Starting phenix.real_space_refine on Sat Feb 24 13:41:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emm_28254/02_2024/8emm_28254_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emm_28254/02_2024/8emm_28254.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emm_28254/02_2024/8emm_28254_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emm_28254/02_2024/8emm_28254_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emm_28254/02_2024/8emm_28254_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emm_28254/02_2024/8emm_28254.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emm_28254/02_2024/8emm_28254.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emm_28254/02_2024/8emm_28254_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emm_28254/02_2024/8emm_28254_updated.pdb" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians K 10 8.98 5 Zn 2 6.06 5 P 4558 5.49 5 Mg 321 5.21 5 S 151 5.16 5 C 71261 2.51 5 N 26509 2.21 5 O 42923 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "c ARG 52": "NH1" <-> "NH2" Residue "c ARG 63": "NH1" <-> "NH2" Residue "c ARG 80": "NH1" <-> "NH2" Residue "c ARG 133": "NH1" <-> "NH2" Residue "c TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 167": "NH1" <-> "NH2" Residue "c ARG 177": "NH1" <-> "NH2" Residue "c ARG 182": "NH1" <-> "NH2" Residue "c ARG 189": "NH1" <-> "NH2" Residue "c ARG 203": "NH1" <-> "NH2" Residue "c ARG 212": "NH1" <-> "NH2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "d ARG 59": "NH1" <-> "NH2" Residue "d ARG 83": "NH1" <-> "NH2" Residue "d ARG 128": "NH1" <-> "NH2" Residue "d ARG 169": "NH1" <-> "NH2" Residue "e ARG 44": "NH1" <-> "NH2" Residue "e ARG 49": "NH1" <-> "NH2" Residue "e ARG 61": "NH1" <-> "NH2" Residue "e ARG 88": "NH1" <-> "NH2" Residue "e ARG 102": "NH1" <-> "NH2" Residue "e ARG 162": "NH1" <-> "NH2" Residue "e ARG 170": "NH1" <-> "NH2" Residue "f ARG 71": "NH1" <-> "NH2" Residue "f ARG 80": "NH1" <-> "NH2" Residue "f ARG 92": "NH1" <-> "NH2" Residue "f ARG 102": "NH1" <-> "NH2" Residue "f ARG 110": "NH1" <-> "NH2" Residue "f ARG 112": "NH1" <-> "NH2" Residue "f ARG 115": "NH1" <-> "NH2" Residue "f ARG 133": "NH1" <-> "NH2" Residue "g ARG 3": "NH1" <-> "NH2" Residue "g ARG 153": "NH1" <-> "NH2" Residue "g ARG 163": "NH1" <-> "NH2" Residue "g ARG 170": "NH1" <-> "NH2" Residue "h ARG 27": "NH1" <-> "NH2" Residue "i ARG 13": "NH1" <-> "NH2" Residue "i ARG 37": "NH1" <-> "NH2" Residue "i ARG 96": "NH1" <-> "NH2" Residue "i ARG 120": "NH1" <-> "NH2" Residue "k ARG 21": "NH1" <-> "NH2" Residue "k ARG 33": "NH1" <-> "NH2" Residue "k ARG 41": "NH1" <-> "NH2" Residue "k ARG 47": "NH1" <-> "NH2" Residue "k ARG 60": "NH1" <-> "NH2" Residue "k ARG 78": "NH1" <-> "NH2" Residue "k ARG 126": "NH1" <-> "NH2" Residue "l ARG 10": "NH1" <-> "NH2" Residue "l ARG 18": "NH1" <-> "NH2" Residue "l ARG 40": "NH1" <-> "NH2" Residue "l ARG 44": "NH1" <-> "NH2" Residue "l ARG 50": "NH1" <-> "NH2" Residue "l ARG 55": "NH1" <-> "NH2" Residue "l ARG 114": "NH1" <-> "NH2" Residue "m ARG 12": "NH1" <-> "NH2" Residue "m ARG 17": "NH1" <-> "NH2" Residue "m ARG 22": "NH1" <-> "NH2" Residue "m ARG 46": "NH1" <-> "NH2" Residue "m ARG 63": "NH1" <-> "NH2" Residue "m ARG 64": "NH1" <-> "NH2" Residue "m ARG 69": "NH1" <-> "NH2" Residue "m ARG 71": "NH1" <-> "NH2" Residue "m ARG 96": "NH1" <-> "NH2" Residue "m ARG 118": "NH1" <-> "NH2" Residue "n ARG 10": "NH1" <-> "NH2" Residue "n ARG 16": "NH1" <-> "NH2" Residue "n ARG 25": "NH1" <-> "NH2" Residue "n ARG 81": "NH1" <-> "NH2" Residue "n ARG 94": "NH1" <-> "NH2" Residue "n ARG 102": "NH1" <-> "NH2" Residue "n ARG 111": "NH1" <-> "NH2" Residue "o ARG 21": "NH1" <-> "NH2" Residue "o ARG 39": "NH1" <-> "NH2" Residue "o ARG 89": "NH1" <-> "NH2" Residue "o ARG 101": "NH1" <-> "NH2" Residue "o ARG 109": "NH1" <-> "NH2" Residue "p ARG 3": "NH1" <-> "NH2" Residue "p ARG 6": "NH1" <-> "NH2" Residue "p ARG 13": "NH1" <-> "NH2" Residue "p ARG 33": "NH1" <-> "NH2" Residue "p ARG 48": "NH1" <-> "NH2" Residue "q ARG 21": "NH1" <-> "NH2" Residue "q ARG 68": "NH1" <-> "NH2" Residue "q ARG 79": "NH1" <-> "NH2" Residue "q ARG 84": "NH1" <-> "NH2" Residue "r ARG 84": "NH1" <-> "NH2" Residue "r ARG 88": "NH1" <-> "NH2" Residue "r ARG 95": "NH1" <-> "NH2" Residue "r ARG 110": "NH1" <-> "NH2" Residue "s ARG 73": "NH1" <-> "NH2" Residue "t ARG 6": "NH1" <-> "NH2" Residue "t ARG 7": "NH1" <-> "NH2" Residue "t ARG 82": "NH1" <-> "NH2" Residue "t ARG 86": "NH1" <-> "NH2" Residue "t ARG 94": "NH1" <-> "NH2" Residue "w ARG 3": "NH1" <-> "NH2" Residue "w ARG 11": "NH1" <-> "NH2" Residue "w ARG 37": "NH1" <-> "NH2" Residue "w ARG 50": "NH1" <-> "NH2" Residue "w ARG 57": "NH1" <-> "NH2" Residue "w ARG 74": "NH1" <-> "NH2" Residue "w TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 29": "NH1" <-> "NH2" Residue "x ARG 47": "NH1" <-> "NH2" Residue "x ARG 52": "NH1" <-> "NH2" Residue "y ARG 11": "NH1" <-> "NH2" Residue "y ARG 30": "NH1" <-> "NH2" Residue "y ARG 45": "NH1" <-> "NH2" Residue "z ARG 10": "NH1" <-> "NH2" Residue "z ARG 16": "NH1" <-> "NH2" Residue "z ARG 52": "NH1" <-> "NH2" Residue "0 ARG 44": "NH1" <-> "NH2" Residue "1 ARG 3": "NH1" <-> "NH2" Residue "1 ARG 12": "NH1" <-> "NH2" Residue "1 ARG 14": "NH1" <-> "NH2" Residue "1 ARG 21": "NH1" <-> "NH2" Residue "1 ARG 33": "NH1" <-> "NH2" Residue "1 ARG 41": "NH1" <-> "NH2" Residue "2 ARG 13": "NH1" <-> "NH2" Residue "2 ARG 30": "NH1" <-> "NH2" Residue "2 ARG 40": "NH1" <-> "NH2" Residue "3 ARG 24": "NH1" <-> "NH2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 56": "OE1" <-> "OE2" Residue "B GLU 118": "OE1" <-> "OE2" Residue "B GLU 142": "OE1" <-> "OE2" Residue "B GLU 223": "OE1" <-> "OE2" Residue "C GLU 28": "OE1" <-> "OE2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D GLU 78": "OE1" <-> "OE2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "D GLU 147": "OE1" <-> "OE2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D GLU 202": "OE1" <-> "OE2" Residue "E GLU 13": "OE1" <-> "OE2" Residue "E GLU 116": "OE1" <-> "OE2" Residue "E GLU 151": "OE1" <-> "OE2" Residue "E GLU 163": "OE1" <-> "OE2" Residue "F GLU 23": "OE1" <-> "OE2" Residue "F GLU 33": "OE1" <-> "OE2" Residue "F GLU 65": "OE1" <-> "OE2" Residue "F GLU 69": "OE1" <-> "OE2" Residue "F GLU 75": "OE1" <-> "OE2" Residue "G GLU 21": "OE1" <-> "OE2" Residue "G GLU 40": "OE1" <-> "OE2" Residue "G GLU 63": "OE1" <-> "OE2" Residue "G GLU 67": "OE1" <-> "OE2" Residue "G GLU 74": "OE1" <-> "OE2" Residue "G GLU 106": "OE1" <-> "OE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "G GLU 139": "OE1" <-> "OE2" Residue "G GLU 146": "OE1" <-> "OE2" Residue "H GLU 42": "OE1" <-> "OE2" Residue "H GLU 43": "OE1" <-> "OE2" Residue "H GLU 47": "OE1" <-> "OE2" Residue "H GLU 58": "OE1" <-> "OE2" Residue "H GLU 73": "OE1" <-> "OE2" Residue "H GLU 124": "OE1" <-> "OE2" Residue "I GLU 36": "OE1" <-> "OE2" Residue "I GLU 42": "OE1" <-> "OE2" Residue "J GLU 47": "OE1" <-> "OE2" Residue "K GLU 68": "OE1" <-> "OE2" Residue "L GLU 25": "OE1" <-> "OE2" Residue "L GLU 62": "OE1" <-> "OE2" Residue "M GLU 50": "OE1" <-> "OE2" Residue "N GLU 86": "OE1" <-> "OE2" Residue "O GLU 6": "OE1" <-> "OE2" Residue "O GLU 45": "OE1" <-> "OE2" Residue "P GLU 34": "OE1" <-> "OE2" Residue "P GLU 77": "OE1" <-> "OE2" Residue "Q GLU 26": "OE1" <-> "OE2" Residue "Q GLU 60": "OE1" <-> "OE2" Residue "R GLU 20": "OE1" <-> "OE2" Residue "R GLU 35": "OE1" <-> "OE2" Residue "S GLU 65": "OE1" <-> "OE2" Residue "S GLU 73": "OE1" <-> "OE2" Residue "T GLU 15": "OE1" <-> "OE2" Residue "T GLU 40": "OE1" <-> "OE2" Residue "U GLU 24": "OE1" <-> "OE2" Residue "U GLU 31": "OE1" <-> "OE2" Residue "U GLU 63": "OE1" <-> "OE2" 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: 145735 Number of models: 1 Model: "" Number of chains: 97 Chain: "a" Number of atoms: 59130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2753, 59130 Classifications: {'RNA': 2753} Modifications used: {'rna2p': 7, 'rna2p_pur': 266, 'rna2p_pyr': 139, 'rna3p': 17, 'rna3p_pur': 1319, 'rna3p_pyr': 1005} Link IDs: {'rna2p': 411, 'rna3p': 2341} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 10 Chain: "b" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2549 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 58, 'rna3p_pyr': 49} Link IDs: {'rna2p': 12, 'rna3p': 106} Chain: "c" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "d" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1566 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEQ:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "f" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "g" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "h" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 303 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "i" 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: "j" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "k" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "l" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1075 Unusual residues: {'MS6': 1} Classifications: {'peptide': 135, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126, None: 2} Not linked: pdbres="4D4 l 81 " pdbres="MS6 l 82 " Not linked: pdbres="MS6 l 82 " pdbres="GLY l 83 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4D4:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 945 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "n" 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: "o" 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: "p" 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: "q" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 101} Chain: "r" 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: "s" 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: "t" 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: "u" 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: "v" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 628 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "w" Number of atoms: 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: "x" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "y" 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: "z" 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: "0" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 417 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "1" 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: "2" 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: "3" 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: "4" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 480 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain breaks: 1 Chain: "Y" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1623 Unusual residues: {'8AN': 1} Classifications: {'RNA': 75, 'undetermined': 1} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 31, 'rna3p_pyr': 32} Link IDs: {'p': 1, 'rna2p': 12, 'rna3p': 62} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "Z" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1623 Unusual residues: {'8AN': 1} Classifications: {'RNA': 75, 'undetermined': 1} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 33, 'rna3p_pyr': 33} Link IDs: {'p': 1, 'rna2p': 9, 'rna3p': 65} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 32612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1519, 32612 Classifications: {'RNA': 1519} Modifications used: {'rna2p': 1, 'rna2p_pur': 120, 'rna2p_pyr': 81, 'rna3p': 10, 'rna3p_pur': 742, 'rna3p_pyr': 565} Link IDs: {'rna2p': 202, 'rna3p': 1316} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 7 Chain: "B" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "C" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "F" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 839 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "G" Number of atoms: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1203 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 5, 'TRANS': 147} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 92} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'IAS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D2T:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 643 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "Q" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 641 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 544 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "S" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 668 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "U" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "X" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 322 Classifications: {'RNA': 15} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 7, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 12} Chain: "a" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 400 Unusual residues: {' K': 9, ' MG': 217, 'SPD': 16, 'SPM': 1} Classifications: {'undetermined': 243} Link IDs: {None: 242} Chain: "b" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "c" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Chain: "Z" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {' MG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "A" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 144 Unusual residues: {' MG': 92, 'PAR': 1, 'SPD': 1} Classifications: {'undetermined': 94} Link IDs: {None: 93} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3031, 3031 Classifications: {'water': 3031} Link IDs: {None: 3030} Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "c" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 86 Classifications: {'water': 86} Link IDs: {None: 85} Chain: "d" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "i" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "j" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "k" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "l" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "m" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "o" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "p" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "q" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "r" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "s" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "u" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "v" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "w" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "x" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "z" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "1" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "2" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "3" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "Z" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 85792 SG CYS 3 11 155.753 86.301 164.776 1.00 40.65 S ATOM 85817 SG CYS 3 14 153.420 83.954 162.198 1.00 39.55 S ATOM 85920 SG CYS 3 27 152.451 84.387 166.017 1.00 40.64 S ATOM 86139 SG CYS 4 16 207.287 154.077 93.942 1.00 98.45 S ATOM 86151 SG CYS 4 18 211.541 154.104 94.988 1.00 99.52 S ATOM 86293 SG CYS 4 37 208.423 150.809 95.053 1.00 95.60 S ATOM 86314 SG CYS 4 40 208.173 153.516 97.406 1.00 95.67 S Time building chain proxies: 59.55, per 1000 atoms: 0.41 Number of scatterers: 145735 At special positions: 0 Unit cell: (231.458, 257.176, 269.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 K 10 19.00 S 151 16.00 P 4558 15.00 Mg 321 11.99 O 42923 8.00 N 26509 7.00 C 71261 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 69.73 Conformation dependent library (CDL) restraints added in 6.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 3 101 " pdb="ZN ZN 3 101 " - pdb=" ND1 HIS 3 33 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 27 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 11 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 14 " pdb=" ZN 4 101 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 16 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 40 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 18 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 37 " Number of angles added : 9 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10274 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 174 helices and 70 sheets defined 39.3% alpha, 20.2% beta 1553 base pairs and 2492 stacking pairs defined. Time for finding SS restraints: 81.75 Creating SS restraints... Processing helix chain 'c' and resid 10 through 15 removed outlier: 5.036A pdb=" N HIS c 15 " --> pdb=" O PRO c 11 " (cutoff:3.500A) Processing helix chain 'c' and resid 30 through 35 removed outlier: 3.946A pdb=" N LEU c 34 " --> pdb=" O PHE c 30 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N GLU c 35 " --> pdb=" O ALA c 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 30 through 35' Processing helix chain 'c' and resid 131 through 136 removed outlier: 3.588A pdb=" N ILE c 135 " --> pdb=" O PRO c 131 " (cutoff:3.500A) Proline residue: c 136 - end of helix No H-bonds generated for 'chain 'c' and resid 131 through 136' Processing helix chain 'c' and resid 207 through 215 removed outlier: 3.924A pdb=" N ALA c 211 " --> pdb=" O LYS c 207 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG c 214 " --> pdb=" O ALA c 210 " (cutoff:3.500A) Processing helix chain 'c' and resid 221 through 226 removed outlier: 3.992A pdb=" N MET c 225 " --> pdb=" O ARG c 221 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ASN c 226 " --> pdb=" O GLY c 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 221 through 226' Processing helix chain 'c' and resid 260 through 268 removed outlier: 3.509A pdb=" N ASP c 264 " --> pdb=" O ASN c 260 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LYS c 265 " --> pdb=" O LYS c 261 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N PHE c 266 " --> pdb=" O ARG c 262 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE c 267 " --> pdb=" O THR c 263 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N VAL c 268 " --> pdb=" O ASP c 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 260 through 268' Processing helix chain 'd' and resid 56 through 61 removed outlier: 5.634A pdb=" N THR d 61 " --> pdb=" O ALA d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 62 through 72 removed outlier: 3.684A pdb=" N ALA d 71 " --> pdb=" O HIS d 67 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 103 removed outlier: 4.197A pdb=" N ALA d 102 " --> pdb=" O VAL d 98 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ASP d 103 " --> pdb=" O GLU d 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 98 through 103' Processing helix chain 'd' and resid 120 through 125 Processing helix chain 'd' and resid 39 through 44 Processing helix chain 'e' and resid 24 through 40 removed outlier: 3.665A pdb=" N ARG e 40 " --> pdb=" O ALA e 36 " (cutoff:3.500A) Processing helix chain 'e' and resid 48 through 53 removed outlier: 6.460A pdb=" N THR e 53 " --> pdb=" O ARG e 49 " (cutoff:3.500A) Processing helix chain 'e' and resid 97 through 116 Processing helix chain 'e' and resid 130 through 142 removed outlier: 3.528A pdb=" N LYS e 139 " --> pdb=" O ALA e 135 " (cutoff:3.500A) Processing helix chain 'e' and resid 154 through 162 removed outlier: 3.938A pdb=" N PHE e 158 " --> pdb=" O ASP e 154 " (cutoff:3.500A) Processing helix chain 'e' and resid 176 through 183 removed outlier: 3.623A pdb=" N ILE e 181 " --> pdb=" O PRO e 177 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE e 183 " --> pdb=" O SER e 179 " (cutoff:3.500A) Processing helix chain 'e' and resid 189 through 201 Processing helix chain 'e' and resid 16 through 21 Processing helix chain 'f' and resid 2 through 21 removed outlier: 5.525A pdb=" N VAL f 13 " --> pdb=" O LYS f 9 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LYS f 14 " --> pdb=" O ASP f 10 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR f 18 " --> pdb=" O LYS f 14 " (cutoff:3.500A) Processing helix chain 'f' and resid 24 through 29 removed outlier: 4.035A pdb=" N VAL f 28 " --> pdb=" O SER f 24 " (cutoff:3.500A) Proline residue: f 29 - end of helix No H-bonds generated for 'chain 'f' and resid 24 through 29' Processing helix chain 'f' and resid 46 through 62 removed outlier: 4.736A pdb=" N LEU f 50 " --> pdb=" O ASP f 46 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP f 51 " --> pdb=" O LYS f 47 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA f 55 " --> pdb=" O ASP f 51 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP f 56 " --> pdb=" O ASN f 52 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA f 58 " --> pdb=" O ALA f 54 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA f 59 " --> pdb=" O ALA f 55 " (cutoff:3.500A) Processing helix chain 'f' and resid 93 through 111 removed outlier: 3.604A pdb=" N TRP f 97 " --> pdb=" O GLY f 93 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG f 102 " --> pdb=" O GLU f 98 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA f 107 " --> pdb=" O LEU f 103 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N VAL f 108 " --> pdb=" O ILE f 104 " (cutoff:3.500A) Proline residue: f 109 - end of helix Processing helix chain 'f' and resid 162 through 174 removed outlier: 3.517A pdb=" N ALA f 172 " --> pdb=" O ALA f 168 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE f 173 " --> pdb=" O LEU f 169 " (cutoff:3.500A) Processing helix chain 'f' and resid 40 through 45 removed outlier: 4.438A pdb=" N ILE f 44 " --> pdb=" O GLY f 41 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA f 45 " --> pdb=" O GLU f 42 " (cutoff:3.500A) Processing helix chain 'f' and resid 134 through 139 removed outlier: 3.917A pdb=" N ILE f 137 " --> pdb=" O GLU f 134 " (cutoff:3.500A) Proline residue: f 139 - end of helix Processing helix chain 'g' and resid 2 through 8 removed outlier: 3.954A pdb=" N ALA g 7 " --> pdb=" O ARG g 3 " (cutoff:3.500A) Proline residue: g 8 - end of helix Processing helix chain 'g' and resid 60 through 81 removed outlier: 5.653A pdb=" N GLN g 64 " --> pdb=" O ASP g 60 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL g 79 " --> pdb=" O MET g 75 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR g 80 " --> pdb=" O VAL g 76 " (cutoff:3.500A) Processing helix chain 'g' and resid 137 through 153 removed outlier: 3.595A pdb=" N TYR g 151 " --> pdb=" O ASP g 147 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ARG g 152 " --> pdb=" O LEU g 148 " (cutoff:3.500A) Processing helix chain 'h' and resid 22 through 28 Processing helix chain 'h' and resid 29 through 34 removed outlier: 3.567A pdb=" N GLY h 34 " --> pdb=" O LEU h 30 " (cutoff:3.500A) Processing helix chain 'i' and resid 24 through 38 removed outlier: 3.801A pdb=" N GLU i 31 " --> pdb=" O ARG i 27 " (cutoff:3.500A) Processing helix chain 'i' and resid 88 through 96 Processing helix chain 'i' and resid 97 through 110 removed outlier: 4.168A pdb=" N ILE i 101 " --> pdb=" O PRO i 97 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET i 108 " --> pdb=" O ALA i 104 " (cutoff:3.500A) Proline residue: i 110 - end of helix Processing helix chain 'i' and resid 112 through 122 removed outlier: 3.542A pdb=" N ARG i 120 " --> pdb=" O ARG i 116 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS i 121 " --> pdb=" O ALA i 117 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU i 122 " --> pdb=" O MET i 118 " (cutoff:3.500A) Processing helix chain 'j' and resid 104 through 109 removed outlier: 4.579A pdb=" N ARG j 108 " --> pdb=" O THR j 104 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N SER j 109 " --> pdb=" O ARG j 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 104 through 109' Processing helix chain 'j' and resid 112 through 119 Processing helix chain 'k' and resid 37 through 42 removed outlier: 3.802A pdb=" N ARG k 41 " --> pdb=" O GLY k 37 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N SER k 42 " --> pdb=" O GLN k 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 37 through 42' Processing helix chain 'k' and resid 56 through 62 removed outlier: 3.509A pdb=" N LEU k 61 " --> pdb=" O LEU k 57 " (cutoff:3.500A) Proline residue: k 62 - end of helix Processing helix chain 'k' and resid 68 through 75 removed outlier: 4.040A pdb=" N ALA k 72 " --> pdb=" O SER k 68 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE k 73 " --> pdb=" O ARG k 69 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ALA k 75 " --> pdb=" O ALA k 71 " (cutoff:3.500A) Processing helix chain 'k' and resid 78 through 85 removed outlier: 3.749A pdb=" N LEU k 82 " --> pdb=" O ARG k 78 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ALA k 83 " --> pdb=" O LEU k 79 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LYS k 84 " --> pdb=" O SER k 80 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL k 85 " --> pdb=" O ASP k 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 78 through 85' Processing helix chain 'k' and resid 91 through 99 Processing helix chain 'k' and resid 128 through 139 removed outlier: 3.723A pdb=" N ALA k 138 " --> pdb=" O ALA k 134 " (cutoff:3.500A) Processing helix chain 'l' and resid 42 through 58 Processing helix chain 'l' and resid 109 through 125 removed outlier: 4.125A pdb=" N LYS l 123 " --> pdb=" O LEU l 119 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU l 124 " --> pdb=" O ALA l 120 " (cutoff:3.500A) Proline residue: l 125 - end of helix Processing helix chain 'm' and resid 13 through 32 Processing helix chain 'm' and resid 37 through 58 removed outlier: 4.404A pdb=" N ARG m 46 " --> pdb=" O LYS m 42 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL m 47 " --> pdb=" O GLU m 43 " (cutoff:3.500A) Proline residue: m 50 - end of helix removed outlier: 4.349A pdb=" N THR m 57 " --> pdb=" O THR m 53 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ASP m 58 " --> pdb=" O LEU m 54 " (cutoff:3.500A) Processing helix chain 'm' and resid 59 through 71 removed outlier: 4.346A pdb=" N THR m 70 " --> pdb=" O ALA m 66 " (cutoff:3.500A) Processing helix chain 'm' and resid 72 through 88 removed outlier: 5.147A pdb=" N GLY m 84 " --> pdb=" O PHE m 80 " (cutoff:3.500A) Proline residue: m 85 - end of helix Processing helix chain 'n' and resid 2 through 22 removed outlier: 4.731A pdb=" N ARG n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ALA n 14 " --> pdb=" O ARG n 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 55 through 63 removed outlier: 5.370A pdb=" N GLN n 61 " --> pdb=" O ALA n 57 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU n 62 " --> pdb=" O ILE n 58 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N LYS n 63 " --> pdb=" O ALA n 59 " (cutoff:3.500A) Processing helix chain 'n' and resid 67 through 86 removed outlier: 4.400A pdb=" N GLU n 84 " --> pdb=" O GLU n 80 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS n 85 " --> pdb=" O ARG n 81 " (cutoff:3.500A) Processing helix chain 'n' and resid 101 through 114 Processing helix chain 'o' and resid 2 through 13 removed outlier: 4.375A pdb=" N GLN o 12 " --> pdb=" O LEU o 8 " (cutoff:3.500A) Processing helix chain 'o' and resid 97 through 104 removed outlier: 4.601A pdb=" N ARG o 101 " --> pdb=" O LEU o 97 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLU o 102 " --> pdb=" O TYR o 98 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG o 103 " --> pdb=" O TYR o 99 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N THR o 104 " --> pdb=" O LEU o 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 97 through 104' Processing helix chain 'p' and resid 6 through 22 removed outlier: 3.701A pdb=" N LYS p 22 " --> pdb=" O LEU p 18 " (cutoff:3.500A) Processing helix chain 'p' and resid 26 through 31 removed outlier: 3.662A pdb=" N ARG p 30 " --> pdb=" O GLY p 26 " (cutoff:3.500A) Processing helix chain 'p' and resid 32 through 37 removed outlier: 3.586A pdb=" N GLN p 37 " --> pdb=" O ARG p 33 " (cutoff:3.500A) Processing helix chain 'p' and resid 39 through 73 removed outlier: 3.671A pdb=" N ARG p 51 " --> pdb=" O TYR p 47 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS p 54 " --> pdb=" O ARG p 50 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG p 55 " --> pdb=" O ARG p 51 " (cutoff:3.500A) Processing helix chain 'p' and resid 75 through 87 Processing helix chain 'p' and resid 91 through 102 Processing helix chain 'p' and resid 103 through 118 Processing helix chain 'r' and resid 13 through 25 removed outlier: 3.841A pdb=" N VAL r 20 " --> pdb=" O LYS r 16 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU r 23 " --> pdb=" O LEU r 19 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE r 24 " --> pdb=" O VAL r 20 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG r 25 " --> pdb=" O ALA r 21 " (cutoff:3.500A) Processing helix chain 'r' and resid 28 through 39 Processing helix chain 'r' and resid 41 through 61 removed outlier: 3.900A pdb=" N VAL r 45 " --> pdb=" O LYS r 41 " (cutoff:3.500A) Processing helix chain 'r' and resid 65 through 70 removed outlier: 3.692A pdb=" N LEU r 69 " --> pdb=" O ASP r 65 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LYS r 70 " --> pdb=" O ILE r 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 65 through 70' Processing helix chain 's' and resid 3 through 11 removed outlier: 4.056A pdb=" N LYS s 9 " --> pdb=" O GLU s 5 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL s 10 " --> pdb=" O ARG s 6 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEU s 11 " --> pdb=" O LEU s 7 " (cutoff:3.500A) Processing helix chain 's' and resid 17 through 27 Processing helix chain 's' and resid 39 through 50 Processing helix chain 't' and resid 66 through 71 removed outlier: 3.996A pdb=" N VAL t 70 " --> pdb=" O GLN t 66 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ALA t 71 " --> pdb=" O VAL t 67 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 66 through 71' Processing helix chain 'u' and resid 13 through 24 Processing helix chain 'u' and resid 43 through 53 removed outlier: 3.630A pdb=" N ALA u 52 " --> pdb=" O MET u 48 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LYS u 53 " --> pdb=" O ASN u 49 " (cutoff:3.500A) Processing helix chain 'u' and resid 54 through 59 removed outlier: 4.095A pdb=" N SER u 58 " --> pdb=" O ALA u 54 " (cutoff:3.500A) Processing helix chain 'w' and resid 52 through 63 Processing helix chain 'w' and resid 64 through 75 Processing helix chain 'x' and resid 2 through 10 removed outlier: 3.823A pdb=" N GLU x 8 " --> pdb=" O LYS x 4 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS x 9 " --> pdb=" O GLU x 5 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N SER x 10 " --> pdb=" O LEU x 6 " (cutoff:3.500A) Processing helix chain 'x' and resid 11 through 35 removed outlier: 3.541A pdb=" N ASN x 20 " --> pdb=" O THR x 16 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA x 33 " --> pdb=" O ARG x 29 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER x 34 " --> pdb=" O MET x 30 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLY x 35 " --> pdb=" O GLN x 31 " (cutoff:3.500A) Processing helix chain 'x' and resid 39 through 62 removed outlier: 4.857A pdb=" N LEU x 43 " --> pdb=" O GLN x 39 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LYS x 44 " --> pdb=" O SER x 40 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY x 62 " --> pdb=" O ASN x 58 " (cutoff:3.500A) Processing helix chain 'y' and resid 17 through 28 Processing helix chain 'y' and resid 41 through 52 Processing helix chain 'z' and resid 9 through 19 removed outlier: 4.827A pdb=" N HIS z 19 " --> pdb=" O MET z 15 " (cutoff:3.500A) Processing helix chain '1' and resid 8 through 16 Processing helix chain '1' and resid 17 through 24 removed outlier: 4.278A pdb=" N THR 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) Processing helix chain '1' and resid 25 through 38 Processing helix chain '2' and resid 7 through 14 removed outlier: 3.802A pdb=" N ARG 2 13 " --> pdb=" O GLY 2 9 " (cutoff:3.500A) Processing helix chain '2' and resid 32 through 37 removed outlier: 4.616A pdb=" N LYS 2 36 " --> pdb=" O ILE 2 32 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ALA 2 37 " --> pdb=" O LEU 2 33 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 32 through 37' Processing helix chain '2' and resid 38 through 46 Proline residue: 2 46 - end of helix Processing helix chain '2' and resid 51 through 63 removed outlier: 4.641A pdb=" N GLY 2 56 " --> pdb=" O LYS 2 52 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU 2 57 " --> pdb=" O GLY 2 53 " (cutoff:3.500A) Proline residue: 2 63 - end of helix Processing helix chain '4' and resid 41 through 46 Processing helix chain '4' and resid 55 through 64 Processing helix chain 'B' and resid 5 through 13 Processing helix chain 'B' and resid 27 through 32 removed outlier: 3.567A pdb=" N ILE B 31 " --> pdb=" O MET B 27 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N PHE B 32 " --> pdb=" O LYS B 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 27 through 32' Processing helix chain 'B' and resid 42 through 64 Proline residue: B 48 - end of helix removed outlier: 4.084A pdb=" N LYS B 64 " --> pdb=" O ILE B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 88 removed outlier: 3.798A pdb=" N CYS B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 124 removed outlier: 4.553A pdb=" N GLN B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 130 removed outlier: 4.509A pdb=" N LEU B 129 " --> pdb=" O THR B 125 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N THR B 130 " --> pdb=" O PHE B 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 125 through 130' Processing helix chain 'B' and resid 131 through 148 removed outlier: 3.746A pdb=" N LEU B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 171 through 180 Processing helix chain 'B' and resid 206 through 227 Processing helix chain 'C' and resid 6 through 12 removed outlier: 3.682A pdb=" N ARG C 11 " --> pdb=" O PRO C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 48 Processing helix chain 'C' and resid 72 through 78 Processing helix chain 'C' and resid 81 through 96 removed outlier: 3.662A pdb=" N GLU C 85 " --> pdb=" O GLY C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 113 removed outlier: 4.026A pdb=" N ASP C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ALA C 113 " --> pdb=" O PRO C 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 108 through 113' Processing helix chain 'C' and resid 114 through 127 Processing helix chain 'C' and resid 129 through 145 Processing helix chain 'D' and resid 7 through 16 removed outlier: 4.445A pdb=" N LEU D 11 " --> pdb=" O PRO D 7 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 removed outlier: 3.844A pdb=" N LYS D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 68 through 83 removed outlier: 5.353A pdb=" N LYS D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 97 removed outlier: 3.743A pdb=" N ARG D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 106 Processing helix chain 'D' and resid 110 through 121 Processing helix chain 'D' and resid 146 through 151 removed outlier: 4.657A pdb=" N LYS D 151 " --> pdb=" O GLU D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 166 removed outlier: 3.504A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLU D 166 " --> pdb=" O ALA D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 192 removed outlier: 3.734A pdb=" N LEU D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N SER D 192 " --> pdb=" O ARG D 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 187 through 192' Processing helix chain 'D' and resid 196 through 206 removed outlier: 3.875A pdb=" N ILE D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 71 removed outlier: 3.828A pdb=" N MET E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 119 Processing helix chain 'E' and resid 132 through 147 Processing helix chain 'E' and resid 149 through 158 Processing helix chain 'E' and resid 160 through 165 Processing helix chain 'F' and resid 14 through 33 removed outlier: 3.741A pdb=" N VAL F 18 " --> pdb=" O GLN F 14 " (cutoff:3.500A) Proline residue: F 19 - end of helix removed outlier: 3.575A pdb=" N GLU F 33 " --> pdb=" O ILE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 82 removed outlier: 5.202A pdb=" N ASP F 82 " --> pdb=" O PHE F 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 31 Processing helix chain 'G' and resid 35 through 55 Processing helix chain 'G' and resid 57 through 70 removed outlier: 3.638A pdb=" N VAL G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 111 Processing helix chain 'G' and resid 115 through 130 removed outlier: 3.581A pdb=" N GLU G 129 " --> pdb=" O SER G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 149 Processing helix chain 'H' and resid 5 through 21 Processing helix chain 'H' and resid 30 through 44 Processing helix chain 'H' and resid 112 through 120 Processing helix chain 'I' and resid 34 through 40 removed outlier: 4.453A pdb=" N GLY I 40 " --> pdb=" O GLU I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 56 Proline residue: I 51 - end of helix Processing helix chain 'I' and resid 71 through 91 Processing helix chain 'I' and resid 94 through 102 Processing helix chain 'J' and resid 14 through 33 Processing helix chain 'J' and resid 80 through 90 removed outlier: 3.624A pdb=" N VAL J 84 " --> pdb=" O THR J 80 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP J 85 " --> pdb=" O GLU J 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 51 removed outlier: 4.001A pdb=" N GLY K 51 " --> pdb=" O ALA K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 59 removed outlier: 4.048A pdb=" N SER K 58 " --> pdb=" O GLY K 54 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N THR K 59 " --> pdb=" O SER K 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 54 through 59' Processing helix chain 'K' and resid 60 through 76 removed outlier: 3.585A pdb=" N LYS K 75 " --> pdb=" O ALA K 71 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N GLU K 76 " --> pdb=" O ASP K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 104 removed outlier: 3.938A pdb=" N THR K 96 " --> pdb=" O GLY K 92 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE K 97 " --> pdb=" O ARG K 93 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY K 104 " --> pdb=" O LEU K 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 11 Proline residue: L 11 - end of helix Processing helix chain 'L' and resid 113 through 118 removed outlier: 3.592A pdb=" N TYR L 117 " --> pdb=" O ALA L 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 22 removed outlier: 3.781A pdb=" N THR M 20 " --> pdb=" O VAL M 16 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ILE M 22 " --> pdb=" O ALA M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 49 through 64 removed outlier: 3.812A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N PHE M 63 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N VAL M 64 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 84 Processing helix chain 'M' and resid 85 through 94 Processing helix chain 'M' and resid 106 through 111 Processing helix chain 'N' and resid 3 through 21 Processing helix chain 'N' and resid 22 through 33 Processing helix chain 'N' and resid 37 through 52 Proline residue: N 52 - end of helix Processing helix chain 'N' and resid 80 through 91 Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 44 removed outlier: 4.151A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 removed outlier: 3.722A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 86 Processing helix chain 'P' and resid 53 through 64 Processing helix chain 'P' and resid 68 through 80 removed outlier: 4.089A pdb=" N LYS P 80 " --> pdb=" O LYS P 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 11 through 17 removed outlier: 3.668A pdb=" N ALA R 15 " --> pdb=" O CYS R 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 34 removed outlier: 4.113A pdb=" N ASN R 31 " --> pdb=" O ALA R 27 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N TYR R 32 " --> pdb=" O THR R 28 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE R 33 " --> pdb=" O LEU R 29 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N THR R 34 " --> pdb=" O LYS R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 46 Processing helix chain 'R' and resid 48 through 66 Processing helix chain 'S' and resid 12 through 26 Processing helix chain 'S' and resid 70 through 76 removed outlier: 4.464A pdb=" N PHE S 74 " --> pdb=" O LYS S 70 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA S 75 " --> pdb=" O LEU S 71 " (cutoff:3.500A) Proline residue: S 76 - end of helix No H-bonds generated for 'chain 'S' and resid 70 through 76' Processing helix chain 'T' and resid 4 through 41 Processing helix chain 'T' and resid 44 through 65 removed outlier: 3.536A pdb=" N LYS T 49 " --> pdb=" O ALA T 45 " (cutoff:3.500A) Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 68 through 87 removed outlier: 3.937A pdb=" N ALA T 87 " --> pdb=" O ILE T 83 " (cutoff:3.500A) Processing helix chain 'U' and resid 11 through 27 Processing helix chain 'U' and resid 28 through 37 removed outlier: 4.752A pdb=" N PHE U 37 " --> pdb=" O ARG U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 69 removed outlier: 4.166A pdb=" N ARG U 67 " --> pdb=" O GLU U 63 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR U 68 " --> pdb=" O ASN U 64 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ARG U 69 " --> pdb=" O ALA U 65 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'c' and resid 2 through 6 removed outlier: 5.788A pdb=" N VAL c 16 " --> pdb=" O CYS c 6 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'c' and resid 73 through 78 removed outlier: 5.004A pdb=" N ILE c 74 " --> pdb=" O SER c 118 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N SER c 118 " --> pdb=" O ILE c 74 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASP c 114 " --> pdb=" O VAL c 78 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLY c 127 " --> pdb=" O GLN c 115 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLN c 117 " --> pdb=" O GLY c 127 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'c' and resid 80 through 83 removed outlier: 3.518A pdb=" N ARG c 80 " --> pdb=" O LEU c 93 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ASN c 90 " --> pdb=" O ALA c 106 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'c' and resid 138 through 142 removed outlier: 4.082A pdb=" N SER c 139 " --> pdb=" O ILE c 164 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR c 173 " --> pdb=" O VAL c 165 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU c 180 " --> pdb=" O LEU c 176 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'd' and resid 3 through 7 removed outlier: 7.150A pdb=" N ASP d 200 " --> pdb=" O THR d 112 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N THR d 112 " --> pdb=" O ASP d 200 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'd' and resid 10 through 16 removed outlier: 3.686A pdb=" N GLY d 10 " --> pdb=" O VAL d 26 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL d 20 " --> pdb=" O THR d 16 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'd' and resid 79 through 84 removed outlier: 5.949A pdb=" N ARG d 46 " --> pdb=" O LEU d 84 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLN d 49 " --> pdb=" O THR d 35 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLN d 94 " --> pdb=" O VAL d 34 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'd' and resid 105 through 108 removed outlier: 6.548A pdb=" N LYS d 105 " --> pdb=" O VAL d 177 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'e' and resid 2 through 6 removed outlier: 4.733A pdb=" N SER e 10 " --> pdb=" O LEU e 5 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'e' and resid 117 through 120 removed outlier: 5.462A pdb=" N ARG e 117 " --> pdb=" O ASP e 184 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'f' and resid 65 through 69 removed outlier: 3.516A pdb=" N GLY f 86 " --> pdb=" O THR f 68 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N GLY f 39 " --> pdb=" O GLY f 151 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLY f 151 " --> pdb=" O GLY f 39 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'g' and resid 15 through 20 removed outlier: 6.041A pdb=" N GLN g 22 " --> pdb=" O LEU g 37 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU g 33 " --> pdb=" O ILE g 26 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY g 28 " --> pdb=" O GLY g 31 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N GLY g 31 " --> pdb=" O GLY g 28 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'g' and resid 40 through 43 No H-bonds generated for sheet with id= 13 Processing sheet with id= 14, first strand: chain 'g' and resid 94 through 99 removed outlier: 6.856A pdb=" N ASN g 101 " --> pdb=" O LEU g 117 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'g' and resid 121 through 125 removed outlier: 5.907A pdb=" N THR g 129 " --> pdb=" O LEU g 89 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL g 90 " --> pdb=" O GLY g 161 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY g 161 " --> pdb=" O VAL g 90 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'h' and resid 16 through 21 removed outlier: 4.489A pdb=" N ASP h 17 " --> pdb=" O LEU h 5 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL h 21 " --> pdb=" O MET h 1 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N GLN h 2 " --> pdb=" O ALA h 39 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LYS h 35 " --> pdb=" O LEU h 6 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'i' and resid 14 through 19 Processing sheet with id= 18, first strand: chain 'i' and resid 74 through 78 removed outlier: 7.492A pdb=" N GLY i 83 " --> pdb=" O THR i 78 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'j' and resid 18 through 21 removed outlier: 4.218A pdb=" N THR j 6 " --> pdb=" O CYS j 21 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ASN j 82 " --> pdb=" O MET j 7 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'j' and resid 38 through 41 Processing sheet with id= 21, first strand: chain 'l' and resid 37 through 40 No H-bonds generated for sheet with id= 21 Processing sheet with id= 22, first strand: chain 'l' and resid 62 through 65 removed outlier: 3.761A pdb=" N TYR l 103 " --> pdb=" O LEU l 33 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU l 33 " --> pdb=" O LEU l 102 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS l 100 " --> pdb=" O ALA l 35 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'l' and resid 73 through 76 removed outlier: 6.790A pdb=" N ILE l 73 " --> pdb=" O GLU l 90 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'l' and resid 30 through 36 removed outlier: 7.760A pdb=" N SER l 30 " --> pdb=" O LYS l 133 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LYS l 127 " --> pdb=" O VAL l 36 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'm' and resid 33 through 36 removed outlier: 5.851A pdb=" N ALA m 108 " --> pdb=" O PHE m 102 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N PHE m 102 " --> pdb=" O ALA m 108 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N MET m 110 " --> pdb=" O CYS m 100 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'n' and resid 49 through 52 removed outlier: 3.766A pdb=" N VAL n 49 " --> pdb=" O VAL n 39 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'o' and resid 38 through 45 removed outlier: 6.482A pdb=" N THR o 25 " --> pdb=" O LYS o 87 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'o' and resid 49 through 52 removed outlier: 3.718A pdb=" N ALA o 49 " --> pdb=" O THR o 60 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N SER o 57 " --> pdb=" O THR o 76 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'q' and resid 11 through 15 removed outlier: 3.677A pdb=" N MET q 40 " --> pdb=" O VAL q 4 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU q 39 " --> pdb=" O GLY q 50 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU q 46 " --> pdb=" O ASN q 43 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'q' and resid 18 through 23 removed outlier: 4.299A pdb=" N GLN q 18 " --> pdb=" O ILE q 98 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASP q 95 " --> pdb=" O VAL q 64 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LYS q 60 " --> pdb=" O THR q 99 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLU q 31 " --> pdb=" O VAL q 63 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'q' and resid 57 through 60 removed outlier: 3.540A pdb=" N VAL q 58 " --> pdb=" O SER q 102 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'q' and resid 65 through 68 removed outlier: 3.582A pdb=" N ALA q 65 " --> pdb=" O ASP q 95 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'q' and resid 71 through 78 removed outlier: 4.179A pdb=" N TYR q 83 " --> pdb=" O ARG q 78 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'r' and resid 2 through 8 Processing sheet with id= 35, first strand: chain 's' and resid 28 through 33 removed outlier: 6.249A pdb=" N ASN s 28 " --> pdb=" O LEU s 87 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS s 66 " --> pdb=" O ARG s 77 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ASP s 79 " --> pdb=" O LYS s 64 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LYS s 64 " --> pdb=" O ASP s 79 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LYS s 81 " --> pdb=" O VAL s 62 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL s 62 " --> pdb=" O LYS s 81 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA s 83 " --> pdb=" O THR s 60 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR s 60 " --> pdb=" O ALA s 83 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL s 85 " --> pdb=" O VAL s 58 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL s 58 " --> pdb=" O VAL s 85 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 't' and resid 40 through 49 removed outlier: 6.336A pdb=" N LEU t 41 " --> pdb=" O GLU t 62 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLU t 62 " --> pdb=" O LEU t 41 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LYS t 43 " --> pdb=" O GLU t 60 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLU t 60 " --> pdb=" O LYS t 43 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N HIS t 45 " --> pdb=" O ILE t 58 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE t 58 " --> pdb=" O HIS t 45 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LYS t 47 " --> pdb=" O GLY t 56 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLY t 56 " --> pdb=" O LYS t 47 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N VAL t 49 " --> pdb=" O GLN t 54 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 't' and resid 83 through 87 Processing sheet with id= 38, first strand: chain 'u' and resid 69 through 72 removed outlier: 6.627A pdb=" N ALA u 39 " --> pdb=" O ARG u 9 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE u 89 " --> pdb=" O PRO u 27 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'v' and resid 51 through 54 removed outlier: 4.205A pdb=" N THR v 58 " --> pdb=" O GLY v 54 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'v' and resid 65 through 71 Processing sheet with id= 41, first strand: chain 'w' and resid 11 through 19 No H-bonds generated for sheet with id= 41 Processing sheet with id= 42, first strand: chain 'w' and resid 34 through 41 removed outlier: 3.515A pdb=" N ARG w 45 " --> pdb=" O VAL w 40 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'y' and resid 33 through 39 removed outlier: 4.290A pdb=" N HIS y 34 " --> pdb=" O GLN y 9 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N MET y 54 " --> pdb=" O THR y 10 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'z' and resid 29 through 32 removed outlier: 4.579A pdb=" N GLU z 36 " --> pdb=" O ASP z 31 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain '0' and resid 19 through 24 removed outlier: 5.849A pdb=" N HIS 0 19 " --> pdb=" O SER 0 13 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ILE 0 48 " --> pdb=" O SER 0 14 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU 0 34 " --> pdb=" O GLU 0 51 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain '2' and resid 22 through 25 removed outlier: 5.657A pdb=" N PHE 2 22 " --> pdb=" O VAL 2 50 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain '3' and resid 1 through 5 removed outlier: 6.428A pdb=" N HIS 3 33 " --> pdb=" O CYS 3 27 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N CYS 3 27 " --> pdb=" O HIS 3 33 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ILE 3 23 " --> pdb=" O GLN 3 37 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain '4' and resid 20 through 26 removed outlier: 4.533A pdb=" N ASN 4 20 " --> pdb=" O CYS 4 16 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER 4 15 " --> pdb=" O LEU 4 32 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'B' and resid 15 through 18 removed outlier: 5.273A pdb=" N HIS B 15 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N HIS B 39 " --> pdb=" O GLY B 17 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'B' and resid 89 through 93 Processing sheet with id= 51, first strand: chain 'C' and resid 54 through 59 removed outlier: 3.586A pdb=" N ARG C 54 " --> pdb=" O HIS C 69 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'C' and resid 164 through 169 removed outlier: 6.260A pdb=" N ASP C 181 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'D' and resid 141 through 144 removed outlier: 3.591A pdb=" N ASP D 141 " --> pdb=" O PHE D 182 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'E' and resid 12 through 16 removed outlier: 6.704A pdb=" N LEU E 36 " --> pdb=" O ILE E 16 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'E' and resid 84 through 88 removed outlier: 3.730A pdb=" N ALA E 99 " --> pdb=" O ASN E 122 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ASN E 122 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'E' and resid 33 through 40 Processing sheet with id= 57, first strand: chain 'F' and resid 38 through 42 removed outlier: 5.642A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG F 86 " --> pdb=" O MET F 9 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'F' and resid 43 through 47 removed outlier: 6.880A pdb=" N HIS F 55 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'G' and resid 72 through 79 removed outlier: 6.458A pdb=" N THR G 72 " --> pdb=" O VAL G 91 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'H' and resid 23 through 29 removed outlier: 6.370A pdb=" N ALA H 23 " --> pdb=" O LEU H 63 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP H 48 " --> pdb=" O THR H 62 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'H' and resid 74 through 77 removed outlier: 3.878A pdb=" N SER H 74 " --> pdb=" O ALA H 130 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS H 127 " --> pdb=" O VAL H 103 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'I' and resid 5 through 11 removed outlier: 3.902A pdb=" N LYS I 60 " --> pdb=" O GLY I 24 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS I 27 " --> pdb=" O LEU I 61 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'J' and resid 39 through 42 removed outlier: 4.469A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'J' and resid 44 through 52 Processing sheet with id= 65, first strand: chain 'K' and resid 42 through 45 removed outlier: 7.068A pdb=" N VAL K 84 " --> pdb=" O THR K 108 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'L' and resid 29 through 32 removed outlier: 5.120A pdb=" N LEU L 81 " --> pdb=" O VAL L 98 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'L' and resid 36 through 41 removed outlier: 3.567A pdb=" N ARG L 36 " --> pdb=" O ARG L 54 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N LYS L 51 " --> pdb=" O ILE L 67 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'P' and resid 4 through 10 removed outlier: 3.592A pdb=" N GLY P 37 " --> pdb=" O VAL P 19 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N GLY P 49 " --> pdb=" O ASN P 40 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'Q' and resid 37 through 48 removed outlier: 6.465A pdb=" N VAL Q 22 " --> pdb=" O VAL Q 13 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLU Q 26 " --> pdb=" O GLN Q 9 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N GLN Q 9 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 13.218A pdb=" N PHE Q 28 " --> pdb=" O THR Q 7 " (cutoff:3.500A) removed outlier: 16.933A pdb=" N THR Q 7 " --> pdb=" O PHE Q 28 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASP Q 57 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'S' and resid 30 through 34 removed outlier: 4.688A pdb=" N LEU S 47 " --> pdb=" O VAL S 62 " (cutoff:3.500A) 1903 hydrogen bonds defined for protein. 5625 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3892 hydrogen bonds 6076 hydrogen bond angles 0 basepair planarities 1553 basepair parallelities 2492 stacking parallelities Total time for adding SS restraints: 556.41 Time building geometry restraints manager: 74.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 15018 1.31 - 1.45: 68826 1.45 - 1.58: 61550 1.58 - 1.71: 8563 1.71 - 1.85: 268 Bond restraints: 154225 Sorted by residual: bond pdb=" C4 5MU a 747 " pdb=" C5 5MU a 747 " ideal model delta sigma weight residual 1.802 1.481 0.321 2.00e-02 2.50e+03 2.58e+02 bond pdb=" C4 5MU a1939 " pdb=" C5 5MU a1939 " ideal model delta sigma weight residual 1.802 1.481 0.321 2.00e-02 2.50e+03 2.58e+02 bond pdb=" N1 5MU a1939 " pdb=" C6 5MU a1939 " ideal model delta sigma weight residual 1.635 1.326 0.309 2.00e-02 2.50e+03 2.38e+02 bond pdb=" N1 5MU a 747 " pdb=" C6 5MU a 747 " ideal model delta sigma weight residual 1.635 1.329 0.306 2.00e-02 2.50e+03 2.34e+02 bond pdb=" C2' 8AN Y 76 " pdb=" C1' 8AN Y 76 " ideal model delta sigma weight residual 1.289 1.528 -0.239 2.00e-02 2.50e+03 1.42e+02 ... (remaining 154220 not shown) Histogram of bond angle deviations from ideal: 92.86 - 101.91: 4736 101.91 - 110.95: 85604 110.95 - 120.00: 79459 120.00 - 129.04: 56582 129.04 - 138.09: 4317 Bond angle restraints: 230698 Sorted by residual: angle pdb=" C1' G7M A 527 " pdb=" N9 G7M A 527 " pdb=" C8 G7M A 527 " ideal model delta sigma weight residual 94.96 126.51 -31.55 3.00e+00 1.11e-01 1.11e+02 angle pdb=" C1' G7M a2069 " pdb=" N9 G7M a2069 " pdb=" C8 G7M a2069 " ideal model delta sigma weight residual 94.96 126.26 -31.30 3.00e+00 1.11e-01 1.09e+02 angle pdb=" C SER t 98 " pdb=" N ASN t 99 " pdb=" CA ASN t 99 " ideal model delta sigma weight residual 121.54 137.66 -16.12 1.91e+00 2.74e-01 7.12e+01 angle pdb=" CA ARG z 40 " pdb=" CB ARG z 40 " pdb=" CG ARG z 40 " ideal model delta sigma weight residual 114.10 127.79 -13.69 2.00e+00 2.50e-01 4.68e+01 angle pdb=" CG ARG z 40 " pdb=" CD ARG z 40 " pdb=" NE ARG z 40 " ideal model delta sigma weight residual 112.00 126.21 -14.21 2.20e+00 2.07e-01 4.17e+01 ... (remaining 230693 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.60: 87144 35.60 - 71.20: 10351 71.20 - 106.81: 1275 106.81 - 142.41: 16 142.41 - 178.01: 10 Dihedral angle restraints: 98796 sinusoidal: 82871 harmonic: 15925 Sorted by residual: dihedral pdb=" CA ASP g 47 " pdb=" C ASP g 47 " pdb=" N ASN g 48 " pdb=" CA ASN g 48 " ideal model delta harmonic sigma weight residual -180.00 -123.18 -56.82 0 5.00e+00 4.00e-02 1.29e+02 dihedral pdb=" O4' U Y 33 " pdb=" C1' U Y 33 " pdb=" N1 U Y 33 " pdb=" C2 U Y 33 " ideal model delta sinusoidal sigma weight residual 200.00 36.23 163.77 1 1.50e+01 4.44e-03 8.36e+01 dihedral pdb=" O4' C Y 32 " pdb=" C1' C Y 32 " pdb=" N1 C Y 32 " pdb=" C2 C Y 32 " ideal model delta sinusoidal sigma weight residual 200.00 37.76 162.24 1 1.50e+01 4.44e-03 8.33e+01 ... (remaining 98793 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 25023 0.073 - 0.146: 3780 0.146 - 0.219: 530 0.219 - 0.292: 41 0.292 - 0.364: 8 Chirality restraints: 29382 Sorted by residual: chirality pdb=" CB D2T L 89 " pdb=" CA D2T L 89 " pdb=" SB D2T L 89 " pdb=" CG D2T L 89 " both_signs ideal model delta sigma weight residual False -3.02 -3.38 0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" C1' A a2430 " pdb=" O4' A a2430 " pdb=" C2' A a2430 " pdb=" N9 A a2430 " both_signs ideal model delta sigma weight residual False 2.46 2.10 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" C1* PSU A 516 " pdb=" O4* PSU A 516 " pdb=" C2* PSU A 516 " pdb=" C5 PSU A 516 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.95e+00 ... (remaining 29379 not shown) Planarity restraints: 12256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1516 " -0.067 2.00e-02 2.50e+03 6.06e-01 8.27e+03 pdb=" C4' 2MG A1516 " -0.442 2.00e-02 2.50e+03 pdb=" O4' 2MG A1516 " -0.592 2.00e-02 2.50e+03 pdb=" C3' 2MG A1516 " 0.593 2.00e-02 2.50e+03 pdb=" O3' 2MG A1516 " 0.668 2.00e-02 2.50e+03 pdb=" C2' 2MG A1516 " 0.151 2.00e-02 2.50e+03 pdb=" O2' 2MG A1516 " -1.007 2.00e-02 2.50e+03 pdb=" C1' 2MG A1516 " -0.234 2.00e-02 2.50e+03 pdb=" N9 2MG A1516 " 0.931 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC A1407 " -0.063 2.00e-02 2.50e+03 6.04e-01 8.21e+03 pdb=" C4' 5MC A1407 " -0.457 2.00e-02 2.50e+03 pdb=" O4' 5MC A1407 " -0.627 2.00e-02 2.50e+03 pdb=" C3' 5MC A1407 " 0.583 2.00e-02 2.50e+03 pdb=" O3' 5MC A1407 " 0.658 2.00e-02 2.50e+03 pdb=" C2' 5MC A1407 " 0.171 2.00e-02 2.50e+03 pdb=" O2' 5MC A1407 " -0.976 2.00e-02 2.50e+03 pdb=" C1' 5MC A1407 " -0.224 2.00e-02 2.50e+03 pdb=" N1 5MC A1407 " 0.934 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a2445 " -0.049 2.00e-02 2.50e+03 5.97e-01 8.03e+03 pdb=" C4' 2MG a2445 " -0.440 2.00e-02 2.50e+03 pdb=" O4' 2MG a2445 " -0.714 2.00e-02 2.50e+03 pdb=" C3' 2MG a2445 " 0.602 2.00e-02 2.50e+03 pdb=" O3' 2MG a2445 " 0.589 2.00e-02 2.50e+03 pdb=" C2' 2MG a2445 " 0.209 2.00e-02 2.50e+03 pdb=" O2' 2MG a2445 " -0.911 2.00e-02 2.50e+03 pdb=" C1' 2MG a2445 " -0.220 2.00e-02 2.50e+03 pdb=" N9 2MG a2445 " 0.934 2.00e-02 2.50e+03 ... (remaining 12253 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.42: 1541 2.42 - 3.10: 99301 3.10 - 3.78: 348818 3.78 - 4.46: 533248 4.46 - 5.14: 692225 Nonbonded interactions: 1675133 Sorted by model distance: nonbonded pdb="MG MG a6243 " pdb=" O HOH a9235 " model vdw 1.741 2.170 nonbonded pdb=" OP1 G a2582 " pdb="MG MG a6238 " model vdw 1.754 2.170 nonbonded pdb=" OP1 A A 533 " pdb="MG MG A1672 " model vdw 1.803 2.170 nonbonded pdb=" OP2 G A1304 " pdb="MG MG A1633 " model vdw 1.850 2.170 nonbonded pdb=" OP1 C A1054 " pdb="MG MG A1617 " model vdw 1.866 2.170 ... (remaining 1675128 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 'Y' selection = (chain 'Z' and (resid 2 through 76 or resid 101)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 24.410 Check model and map are aligned: 1.690 Set scattering table: 1.030 Process input model: 897.420 Find NCS groups from input model: 3.080 Set up NCS constraints: 0.440 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 944.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 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 : 0.010 0.321 154225 Z= 0.603 Angle : 1.020 31.554 230698 Z= 0.510 Chirality : 0.054 0.364 29382 Planarity : 0.020 0.606 12256 Dihedral : 22.765 178.009 88522 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.45 % Favored : 96.48 % Rotamer: Outliers : 1.11 % Allowed : 13.57 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.10), residues: 5480 helix: -0.76 (0.11), residues: 1873 sheet: -0.47 (0.15), residues: 1061 loop : -0.89 (0.11), residues: 2546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.004 TRP e 78 HIS 0.037 0.004 HIS r 7 PHE 0.035 0.004 PHE v 79 TYR 0.053 0.004 TYR 0 49 ARG 0.029 0.002 ARG e 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1157 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 1106 time to evaluate : 6.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 26 MET cc_start: 0.7729 (mmm) cc_final: 0.7529 (mmm) REVERT: f 85 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7334 (pp) REVERT: g 139 GLN cc_start: 0.8325 (tm-30) cc_final: 0.8083 (tm-30) REVERT: i 128 ASN cc_start: 0.8476 (t0) cc_final: 0.8251 (t0) REVERT: k 123 ARG cc_start: 0.7446 (ttm170) cc_final: 0.7215 (mtm-85) REVERT: n 104 GLN cc_start: 0.8608 (tt0) cc_final: 0.8123 (tt0) REVERT: t 6 ARG cc_start: 0.8433 (mtt180) cc_final: 0.8169 (mtm180) REVERT: t 24 LYS cc_start: 0.7992 (ttpm) cc_final: 0.7783 (ttmm) REVERT: t 62 GLU cc_start: 0.7692 (mp0) cc_final: 0.7418 (mp0) REVERT: v 64 ASP cc_start: 0.8347 (m-30) cc_final: 0.8117 (m-30) REVERT: x 45 GLN cc_start: 0.7569 (mt0) cc_final: 0.7331 (mt0) REVERT: z 12 LYS cc_start: 0.8413 (mmtt) cc_final: 0.8050 (mmtm) REVERT: 4 6 HIS cc_start: 0.7656 (m-70) cc_final: 0.7436 (m-70) REVERT: 4 33 ASN cc_start: 0.6937 (m-40) cc_final: 0.6629 (m110) REVERT: C 49 LYS cc_start: 0.8503 (tppp) cc_final: 0.8269 (mptt) REVERT: C 142 MET cc_start: 0.8763 (mmm) cc_final: 0.8500 (mmp) REVERT: D 148 LYS cc_start: 0.7565 (tmmt) cc_final: 0.7298 (ptmm) REVERT: D 178 MET cc_start: 0.7352 (mtm) cc_final: 0.7001 (mtt) REVERT: F 1 MET cc_start: 0.6742 (mtp) cc_final: 0.6350 (mtp) REVERT: H 27 MET cc_start: 0.9009 (ptp) cc_final: 0.8696 (ptp) REVERT: I 41 ARG cc_start: 0.7056 (ttt90) cc_final: 0.6802 (ttt-90) REVERT: K 64 GLN cc_start: 0.8619 (tt0) cc_final: 0.8406 (tt0) REVERT: L 36 ARG cc_start: 0.7618 (ttp80) cc_final: 0.7377 (ttt180) REVERT: M 48 LEU cc_start: 0.7935 (mt) cc_final: 0.7712 (mt) REVERT: P 76 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7298 (pttm) REVERT: T 68 HIS cc_start: 0.8531 (t-90) cc_final: 0.8294 (t-90) REVERT: U 62 ARG cc_start: 0.5199 (mtt180) cc_final: 0.4386 (mmm-85) outliers start: 51 outliers final: 18 residues processed: 1148 average time/residue: 2.5386 time to fit residues: 4019.5716 Evaluate side-chains 894 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 874 time to evaluate : 6.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 110 THR Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain n residue 103 VAL Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain w residue 40 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain P residue 76 LYS Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain U residue 22 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 989 random chunks: chunk 835 optimal weight: 3.9990 chunk 749 optimal weight: 30.0000 chunk 415 optimal weight: 10.0000 chunk 256 optimal weight: 0.8980 chunk 505 optimal weight: 2.9990 chunk 400 optimal weight: 6.9990 chunk 775 optimal weight: 10.0000 chunk 299 optimal weight: 0.1980 chunk 471 optimal weight: 2.9990 chunk 576 optimal weight: 0.7980 chunk 898 optimal weight: 7.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 70 ASN c 86 ASN c 115 GLN c 197 ASN c 243 HIS d 32 ASN d 42 ASN e 136 GLN e 195 GLN g 22 GLN g 30 ASN h 20 ASN j 90 ASN l 13 HIS l 22 GLN m 31 HIS n 38 GLN n 98 GLN n 100 HIS o 12 GLN p 37 GLN ** p 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 18 GLN ** q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 86 GLN r 7 HIS s 28 ASN s 48 GLN t 53 ASN t 74 ASN u 49 ASN v 57 HIS w 20 HIS x 15 ASN x 45 GLN z 6 ASN 1 26 ASN ** 3 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 20 ASN ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN C 8 ASN C 139 GLN D 74 ASN E 78 ASN ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 GLN I 31 ASN J 56 HIS K 40 ASN M 12 HIS N 62 ASN O 40 GLN O 62 GLN P 29 ASN P 40 ASN R 54 GLN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 154225 Z= 0.152 Angle : 0.631 14.989 230698 Z= 0.342 Chirality : 0.036 0.395 29382 Planarity : 0.006 0.132 12256 Dihedral : 23.114 176.881 77508 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.68 % Favored : 97.26 % Rotamer: Outliers : 2.45 % Allowed : 17.09 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.11), residues: 5480 helix: 0.78 (0.12), residues: 1884 sheet: -0.12 (0.16), residues: 1039 loop : -0.46 (0.12), residues: 2557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 201 HIS 0.011 0.001 HIS l 13 PHE 0.018 0.001 PHE B 90 TYR 0.017 0.001 TYR C 42 ARG 0.012 0.000 ARG p 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1033 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 921 time to evaluate : 6.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 17 MET cc_start: 0.6790 (mmm) cc_final: 0.6511 (mtp) REVERT: f 38 MET cc_start: 0.7129 (mtm) cc_final: 0.6625 (mtt) REVERT: f 42 GLU cc_start: 0.6019 (OUTLIER) cc_final: 0.5719 (pp20) REVERT: f 85 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7383 (pp) REVERT: f 120 LYS cc_start: 0.6856 (mptm) cc_final: 0.6581 (tppt) REVERT: f 148 ARG cc_start: 0.6108 (tpp80) cc_final: 0.5404 (mtp85) REVERT: f 165 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7446 (mp0) REVERT: g 69 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7810 (tpt-90) REVERT: g 152 ARG cc_start: 0.7801 (tpp-160) cc_final: 0.7385 (mmt180) REVERT: l 110 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7317 (tt0) REVERT: l 127 LYS cc_start: 0.8227 (tppt) cc_final: 0.7867 (tptt) REVERT: q 97 LYS cc_start: 0.8260 (ttmm) cc_final: 0.8055 (ttmp) REVERT: t 24 LYS cc_start: 0.7954 (ttpm) cc_final: 0.7698 (ttmm) REVERT: z 12 LYS cc_start: 0.8395 (mmtt) cc_final: 0.8140 (mmtm) REVERT: 4 6 HIS cc_start: 0.7757 (m-70) cc_final: 0.7545 (m-70) REVERT: 4 33 ASN cc_start: 0.7008 (m-40) cc_final: 0.6784 (m110) REVERT: B 58 ASN cc_start: 0.7591 (t0) cc_final: 0.7328 (t0) REVERT: B 141 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7506 (tp) REVERT: B 205 ASP cc_start: 0.7164 (OUTLIER) cc_final: 0.6861 (p0) REVERT: B 223 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6618 (mt-10) REVERT: D 178 MET cc_start: 0.7291 (mtm) cc_final: 0.6937 (mtt) REVERT: F 94 HIS cc_start: 0.7337 (OUTLIER) cc_final: 0.7102 (m90) REVERT: H 27 MET cc_start: 0.9066 (ptp) cc_final: 0.8820 (ptp) REVERT: H 91 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7258 (mp0) REVERT: L 54 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8380 (tpt170) REVERT: M 71 ARG cc_start: 0.7273 (ptp-110) cc_final: 0.6829 (mtm-85) REVERT: N 41 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.6975 (ttp80) REVERT: O 35 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7763 (mm-40) REVERT: U 62 ARG cc_start: 0.5126 (mtt180) cc_final: 0.4330 (mmm-85) outliers start: 112 outliers final: 43 residues processed: 994 average time/residue: 2.4068 time to fit residues: 3341.2556 Evaluate side-chains 891 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 835 time to evaluate : 6.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 110 THR Chi-restraints excluded: chain e residue 22 ASP Chi-restraints excluded: chain f residue 24 SER Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 42 GLU Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 157 THR Chi-restraints excluded: chain f residue 164 GLU Chi-restraints excluded: chain f residue 165 GLU Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 69 ARG Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain i residue 96 ARG Chi-restraints excluded: chain j residue 111 LYS Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 110 GLU Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain o residue 19 SER Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain w residue 35 SER Chi-restraints excluded: chain w residue 40 VAL Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain 4 residue 15 SER Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 68 ASP Chi-restraints excluded: chain N residue 41 ARG Chi-restraints excluded: chain N residue 80 SER Chi-restraints excluded: chain O residue 35 GLN Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 51 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 989 random chunks: chunk 499 optimal weight: 1.9990 chunk 278 optimal weight: 20.0000 chunk 747 optimal weight: 8.9990 chunk 611 optimal weight: 20.0000 chunk 247 optimal weight: 10.0000 chunk 899 optimal weight: 8.9990 chunk 971 optimal weight: 1.9990 chunk 801 optimal weight: 7.9990 chunk 892 optimal weight: 0.0370 chunk 306 optimal weight: 0.8980 chunk 721 optimal weight: 20.0000 overall best weight: 2.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 70 ASN c 115 GLN e 90 GLN e 195 GLN i 128 ASN l 22 GLN n 61 GLN n 98 GLN ** p 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 18 GLN q 86 GLN r 31 GLN s 28 ASN w 20 HIS x 15 ASN x 20 ASN x 45 GLN 0 45 GLN ** 4 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN C 139 GLN D 198 HIS F 37 HIS ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 HIS N 62 ASN P 29 ASN P 40 ASN R 54 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 154225 Z= 0.187 Angle : 0.617 15.045 230698 Z= 0.336 Chirality : 0.036 0.410 29382 Planarity : 0.006 0.140 12256 Dihedral : 22.994 177.234 77492 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.99 % Favored : 96.97 % Rotamer: Outliers : 2.82 % Allowed : 17.78 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.11), residues: 5480 helix: 1.28 (0.12), residues: 1889 sheet: 0.06 (0.16), residues: 1067 loop : -0.31 (0.12), residues: 2524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 201 HIS 0.008 0.001 HIS y 20 PHE 0.017 0.002 PHE v 79 TYR 0.018 0.002 TYR l 103 ARG 0.006 0.001 ARG M 93 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1004 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 875 time to evaluate : 6.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 100 MET cc_start: 0.8981 (mtp) cc_final: 0.8737 (mtp) REVERT: e 195 GLN cc_start: 0.8341 (mt0) cc_final: 0.8032 (mt0) REVERT: f 17 MET cc_start: 0.6707 (mmm) cc_final: 0.6370 (mtp) REVERT: f 27 GLN cc_start: 0.7748 (tt0) cc_final: 0.7476 (mt0) REVERT: f 38 MET cc_start: 0.7173 (mtm) cc_final: 0.6803 (mtt) REVERT: f 47 LYS cc_start: 0.6710 (tptm) cc_final: 0.6303 (mmtm) REVERT: f 85 ILE cc_start: 0.7833 (OUTLIER) cc_final: 0.7486 (pp) REVERT: f 120 LYS cc_start: 0.6821 (mptm) cc_final: 0.6541 (tppt) REVERT: f 135 GLN cc_start: 0.7261 (pm20) cc_final: 0.6981 (pm20) REVERT: f 165 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7585 (mp0) REVERT: g 69 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7842 (tpt-90) REVERT: g 139 GLN cc_start: 0.8124 (tm-30) cc_final: 0.7868 (tm130) REVERT: g 152 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7353 (mmt180) REVERT: i 23 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.7845 (mmtm) REVERT: k 1 MET cc_start: 0.8403 (ttp) cc_final: 0.8049 (ttp) REVERT: k 81 ASP cc_start: 0.7507 (m-30) cc_final: 0.7292 (m-30) REVERT: k 84 LYS cc_start: 0.7744 (mttp) cc_final: 0.7535 (mttt) REVERT: l 110 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7344 (tt0) REVERT: l 127 LYS cc_start: 0.8195 (tppt) cc_final: 0.7910 (tptt) REVERT: n 20 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.7093 (tm-30) REVERT: n 69 ASP cc_start: 0.7490 (m-30) cc_final: 0.7151 (m-30) REVERT: p 102 ASP cc_start: 0.7829 (t0) cc_final: 0.7552 (t0) REVERT: t 10 GLU cc_start: 0.7534 (tp30) cc_final: 0.7207 (tm-30) REVERT: t 24 LYS cc_start: 0.7981 (ttpm) cc_final: 0.7716 (ttmm) REVERT: z 12 LYS cc_start: 0.8458 (mmtt) cc_final: 0.8074 (mmtm) REVERT: 4 6 HIS cc_start: 0.7731 (m-70) cc_final: 0.7494 (m-70) REVERT: B 58 ASN cc_start: 0.7568 (t0) cc_final: 0.7253 (t0) REVERT: B 81 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7505 (ttpt) REVERT: B 140 GLU cc_start: 0.6702 (mt-10) cc_final: 0.6439 (mm-30) REVERT: B 154 MET cc_start: 0.7977 (ttp) cc_final: 0.7774 (mtm) REVERT: B 223 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6725 (mt-10) REVERT: D 178 MET cc_start: 0.7402 (mtm) cc_final: 0.6989 (mtt) REVERT: H 27 MET cc_start: 0.9119 (ptp) cc_final: 0.8885 (ptp) REVERT: H 91 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7225 (mp0) REVERT: L 54 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8525 (tpt170) REVERT: M 47 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6992 (mm-30) REVERT: M 71 ARG cc_start: 0.7296 (ptp-110) cc_final: 0.6901 (mtm-85) REVERT: N 41 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7037 (ttp80) REVERT: O 35 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7761 (mm-40) REVERT: U 62 ARG cc_start: 0.5028 (mtt180) cc_final: 0.4375 (mmm-85) outliers start: 129 outliers final: 47 residues processed: 953 average time/residue: 2.3500 time to fit residues: 3146.2556 Evaluate side-chains 897 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 837 time to evaluate : 6.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 110 THR Chi-restraints excluded: chain e residue 13 THR Chi-restraints excluded: chain e residue 22 ASP Chi-restraints excluded: chain e residue 166 LYS Chi-restraints excluded: chain f residue 24 SER Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 164 GLU Chi-restraints excluded: chain f residue 165 GLU Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 69 ARG Chi-restraints excluded: chain g residue 152 ARG Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain i residue 23 LYS Chi-restraints excluded: chain j residue 111 LYS Chi-restraints excluded: chain l residue 110 GLU Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain n residue 20 GLU Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain o residue 19 SER Chi-restraints excluded: chain q residue 48 LYS Chi-restraints excluded: chain q residue 64 VAL Chi-restraints excluded: chain r residue 73 LYS Chi-restraints excluded: chain s residue 93 LEU Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain w residue 35 SER Chi-restraints excluded: chain w residue 40 VAL Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain y residue 41 THR Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain 4 residue 15 SER Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain N residue 41 ARG Chi-restraints excluded: chain N residue 80 SER Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 35 GLN Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 22 SER Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 51 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 989 random chunks: chunk 888 optimal weight: 6.9990 chunk 676 optimal weight: 10.0000 chunk 466 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 429 optimal weight: 9.9990 chunk 604 optimal weight: 30.0000 chunk 902 optimal weight: 8.9990 chunk 955 optimal weight: 20.0000 chunk 471 optimal weight: 10.0000 chunk 855 optimal weight: 10.0000 chunk 257 optimal weight: 10.0000 overall best weight: 9.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 70 ASN c 115 GLN i 128 ASN j 90 ASN l 22 GLN n 98 GLN p 81 ASN q 66 HIS s 28 ASN u 5 ASN w 20 HIS x 15 ASN x 20 ASN x 45 GLN z 42 HIS 0 45 GLN 4 33 ASN ** 4 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN C 139 GLN D 198 HIS E 73 ASN E 77 ASN E 148 ASN ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 ASN ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 HIS N 62 ASN P 29 ASN P 40 ASN T 3 ASN ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.102 154225 Z= 0.520 Angle : 0.900 21.032 230698 Z= 0.457 Chirality : 0.049 0.418 29382 Planarity : 0.009 0.160 12256 Dihedral : 23.153 178.175 77488 Min Nonbonded Distance : 1.668 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.65 % Favored : 96.28 % Rotamer: Outliers : 3.67 % Allowed : 17.61 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.11), residues: 5480 helix: 0.97 (0.12), residues: 1886 sheet: -0.07 (0.15), residues: 1087 loop : -0.45 (0.12), residues: 2507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP f 97 HIS 0.017 0.003 HIS k 35 PHE 0.029 0.003 PHE v 79 TYR 0.026 0.003 TYR L 117 ARG 0.012 0.001 ARG p 48 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1027 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 859 time to evaluate : 6.667 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: f 17 MET cc_start: 0.6715 (mmm) cc_final: 0.6392 (mtp) REVERT: f 27 GLN cc_start: 0.7748 (tt0) cc_final: 0.7460 (mt0) REVERT: f 38 MET cc_start: 0.7225 (mtm) cc_final: 0.6850 (mtt) REVERT: f 47 LYS cc_start: 0.6701 (tptm) cc_final: 0.6245 (mmtm) REVERT: f 120 LYS cc_start: 0.6820 (mptm) cc_final: 0.6562 (tppt) REVERT: g 69 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.6690 (tpt90) REVERT: g 76 VAL cc_start: 0.7441 (OUTLIER) cc_final: 0.7168 (m) REVERT: g 77 ILE cc_start: 0.8139 (mt) cc_final: 0.7859 (mp) REVERT: i 23 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.7923 (mmtm) REVERT: l 5 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8264 (mttm) REVERT: l 110 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7438 (tt0) REVERT: l 127 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7567 (mtpt) REVERT: n 20 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7149 (tm-30) REVERT: n 80 GLU cc_start: 0.7054 (mt-10) cc_final: 0.6738 (mt-10) REVERT: p 102 ASP cc_start: 0.8051 (t0) cc_final: 0.7780 (t0) REVERT: q 34 GLU cc_start: 0.6945 (mm-30) cc_final: 0.6679 (mm-30) REVERT: q 60 LYS cc_start: 0.8086 (mttm) cc_final: 0.7783 (mmtp) REVERT: s 6 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7545 (tpt-90) REVERT: t 10 GLU cc_start: 0.7572 (tp30) cc_final: 0.7229 (tm-30) REVERT: t 24 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7851 (ttmm) REVERT: y 58 GLU cc_start: 0.6611 (mp0) cc_final: 0.6364 (mp0) REVERT: 4 6 HIS cc_start: 0.7790 (m-70) cc_final: 0.7476 (m-70) REVERT: B 81 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7491 (ttpt) REVERT: B 133 GLU cc_start: 0.5865 (mm-30) cc_final: 0.5658 (mm-30) REVERT: B 154 MET cc_start: 0.8049 (ttp) cc_final: 0.7830 (mtm) REVERT: D 128 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.6948 (mtm180) REVERT: D 178 MET cc_start: 0.7543 (mtm) cc_final: 0.7303 (mtp) REVERT: F 14 GLN cc_start: 0.6626 (OUTLIER) cc_final: 0.6371 (mp10) REVERT: H 27 MET cc_start: 0.9151 (ptp) cc_final: 0.8842 (ptp) REVERT: H 91 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7257 (mp0) REVERT: M 47 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6907 (mm-30) REVERT: M 62 LYS cc_start: 0.7403 (OUTLIER) cc_final: 0.7169 (mttt) REVERT: N 26 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7245 (tt0) REVERT: O 35 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7918 (mm110) REVERT: P 20 VAL cc_start: 0.9109 (m) cc_final: 0.8889 (m) REVERT: P 47 GLU cc_start: 0.6624 (OUTLIER) cc_final: 0.6302 (pt0) REVERT: U 4 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8067 (mp) REVERT: U 62 ARG cc_start: 0.5183 (mtt180) cc_final: 0.4423 (mmm-85) outliers start: 168 outliers final: 83 residues processed: 968 average time/residue: 2.3229 time to fit residues: 3172.1616 Evaluate side-chains 930 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 828 time to evaluate : 6.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 97 LYS Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain e residue 22 ASP Chi-restraints excluded: chain e residue 166 LYS Chi-restraints excluded: chain e residue 194 LYS Chi-restraints excluded: chain f residue 3 LYS Chi-restraints excluded: chain f residue 24 SER Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 153 ASP Chi-restraints excluded: chain f residue 157 THR Chi-restraints excluded: chain f residue 164 GLU Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 69 ARG Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain g residue 101 ASN Chi-restraints excluded: chain g residue 152 ARG Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 23 LYS Chi-restraints excluded: chain j residue 111 LYS Chi-restraints excluded: chain k residue 121 THR Chi-restraints excluded: chain l residue 5 LYS Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 110 GLU Chi-restraints excluded: chain l residue 127 LYS Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain n residue 20 GLU Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 103 VAL Chi-restraints excluded: chain o residue 19 SER Chi-restraints excluded: chain q residue 64 VAL Chi-restraints excluded: chain q residue 72 VAL Chi-restraints excluded: chain q residue 95 ASP Chi-restraints excluded: chain r residue 73 LYS Chi-restraints excluded: chain s residue 6 ARG Chi-restraints excluded: chain s residue 93 LEU Chi-restraints excluded: chain t residue 24 LYS Chi-restraints excluded: chain t residue 27 ASN Chi-restraints excluded: chain t residue 72 ILE Chi-restraints excluded: chain t residue 102 THR Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain w residue 35 SER Chi-restraints excluded: chain w residue 40 VAL Chi-restraints excluded: chain x residue 19 LEU Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain y residue 41 THR Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain 4 residue 15 SER Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain G residue 131 LYS Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 62 LYS Chi-restraints excluded: chain N residue 26 GLU Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 41 ARG Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain O residue 35 GLN Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain T residue 3 ASN Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 22 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 989 random chunks: chunk 796 optimal weight: 10.0000 chunk 542 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 711 optimal weight: 10.0000 chunk 394 optimal weight: 2.9990 chunk 815 optimal weight: 0.0020 chunk 660 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 488 optimal weight: 1.9990 chunk 858 optimal weight: 9.9990 chunk 241 optimal weight: 5.9990 overall best weight: 2.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 70 ASN c 115 GLN d 32 ASN e 165 HIS e 195 GLN g 20 ASN i 128 ASN j 90 ASN l 22 GLN n 38 GLN ** q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 28 ASN u 5 ASN w 20 HIS x 15 ASN x 20 ASN x 45 GLN 0 45 GLN 4 33 ASN 4 48 GLN B 93 ASN C 8 ASN D 59 GLN D 74 ASN D 136 GLN ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 ASN ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 HIS P 40 ASN T 3 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 154225 Z= 0.174 Angle : 0.615 14.439 230698 Z= 0.336 Chirality : 0.036 0.414 29382 Planarity : 0.006 0.136 12256 Dihedral : 23.014 177.137 77487 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.90 % Favored : 97.06 % Rotamer: Outliers : 2.64 % Allowed : 18.90 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.11), residues: 5480 helix: 1.46 (0.12), residues: 1888 sheet: 0.14 (0.16), residues: 1064 loop : -0.31 (0.12), residues: 2528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 201 HIS 0.010 0.001 HIS F 3 PHE 0.016 0.001 PHE t 96 TYR 0.014 0.001 TYR r 38 ARG 0.006 0.000 ARG T 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 973 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 852 time to evaluate : 6.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 121 ASP cc_start: 0.6676 (p0) cc_final: 0.6353 (p0) REVERT: e 100 MET cc_start: 0.8969 (mtp) cc_final: 0.8742 (mtp) REVERT: f 17 MET cc_start: 0.6696 (mmm) cc_final: 0.6422 (mtp) REVERT: f 27 GLN cc_start: 0.7738 (tt0) cc_final: 0.7412 (mt0) REVERT: f 38 MET cc_start: 0.7171 (mtm) cc_final: 0.6879 (mtt) REVERT: f 47 LYS cc_start: 0.6770 (tptm) cc_final: 0.6325 (mmtm) REVERT: f 89 VAL cc_start: 0.8437 (OUTLIER) cc_final: 0.8237 (t) REVERT: f 120 LYS cc_start: 0.6778 (mptm) cc_final: 0.6522 (tppt) REVERT: g 69 ARG cc_start: 0.8033 (tpt90) cc_final: 0.7785 (tpt-90) REVERT: g 152 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7377 (mmt180) REVERT: g 170 ARG cc_start: 0.6621 (OUTLIER) cc_final: 0.6164 (ptt90) REVERT: i 23 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.7863 (mmtm) REVERT: k 1 MET cc_start: 0.8324 (ttp) cc_final: 0.8115 (ttp) REVERT: k 136 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6859 (mt-10) REVERT: l 110 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7312 (tt0) REVERT: l 127 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7921 (tptt) REVERT: n 69 ASP cc_start: 0.7507 (m-30) cc_final: 0.7214 (m-30) REVERT: p 102 ASP cc_start: 0.7873 (t0) cc_final: 0.7634 (t0) REVERT: s 6 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7512 (tpt-90) REVERT: s 42 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7577 (mt-10) REVERT: t 10 GLU cc_start: 0.7599 (tp30) cc_final: 0.7260 (tm-30) REVERT: t 24 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7850 (ttmm) REVERT: u 61 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7990 (mt) REVERT: y 58 GLU cc_start: 0.6571 (mp0) cc_final: 0.6327 (mp0) REVERT: 4 6 HIS cc_start: 0.7708 (m-70) cc_final: 0.7456 (m-70) REVERT: B 81 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7500 (ttpt) REVERT: B 133 GLU cc_start: 0.5920 (mm-30) cc_final: 0.5522 (mm-30) REVERT: B 154 MET cc_start: 0.8041 (ttp) cc_final: 0.7823 (mtm) REVERT: D 128 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.6938 (mtm180) REVERT: D 178 MET cc_start: 0.7470 (mtm) cc_final: 0.7218 (mtt) REVERT: H 27 MET cc_start: 0.9126 (ptp) cc_final: 0.8884 (ptp) REVERT: H 91 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7211 (mp0) REVERT: M 47 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6918 (mm-30) REVERT: M 71 ARG cc_start: 0.7364 (ptp-110) cc_final: 0.6962 (mtm-85) REVERT: O 35 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7787 (mm-40) REVERT: P 47 GLU cc_start: 0.6455 (OUTLIER) cc_final: 0.6087 (pt0) REVERT: T 3 ASN cc_start: 0.8215 (OUTLIER) cc_final: 0.7872 (p0) REVERT: U 4 ILE cc_start: 0.8415 (OUTLIER) cc_final: 0.8061 (mp) REVERT: U 62 ARG cc_start: 0.5124 (mtt180) cc_final: 0.4308 (mmm-85) REVERT: Y 101 MET cc_start: 0.8033 (mmt) cc_final: 0.7757 (mmt) outliers start: 121 outliers final: 48 residues processed: 931 average time/residue: 2.3966 time to fit residues: 3148.5779 Evaluate side-chains 891 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 826 time to evaluate : 6.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 110 THR Chi-restraints excluded: chain e residue 22 ASP Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain f residue 24 SER Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 140 GLU Chi-restraints excluded: chain f residue 153 ASP Chi-restraints excluded: chain f residue 157 THR Chi-restraints excluded: chain f residue 164 GLU Chi-restraints excluded: chain f residue 174 ASP Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 101 ASN Chi-restraints excluded: chain g residue 152 ARG Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain g residue 170 ARG Chi-restraints excluded: chain i residue 23 LYS Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 110 GLU Chi-restraints excluded: chain l residue 127 LYS Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain o residue 19 SER Chi-restraints excluded: chain q residue 48 LYS Chi-restraints excluded: chain r residue 73 LYS Chi-restraints excluded: chain s residue 6 ARG Chi-restraints excluded: chain t residue 24 LYS Chi-restraints excluded: chain u residue 25 LYS Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain w residue 35 SER Chi-restraints excluded: chain w residue 40 VAL Chi-restraints excluded: chain x residue 19 LEU Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain y residue 41 THR Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 35 GLN Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain T residue 3 ASN Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 22 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 989 random chunks: chunk 321 optimal weight: 10.0000 chunk 860 optimal weight: 8.9990 chunk 188 optimal weight: 9.9990 chunk 561 optimal weight: 20.0000 chunk 235 optimal weight: 9.9990 chunk 956 optimal weight: 20.0000 chunk 794 optimal weight: 8.9990 chunk 443 optimal weight: 0.1980 chunk 79 optimal weight: 10.0000 chunk 316 optimal weight: 5.9990 chunk 502 optimal weight: 10.0000 overall best weight: 6.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 70 ASN c 115 GLN e 195 GLN i 128 ASN j 90 ASN l 22 GLN o 3 ASN s 28 ASN u 5 ASN w 20 HIS x 15 ASN x 20 ASN x 45 GLN 0 45 GLN 4 33 ASN C 8 ASN C 139 GLN D 59 GLN D 74 ASN D 198 HIS ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 ASN H 76 GLN ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 HIS P 40 ASN T 3 ASN T 13 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 154225 Z= 0.400 Angle : 0.783 18.834 230698 Z= 0.407 Chirality : 0.044 0.423 29382 Planarity : 0.008 0.154 12256 Dihedral : 23.059 177.994 77483 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.56 % Favored : 96.39 % Rotamer: Outliers : 3.06 % Allowed : 18.48 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.11), residues: 5480 helix: 1.27 (0.12), residues: 1892 sheet: 0.02 (0.15), residues: 1091 loop : -0.37 (0.12), residues: 2497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 201 HIS 0.015 0.002 HIS k 35 PHE 0.022 0.002 PHE S 10 TYR 0.022 0.002 TYR L 117 ARG 0.008 0.001 ARG d 124 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 976 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 836 time to evaluate : 6.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 55 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7709 (tttp) REVERT: e 100 MET cc_start: 0.9021 (mtp) cc_final: 0.8780 (mtp) REVERT: f 17 MET cc_start: 0.6701 (mmm) cc_final: 0.6389 (mtp) REVERT: f 27 GLN cc_start: 0.7768 (tt0) cc_final: 0.7469 (mt0) REVERT: f 38 MET cc_start: 0.7222 (mtm) cc_final: 0.6922 (mtt) REVERT: f 47 LYS cc_start: 0.6710 (tptm) cc_final: 0.6447 (mmtm) REVERT: f 89 VAL cc_start: 0.8509 (OUTLIER) cc_final: 0.8246 (t) REVERT: f 120 LYS cc_start: 0.6776 (mptm) cc_final: 0.6500 (tppt) REVERT: g 69 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.6706 (tpt90) REVERT: g 152 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7362 (mmt180) REVERT: g 170 ARG cc_start: 0.6589 (OUTLIER) cc_final: 0.6114 (ptt90) REVERT: i 23 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.7874 (mmtm) REVERT: l 110 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7370 (tt0) REVERT: l 127 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7543 (mtpt) REVERT: n 80 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6817 (mt-10) REVERT: p 102 ASP cc_start: 0.7996 (t0) cc_final: 0.7757 (t0) REVERT: q 34 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6765 (mt-10) REVERT: s 6 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7495 (tpt-90) REVERT: s 42 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7568 (mt-10) REVERT: t 10 GLU cc_start: 0.7602 (tp30) cc_final: 0.7286 (tm-30) REVERT: u 61 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8052 (mt) REVERT: y 58 GLU cc_start: 0.6609 (mp0) cc_final: 0.6369 (mp0) REVERT: 4 6 HIS cc_start: 0.7766 (m-70) cc_final: 0.7494 (m-70) REVERT: B 81 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7504 (ttpt) REVERT: B 133 GLU cc_start: 0.5900 (mm-30) cc_final: 0.5679 (mm-30) REVERT: B 154 MET cc_start: 0.8059 (ttp) cc_final: 0.7830 (mtm) REVERT: D 128 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.6932 (mtm180) REVERT: E 29 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.7976 (mtt-85) REVERT: F 14 GLN cc_start: 0.6619 (OUTLIER) cc_final: 0.6407 (mp10) REVERT: H 27 MET cc_start: 0.9151 (ptp) cc_final: 0.8830 (ptp) REVERT: H 91 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: M 47 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6916 (mm-30) REVERT: P 47 GLU cc_start: 0.6608 (OUTLIER) cc_final: 0.6269 (pt0) REVERT: U 4 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8056 (mp) REVERT: U 54 LYS cc_start: 0.7196 (OUTLIER) cc_final: 0.6966 (tppp) REVERT: U 62 ARG cc_start: 0.5156 (mtt180) cc_final: 0.4416 (mmm-85) outliers start: 140 outliers final: 79 residues processed: 918 average time/residue: 2.4078 time to fit residues: 3103.4547 Evaluate side-chains 922 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 823 time to evaluate : 6.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 55 LYS Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain d residue 110 THR Chi-restraints excluded: chain e residue 2 GLU Chi-restraints excluded: chain e residue 22 ASP Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 166 LYS Chi-restraints excluded: chain f residue 3 LYS Chi-restraints excluded: chain f residue 24 SER Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 140 GLU Chi-restraints excluded: chain f residue 153 ASP Chi-restraints excluded: chain f residue 157 THR Chi-restraints excluded: chain f residue 164 GLU Chi-restraints excluded: chain f residue 174 ASP Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 69 ARG Chi-restraints excluded: chain g residue 101 ASN Chi-restraints excluded: chain g residue 152 ARG Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain g residue 170 ARG Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 23 LYS Chi-restraints excluded: chain j residue 111 LYS Chi-restraints excluded: chain k residue 121 THR Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 110 GLU Chi-restraints excluded: chain l residue 127 LYS Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 103 VAL Chi-restraints excluded: chain o residue 19 SER Chi-restraints excluded: chain q residue 34 GLU Chi-restraints excluded: chain q residue 62 GLU Chi-restraints excluded: chain q residue 72 VAL Chi-restraints excluded: chain q residue 95 ASP Chi-restraints excluded: chain r residue 28 LYS Chi-restraints excluded: chain r residue 73 LYS Chi-restraints excluded: chain s residue 6 ARG Chi-restraints excluded: chain t residue 72 ILE Chi-restraints excluded: chain t residue 102 THR Chi-restraints excluded: chain u residue 25 LYS Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain u residue 63 ILE Chi-restraints excluded: chain w residue 35 SER Chi-restraints excluded: chain w residue 40 VAL Chi-restraints excluded: chain x residue 19 LEU Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain y residue 41 THR Chi-restraints excluded: chain y residue 56 LYS Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain 4 residue 15 SER Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 11 LYS Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 41 ARG Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 35 GLN Chi-restraints excluded: chain O residue 40 GLN Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 22 SER Chi-restraints excluded: chain U residue 54 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 989 random chunks: chunk 922 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 545 optimal weight: 1.9990 chunk 698 optimal weight: 10.0000 chunk 541 optimal weight: 10.0000 chunk 805 optimal weight: 20.0000 chunk 534 optimal weight: 7.9990 chunk 953 optimal weight: 20.0000 chunk 596 optimal weight: 20.0000 chunk 581 optimal weight: 8.9990 chunk 440 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 70 ASN c 115 GLN e 165 HIS e 195 GLN i 128 ASN j 90 ASN l 22 GLN o 3 ASN s 28 ASN u 5 ASN w 20 HIS x 15 ASN x 20 ASN x 45 GLN 0 45 GLN 4 33 ASN C 8 ASN C 139 GLN D 59 GLN D 74 ASN ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 ASN H 76 GLN ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 HIS P 40 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 154225 Z= 0.375 Angle : 0.766 18.107 230698 Z= 0.400 Chirality : 0.043 0.408 29382 Planarity : 0.007 0.152 12256 Dihedral : 23.070 177.708 77483 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.36 % Favored : 96.59 % Rotamer: Outliers : 3.10 % Allowed : 18.51 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.11), residues: 5480 helix: 1.24 (0.12), residues: 1891 sheet: 0.01 (0.15), residues: 1089 loop : -0.39 (0.12), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 201 HIS 0.015 0.002 HIS F 3 PHE 0.021 0.002 PHE S 10 TYR 0.022 0.002 TYR L 117 ARG 0.009 0.001 ARG i 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 979 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 837 time to evaluate : 6.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 17 MET cc_start: 0.6650 (mmm) cc_final: 0.6399 (mtp) REVERT: f 27 GLN cc_start: 0.7761 (tt0) cc_final: 0.7460 (mt0) REVERT: f 38 MET cc_start: 0.7258 (mtm) cc_final: 0.6960 (mtt) REVERT: f 47 LYS cc_start: 0.6662 (tptm) cc_final: 0.6422 (tppt) REVERT: f 89 VAL cc_start: 0.8502 (OUTLIER) cc_final: 0.8242 (t) REVERT: f 120 LYS cc_start: 0.6782 (mptm) cc_final: 0.6549 (tppt) REVERT: g 69 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.6670 (tpt90) REVERT: g 152 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7343 (mmt180) REVERT: g 170 ARG cc_start: 0.6584 (OUTLIER) cc_final: 0.6117 (ptt90) REVERT: i 23 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.7883 (mmtm) REVERT: k 136 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6999 (mt-10) REVERT: l 5 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8232 (mttm) REVERT: l 110 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7383 (tt0) REVERT: l 127 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7529 (mtpt) REVERT: n 80 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6810 (mt-10) REVERT: o 7 GLN cc_start: 0.7505 (tm-30) cc_final: 0.6996 (tm-30) REVERT: p 102 ASP cc_start: 0.7962 (t0) cc_final: 0.7730 (t0) REVERT: s 6 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7498 (tpt-90) REVERT: s 42 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7562 (mt-10) REVERT: t 10 GLU cc_start: 0.7602 (tp30) cc_final: 0.7287 (tm-30) REVERT: t 24 LYS cc_start: 0.8035 (ttpp) cc_final: 0.7808 (ttmm) REVERT: u 61 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8008 (mt) REVERT: y 58 GLU cc_start: 0.6637 (mp0) cc_final: 0.6403 (mp0) REVERT: 4 6 HIS cc_start: 0.7769 (m-70) cc_final: 0.7527 (m-70) REVERT: B 81 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7480 (ttpt) REVERT: B 135 LEU cc_start: 0.6672 (tp) cc_final: 0.6385 (mm) REVERT: B 154 MET cc_start: 0.8026 (ttp) cc_final: 0.7805 (mtm) REVERT: B 205 ASP cc_start: 0.7019 (OUTLIER) cc_final: 0.6573 (p0) REVERT: D 128 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.6923 (mtm180) REVERT: H 27 MET cc_start: 0.9150 (ptp) cc_final: 0.8819 (ptp) REVERT: H 91 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7234 (mp0) REVERT: M 47 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6938 (mm-30) REVERT: P 20 VAL cc_start: 0.9098 (m) cc_final: 0.8883 (m) REVERT: U 4 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8067 (mp) REVERT: U 54 LYS cc_start: 0.7176 (OUTLIER) cc_final: 0.6940 (tppp) REVERT: U 62 ARG cc_start: 0.5155 (mtt180) cc_final: 0.4407 (mmm-85) outliers start: 142 outliers final: 77 residues processed: 928 average time/residue: 2.4224 time to fit residues: 3160.6997 Evaluate side-chains 920 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 826 time to evaluate : 6.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain d residue 110 THR Chi-restraints excluded: chain e residue 2 GLU Chi-restraints excluded: chain e residue 22 ASP Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 165 HIS Chi-restraints excluded: chain f residue 24 SER Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 63 GLN Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 140 GLU Chi-restraints excluded: chain f residue 153 ASP Chi-restraints excluded: chain f residue 157 THR Chi-restraints excluded: chain f residue 164 GLU Chi-restraints excluded: chain f residue 174 ASP Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 69 ARG Chi-restraints excluded: chain g residue 101 ASN Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain g residue 152 ARG Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain g residue 170 ARG Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 23 LYS Chi-restraints excluded: chain j residue 111 LYS Chi-restraints excluded: chain k residue 121 THR Chi-restraints excluded: chain l residue 5 LYS Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 110 GLU Chi-restraints excluded: chain l residue 127 LYS Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain o residue 19 SER Chi-restraints excluded: chain q residue 62 GLU Chi-restraints excluded: chain q residue 72 VAL Chi-restraints excluded: chain q residue 95 ASP Chi-restraints excluded: chain r residue 28 LYS Chi-restraints excluded: chain r residue 73 LYS Chi-restraints excluded: chain s residue 6 ARG Chi-restraints excluded: chain t residue 72 ILE Chi-restraints excluded: chain t residue 102 THR Chi-restraints excluded: chain u residue 25 LYS Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain w residue 35 SER Chi-restraints excluded: chain w residue 40 VAL Chi-restraints excluded: chain x residue 19 LEU Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain y residue 41 THR Chi-restraints excluded: chain y residue 56 LYS Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 11 LYS Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 80 SER Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 35 GLN Chi-restraints excluded: chain O residue 40 GLN Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 22 SER Chi-restraints excluded: chain U residue 54 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 989 random chunks: chunk 589 optimal weight: 8.9990 chunk 380 optimal weight: 1.9990 chunk 569 optimal weight: 6.9990 chunk 287 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 chunk 184 optimal weight: 10.0000 chunk 606 optimal weight: 20.0000 chunk 649 optimal weight: 20.0000 chunk 471 optimal weight: 10.0000 chunk 88 optimal weight: 30.0000 chunk 749 optimal weight: 30.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 70 ASN c 115 GLN e 165 HIS e 195 GLN i 128 ASN j 90 ASN l 22 GLN o 3 ASN s 28 ASN u 5 ASN w 20 HIS x 15 ASN x 20 ASN x 45 GLN 0 45 GLN 4 33 ASN C 8 ASN C 139 GLN D 74 ASN ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 ASN H 76 GLN ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 40 ASN T 70 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 154225 Z= 0.325 Angle : 0.727 17.489 230698 Z= 0.384 Chirality : 0.041 0.413 29382 Planarity : 0.007 0.149 12256 Dihedral : 23.063 177.466 77483 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.39 % Favored : 96.55 % Rotamer: Outliers : 2.73 % Allowed : 19.12 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.11), residues: 5480 helix: 1.33 (0.12), residues: 1890 sheet: 0.03 (0.15), residues: 1098 loop : -0.38 (0.12), residues: 2492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 201 HIS 0.014 0.002 HIS F 3 PHE 0.020 0.002 PHE S 10 TYR 0.019 0.002 TYR L 117 ARG 0.008 0.001 ARG i 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 965 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 840 time to evaluate : 6.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 100 MET cc_start: 0.9007 (mtp) cc_final: 0.8773 (mtp) REVERT: f 27 GLN cc_start: 0.7780 (tt0) cc_final: 0.7457 (mt0) REVERT: f 38 MET cc_start: 0.7237 (mtm) cc_final: 0.6943 (mtt) REVERT: f 89 VAL cc_start: 0.8497 (OUTLIER) cc_final: 0.8238 (t) REVERT: f 120 LYS cc_start: 0.6801 (mptm) cc_final: 0.6559 (tppt) REVERT: g 69 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.6678 (tpt90) REVERT: g 134 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7578 (tppp) REVERT: g 152 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7381 (mmt180) REVERT: g 170 ARG cc_start: 0.6569 (OUTLIER) cc_final: 0.6099 (ptt90) REVERT: i 23 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.7887 (mmtm) REVERT: k 136 GLU cc_start: 0.7294 (mt-10) cc_final: 0.7034 (mt-10) REVERT: l 110 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7368 (tt0) REVERT: l 127 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7530 (mtpt) REVERT: n 69 ASP cc_start: 0.7513 (m-30) cc_final: 0.7219 (m-30) REVERT: n 80 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6820 (mt-10) REVERT: p 102 ASP cc_start: 0.7954 (t0) cc_final: 0.7731 (t0) REVERT: s 6 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7501 (tpt-90) REVERT: s 42 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7568 (mt-10) REVERT: t 10 GLU cc_start: 0.7603 (tp30) cc_final: 0.7240 (tm-30) REVERT: t 24 LYS cc_start: 0.8039 (ttpp) cc_final: 0.7822 (ttmm) REVERT: t 60 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6547 (mm-30) REVERT: u 61 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8031 (mt) REVERT: y 58 GLU cc_start: 0.6615 (mp0) cc_final: 0.6381 (mp0) REVERT: 4 6 HIS cc_start: 0.7705 (m-70) cc_final: 0.7466 (m-70) REVERT: B 81 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7491 (ttpt) REVERT: B 154 MET cc_start: 0.8062 (ttp) cc_final: 0.7832 (mtm) REVERT: D 128 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.6902 (mtm180) REVERT: F 14 GLN cc_start: 0.6640 (OUTLIER) cc_final: 0.5290 (mp10) REVERT: H 27 MET cc_start: 0.9149 (ptp) cc_final: 0.8830 (ptp) REVERT: H 91 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: M 47 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6937 (mm-30) REVERT: M 71 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.7005 (mtm-85) REVERT: U 4 ILE cc_start: 0.8415 (OUTLIER) cc_final: 0.8076 (mp) REVERT: U 54 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6979 (tppp) REVERT: U 62 ARG cc_start: 0.5203 (mtt180) cc_final: 0.4447 (mmm-85) outliers start: 125 outliers final: 78 residues processed: 917 average time/residue: 2.3741 time to fit residues: 3055.1769 Evaluate side-chains 930 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 833 time to evaluate : 6.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain d residue 110 THR Chi-restraints excluded: chain e residue 2 GLU Chi-restraints excluded: chain e residue 22 ASP Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain f residue 3 LYS Chi-restraints excluded: chain f residue 24 SER Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 140 GLU Chi-restraints excluded: chain f residue 153 ASP Chi-restraints excluded: chain f residue 157 THR Chi-restraints excluded: chain f residue 164 GLU Chi-restraints excluded: chain f residue 174 ASP Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 69 ARG Chi-restraints excluded: chain g residue 101 ASN Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain g residue 134 LYS Chi-restraints excluded: chain g residue 152 ARG Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain g residue 170 ARG Chi-restraints excluded: chain i residue 23 LYS Chi-restraints excluded: chain j residue 111 LYS Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 110 GLU Chi-restraints excluded: chain l residue 127 LYS Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 103 VAL Chi-restraints excluded: chain o residue 19 SER Chi-restraints excluded: chain q residue 62 GLU Chi-restraints excluded: chain q residue 95 ASP Chi-restraints excluded: chain r residue 28 LYS Chi-restraints excluded: chain r residue 73 LYS Chi-restraints excluded: chain s residue 6 ARG Chi-restraints excluded: chain t residue 27 ASN Chi-restraints excluded: chain t residue 60 GLU Chi-restraints excluded: chain t residue 102 THR Chi-restraints excluded: chain u residue 25 LYS Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain w residue 35 SER Chi-restraints excluded: chain w residue 40 VAL Chi-restraints excluded: chain x residue 19 LEU Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain y residue 41 THR Chi-restraints excluded: chain y residue 56 LYS Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain 4 residue 15 SER Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 11 LYS Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 124 ARG Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 35 GLN Chi-restraints excluded: chain O residue 40 GLN Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 22 SER Chi-restraints excluded: chain U residue 54 LYS Chi-restraints excluded: chain Z residue 101 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 989 random chunks: chunk 867 optimal weight: 8.9990 chunk 913 optimal weight: 0.6980 chunk 833 optimal weight: 3.9990 chunk 888 optimal weight: 0.9980 chunk 912 optimal weight: 10.0000 chunk 534 optimal weight: 10.0000 chunk 386 optimal weight: 6.9990 chunk 697 optimal weight: 8.9990 chunk 272 optimal weight: 10.0000 chunk 802 optimal weight: 20.0000 chunk 840 optimal weight: 5.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 70 ASN c 115 GLN e 165 HIS e 195 GLN g 128 GLN ** i 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 90 ASN l 22 GLN o 3 ASN s 28 ASN u 5 ASN w 20 HIS x 15 ASN x 20 ASN x 45 GLN 0 45 GLN 4 33 ASN C 8 ASN C 139 GLN D 59 GLN D 74 ASN ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 ASN H 76 GLN ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 40 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 154225 Z= 0.250 Angle : 0.678 16.842 230698 Z= 0.365 Chirality : 0.039 0.409 29382 Planarity : 0.007 0.145 12256 Dihedral : 23.072 177.194 77483 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.39 % Favored : 96.55 % Rotamer: Outliers : 2.45 % Allowed : 19.51 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.11), residues: 5480 helix: 1.41 (0.12), residues: 1890 sheet: 0.04 (0.16), residues: 1081 loop : -0.36 (0.12), residues: 2509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 201 HIS 0.017 0.002 HIS e 165 PHE 0.017 0.002 PHE t 96 TYR 0.017 0.002 TYR L 117 ARG 0.008 0.001 ARG K 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 954 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 842 time to evaluate : 7.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 100 MET cc_start: 0.9001 (mtp) cc_final: 0.8775 (mtp) REVERT: f 27 GLN cc_start: 0.7775 (tt0) cc_final: 0.7441 (mt0) REVERT: f 38 MET cc_start: 0.7247 (mtm) cc_final: 0.6961 (mtt) REVERT: f 89 VAL cc_start: 0.8474 (OUTLIER) cc_final: 0.8224 (t) REVERT: f 120 LYS cc_start: 0.6799 (mptm) cc_final: 0.6560 (tppt) REVERT: g 134 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7568 (tppp) REVERT: g 152 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7396 (mmt180) REVERT: g 170 ARG cc_start: 0.6573 (OUTLIER) cc_final: 0.6108 (ptt90) REVERT: i 23 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.7875 (mmtm) REVERT: k 136 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6965 (mt-10) REVERT: l 110 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7348 (tt0) REVERT: l 127 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7510 (mtpt) REVERT: n 20 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7140 (tm-30) REVERT: n 69 ASP cc_start: 0.7497 (m-30) cc_final: 0.7198 (m-30) REVERT: n 80 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6820 (mt-10) REVERT: p 102 ASP cc_start: 0.7928 (t0) cc_final: 0.7679 (t0) REVERT: s 6 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7511 (tpt-90) REVERT: t 10 GLU cc_start: 0.7602 (tp30) cc_final: 0.7276 (tm-30) REVERT: t 24 LYS cc_start: 0.8018 (ttpp) cc_final: 0.7806 (ttmm) REVERT: u 61 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8037 (mt) REVERT: y 58 GLU cc_start: 0.6604 (mp0) cc_final: 0.6370 (mp0) REVERT: 4 6 HIS cc_start: 0.7702 (m-70) cc_final: 0.7465 (m-70) REVERT: B 81 LYS cc_start: 0.7797 (OUTLIER) cc_final: 0.7487 (ttpt) REVERT: B 136 MET cc_start: 0.5859 (mmp) cc_final: 0.5395 (mmt) REVERT: B 154 MET cc_start: 0.8058 (ttp) cc_final: 0.7830 (mtm) REVERT: D 128 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.6903 (mtm180) REVERT: F 14 GLN cc_start: 0.6665 (OUTLIER) cc_final: 0.5315 (mp10) REVERT: G 5 ARG cc_start: 0.6162 (tmm160) cc_final: 0.5953 (ttp80) REVERT: H 27 MET cc_start: 0.9145 (ptp) cc_final: 0.8870 (ptp) REVERT: H 91 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: M 47 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6918 (mm-30) REVERT: U 4 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8067 (mp) REVERT: U 54 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6982 (tppp) REVERT: U 62 ARG cc_start: 0.5197 (mtt180) cc_final: 0.4445 (mmm-85) outliers start: 112 outliers final: 78 residues processed: 912 average time/residue: 2.4447 time to fit residues: 3130.8993 Evaluate side-chains 923 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 828 time to evaluate : 6.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 97 LYS Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain d residue 110 THR Chi-restraints excluded: chain e residue 2 GLU Chi-restraints excluded: chain e residue 22 ASP Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain f residue 3 LYS Chi-restraints excluded: chain f residue 24 SER Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 140 GLU Chi-restraints excluded: chain f residue 153 ASP Chi-restraints excluded: chain f residue 157 THR Chi-restraints excluded: chain f residue 164 GLU Chi-restraints excluded: chain f residue 174 ASP Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 101 ASN Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain g residue 134 LYS Chi-restraints excluded: chain g residue 152 ARG Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain g residue 170 ARG Chi-restraints excluded: chain i residue 23 LYS Chi-restraints excluded: chain j residue 111 LYS Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 110 GLU Chi-restraints excluded: chain l residue 127 LYS Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain n residue 20 GLU Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 103 VAL Chi-restraints excluded: chain o residue 19 SER Chi-restraints excluded: chain q residue 62 GLU Chi-restraints excluded: chain q residue 72 VAL Chi-restraints excluded: chain q residue 95 ASP Chi-restraints excluded: chain r residue 28 LYS Chi-restraints excluded: chain r residue 73 LYS Chi-restraints excluded: chain s residue 6 ARG Chi-restraints excluded: chain t residue 27 ASN Chi-restraints excluded: chain t residue 102 THR Chi-restraints excluded: chain u residue 25 LYS Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain w residue 35 SER Chi-restraints excluded: chain w residue 40 VAL Chi-restraints excluded: chain x residue 19 LEU Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain y residue 41 THR Chi-restraints excluded: chain y residue 56 LYS Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain 4 residue 15 SER Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 11 LYS Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 80 SER Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 35 GLN Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain R residue 12 ARG Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 22 SER Chi-restraints excluded: chain U residue 54 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 989 random chunks: chunk 885 optimal weight: 6.9990 chunk 583 optimal weight: 9.9990 chunk 939 optimal weight: 4.9990 chunk 573 optimal weight: 0.7980 chunk 445 optimal weight: 2.9990 chunk 652 optimal weight: 40.0000 chunk 985 optimal weight: 2.9990 chunk 906 optimal weight: 20.0000 chunk 784 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 606 optimal weight: 20.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 70 ASN c 115 GLN e 165 HIS e 195 GLN ** i 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 90 ASN l 22 GLN o 3 ASN s 28 ASN u 5 ASN w 20 HIS x 15 ASN x 20 ASN x 45 GLN 0 45 GLN 4 33 ASN C 8 ASN C 139 GLN D 59 GLN D 74 ASN ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 ASN H 76 GLN ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 40 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 154225 Z= 0.249 Angle : 0.676 15.807 230698 Z= 0.363 Chirality : 0.039 0.418 29382 Planarity : 0.007 0.144 12256 Dihedral : 23.050 177.279 77481 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.36 % Favored : 96.61 % Rotamer: Outliers : 2.14 % Allowed : 19.86 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.11), residues: 5480 helix: 1.45 (0.12), residues: 1892 sheet: 0.07 (0.16), residues: 1074 loop : -0.33 (0.12), residues: 2514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP Q 73 HIS 0.013 0.001 HIS F 3 PHE 0.017 0.002 PHE t 96 TYR 0.019 0.002 TYR L 117 ARG 0.009 0.001 ARG K 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 930 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 832 time to evaluate : 6.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 100 MET cc_start: 0.8998 (mtp) cc_final: 0.8780 (mtp) REVERT: f 27 GLN cc_start: 0.7771 (tt0) cc_final: 0.7439 (mt0) REVERT: f 38 MET cc_start: 0.7251 (mtm) cc_final: 0.6966 (mtt) REVERT: f 89 VAL cc_start: 0.8458 (OUTLIER) cc_final: 0.8209 (t) REVERT: f 120 LYS cc_start: 0.6798 (mptm) cc_final: 0.6564 (tppt) REVERT: g 152 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7396 (mmt180) REVERT: g 170 ARG cc_start: 0.6608 (OUTLIER) cc_final: 0.6146 (ptt90) REVERT: i 23 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.7871 (mmtm) REVERT: k 136 GLU cc_start: 0.7240 (mt-10) cc_final: 0.6980 (mt-10) REVERT: l 110 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7328 (tt0) REVERT: l 127 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7503 (mtpt) REVERT: n 20 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7121 (tm-30) REVERT: n 69 ASP cc_start: 0.7517 (m-30) cc_final: 0.7226 (m-30) REVERT: n 80 GLU cc_start: 0.7078 (mt-10) cc_final: 0.6801 (mt-10) REVERT: p 102 ASP cc_start: 0.7924 (t0) cc_final: 0.7679 (t0) REVERT: s 6 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7515 (tpt-90) REVERT: t 10 GLU cc_start: 0.7604 (tp30) cc_final: 0.7237 (tm-30) REVERT: t 24 LYS cc_start: 0.8027 (ttpp) cc_final: 0.7814 (ttmm) REVERT: u 61 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8037 (mt) REVERT: y 58 GLU cc_start: 0.6604 (mp0) cc_final: 0.6366 (mp0) REVERT: 4 6 HIS cc_start: 0.7694 (m-70) cc_final: 0.7448 (m-70) REVERT: B 81 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7515 (ttpt) REVERT: B 154 MET cc_start: 0.8060 (ttp) cc_final: 0.7830 (mtm) REVERT: D 128 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.6904 (mtm180) REVERT: E 29 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7962 (mtt-85) REVERT: F 14 GLN cc_start: 0.6669 (OUTLIER) cc_final: 0.5318 (mp10) REVERT: H 27 MET cc_start: 0.9139 (ptp) cc_final: 0.8875 (ptp) REVERT: H 91 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: M 47 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6917 (mm-30) REVERT: U 4 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8047 (mp) REVERT: U 54 LYS cc_start: 0.7206 (OUTLIER) cc_final: 0.6981 (tppp) REVERT: U 62 ARG cc_start: 0.5195 (mtt180) cc_final: 0.4445 (mmm-85) outliers start: 98 outliers final: 76 residues processed: 894 average time/residue: 2.4361 time to fit residues: 3058.1256 Evaluate side-chains 917 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 824 time to evaluate : 6.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 97 LYS Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain d residue 110 THR Chi-restraints excluded: chain e residue 2 GLU Chi-restraints excluded: chain e residue 22 ASP Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain f residue 3 LYS Chi-restraints excluded: chain f residue 24 SER Chi-restraints excluded: chain f residue 63 GLN Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 140 GLU Chi-restraints excluded: chain f residue 153 ASP Chi-restraints excluded: chain f residue 157 THR Chi-restraints excluded: chain f residue 164 GLU Chi-restraints excluded: chain f residue 174 ASP Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 101 ASN Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain g residue 152 ARG Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain g residue 170 ARG Chi-restraints excluded: chain i residue 23 LYS Chi-restraints excluded: chain j residue 111 LYS Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 110 GLU Chi-restraints excluded: chain l residue 127 LYS Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain n residue 20 GLU Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 103 VAL Chi-restraints excluded: chain o residue 19 SER Chi-restraints excluded: chain q residue 62 GLU Chi-restraints excluded: chain q residue 72 VAL Chi-restraints excluded: chain q residue 95 ASP Chi-restraints excluded: chain r residue 28 LYS Chi-restraints excluded: chain r residue 73 LYS Chi-restraints excluded: chain s residue 6 ARG Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain t residue 27 ASN Chi-restraints excluded: chain t residue 102 THR Chi-restraints excluded: chain u residue 25 LYS Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain w residue 35 SER Chi-restraints excluded: chain w residue 40 VAL Chi-restraints excluded: chain x residue 19 LEU Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain y residue 41 THR Chi-restraints excluded: chain y residue 56 LYS Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain 4 residue 15 SER Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 11 LYS Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 88 MET Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 80 SER Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 35 GLN Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 22 SER Chi-restraints excluded: chain U residue 54 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 989 random chunks: chunk 481 optimal weight: 0.7980 chunk 623 optimal weight: 20.0000 chunk 835 optimal weight: 4.9990 chunk 240 optimal weight: 10.0000 chunk 723 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 218 optimal weight: 10.0000 chunk 785 optimal weight: 7.9990 chunk 328 optimal weight: 9.9990 chunk 806 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 overall best weight: 6.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 70 ASN c 115 GLN e 165 HIS e 195 GLN ** i 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 90 ASN j 93 GLN l 22 GLN o 3 ASN s 28 ASN u 5 ASN w 20 HIS x 15 ASN x 20 ASN x 45 GLN 0 45 GLN C 8 ASN C 139 GLN D 59 GLN D 74 ASN ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 ASN H 76 GLN ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 40 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.127733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.091404 restraints weight = 171091.700| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 0.80 r_work: 0.2903 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 154225 Z= 0.375 Angle : 0.766 19.086 230698 Z= 0.401 Chirality : 0.043 0.413 29382 Planarity : 0.007 0.153 12256 Dihedral : 23.066 177.797 77481 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.61 % Favored : 96.33 % Rotamer: Outliers : 2.51 % Allowed : 19.73 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.11), residues: 5480 helix: 1.28 (0.12), residues: 1900 sheet: 0.02 (0.15), residues: 1101 loop : -0.41 (0.12), residues: 2479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Q 73 HIS 0.015 0.002 HIS F 3 PHE 0.022 0.002 PHE S 10 TYR 0.026 0.002 TYR L 117 ARG 0.010 0.001 ARG G 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 49553.51 seconds wall clock time: 861 minutes 4.09 seconds (51664.09 seconds total)