi-restraints excluded: chain UA residue 74 ILE Chi-restraints excluded: chain UA residue 84 ILE Chi-restraints excluded: chain UA residue 89 ASP Chi-restraints excluded: chain VA residue 26 LYS Chi-restraints excluded: chain VA residue 36 GLN Chi-restraints excluded: chain WA residue 17 LEU Chi-restraints excluded: chain WA residue 52 LEU Chi-restraints excluded: chain WA residue 83 THR Chi-restraints excluded: chain WA residue 97 ASP Chi-restraints excluded: chain XA residue 30 ILE Chi-restraints excluded: chain XA residue 45 THR Chi-restraints excluded: chain XA residue 80 ASN Chi-restraints excluded: chain YA residue 2 THR Chi-restraints excluded: chain YA residue 40 THR Chi-restraints excluded: chain YA residue 75 GLU Chi-restraints excluded: chain YA residue 111 GLN Chi-restraints excluded: chain ZA residue 8 ILE Chi-restraints excluded: chain ZA residue 11 HIS Chi-restraints excluded: chain ZA residue 84 CYS Chi-restraints excluded: chain AB residue 58 SER Chi-restraints excluded: chain AB residue 62 ASN Chi-restraints excluded: chain AB residue 64 CYS Chi-restraints excluded: chain AB residue 67 THR Chi-restraints excluded: chain BB residue 88 ARG Chi-restraints excluded: chain CB residue 19 VAL Chi-restraints excluded: chain DB residue 19 SER Chi-restraints excluded: chain DB residue 76 ARG Chi-restraints excluded: chain DB residue 82 VAL Chi-restraints excluded: chain EB residue 25 ILE Chi-restraints excluded: chain FB residue 5 LYS Chi-restraints excluded: chain FB residue 14 LEU Chi-restraints excluded: chain FB residue 46 LEU Chi-restraints excluded: chain FB residue 57 VAL Chi-restraints excluded: chain GB residue 81 GLN Chi-restraints excluded: chain HB residue 12 ASP Chi-restraints excluded: chain HB residue 13 VAL Chi-restraints excluded: chain HB residue 18 PHE Chi-restraints excluded: chain HB residue 22 CYS Chi-restraints excluded: chain HB residue 63 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1099 random chunks: chunk 1025 optimal weight: 50.0000 chunk 119 optimal weight: 30.0000 chunk 605 optimal weight: 30.0000 chunk 776 optimal weight: 0.0870 chunk 601 optimal weight: 40.0000 chunk 895 optimal weight: 20.0000 chunk 593 optimal weight: 7.9990 chunk 1059 optimal weight: 20.0000 chunk 662 optimal weight: 20.0000 chunk 645 optimal weight: 5.9990 chunk 489 optimal weight: 30.0000 overall best weight: 10.8170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 11 GLN ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 65 GLN ** CA 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HA 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** MA 91 GLN ** QA 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** QA 135 GLN ** SA 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SA 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TA 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** UA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XA 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** YA 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** YA 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GB 81 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.6199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 165304 Z= 0.313 Angle : 0.666 18.306 246624 Z= 0.336 Chirality : 0.035 0.325 31435 Planarity : 0.005 0.077 13698 Dihedral : 24.345 179.697 81109 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 31.23 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.93 % Favored : 89.93 % Rotamer: Outliers : 3.86 % Allowed : 20.59 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.10 % 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: -1.79 (0.10), residues: 6412 helix: -0.03 (0.11), residues: 2158 sheet: -1.20 (0.15), residues: 1140 loop : -2.03 (0.11), residues: 3114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPMA 55 HIS 0.017 0.002 HISPA 5 PHE 0.036 0.002 PHEMA 132 TYR 0.016 0.002 TYRQA 64 ARG 0.014 0.001 ARG V 84 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12824 Ramachandran restraints generated. 6412 Oldfield, 0 Emsley, 6412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12824 Ramachandran restraints generated. 6412 Oldfield, 0 Emsley, 6412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 5312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 615 time to evaluate : 6.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 97 MET cc_start: 0.2445 (mpp) cc_final: 0.2143 (mmt) REVERT: E 218 MET cc_start: 0.4720 (mtm) cc_final: 0.3226 (mtt) REVERT: K 15 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.7977 (mt) REVERT: K 66 ASN cc_start: 0.9071 (m-40) cc_final: 0.8510 (m-40) REVERT: K 132 PHE cc_start: 0.9016 (m-80) cc_final: 0.8752 (m-80) REVERT: K 135 HIS cc_start: 0.8988 (t-90) cc_final: 0.8572 (t-90) REVERT: K 143 ILE cc_start: 0.9603 (mm) cc_final: 0.9245 (tp) REVERT: L 38 MET cc_start: -0.1105 (mtt) cc_final: -0.1693 (mtt) REVERT: L 52 MET cc_start: 0.4948 (tpt) cc_final: 0.4453 (tpt) REVERT: M 16 MET cc_start: 0.4422 (tmm) cc_final: 0.4105 (ppp) REVERT: M 20 SER cc_start: 0.6878 (t) cc_final: 0.6626 (m) REVERT: M 124 MET cc_start: 0.8863 (mmm) cc_final: 0.8496 (mmm) REVERT: N 108 MET cc_start: 0.7963 (mmm) cc_final: 0.7497 (mmm) REVERT: O 32 TYR cc_start: 0.7596 (OUTLIER) cc_final: 0.7099 (p90) REVERT: W 19 LEU cc_start: 0.9074 (pp) cc_final: 0.8781 (tp) REVERT: W 69 LEU cc_start: 0.8565 (tp) cc_final: 0.7981 (mt) REVERT: X 1 MET cc_start: 0.4671 (ptp) cc_final: 0.3777 (ptm) REVERT: X 37 ASP cc_start: 0.8548 (p0) cc_final: 0.8169 (p0) REVERT: Z 86 LEU cc_start: 0.8130 (pt) cc_final: 0.7907 (pt) REVERT: FA 47 TYR cc_start: 0.8267 (m-10) cc_final: 0.8021 (m-10) REVERT: MA 127 PHE cc_start: 0.8244 (t80) cc_final: 0.8014 (t80) REVERT: MA 339 MET cc_start: 0.8570 (pmm) cc_final: 0.8364 (pmm) REVERT: OA 48 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8652 (tmm) REVERT: OA 119 GLN cc_start: 0.9552 (mt0) cc_final: 0.9218 (tt0) REVERT: RA 63 MET cc_start: 0.8696 (ppp) cc_final: 0.8427 (ppp) REVERT: RA 151 MET cc_start: 0.9172 (ppp) cc_final: 0.8710 (ppp) REVERT: SA 88 MET cc_start: 0.8682 (tpt) cc_final: 0.8472 (tpp) REVERT: TA 30 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8227 (tmm) REVERT: UA 89 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.8140 (p0) REVERT: YA 75 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7505 (tp30) REVERT: AB 58 SER cc_start: 0.8750 (OUTLIER) cc_final: 0.8417 (t) REVERT: DB 16 MET cc_start: 0.7784 (mmt) cc_final: 0.7528 (mmp) REVERT: DB 49 ASN cc_start: 0.8547 (p0) cc_final: 0.8081 (p0) outliers start: 205 outliers final: 167 residues processed: 760 average time/residue: 1.3016 time to fit residues: 1737.2998 Evaluate side-chains 739 residues out of total 5312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 565 time to evaluate : 6.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 186 LYS Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 82 TYR Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 263 ASP Chi-restraints excluded: chain G residue 8 LYS Chi-restraints excluded: chain G residue 11 MET Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain I residue 25 MET Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain I residue 99 PHE Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 19 ASN Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 17 ASP Chi-restraints excluded: chain K residue 40 THR Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 141 LYS Chi-restraints excluded: chain L residue 86 MET Chi-restraints excluded: chain M residue 33 ASN Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 85 ILE Chi-restraints excluded: chain N residue 25 LEU Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain N residue 84 ILE Chi-restraints excluded: chain O residue 32 TYR Chi-restraints excluded: chain O residue 37 ASP Chi-restraints excluded: chain O residue 52 VAL Chi-restraints excluded: chain O residue 56 ASP Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 69 VAL Chi-restraints excluded: chain O residue 110 GLU Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain P residue 77 ILE Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 70 ASP Chi-restraints excluded: chain Q residue 73 ILE Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 102 LEU Chi-restraints excluded: chain Q residue 134 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 13 ASN Chi-restraints excluded: chain R residue 43 GLU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 69 ASP Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain S residue 87 ILE Chi-restraints excluded: chain T residue 15 ASP Chi-restraints excluded: chain T residue 83 ILE Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain V residue 40 MET Chi-restraints excluded: chain V residue 46 GLU Chi-restraints excluded: chain V residue 98 ILE Chi-restraints excluded: chain W residue 7 HIS Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain W residue 109 ASP Chi-restraints excluded: chain Y residue 7 ASP Chi-restraints excluded: chain Y residue 27 VAL Chi-restraints excluded: chain Y residue 29 SER Chi-restraints excluded: chain Y residue 71 ILE Chi-restraints excluded: chain Y residue 88 ASP Chi-restraints excluded: chain Z residue 43 ASP Chi-restraints excluded: chain Z residue 56 PHE Chi-restraints excluded: chain Z residue 61 LEU Chi-restraints excluded: chain Z residue 63 ILE Chi-restraints excluded: chain Z residue 66 ASP Chi-restraints excluded: chain Z residue 77 VAL Chi-restraints excluded: chain Z residue 89 ILE Chi-restraints excluded: chain AA residue 52 ASP Chi-restraints excluded: chain AA residue 78 ILE Chi-restraints excluded: chain BA residue 39 VAL Chi-restraints excluded: chain BA residue 58 ILE Chi-restraints excluded: chain CA residue 4 LYS Chi-restraints excluded: chain CA residue 7 ARG Chi-restraints excluded: chain DA residue 26 LEU Chi-restraints excluded: chain DA residue 56 VAL Chi-restraints excluded: chain EA residue 39 LYS Chi-restraints excluded: chain FA residue 8 THR Chi-restraints excluded: chain FA residue 22 THR Chi-restraints excluded: chain GA residue 4 ILE Chi-restraints excluded: chain GA residue 8 ILE Chi-restraints excluded: chain GA residue 47 ILE Chi-restraints excluded: chain HA residue 8 SER Chi-restraints excluded: chain HA residue 43 THR Chi-restraints excluded: chain IA residue 53 ASP Chi-restraints excluded: chain IA residue 61 LEU Chi-restraints excluded: chain MA residue 12 LEU Chi-restraints excluded: chain MA residue 115 VAL Chi-restraints excluded: chain MA residue 162 ILE Chi-restraints excluded: chain MA residue 166 ILE Chi-restraints excluded: chain MA residue 176 LYS Chi-restraints excluded: chain MA residue 184 VAL Chi-restraints excluded: chain MA residue 255 VAL Chi-restraints excluded: chain OA residue 7 ASP Chi-restraints excluded: chain OA residue 48 MET Chi-restraints excluded: chain OA residue 87 ASP Chi-restraints excluded: chain OA residue 124 THR Chi-restraints excluded: chain PA residue 30 ASP Chi-restraints excluded: chain PA residue 51 VAL Chi-restraints excluded: chain PA residue 101 ASN Chi-restraints excluded: chain PA residue 106 ARG Chi-restraints excluded: chain QA residue 19 PHE Chi-restraints excluded: chain RA residue 14 LEU Chi-restraints excluded: chain RA residue 17 VAL Chi-restraints excluded: chain RA residue 77 ASN Chi-restraints excluded: chain RA residue 105 ILE Chi-restraints excluded: chain RA residue 130 THR Chi-restraints excluded: chain SA residue 16 GLU Chi-restraints excluded: chain SA residue 30 THR Chi-restraints excluded: chain SA residue 82 ASP Chi-restraints excluded: chain TA residue 30 MET Chi-restraints excluded: chain UA residue 74 ILE Chi-restraints excluded: chain UA residue 84 ILE Chi-restraints excluded: chain UA residue 89 ASP Chi-restraints excluded: chain VA residue 26 LYS Chi-restraints excluded: chain VA residue 36 GLN Chi-restraints excluded: chain WA residue 17 LEU Chi-restraints excluded: chain WA residue 52 LEU Chi-restraints excluded: chain WA residue 83 THR Chi-restraints excluded: chain WA residue 97 ASP Chi-restraints excluded: chain XA residue 30 ILE Chi-restraints excluded: chain XA residue 45 THR Chi-restraints excluded: chain XA residue 80 ASN Chi-restraints excluded: chain YA residue 2 THR Chi-restraints excluded: chain YA residue 40 THR Chi-restraints excluded: chain YA residue 72 ASN Chi-restraints excluded: chain YA residue 75 GLU Chi-restraints excluded: chain YA residue 111 GLN Chi-restraints excluded: chain ZA residue 8 ILE Chi-restraints excluded: chain ZA residue 11 HIS Chi-restraints excluded: chain ZA residue 84 CYS Chi-restraints excluded: chain AB residue 58 SER Chi-restraints excluded: chain AB residue 62 ASN Chi-restraints excluded: chain AB residue 64 CYS Chi-restraints excluded: chain AB residue 67 THR Chi-restraints excluded: chain BB residue 88 ARG Chi-restraints excluded: chain CB residue 19 VAL Chi-restraints excluded: chain DB residue 19 SER Chi-restraints excluded: chain DB residue 37 ILE Chi-restraints excluded: chain DB residue 54 ILE Chi-restraints excluded: chain DB residue 76 ARG Chi-restraints excluded: chain DB residue 82 VAL Chi-restraints excluded: chain EB residue 25 ILE Chi-restraints excluded: chain FB residue 5 LYS Chi-restraints excluded: chain FB residue 14 LEU Chi-restraints excluded: chain FB residue 57 VAL Chi-restraints excluded: chain FB residue 78 THR Chi-restraints excluded: chain GB residue 11 ILE Chi-restraints excluded: chain GB residue 81 GLN Chi-restraints excluded: chain HB residue 12 ASP Chi-restraints excluded: chain HB residue 13 VAL Chi-restraints excluded: chain HB residue 18 PHE Chi-restraints excluded: chain HB residue 22 CYS Chi-restraints excluded: chain HB residue 63 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1099 random chunks: chunk 655 optimal weight: 30.0000 chunk 423 optimal weight: 20.0000 chunk 632 optimal weight: 6.9990 chunk 319 optimal weight: 20.0000 chunk 208 optimal weight: 20.0000 chunk 205 optimal weight: 20.0000 chunk 673 optimal weight: 5.9990 chunk 721 optimal weight: 20.0000 chunk 523 optimal weight: 10.0000 chunk 98 optimal weight: 30.0000 chunk 832 optimal weight: 30.0000 overall best weight: 12.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 ASN ** H 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 8 ASN ** CA 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GA 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HA 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HA 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** OA 50 ASN ** OA 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** QA 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SA 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SA 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TA 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** UA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** WA 56 HIS ** XA 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** YA 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** YA 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GB 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GB 81 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.6774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 165304 Z= 0.358 Angle : 0.717 14.156 246624 Z= 0.361 Chirality : 0.037 0.295 31435 Planarity : 0.005 0.076 13698 Dihedral : 24.601 178.300 81109 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 36.41 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.37 % Favored : 89.49 % Rotamer: Outliers : 4.14 % Allowed : 20.84 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.08 % 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: -1.91 (0.10), residues: 6412 helix: -0.25 (0.11), residues: 2138 sheet: -1.28 (0.15), residues: 1143 loop : -1.99 (0.11), residues: 3131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRPMA 55 HIS 0.015 0.002 HISMA 264 PHE 0.034 0.003 PHEWA 49 TYR 0.021 0.002 TYRDB 33 ARG 0.012 0.001 ARGAA 7 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12824 Ramachandran restraints generated. 6412 Oldfield, 0 Emsley, 6412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12824 Ramachandran restraints generated. 6412 Oldfield, 0 Emsley, 6412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 5312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 588 time to evaluate : 6.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 97 MET cc_start: 0.2603 (mpp) cc_final: 0.2312 (mmt) REVERT: E 218 MET cc_start: 0.4532 (mtm) cc_final: 0.3192 (mtt) REVERT: H 62 GLN cc_start: 0.6946 (OUTLIER) cc_final: 0.5957 (tp40) REVERT: J 74 MET cc_start: 0.8969 (mpp) cc_final: 0.8617 (mtp) REVERT: K 15 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8159 (mt) REVERT: K 66 ASN cc_start: 0.9050 (m-40) cc_final: 0.8511 (m-40) REVERT: K 123 ARG cc_start: 0.8839 (mtt180) cc_final: 0.8527 (mmm-85) REVERT: K 132 PHE cc_start: 0.8967 (m-80) cc_final: 0.8715 (m-80) REVERT: K 135 HIS cc_start: 0.8950 (t-90) cc_final: 0.8522 (t-90) REVERT: L 38 MET cc_start: -0.0916 (mtt) cc_final: -0.1586 (mtt) REVERT: L 52 MET cc_start: 0.4679 (tpt) cc_final: 0.4180 (tpt) REVERT: M 20 SER cc_start: 0.6919 (t) cc_final: 0.6686 (m) REVERT: M 124 MET cc_start: 0.8889 (mmm) cc_final: 0.8481 (mmm) REVERT: O 32 TYR cc_start: 0.7693 (OUTLIER) cc_final: 0.7211 (p90) REVERT: W 69 LEU cc_start: 0.8538 (tp) cc_final: 0.7976 (mt) REVERT: X 1 MET cc_start: 0.5103 (ptp) cc_final: 0.4254 (ptm) REVERT: X 37 ASP cc_start: 0.8873 (p0) cc_final: 0.8549 (p0) REVERT: IA 48 MET cc_start: 0.8223 (tpp) cc_final: 0.7682 (tpp) REVERT: MA 127 PHE cc_start: 0.8274 (t80) cc_final: 0.8053 (t80) REVERT: MA 269 LYS cc_start: 0.9020 (pttt) cc_final: 0.8438 (pttt) REVERT: OA 48 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8583 (tmm) REVERT: RA 151 MET cc_start: 0.9120 (ppp) cc_final: 0.8783 (ppp) REVERT: SA 1 MET cc_start: 0.7285 (tpp) cc_final: 0.6911 (tpp) REVERT: SA 88 MET cc_start: 0.8763 (tpt) cc_final: 0.8541 (tpp) REVERT: TA 30 MET cc_start: 0.8460 (ttt) cc_final: 0.8077 (tmm) REVERT: UA 58 LEU cc_start: 0.8347 (tp) cc_final: 0.8142 (tt) REVERT: UA 89 ASP cc_start: 0.8461 (OUTLIER) cc_final: 0.8195 (p0) REVERT: UA 110 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8088 (pmm) REVERT: YA 75 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7473 (tp30) REVERT: ZA 80 MET cc_start: 0.8642 (mmp) cc_final: 0.8412 (mmt) REVERT: AB 58 SER cc_start: 0.8841 (OUTLIER) cc_final: 0.8556 (t) REVERT: AB 64 CYS cc_start: 0.5166 (OUTLIER) cc_final: 0.4737 (p) REVERT: BB 58 MET cc_start: 0.8236 (ptp) cc_final: 0.7805 (ptp) REVERT: DB 16 MET cc_start: 0.7695 (mmt) cc_final: 0.7474 (mmp) REVERT: HB 35 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7661 (pp20) outliers start: 220 outliers final: 177 residues processed: 749 average time/residue: 1.3469 time to fit residues: 1766.2151 Evaluate side-chains 727 residues out of total 5312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 540 time to evaluate : 6.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 186 LYS Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 82 TYR Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 263 ASP Chi-restraints excluded: chain G residue 8 LYS Chi-restraints excluded: chain G residue 11 MET Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 62 GLN Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain I residue 99 PHE Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 19 ASN Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 17 ASP Chi-restraints excluded: chain K residue 40 THR Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 141 LYS Chi-restraints excluded: chain L residue 86 MET Chi-restraints excluded: chain M residue 33 ASN Chi-restraints excluded: chain M residue 61 TYR Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 85 ILE Chi-restraints excluded: chain N residue 25 LEU Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain N residue 84 ILE Chi-restraints excluded: chain O residue 32 TYR Chi-restraints excluded: chain O residue 37 ASP Chi-restraints excluded: chain O residue 56 ASP Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 69 VAL Chi-restraints excluded: chain O residue 110 GLU Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain P residue 77 ILE Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 70 ASP Chi-restraints excluded: chain Q residue 73 ILE Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 102 LEU Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 134 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 13 ASN Chi-restraints excluded: chain R residue 35 LYS Chi-restraints excluded: chain R residue 43 GLU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain S residue 4 LYS Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 48 LEU Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain S residue 69 ASP Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain S residue 87 ILE Chi-restraints excluded: chain T residue 15 ASP Chi-restraints excluded: chain T residue 83 ILE Chi-restraints excluded: chain U residue 16 ILE Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain V residue 40 MET Chi-restraints excluded: chain V residue 46 GLU Chi-restraints excluded: chain V residue 98 ILE Chi-restraints excluded: chain W residue 7 HIS Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain W residue 51 LEU Chi-restraints excluded: chain W residue 109 ASP Chi-restraints excluded: chain Y residue 27 VAL Chi-restraints excluded: chain Y residue 29 SER Chi-restraints excluded: chain Y residue 71 ILE Chi-restraints excluded: chain Z residue 43 ASP Chi-restraints excluded: chain Z residue 56 PHE Chi-restraints excluded: chain Z residue 61 LEU Chi-restraints excluded: chain Z residue 63 ILE Chi-restraints excluded: chain Z residue 66 ASP Chi-restraints excluded: chain Z residue 77 VAL Chi-restraints excluded: chain Z residue 89 ILE Chi-restraints excluded: chain AA residue 52 ASP Chi-restraints excluded: chain AA residue 78 ILE Chi-restraints excluded: chain BA residue 39 VAL Chi-restraints excluded: chain BA residue 58 ILE Chi-restraints excluded: chain CA residue 4 LYS Chi-restraints excluded: chain CA residue 7 ARG Chi-restraints excluded: chain DA residue 26 LEU Chi-restraints excluded: chain DA residue 56 VAL Chi-restraints excluded: chain EA residue 39 LYS Chi-restraints excluded: chain EA residue 66 ILE Chi-restraints excluded: chain FA residue 22 THR Chi-restraints excluded: chain FA residue 56 LYS Chi-restraints excluded: chain GA residue 4 ILE Chi-restraints excluded: chain GA residue 8 ILE Chi-restraints excluded: chain GA residue 47 ILE Chi-restraints excluded: chain HA residue 8 SER Chi-restraints excluded: chain HA residue 43 THR Chi-restraints excluded: chain IA residue 53 ASP Chi-restraints excluded: chain IA residue 61 LEU Chi-restraints excluded: chain JA residue 26 ILE Chi-restraints excluded: chain MA residue 12 LEU Chi-restraints excluded: chain MA residue 75 ARG Chi-restraints excluded: chain MA residue 166 ILE Chi-restraints excluded: chain MA residue 176 LYS Chi-restraints excluded: chain MA residue 184 VAL Chi-restraints excluded: chain MA residue 206 MET Chi-restraints excluded: chain MA residue 255 VAL Chi-restraints excluded: chain OA residue 7 ASP Chi-restraints excluded: chain OA residue 48 MET Chi-restraints excluded: chain OA residue 87 ASP Chi-restraints excluded: chain OA residue 198 VAL Chi-restraints excluded: chain PA residue 30 ASP Chi-restraints excluded: chain PA residue 51 VAL Chi-restraints excluded: chain PA residue 101 ASN Chi-restraints excluded: chain PA residue 106 ARG Chi-restraints excluded: chain QA residue 19 PHE Chi-restraints excluded: chain QA residue 170 LEU Chi-restraints excluded: chain RA residue 17 VAL Chi-restraints excluded: chain RA residue 77 ASN Chi-restraints excluded: chain RA residue 130 THR Chi-restraints excluded: chain SA residue 16 GLU Chi-restraints excluded: chain SA residue 30 THR Chi-restraints excluded: chain SA residue 82 ASP Chi-restraints excluded: chain UA residue 74 ILE Chi-restraints excluded: chain UA residue 84 ILE Chi-restraints excluded: chain UA residue 89 ASP Chi-restraints excluded: chain UA residue 110 MET Chi-restraints excluded: chain VA residue 26 LYS Chi-restraints excluded: chain VA residue 36 GLN Chi-restraints excluded: chain WA residue 17 LEU Chi-restraints excluded: chain WA residue 52 LEU Chi-restraints excluded: chain WA residue 83 THR Chi-restraints excluded: chain WA residue 91 ASP Chi-restraints excluded: chain WA residue 97 ASP Chi-restraints excluded: chain XA residue 15 VAL Chi-restraints excluded: chain XA residue 30 ILE Chi-restraints excluded: chain XA residue 31 VAL Chi-restraints excluded: chain XA residue 45 THR Chi-restraints excluded: chain XA residue 80 ASN Chi-restraints excluded: chain YA residue 2 THR Chi-restraints excluded: chain YA residue 40 THR Chi-restraints excluded: chain YA residue 72 ASN Chi-restraints excluded: chain YA residue 75 GLU Chi-restraints excluded: chain YA residue 110 LYS Chi-restraints excluded: chain YA residue 111 GLN Chi-restraints excluded: chain ZA residue 8 ILE Chi-restraints excluded: chain ZA residue 11 HIS Chi-restraints excluded: chain ZA residue 84 CYS Chi-restraints excluded: chain AB residue 30 ILE Chi-restraints excluded: chain AB residue 58 SER Chi-restraints excluded: chain AB residue 62 ASN Chi-restraints excluded: chain AB residue 64 CYS Chi-restraints excluded: chain AB residue 67 THR Chi-restraints excluded: chain CB residue 19 VAL Chi-restraints excluded: chain CB residue 52 LEU Chi-restraints excluded: chain DB residue 19 SER Chi-restraints excluded: chain DB residue 37 ILE Chi-restraints excluded: chain DB residue 76 ARG Chi-restraints excluded: chain DB residue 82 VAL Chi-restraints excluded: chain EB residue 25 ILE Chi-restraints excluded: chain FB residue 5 LYS Chi-restraints excluded: chain FB residue 14 LEU Chi-restraints excluded: chain FB residue 39 ILE Chi-restraints excluded: chain FB residue 57 VAL Chi-restraints excluded: chain FB residue 78 THR Chi-restraints excluded: chain GB residue 11 ILE Chi-restraints excluded: chain HB residue 12 ASP Chi-restraints excluded: chain HB residue 13 VAL Chi-restraints excluded: chain HB residue 18 PHE Chi-restraints excluded: chain HB residue 22 CYS Chi-restraints excluded: chain HB residue 35 GLU Chi-restraints excluded: chain HB residue 37 TYR Chi-restraints excluded: chain HB residue 63 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1099 random chunks: chunk 963 optimal weight: 0.9990 chunk 1014 optimal weight: 6.9990 chunk 925 optimal weight: 0.0370 chunk 987 optimal weight: 0.9990 chunk 594 optimal weight: 7.9990 chunk 430 optimal weight: 20.0000 chunk 775 optimal weight: 10.0000 chunk 302 optimal weight: 20.0000 chunk 891 optimal weight: 10.0000 chunk 933 optimal weight: 20.0000 chunk 983 optimal weight: 30.0000 overall best weight: 3.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 ASN H 165 HIS J 37 ASN J 63 GLN ** J 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 138 GLN ** O 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 68 ASN ** CA 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GA 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GA 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** HA 13 ASN ** HA 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** OA 50 ASN ** OA 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** PA 122 GLN ** QA 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SA 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SA 46 GLN ** TA 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** UA 15 ASN ** UA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XA 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** YA 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EB 18 GLN ** GB 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.6525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 165304 Z= 0.161 Angle : 0.618 25.467 246624 Z= 0.308 Chirality : 0.033 0.455 31435 Planarity : 0.004 0.075 13698 Dihedral : 24.333 179.842 81109 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 21.52 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.53 % Favored : 91.33 % Rotamer: Outliers : 2.56 % Allowed : 22.97 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.08 % 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: -1.58 (0.10), residues: 6412 helix: 0.02 (0.11), residues: 2171 sheet: -1.02 (0.16), residues: 1119 loop : -1.83 (0.11), residues: 3122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRPMA 55 HIS 0.006 0.001 HISMA 279 PHE 0.031 0.002 PHE V 77 TYR 0.019 0.001 TYRXA 76 ARG 0.016 0.001 ARG V 84 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12824 Ramachandran restraints generated. 6412 Oldfield, 0 Emsley, 6412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12824 Ramachandran restraints generated. 6412 Oldfield, 0 Emsley, 6412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 5312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 635 time to evaluate : 6.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 97 MET cc_start: 0.2568 (mpp) cc_final: 0.2180 (mmt) REVERT: E 121 MET cc_start: 0.4975 (mmm) cc_final: 0.4769 (mmm) REVERT: E 218 MET cc_start: 0.4157 (mtm) cc_final: 0.2472 (mtt) REVERT: J 74 MET cc_start: 0.8983 (mpp) cc_final: 0.8537 (mtp) REVERT: K 15 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7903 (mt) REVERT: K 66 ASN cc_start: 0.9010 (m-40) cc_final: 0.8451 (m-40) REVERT: K 89 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8184 (tmtt) REVERT: K 132 PHE cc_start: 0.8934 (m-80) cc_final: 0.8723 (m-80) REVERT: K 135 HIS cc_start: 0.8939 (t-90) cc_final: 0.8513 (t-90) REVERT: L 3 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8383 (mt) REVERT: L 31 ARG cc_start: 0.7411 (mmt-90) cc_final: 0.6855 (mmt-90) REVERT: L 38 MET cc_start: -0.0909 (mtt) cc_final: -0.1563 (mtt) REVERT: M 20 SER cc_start: 0.6745 (t) cc_final: 0.6505 (m) REVERT: M 124 MET cc_start: 0.8972 (mmm) cc_final: 0.8559 (mmm) REVERT: M 135 MET cc_start: 0.4288 (mmt) cc_final: 0.4066 (mmt) REVERT: O 32 TYR cc_start: 0.7552 (OUTLIER) cc_final: 0.6964 (p90) REVERT: O 113 MET cc_start: 0.7226 (mmt) cc_final: 0.6910 (pmm) REVERT: Q 124 LEU cc_start: 0.8544 (mm) cc_final: 0.8327 (mm) REVERT: T 101 GLU cc_start: 0.8903 (pm20) cc_final: 0.8697 (pm20) REVERT: V 55 ASP cc_start: 0.8989 (p0) cc_final: 0.8264 (p0) REVERT: W 69 LEU cc_start: 0.8443 (tp) cc_final: 0.7939 (mt) REVERT: X 1 MET cc_start: 0.4770 (ptp) cc_final: 0.3986 (ptm) REVERT: Z 86 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7852 (pt) REVERT: EA 10 GLU cc_start: 0.8210 (mp0) cc_final: 0.7570 (mp0) REVERT: MA 112 PHE cc_start: 0.8289 (m-80) cc_final: 0.7650 (m-80) REVERT: MA 127 PHE cc_start: 0.8193 (t80) cc_final: 0.7967 (t80) REVERT: MA 177 PHE cc_start: 0.8062 (m-80) cc_final: 0.7793 (m-80) REVERT: MA 274 LEU cc_start: 0.8753 (pp) cc_final: 0.8513 (tt) REVERT: RA 151 MET cc_start: 0.8954 (ppp) cc_final: 0.8591 (ppp) REVERT: SA 1 MET cc_start: 0.7026 (tpp) cc_final: 0.6782 (tpp) REVERT: UA 58 LEU cc_start: 0.8398 (tp) cc_final: 0.7950 (tt) REVERT: UA 89 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.8076 (p0) REVERT: VA 35 GLU cc_start: 0.9418 (mp0) cc_final: 0.9160 (pm20) REVERT: VA 111 GLU cc_start: 0.8250 (pm20) cc_final: 0.7967 (pm20) REVERT: ZA 47 LEU cc_start: 0.9037 (mt) cc_final: 0.8736 (tp) REVERT: BB 88 ARG cc_start: 0.5992 (OUTLIER) cc_final: 0.3970 (mmm160) REVERT: DB 76 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.8081 (ttp80) outliers start: 136 outliers final: 104 residues processed: 732 average time/residue: 1.2999 time to fit residues: 1667.2569 Evaluate side-chains 695 residues out of total 5312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 583 time to evaluate : 6.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain G residue 11 MET Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain I residue 99 PHE Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 19 ASN Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 89 LYS Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain K residue 141 LYS Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 86 MET Chi-restraints excluded: chain M residue 33 ASN Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 85 ILE Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain N residue 84 ILE Chi-restraints excluded: chain O residue 32 TYR Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 69 VAL Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain Q residue 70 ASP Chi-restraints excluded: chain Q residue 73 ILE Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 134 THR Chi-restraints excluded: chain R residue 13 ASN Chi-restraints excluded: chain R residue 35 LYS Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain S residue 69 ASP Chi-restraints excluded: chain T residue 15 ASP Chi-restraints excluded: chain T residue 83 ILE Chi-restraints excluded: chain U residue 16 ILE Chi-restraints excluded: chain V residue 46 GLU Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain Y residue 27 VAL Chi-restraints excluded: chain Z residue 43 ASP Chi-restraints excluded: chain Z residue 56 PHE Chi-restraints excluded: chain Z residue 61 LEU Chi-restraints excluded: chain Z residue 66 ASP Chi-restraints excluded: chain Z residue 77 VAL Chi-restraints excluded: chain Z residue 86 LEU Chi-restraints excluded: chain AA residue 78 ILE Chi-restraints excluded: chain BA residue 39 VAL Chi-restraints excluded: chain BA residue 58 ILE Chi-restraints excluded: chain CA residue 7 ARG Chi-restraints excluded: chain DA residue 26 LEU Chi-restraints excluded: chain DA residue 56 VAL Chi-restraints excluded: chain GA residue 4 ILE Chi-restraints excluded: chain GA residue 8 ILE Chi-restraints excluded: chain HA residue 8 SER Chi-restraints excluded: chain HA residue 43 THR Chi-restraints excluded: chain IA residue 53 ASP Chi-restraints excluded: chain IA residue 61 LEU Chi-restraints excluded: chain MA residue 12 LEU Chi-restraints excluded: chain MA residue 176 LYS Chi-restraints excluded: chain MA residue 184 VAL Chi-restraints excluded: chain MA residue 255 VAL Chi-restraints excluded: chain PA residue 51 VAL Chi-restraints excluded: chain PA residue 106 ARG Chi-restraints excluded: chain QA residue 170 LEU Chi-restraints excluded: chain RA residue 17 VAL Chi-restraints excluded: chain RA residue 105 ILE Chi-restraints excluded: chain RA residue 130 THR Chi-restraints excluded: chain SA residue 16 GLU Chi-restraints excluded: chain SA residue 30 THR Chi-restraints excluded: chain UA residue 84 ILE Chi-restraints excluded: chain UA residue 89 ASP Chi-restraints excluded: chain WA residue 17 LEU Chi-restraints excluded: chain WA residue 52 LEU Chi-restraints excluded: chain WA residue 83 THR Chi-restraints excluded: chain WA residue 97 ASP Chi-restraints excluded: chain XA residue 30 ILE Chi-restraints excluded: chain XA residue 31 VAL Chi-restraints excluded: chain XA residue 45 THR Chi-restraints excluded: chain YA residue 2 THR Chi-restraints excluded: chain YA residue 40 THR Chi-restraints excluded: chain YA residue 111 GLN Chi-restraints excluded: chain ZA residue 8 ILE Chi-restraints excluded: chain ZA residue 11 HIS Chi-restraints excluded: chain AB residue 67 THR Chi-restraints excluded: chain BB residue 88 ARG Chi-restraints excluded: chain CB residue 52 LEU Chi-restraints excluded: chain DB residue 19 SER Chi-restraints excluded: chain DB residue 76 ARG Chi-restraints excluded: chain EB residue 25 ILE Chi-restraints excluded: chain FB residue 5 LYS Chi-restraints excluded: chain FB residue 14 LEU Chi-restraints excluded: chain FB residue 57 VAL Chi-restraints excluded: chain FB residue 72 GLU Chi-restraints excluded: chain GB residue 11 ILE Chi-restraints excluded: chain HB residue 13 VAL Chi-restraints excluded: chain HB residue 18 PHE Chi-restraints excluded: chain HB residue 22 CYS Chi-restraints excluded: chain HB residue 27 VAL Chi-restraints excluded: chain HB residue 63 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1099 random chunks: chunk 648 optimal weight: 6.9990 chunk 1043 optimal weight: 1.9990 chunk 637 optimal weight: 0.9990 chunk 495 optimal weight: 6.9990 chunk 725 optimal weight: 20.0000 chunk 1094 optimal weight: 6.9990 chunk 1007 optimal weight: 9.9990 chunk 871 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 chunk 673 optimal weight: 5.9990 chunk 534 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 5 GLN ** Q 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EA 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GA 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GA 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** HA 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MA 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OA 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** PA 138 GLN ** QA 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** RA 77 ASN ** SA 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** TA 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** UA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** WA 56 HIS ** WA 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XA 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** YA 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** YA 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ZA 90 HIS ** DB 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EB 18 GLN ** GB 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.6597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 165304 Z= 0.178 Angle : 0.621 21.178 246624 Z= 0.309 Chirality : 0.033 0.389 31435 Planarity : 0.004 0.075 13698 Dihedral : 24.245 179.293 81109 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 23.75 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.66 % Favored : 91.19 % Rotamer: Outliers : 2.24 % Allowed : 23.78 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.08 % 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: -1.56 (0.10), residues: 6412 helix: 0.05 (0.11), residues: 2174 sheet: -1.02 (0.16), residues: 1138 loop : -1.83 (0.11), residues: 3100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRPMA 55 HIS 0.006 0.001 HIS T 76 PHE 0.053 0.002 PHEMA 132 TYR 0.020 0.001 TYRDB 33 ARG 0.014 0.001 ARGBB 57 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12824 Ramachandran restraints generated. 6412 Oldfield, 0 Emsley, 6412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12824 Ramachandran restraints generated. 6412 Oldfield, 0 Emsley, 6412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 5312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 615 time to evaluate : 6.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 97 MET cc_start: 0.2665 (mpp) cc_final: 0.2261 (mmt) REVERT: E 121 MET cc_start: 0.5129 (mmm) cc_final: 0.4823 (mmm) REVERT: E 218 MET cc_start: 0.4090 (mtm) cc_final: 0.2467 (mtt) REVERT: G 11 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7408 (tmm) REVERT: G 161 MET cc_start: 0.8203 (pmm) cc_final: 0.7777 (pmm) REVERT: I 98 PHE cc_start: 0.8647 (t80) cc_final: 0.8297 (t80) REVERT: J 74 MET cc_start: 0.8942 (mpp) cc_final: 0.8577 (mtp) REVERT: K 15 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.7936 (mt) REVERT: K 66 ASN cc_start: 0.9021 (m-40) cc_final: 0.8471 (m-40) REVERT: K 135 HIS cc_start: 0.8971 (t-90) cc_final: 0.8526 (t-90) REVERT: L 3 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8368 (mt) REVERT: L 31 ARG cc_start: 0.7486 (mmt-90) cc_final: 0.6767 (mmt-90) REVERT: L 38 MET cc_start: -0.0999 (mtt) cc_final: -0.1618 (mtt) REVERT: M 20 SER cc_start: 0.6770 (t) cc_final: 0.6529 (m) REVERT: M 124 MET cc_start: 0.8990 (mmm) cc_final: 0.8555 (mmm) REVERT: M 135 MET cc_start: 0.3779 (mmt) cc_final: 0.3575 (mmt) REVERT: O 5 GLN cc_start: 0.7139 (OUTLIER) cc_final: 0.6727 (tm-30) REVERT: O 32 TYR cc_start: 0.7602 (OUTLIER) cc_final: 0.6966 (p90) REVERT: O 113 MET cc_start: 0.7241 (mmt) cc_final: 0.6921 (pmm) REVERT: R 20 MET cc_start: 0.8737 (ppp) cc_final: 0.8302 (ppp) REVERT: W 69 LEU cc_start: 0.8503 (tp) cc_final: 0.7958 (mt) REVERT: X 1 MET cc_start: 0.5006 (ptp) cc_final: 0.4161 (ptm) REVERT: X 7 LEU cc_start: 0.9346 (mp) cc_final: 0.9126 (tp) REVERT: BA 55 MET cc_start: 0.8797 (tpp) cc_final: 0.8564 (tpp) REVERT: EA 1 MET cc_start: 0.7239 (mmm) cc_final: 0.6868 (mmm) REVERT: MA 127 PHE cc_start: 0.8197 (t80) cc_final: 0.7955 (t80) REVERT: MA 177 PHE cc_start: 0.8058 (m-80) cc_final: 0.7802 (m-80) REVERT: MA 269 LYS cc_start: 0.8909 (pttt) cc_final: 0.8277 (pttt) REVERT: RA 151 MET cc_start: 0.9029 (ppp) cc_final: 0.8694 (ppp) REVERT: UA 58 LEU cc_start: 0.8282 (tp) cc_final: 0.7989 (tt) REVERT: UA 89 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.7994 (p0) REVERT: UA 110 MET cc_start: 0.8406 (ppp) cc_final: 0.7958 (pmm) REVERT: VA 35 GLU cc_start: 0.9410 (mp0) cc_final: 0.9134 (pm20) REVERT: VA 111 GLU cc_start: 0.8267 (pm20) cc_final: 0.7979 (pm20) REVERT: ZA 47 LEU cc_start: 0.9033 (mt) cc_final: 0.8805 (tp) REVERT: BB 88 ARG cc_start: 0.5722 (OUTLIER) cc_final: 0.3608 (mmm-85) outliers start: 119 outliers final: 100 residues processed: 700 average time/residue: 1.3563 time to fit residues: 1672.5508 Evaluate side-chains 681 residues out of total 5312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 574 time to evaluate : 6.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain G residue 11 MET Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain I residue 99 PHE Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 19 ASN Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 141 LYS Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 52 MET Chi-restraints excluded: chain L residue 86 MET Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 33 ASN Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 85 ILE Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain N residue 84 ILE Chi-restraints excluded: chain O residue 5 GLN Chi-restraints excluded: chain O residue 32 TYR Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 69 VAL Chi-restraints excluded: chain O residue 110 GLU Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain Q residue 70 ASP Chi-restraints excluded: chain Q residue 73 ILE Chi-restraints excluded: chain Q residue 134 THR Chi-restraints excluded: chain R residue 13 ASN Chi-restraints excluded: chain R residue 35 LYS Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 69 ASP Chi-restraints excluded: chain T residue 15 ASP Chi-restraints excluded: chain T residue 83 ILE Chi-restraints excluded: chain U residue 16 ILE Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain Y residue 27 VAL Chi-restraints excluded: chain Z residue 43 ASP Chi-restraints excluded: chain Z residue 56 PHE Chi-restraints excluded: chain Z residue 61 LEU Chi-restraints excluded: chain Z residue 66 ASP Chi-restraints excluded: chain Z residue 77 VAL Chi-restraints excluded: chain AA residue 78 ILE Chi-restraints excluded: chain BA residue 39 VAL Chi-restraints excluded: chain BA residue 58 ILE Chi-restraints excluded: chain CA residue 7 ARG Chi-restraints excluded: chain CA residue 11 VAL Chi-restraints excluded: chain DA residue 26 LEU Chi-restraints excluded: chain DA residue 56 VAL Chi-restraints excluded: chain EA residue 66 ILE Chi-restraints excluded: chain GA residue 4 ILE Chi-restraints excluded: chain GA residue 8 ILE Chi-restraints excluded: chain HA residue 8 SER Chi-restraints excluded: chain HA residue 43 THR Chi-restraints excluded: chain IA residue 53 ASP Chi-restraints excluded: chain MA residue 12 LEU Chi-restraints excluded: chain MA residue 176 LYS Chi-restraints excluded: chain MA residue 184 VAL Chi-restraints excluded: chain MA residue 255 VAL Chi-restraints excluded: chain OA residue 198 VAL Chi-restraints excluded: chain PA residue 51 VAL Chi-restraints excluded: chain PA residue 106 ARG Chi-restraints excluded: chain PA residue 138 GLN Chi-restraints excluded: chain RA residue 17 VAL Chi-restraints excluded: chain RA residue 130 THR Chi-restraints excluded: chain SA residue 16 GLU Chi-restraints excluded: chain UA residue 84 ILE Chi-restraints excluded: chain UA residue 89 ASP Chi-restraints excluded: chain WA residue 17 LEU Chi-restraints excluded: chain WA residue 52 LEU Chi-restraints excluded: chain WA residue 83 THR Chi-restraints excluded: chain WA residue 97 ASP Chi-restraints excluded: chain XA residue 15 VAL Chi-restraints excluded: chain XA residue 30 ILE Chi-restraints excluded: chain XA residue 31 VAL Chi-restraints excluded: chain XA residue 45 THR Chi-restraints excluded: chain YA residue 2 THR Chi-restraints excluded: chain YA residue 40 THR Chi-restraints excluded: chain YA residue 111 GLN Chi-restraints excluded: chain ZA residue 11 HIS Chi-restraints excluded: chain AB residue 67 THR Chi-restraints excluded: chain BB residue 88 ARG Chi-restraints excluded: chain CB residue 52 LEU Chi-restraints excluded: chain DB residue 19 SER Chi-restraints excluded: chain DB residue 76 ARG Chi-restraints excluded: chain EB residue 25 ILE Chi-restraints excluded: chain FB residue 5 LYS Chi-restraints excluded: chain FB residue 14 LEU Chi-restraints excluded: chain FB residue 57 VAL Chi-restraints excluded: chain HB residue 13 VAL Chi-restraints excluded: chain HB residue 18 PHE Chi-restraints excluded: chain HB residue 22 CYS Chi-restraints excluded: chain HB residue 63 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1099 random chunks: chunk 692 optimal weight: 6.9990 chunk 928 optimal weight: 9.9990 chunk 267 optimal weight: 20.0000 chunk 803 optimal weight: 50.0000 chunk 128 optimal weight: 30.0000 chunk 242 optimal weight: 40.0000 chunk 873 optimal weight: 0.0670 chunk 365 optimal weight: 40.0000 chunk 896 optimal weight: 30.0000 chunk 110 optimal weight: 30.0000 chunk 160 optimal weight: 30.0000 overall best weight: 13.4130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 133 ASN ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 ASN ** J 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 72 ASN ** CA 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GA 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GA 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** HA 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MA 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** OA 50 ASN OA 177 ASN ** OA 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** PA 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** QA 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** QA 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RA 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RA 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SA 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** TA 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TA 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** UA 15 ASN ** UA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** WA 56 HIS ** WA 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XA 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** YA 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** YA 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FB 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** GB 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.020299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2427 r_free = 0.2427 target = 0.015253 restraints weight = 2469109.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2460 r_free = 0.2460 target = 0.015732 restraints weight = 946658.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2477 r_free = 0.2477 target = 0.016030 restraints weight = 565079.023| |-----------------------------------------------------------------------------| r_work (final): 0.2460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9088 moved from start: 0.7099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 165304 Z= 0.374 Angle : 0.740 22.118 246624 Z= 0.369 Chirality : 0.037 0.388 31435 Planarity : 0.005 0.081 13698 Dihedral : 24.523 178.195 81109 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 38.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.59 % Favored : 89.29 % Rotamer: Outliers : 2.62 % Allowed : 23.57 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.08 % 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: -1.80 (0.10), residues: 6412 helix: -0.19 (0.11), residues: 2169 sheet: -1.19 (0.15), residues: 1144 loop : -1.92 (0.11), residues: 3099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRPMA 55 HIS 0.009 0.002 HISFB 51 PHE 0.029 0.002 PHEBA 37 TYR 0.029 0.002 TYRXA 76 ARG 0.014 0.001 ARG L 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32744.48 seconds wall clock time: 580 minutes 41.29 seconds (34841.29 seconds total)