Starting phenix.real_space_refine (version: 1.21rc1) on Wed Oct 18 18:29:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jap_3048/10_2023/3jap_3048_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jap_3048/10_2023/3jap_3048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jap_3048/10_2023/3jap_3048.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jap_3048/10_2023/3jap_3048.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jap_3048/10_2023/3jap_3048_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jap_3048/10_2023/3jap_3048_updated.pdb" } resolution = 4.9 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= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 1872 5.49 5 Mg 81 5.21 5 S 149 5.16 5 C 54790 2.51 5 N 17666 2.21 5 O 23771 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 12": "OE1" <-> "OE2" Residue "A GLU 55": "OE1" <-> "OE2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A GLU 117": "OE1" <-> "OE2" Residue "A GLU 135": "OE1" <-> "OE2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "C GLU 60": "OE1" <-> "OE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C GLU 125": "OE1" <-> "OE2" Residue "C GLU 213": "OE1" <-> "OE2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D GLU 103": "OE1" <-> "OE2" Residue "D ARG 124": "NH1" <-> "NH2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D GLU 135": "OE1" <-> "OE2" Residue "D PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 210": "OE1" <-> "OE2" Residue "D GLU 213": "OE1" <-> "OE2" Residue "D GLU 215": "OE1" <-> "OE2" Residue "E ARG 59": "NH1" <-> "NH2" Residue "E GLU 93": "OE1" <-> "OE2" Residue "E PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 118": "OE1" <-> "OE2" Residue "F GLU 26": "OE1" <-> "OE2" Residue "F GLU 41": "OE1" <-> "OE2" Residue "F GLU 54": "OE1" <-> "OE2" Residue "F GLU 146": "OE1" <-> "OE2" Residue "F GLU 183": "OE1" <-> "OE2" Residue "F GLU 198": "OE1" <-> "OE2" Residue "F GLU 218": "OE1" <-> "OE2" Residue "F ARG 227": "NH1" <-> "NH2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G GLU 44": "OE1" <-> "OE2" Residue "G GLU 118": "OE1" <-> "OE2" Residue "G GLU 122": "OE1" <-> "OE2" Residue "G GLU 203": "OE1" <-> "OE2" Residue "G GLU 207": "OE1" <-> "OE2" Residue "G GLU 218": "OE1" <-> "OE2" Residue "G GLU 225": "OE1" <-> "OE2" Residue "H GLU 48": "OE1" <-> "OE2" Residue "H GLU 82": "OE1" <-> "OE2" Residue "I ARG 74": "NH1" <-> "NH2" Residue "I ARG 92": "NH1" <-> "NH2" Residue "J ARG 6": "NH1" <-> "NH2" Residue "J GLU 64": "OE1" <-> "OE2" Residue "J ARG 69": "NH1" <-> "NH2" Residue "J ARG 82": "NH1" <-> "NH2" Residue "J ARG 171": "NH1" <-> "NH2" Residue "J ARG 176": "NH1" <-> "NH2" Residue "K GLU 6": "OE1" <-> "OE2" Residue "K GLU 18": "OE1" <-> "OE2" Residue "K GLU 34": "OE1" <-> "OE2" Residue "K GLU 78": "OE1" <-> "OE2" Residue "L GLU 10": "OE1" <-> "OE2" Residue "L TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 50": "OE1" <-> "OE2" Residue "L GLU 101": "OE1" <-> "OE2" Residue "L PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 18": "OE1" <-> "OE2" Residue "M GLU 40": "OE1" <-> "OE2" Residue "M GLU 57": "OE1" <-> "OE2" Residue "M GLU 61": "OE1" <-> "OE2" Residue "N GLU 142": "OE1" <-> "OE2" Residue "O GLU 37": "OE1" <-> "OE2" Residue "O GLU 116": "OE1" <-> "OE2" Residue "P GLU 23": "OE1" <-> "OE2" Residue "P GLU 69": "OE1" <-> "OE2" Residue "P GLU 71": "OE1" <-> "OE2" Residue "P GLU 106": "OE1" <-> "OE2" Residue "P GLU 118": "OE1" <-> "OE2" Residue "Q GLU 50": "OE1" <-> "OE2" Residue "Q GLU 125": "OE1" <-> "OE2" Residue "R GLU 37": "OE1" <-> "OE2" Residue "R GLU 76": "OE1" <-> "OE2" Residue "S GLU 64": "OE1" <-> "OE2" Residue "S GLU 65": "OE1" <-> "OE2" Residue "S GLU 67": "OE1" <-> "OE2" Residue "S GLU 106": "OE1" <-> "OE2" Residue "S GLU 114": "OE1" <-> "OE2" Residue "T PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 143": "OE1" <-> "OE2" Residue "U GLU 16": "OE1" <-> "OE2" Residue "U GLU 115": "OE1" <-> "OE2" Residue "V GLU 2": "OE1" <-> "OE2" Residue "V GLU 10": "OE1" <-> "OE2" Residue "V GLU 41": "OE1" <-> "OE2" Residue "V GLU 42": "OE1" <-> "OE2" Residue "V GLU 49": "OE1" <-> "OE2" Residue "V ARG 62": "NH1" <-> "NH2" Residue "W GLU 51": "OE1" <-> "OE2" Residue "W GLU 87": "OE1" <-> "OE2" Residue "W ARG 97": "NH1" <-> "NH2" Residue "X GLU 138": "OE1" <-> "OE2" Residue "Y ARG 8": "NH1" <-> "NH2" Residue "Y GLU 39": "OE1" <-> "OE2" Residue "Y GLU 46": "OE1" <-> "OE2" Residue "Y GLU 86": "OE1" <-> "OE2" Residue "Y GLU 98": "OE1" <-> "OE2" Residue "Y ARG 131": "NH1" <-> "NH2" Residue "Z GLU 84": "OE1" <-> "OE2" Residue "Z GLU 86": "OE1" <-> "OE2" Residue "a ARG 51": "NH1" <-> "NH2" Residue "b GLU 75": "OE1" <-> "OE2" Residue "c GLU 50": "OE1" <-> "OE2" Residue "c GLU 60": "OE1" <-> "OE2" Residue "c ARG 64": "NH1" <-> "NH2" Residue "d PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 22": "OE1" <-> "OE2" Residue "e GLU 25": "OE1" <-> "OE2" Residue "f GLU 111": "OE1" <-> "OE2" Residue "f PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 52": "OE1" <-> "OE2" Residue "g GLU 101": "OE1" <-> "OE2" Residue "g GLU 280": "OE1" <-> "OE2" Residue "i ARG 13": "NH1" <-> "NH2" Residue "i ARG 14": "NH1" <-> "NH2" Residue "i GLU 31": "OE1" <-> "OE2" Residue "i GLU 34": "OE1" <-> "OE2" Residue "i GLU 48": "OE1" <-> "OE2" Residue "i GLU 99": "OE1" <-> "OE2" Residue "j GLU 10": "OE1" <-> "OE2" Residue "j GLU 29": "OE1" <-> "OE2" Residue "j GLU 43": "OE1" <-> "OE2" Residue "j ARG 53": "NH1" <-> "NH2" Residue "j ARG 54": "NH1" <-> "NH2" Residue "j ARG 64": "NH1" <-> "NH2" Residue "j ARG 88": "NH1" <-> "NH2" Residue "j GLU 93": "OE1" <-> "OE2" Residue "j GLU 100": "OE1" <-> "OE2" Residue "j GLU 125": "OE1" <-> "OE2" Residue "j GLU 152": "OE1" <-> "OE2" Residue "j GLU 159": "OE1" <-> "OE2" Residue "j GLU 168": "OE1" <-> "OE2" Residue "j GLU 209": "OE1" <-> "OE2" Residue "k GLU 231": "OE1" <-> "OE2" Residue "k GLU 383": "OE1" <-> "OE2" Residue "k GLU 494": "OE1" <-> "OE2" Residue "k GLU 506": "OE1" <-> "OE2" Residue "m ARG 29": "NH1" <-> "NH2" Residue "m GLU 48": "OE1" <-> "OE2" Residue "m GLU 73": "OE1" <-> "OE2" Residue "m GLU 76": "OE1" <-> "OE2" Residue "o GLU 9": "OE1" <-> "OE2" Residue "o GLU 61": "OE1" <-> "OE2" Residue "o GLU 101": "OE1" <-> "OE2" Residue "o PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 392": "OE1" <-> "OE2" Residue "o PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 141": "OE1" <-> "OE2" Residue "q GLU 187": "OE1" <-> "OE2" Residue "q GLU 285": "OE1" <-> "OE2" Residue "q PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 725": "OE1" <-> "OE2" Residue "r PHE 733": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 61": "OE1" <-> "OE2" Residue "s GLU 80": "OE1" <-> "OE2" Residue "s GLU 91": "OE1" <-> "OE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 98333 Number of models: 1 Model: "" Number of chains: 53 Chain: "1" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1607 Classifications: {'RNA': 75} Modifications used: {'p5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 6, 'rna3p_pur': 30, 'rna3p_pyr': 28} Link IDs: {'rna2p': 16, 'rna3p': 58} Chain: "2" Number of atoms: 37797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1780, 37797 Classifications: {'RNA': 1780} Modifications used: {'rna2p_pur': 152, 'rna2p_pyr': 153, 'rna3p_pur': 785, 'rna3p_pyr': 690} Link IDs: {'rna2p': 305, 'rna3p': 1474} Chain breaks: 1 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {' G%rna3p_pur:plan2': 5, ' C%rna3p_pyr:plan': 4, ' A%rna3p_pur:plan2': 4, ' U%rna3p_pyr:plan': 1, ' C%rna3p_pyr:plan2': 4, ' G%rna3p_pur:plan': 5, ' A%rna3p_pur:plan': 4} Unresolved non-hydrogen planarities: 161 Chain: "3" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 287 Classifications: {'RNA': 14} Modifications used: {'rna2p_pyr': 6, 'rna3p_pur': 3, 'rna3p_pyr': 5} Link IDs: {'rna2p': 6, 'rna3p': 7} Chain: "A" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1626 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 191} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1769 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 216} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1629 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain: "D" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1744 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 8, 'TRANS': 214} Chain: "E" Number of atoms: 2078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2078 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 13, 'TRANS': 246} Chain: "F" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1609 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "G" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1812 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 9, 'TRANS': 216} Chain: "H" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1483 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 9, 'TRANS': 174} Chain: "I" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1489 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 183} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1471 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "K" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 809 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "L" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1248 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "M" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 885 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "N" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1187 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 7, 'TRANS': 142} Chain: "O" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 942 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "P" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 927 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "Q" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1105 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 6, 'TRANS': 134} Chain: "R" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 959 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain breaks: 1 Chain: "S" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1193 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 2, 'TRANS': 142} Chain: "T" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1110 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "U" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 845 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "V" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 687 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "W" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "X" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1119 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "Y" Number of atoms: 1061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1061 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "Z" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 558 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "a" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 779 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "b" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 609 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "c" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 487 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 1, 'TRANS': 60} Chain: "d" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain: "e" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 433 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 48} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "f" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 546 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 65} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "g" Number of atoms: 2466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2466 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 8, 'TRANS': 309} Chain breaks: 2 Chain: "h" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 233 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "i" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 884 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 2, 'TRANS': 108} Chain: "j" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2006 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 6, 'TRANS': 242} Chain breaks: 2 Chain: "k" Number of atoms: 3034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3034 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 375} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "l" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1036 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain breaks: 3 Chain: "m" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 716 Classifications: {'peptide': 90} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 87} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "o" Number of atoms: 4189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4189 Classifications: {'peptide': 550} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 14, 'TRANS': 535} Chain breaks: 9 Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'UNK:plan-1': 93} Unresolved non-hydrogen planarities: 93 Chain: "p" Number of atoms: 4899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 4899 Classifications: {'peptide': 634} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 17, 'TRANS': 616} Chain breaks: 7 Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 276 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'UNK:plan-1': 76, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 93 Chain: "q" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2693 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 11, 'TRANS': 330} Chain: "r" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 277 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "s" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 418 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "2" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Unusual residues: {' MG': 80} Classifications: {'undetermined': 80} Link IDs: {None: 79} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 41 Unusual residues: {' MG': 1, 'GCP': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "l" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 72229 SG CYS a 23 117.596 88.736 141.989 1.00 50.00 S ATOM 72250 SG CYS a 26 118.804 88.208 138.453 1.00 50.00 S ATOM 72652 SG CYS a 77 115.262 88.861 138.053 1.00 50.00 S ATOM 73277 SG CYS b 59 136.999 129.935 198.479 1.00 50.00 S ATOM 75147 SG CYS f 121 65.417 90.751 29.611 1.00 50.00 S ATOM 75165 SG CYS f 124 64.160 91.125 33.110 1.00 50.00 S ATOM 75282 SG CYS f 139 67.822 90.647 32.461 1.00 50.00 S ATOM 84766 SG CYS l 236 135.148 48.057 65.219 1.00 50.00 S ATOM 84963 SG CYS l 262 136.170 45.245 62.740 1.00 50.00 S Time building chain proxies: 37.59, per 1000 atoms: 0.38 Number of scatterers: 98333 At special positions: 0 Unit cell: (253.26, 230.48, 262.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 149 16.00 P 1872 15.00 Mg 81 11.99 O 23771 8.00 N 17666 7.00 C 54790 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 36.57 Conformation dependent library (CDL) restraints added in 6.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN a 500 " pdb="ZN ZN a 500 " - pdb=" SG CYS a 23 " pdb="ZN ZN a 500 " - pdb=" SG CYS a 77 " pdb="ZN ZN a 500 " - pdb=" SG CYS a 26 " pdb=" ZN b 101 " pdb="ZN ZN b 101 " - pdb=" SG CYS b 59 " pdb=" ZN f 501 " pdb="ZN ZN f 501 " - pdb=" SG CYS f 121 " pdb="ZN ZN f 501 " - pdb=" SG CYS f 139 " pdb="ZN ZN f 501 " - pdb=" SG CYS f 124 " pdb=" ZN l 301 " pdb="ZN ZN l 301 " - pdb=" SG CYS l 236 " pdb="ZN ZN l 301 " - pdb=" SG CYS l 262 " 14298 Ramachandran restraints generated. 7149 Oldfield, 0 Emsley, 7149 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13960 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 235 helices and 72 sheets defined 34.4% alpha, 14.2% beta 473 base pairs and 892 stacking pairs defined. Time for finding SS restraints: 35.15 Creating SS restraints... Processing helix chain 'A' and resid 11 through 20 Processing helix chain 'A' and resid 50 through 66 Processing helix chain 'A' and resid 80 through 92 removed outlier: 6.237A pdb=" N ARG A 84 " --> pdb=" O TYR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 138 Processing helix chain 'A' and resid 169 through 185 Processing helix chain 'A' and resid 199 through 201 No H-bonds generated for 'chain 'A' and resid 199 through 201' Processing helix chain 'B' and resid 24 through 26 No H-bonds generated for 'chain 'B' and resid 24 through 26' Processing helix chain 'B' and resid 77 through 79 No H-bonds generated for 'chain 'B' and resid 77 through 79' Processing helix chain 'B' and resid 107 through 113 Processing helix chain 'B' and resid 158 through 175 Processing helix chain 'B' and resid 181 through 189 Processing helix chain 'B' and resid 192 through 203 removed outlier: 5.016A pdb=" N ASP B 203 " --> pdb=" O ASN B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'C' and resid 45 through 52 Processing helix chain 'C' and resid 58 through 64 Processing helix chain 'C' and resid 71 through 77 Processing helix chain 'C' and resid 126 through 140 Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 212 through 226 removed outlier: 3.553A pdb=" N THR C 226 " --> pdb=" O ALA C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 247 No H-bonds generated for 'chain 'C' and resid 244 through 247' Processing helix chain 'D' and resid 7 through 28 Processing helix chain 'D' and resid 56 through 59 No H-bonds generated for 'chain 'D' and resid 56 through 59' Processing helix chain 'D' and resid 64 through 76 Processing helix chain 'D' and resid 98 through 111 Processing helix chain 'D' and resid 115 through 129 Processing helix chain 'D' and resid 162 through 164 No H-bonds generated for 'chain 'D' and resid 162 through 164' Processing helix chain 'D' and resid 192 through 195 No H-bonds generated for 'chain 'D' and resid 192 through 195' Processing helix chain 'E' and resid 16 through 18 No H-bonds generated for 'chain 'E' and resid 16 through 18' Processing helix chain 'E' and resid 46 through 49 No H-bonds generated for 'chain 'E' and resid 46 through 49' Processing helix chain 'E' and resid 58 through 66 Processing helix chain 'E' and resid 116 through 119 No H-bonds generated for 'chain 'E' and resid 116 through 119' Processing helix chain 'E' and resid 133 through 135 No H-bonds generated for 'chain 'E' and resid 133 through 135' Processing helix chain 'E' and resid 186 through 188 No H-bonds generated for 'chain 'E' and resid 186 through 188' Processing helix chain 'E' and resid 222 through 224 No H-bonds generated for 'chain 'E' and resid 222 through 224' Processing helix chain 'E' and resid 248 through 257 Processing helix chain 'F' and resid 33 through 36 No H-bonds generated for 'chain 'F' and resid 33 through 36' Processing helix chain 'F' and resid 38 through 41 No H-bonds generated for 'chain 'F' and resid 38 through 41' Processing helix chain 'F' and resid 85 through 88 removed outlier: 3.644A pdb=" N GLN F 88 " --> pdb=" O ARG F 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 85 through 88' Processing helix chain 'F' and resid 91 through 99 Processing helix chain 'F' and resid 109 through 125 Processing helix chain 'F' and resid 131 through 142 Processing helix chain 'F' and resid 166 through 185 Processing helix chain 'F' and resid 192 through 204 Processing helix chain 'F' and resid 211 through 225 Processing helix chain 'G' and resid 21 through 24 No H-bonds generated for 'chain 'G' and resid 21 through 24' Processing helix chain 'G' and resid 38 through 41 No H-bonds generated for 'chain 'G' and resid 38 through 41' Processing helix chain 'G' and resid 58 through 60 No H-bonds generated for 'chain 'G' and resid 58 through 60' Processing helix chain 'G' and resid 138 through 145 Processing helix chain 'G' and resid 181 through 221 Processing helix chain 'H' and resid 6 through 8 No H-bonds generated for 'chain 'H' and resid 6 through 8' Processing helix chain 'H' and resid 15 through 30 removed outlier: 3.941A pdb=" N ASN H 29 " --> pdb=" O ILE H 25 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ASN H 30 " --> pdb=" O ASP H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 73 Processing helix chain 'H' and resid 75 through 84 Processing helix chain 'H' and resid 118 through 129 Processing helix chain 'H' and resid 159 through 161 No H-bonds generated for 'chain 'H' and resid 159 through 161' Processing helix chain 'H' and resid 166 through 176 Processing helix chain 'I' and resid 26 through 28 No H-bonds generated for 'chain 'I' and resid 26 through 28' Processing helix chain 'I' and resid 88 through 93 Processing helix chain 'I' and resid 107 through 116 Processing helix chain 'I' and resid 138 through 147 Processing helix chain 'I' and resid 155 through 163 Processing helix chain 'I' and resid 174 through 177 No H-bonds generated for 'chain 'I' and resid 174 through 177' Processing helix chain 'I' and resid 188 through 200 Processing helix chain 'J' and resid 21 through 34 Processing helix chain 'J' and resid 39 through 61 Processing helix chain 'J' and resid 67 through 83 removed outlier: 3.505A pdb=" N ASN J 74 " --> pdb=" O LEU J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 106 Processing helix chain 'J' and resid 109 through 116 removed outlier: 4.138A pdb=" N TYR J 114 " --> pdb=" O GLN J 110 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU J 116 " --> pdb=" O GLN J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 130 Processing helix chain 'J' and resid 150 through 155 Processing helix chain 'J' and resid 172 through 181 Processing helix chain 'K' and resid 5 through 18 Processing helix chain 'K' and resid 39 through 52 Processing helix chain 'K' and resid 60 through 62 No H-bonds generated for 'chain 'K' and resid 60 through 62' Processing helix chain 'K' and resid 70 through 80 Processing helix chain 'L' and resid 46 through 50 Processing helix chain 'M' and resid 19 through 31 removed outlier: 4.330A pdb=" N VAL M 23 " --> pdb=" O ASP M 19 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N VAL M 24 " --> pdb=" O ALA M 20 " (cutoff:3.500A) Processing helix chain 'M' and resid 39 through 46 Processing helix chain 'M' and resid 63 through 73 Processing helix chain 'M' and resid 85 through 92 Processing helix chain 'M' and resid 124 through 131 removed outlier: 4.077A pdb=" N LEU M 128 " --> pdb=" O ARG M 124 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 43 Processing helix chain 'N' and resid 47 through 57 Processing helix chain 'N' and resid 63 through 67 Processing helix chain 'N' and resid 71 through 78 Processing helix chain 'N' and resid 86 through 104 Processing helix chain 'N' and resid 110 through 132 Processing helix chain 'N' and resid 144 through 150 Processing helix chain 'O' and resid 44 through 47 No H-bonds generated for 'chain 'O' and resid 44 through 47' Processing helix chain 'O' and resid 51 through 54 Processing helix chain 'O' and resid 57 through 74 Processing helix chain 'O' and resid 97 through 106 Processing helix chain 'P' and resid 24 through 26 No H-bonds generated for 'chain 'P' and resid 24 through 26' Processing helix chain 'P' and resid 30 through 35 Processing helix chain 'P' and resid 39 through 46 Processing helix chain 'P' and resid 56 through 66 Processing helix chain 'P' and resid 116 through 118 No H-bonds generated for 'chain 'P' and resid 116 through 118' Processing helix chain 'Q' and resid 45 through 55 removed outlier: 3.584A pdb=" N TYR Q 49 " --> pdb=" O ARG Q 45 " (cutoff:3.500A) Proline residue: Q 51 - end of helix Processing helix chain 'Q' and resid 57 through 60 Processing helix chain 'Q' and resid 75 through 96 Processing helix chain 'Q' and resid 99 through 111 Processing helix chain 'R' and resid 7 through 19 Processing helix chain 'R' and resid 28 through 38 Processing helix chain 'R' and resid 45 through 63 Processing helix chain 'R' and resid 72 through 80 removed outlier: 3.664A pdb=" N GLU R 77 " --> pdb=" O LEU R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 113 Processing helix chain 'S' and resid 17 through 19 No H-bonds generated for 'chain 'S' and resid 17 through 19' Processing helix chain 'S' and resid 29 through 34 removed outlier: 3.951A pdb=" N THR S 34 " --> pdb=" O TYR S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 50 Processing helix chain 'S' and resid 63 through 74 Processing helix chain 'S' and resid 105 through 118 Processing helix chain 'S' and resid 122 through 129 Processing helix chain 'T' and resid 6 through 8 No H-bonds generated for 'chain 'T' and resid 6 through 8' Processing helix chain 'T' and resid 12 through 24 Processing helix chain 'T' and resid 54 through 67 Processing helix chain 'T' and resid 73 through 79 Processing helix chain 'T' and resid 98 through 111 Processing helix chain 'T' and resid 126 through 143 Processing helix chain 'U' and resid 32 through 48 Processing helix chain 'U' and resid 98 through 104 Processing helix chain 'V' and resid 57 through 62 Processing helix chain 'V' and resid 65 through 75 Processing helix chain 'W' and resid 6 through 20 Processing helix chain 'W' and resid 32 through 44 Processing helix chain 'W' and resid 83 through 93 removed outlier: 3.642A pdb=" N GLU W 87 " --> pdb=" O ALA W 84 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 119 Processing helix chain 'X' and resid 13 through 23 Processing helix chain 'X' and resid 27 through 34 Processing helix chain 'X' and resid 36 through 39 No H-bonds generated for 'chain 'X' and resid 36 through 39' Processing helix chain 'X' and resid 91 through 96 Processing helix chain 'X' and resid 132 through 137 Processing helix chain 'Y' and resid 37 through 45 Processing helix chain 'Y' and resid 52 through 54 No H-bonds generated for 'chain 'Y' and resid 52 through 54' Processing helix chain 'Y' and resid 79 through 83 Processing helix chain 'Y' and resid 88 through 94 Processing helix chain 'Y' and resid 105 through 117 Processing helix chain 'Y' and resid 123 through 134 removed outlier: 3.850A pdb=" N ALA Y 134 " --> pdb=" O ALA Y 130 " (cutoff:3.500A) Processing helix chain 'Z' and resid 44 through 54 Processing helix chain 'Z' and resid 62 through 67 Processing helix chain 'Z' and resid 74 through 83 removed outlier: 3.865A pdb=" N VAL Z 78 " --> pdb=" O SER Z 74 " (cutoff:3.500A) Processing helix chain 'a' and resid 50 through 56 Processing helix chain 'a' and resid 75 through 81 removed outlier: 4.169A pdb=" N ILE a 79 " --> pdb=" O ILE a 75 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS a 80 " --> pdb=" O SER a 76 " (cutoff:3.500A) Processing helix chain 'b' and resid 12 through 17 Processing helix chain 'd' and resid 33 through 35 No H-bonds generated for 'chain 'd' and resid 33 through 35' Processing helix chain 'd' and resid 41 through 50 removed outlier: 5.688A pdb=" N ASN d 48 " --> pdb=" O ARG d 44 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ASP d 49 " --> pdb=" O GLU d 45 " (cutoff:3.500A) Processing helix chain 'e' and resid 13 through 17 removed outlier: 3.621A pdb=" N GLN e 17 " --> pdb=" O LYS e 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 13 through 17' Processing helix chain 'e' and resid 33 through 44 Processing helix chain 'h' and resid 3 through 24 Processing helix chain 'i' and resid 12 through 14 No H-bonds generated for 'chain 'i' and resid 12 through 14' Processing helix chain 'i' and resid 97 through 106 Processing helix chain 'j' and resid 92 through 111 removed outlier: 4.274A pdb=" N ILE j 96 " --> pdb=" O SER j 92 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LYS j 97 " --> pdb=" O GLU j 93 " (cutoff:3.500A) Processing helix chain 'j' and resid 114 through 119 Processing helix chain 'j' and resid 123 through 134 removed outlier: 4.237A pdb=" N TRP j 132 " --> pdb=" O LYS j 128 " (cutoff:3.500A) Proline residue: j 133 - end of helix Processing helix chain 'j' and resid 142 through 150 Processing helix chain 'j' and resid 154 through 157 No H-bonds generated for 'chain 'j' and resid 154 through 157' Processing helix chain 'j' and resid 163 through 173 Processing helix chain 'j' and resid 197 through 208 removed outlier: 3.603A pdb=" N SER j 207 " --> pdb=" O ASP j 203 " (cutoff:3.500A) Processing helix chain 'j' and resid 241 through 257 removed outlier: 3.559A pdb=" N GLU j 245 " --> pdb=" O ILE j 241 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER j 246 " --> pdb=" O GLU j 242 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR j 256 " --> pdb=" O THR j 252 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS j 257 " --> pdb=" O GLU j 253 " (cutoff:3.500A) Processing helix chain 'k' and resid 113 through 121 Processing helix chain 'k' and resid 131 through 134 No H-bonds generated for 'chain 'k' and resid 131 through 134' Processing helix chain 'k' and resid 202 through 208 Processing helix chain 'k' and resid 227 through 238 Processing helix chain 'k' and resid 258 through 269 Processing helix chain 'k' and resid 291 through 300 Processing helix chain 'l' and resid 132 through 140 Processing helix chain 'l' and resid 177 through 184 Processing helix chain 'l' and resid 188 through 198 removed outlier: 3.517A pdb=" N ILE l 192 " --> pdb=" O PRO l 188 " (cutoff:3.500A) Processing helix chain 'l' and resid 221 through 233 Processing helix chain 'm' and resid 51 through 61 Processing helix chain 'm' and resid 86 through 94 Processing helix chain 'o' and resid 8 through 21 Processing helix chain 'o' and resid 25 through 35 Processing helix chain 'o' and resid 49 through 62 Processing helix chain 'o' and resid 65 through 79 Processing helix chain 'o' and resid 83 through 119 removed outlier: 3.619A pdb=" N LYS o 116 " --> pdb=" O ASP o 112 " (cutoff:3.500A) Processing helix chain 'o' and resid 151 through 169 Processing helix chain 'o' and resid 177 through 192 Processing helix chain 'o' and resid 197 through 218 removed outlier: 4.599A pdb=" N SER o 218 " --> pdb=" O ASN o 214 " (cutoff:3.500A) Processing helix chain 'o' and resid 231 through 249 Processing helix chain 'o' and resid 254 through 269 Processing helix chain 'o' and resid 278 through 291 removed outlier: 3.799A pdb=" N PHE o 291 " --> pdb=" O VAL o 287 " (cutoff:3.500A) Processing helix chain 'o' and resid 296 through 312 removed outlier: 3.817A pdb=" N THR o 312 " --> pdb=" O LYS o 308 " (cutoff:3.500A) Processing helix chain 'o' and resid 318 through 334 Processing helix chain 'o' and resid 347 through 350 removed outlier: 3.575A pdb=" N ARG o 350 " --> pdb=" O PRO o 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 347 through 350' Processing helix chain 'o' and resid 363 through 371 Processing helix chain 'o' and resid 374 through 377 No H-bonds generated for 'chain 'o' and resid 374 through 377' Processing helix chain 'o' and resid 382 through 391 Processing helix chain 'o' and resid 397 through 413 removed outlier: 4.735A pdb=" N VAL o 409 " --> pdb=" O GLU o 405 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LYS o 410 " --> pdb=" O ASN o 406 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER o 413 " --> pdb=" O VAL o 409 " (cutoff:3.500A) Processing helix chain 'o' and resid 422 through 439 Processing helix chain 'o' and resid 445 through 452 Processing helix chain 'o' and resid 462 through 474 Processing helix chain 'o' and resid 754 through 768 Processing helix chain 'o' and resid 773 through 784 Processing helix chain 'o' and resid 789 through 801 Processing helix chain 'o' and resid 807 through 817 Processing helix chain 'o' and resid 830 through 833 No H-bonds generated for 'chain 'o' and resid 830 through 833' Processing helix chain 'o' and resid 838 through 845 Processing helix chain 'o' and resid 851 through 865 Processing helix chain 'p' and resid 21 through 31 Processing helix chain 'p' and resid 117 through 134 Processing helix chain 'p' and resid 141 through 147 Processing helix chain 'p' and resid 151 through 157 Processing helix chain 'p' and resid 171 through 184 Processing helix chain 'p' and resid 196 through 205 Processing helix chain 'p' and resid 212 through 217 Processing helix chain 'p' and resid 252 through 266 Processing helix chain 'p' and resid 272 through 285 Processing helix chain 'p' and resid 289 through 306 Proline residue: p 301 - end of helix Processing helix chain 'p' and resid 315 through 335 Processing helix chain 'p' and resid 338 through 340 No H-bonds generated for 'chain 'p' and resid 338 through 340' Processing helix chain 'p' and resid 369 through 386 Processing helix chain 'p' and resid 392 through 418 removed outlier: 3.811A pdb=" N GLU p 401 " --> pdb=" O ARG p 397 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLN p 402 " --> pdb=" O LEU p 398 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER p 403 " --> pdb=" O ARG p 399 " (cutoff:3.500A) Processing helix chain 'p' and resid 422 through 438 removed outlier: 4.923A pdb=" N ARG p 431 " --> pdb=" O ARG p 427 " (cutoff:3.500A) Proline residue: p 432 - end of helix Processing helix chain 'p' and resid 445 through 458 Processing helix chain 'p' and resid 478 through 490 Processing helix chain 'p' and resid 496 through 513 Processing helix chain 'p' and resid 516 through 526 Processing helix chain 'p' and resid 538 through 557 Processing helix chain 'p' and resid 560 through 568 Processing helix chain 'p' and resid 586 through 589 No H-bonds generated for 'chain 'p' and resid 586 through 589' Processing helix chain 'p' and resid 614 through 638 removed outlier: 3.584A pdb=" N ILE p 630 " --> pdb=" O LEU p 626 " (cutoff:3.500A) Proline residue: p 631 - end of helix Processing helix chain 'p' and resid 652 through 661 Processing helix chain 'p' and resid 671 through 684 Processing helix chain 'p' and resid 688 through 696 Processing helix chain 'p' and resid 698 through 700 No H-bonds generated for 'chain 'p' and resid 698 through 700' Processing helix chain 'p' and resid 707 through 728 Processing helix chain 'p' and resid 738 through 744 Processing helix chain 'p' and resid 749 through 763 Processing helix chain 'p' and resid 783 through 793 Processing helix chain 'q' and resid 324 through 328 Processing helix chain 'q' and resid 335 through 340 Processing helix chain 'r' and resid 705 through 726 Processing helix chain 's' and resid 47 through 53 Processing helix chain 's' and resid 59 through 61 No H-bonds generated for 'chain 's' and resid 59 through 61' Processing helix chain 's' and resid 87 through 95 Processing sheet with id= A, first strand: chain 'A' and resid 96 through 99 removed outlier: 6.516A pdb=" N LEU A 120 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE A 76 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE A 122 " --> pdb=" O ILE A 76 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 42 through 49 removed outlier: 6.820A pdb=" N ILE B 32 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LYS B 45 " --> pdb=" O TYR B 30 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TYR B 30 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU B 47 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLU B 28 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU B 97 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N VAL B 91 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 65 through 69 removed outlier: 5.585A pdb=" N ARG B 87 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N PHE B 100 " --> pdb=" O ARG B 87 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 120 through 127 removed outlier: 6.201A pdb=" N ARG B 136 " --> pdb=" O LEU B 217 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N LEU B 217 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N PHE B 138 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL B 215 " --> pdb=" O PHE B 138 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 116 through 123 removed outlier: 3.937A pdb=" N ASN C 87 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL C 108 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N VAL C 85 " --> pdb=" O VAL C 108 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 163 through 167 Processing sheet with id= G, first strand: chain 'D' and resid 84 through 90 removed outlier: 6.301A pdb=" N THR D 46 " --> pdb=" O ALA D 85 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N TYR D 87 " --> pdb=" O THR D 46 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE D 48 " --> pdb=" O TYR D 87 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N GLU D 89 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ILE D 50 " --> pdb=" O GLU D 89 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 147 through 154 removed outlier: 5.561A pdb=" N LYS D 141 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL D 181 " --> pdb=" O LYS D 141 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 70 through 72 Processing sheet with id= J, first strand: chain 'E' and resid 122 through 125 removed outlier: 3.636A pdb=" N ASP E 171 " --> pdb=" O LYS E 161 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 146 through 148 Processing sheet with id= L, first strand: chain 'E' and resid 207 through 210 Processing sheet with id= M, first strand: chain 'E' and resid 180 through 183 removed outlier: 5.776A pdb=" N TYR E 182 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N VAL E 227 " --> pdb=" O TYR E 182 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 146 through 149 Processing sheet with id= O, first strand: chain 'G' and resid 12 through 17 removed outlier: 3.561A pdb=" N THR G 114 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL G 49 " --> pdb=" O THR G 114 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN G 34 " --> pdb=" O ILE G 52 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 73 through 77 Processing sheet with id= Q, first strand: chain 'G' and resid 160 through 163 Processing sheet with id= R, first strand: chain 'G' and resid 55 through 57 Processing sheet with id= S, first strand: chain 'H' and resid 46 through 50 Processing sheet with id= T, first strand: chain 'H' and resid 138 through 142 removed outlier: 6.458A pdb=" N GLN H 180 " --> pdb=" O GLN H 150 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ILE H 152 " --> pdb=" O GLN H 180 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL H 182 " --> pdb=" O ILE H 152 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N LEU H 154 " --> pdb=" O VAL H 182 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N GLU H 184 " --> pdb=" O LEU H 154 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 72 through 77 removed outlier: 3.537A pdb=" N VAL I 72 " --> pdb=" O TRP I 67 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ARG I 74 " --> pdb=" O PHE I 65 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE I 65 " --> pdb=" O ARG I 74 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY I 182 " --> pdb=" O ASN I 64 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA I 100 " --> pdb=" O ILE I 170 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLY I 80 " --> pdb=" O GLN I 103 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 44 through 48 removed outlier: 3.558A pdb=" N LYS I 54 " --> pdb=" O VAL I 46 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASN I 52 " --> pdb=" O THR I 48 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'K' and resid 55 through 58 removed outlier: 3.834A pdb=" N THR K 67 " --> pdb=" O LYS K 56 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'L' and resid 106 through 110 removed outlier: 6.012A pdb=" N ARG L 87 " --> pdb=" O VAL L 75 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N VAL L 75 " --> pdb=" O ARG L 87 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N GLY L 126 " --> pdb=" O VAL L 139 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL L 139 " --> pdb=" O GLY L 126 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'L' and resid 90 through 94 removed outlier: 3.706A pdb=" N TYR L 90 " --> pdb=" O ARG L 103 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG L 99 " --> pdb=" O VAL L 94 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'M' and resid 52 through 55 Processing sheet with id= AA, first strand: chain 'O' and resid 19 through 21 Processing sheet with id= AB, first strand: chain 'O' and resid 78 through 83 removed outlier: 7.164A pdb=" N ARG O 111 " --> pdb=" O VAL O 79 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ILE O 81 " --> pdb=" O ARG O 111 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N GLY O 113 " --> pdb=" O ILE O 81 " (cutoff:3.500A) removed outlier: 10.025A pdb=" N ILE O 83 " --> pdb=" O GLY O 113 " (cutoff:3.500A) removed outlier: 9.821A pdb=" N ILE O 115 " --> pdb=" O ILE O 83 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'P' and resid 76 through 78 Processing sheet with id= AD, first strand: chain 'Q' and resid 7 through 9 removed outlier: 5.895A pdb=" N LEU Q 28 " --> pdb=" O ILE Q 65 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N VAL Q 67 " --> pdb=" O LEU Q 28 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LYS Q 30 " --> pdb=" O VAL Q 67 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VAL Q 69 " --> pdb=" O LYS Q 30 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'R' and resid 100 through 102 Processing sheet with id= AF, first strand: chain 'T' and resid 81 through 84 removed outlier: 3.736A pdb=" N GLY T 82 " --> pdb=" O VAL T 94 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS T 92 " --> pdb=" O LYS T 84 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'T' and resid 114 through 116 Processing sheet with id= AH, first strand: chain 'U' and resid 113 through 116 removed outlier: 3.958A pdb=" N ASP U 92 " --> pdb=" O LYS U 53 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL U 51 " --> pdb=" O GLU U 94 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'U' and resid 61 through 68 Processing sheet with id= AJ, first strand: chain 'V' and resid 32 through 37 Processing sheet with id= AK, first strand: chain 'W' and resid 24 through 27 Processing sheet with id= AL, first strand: chain 'W' and resid 109 through 111 removed outlier: 5.059A pdb=" N THR W 105 " --> pdb=" O ILE W 125 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ILE W 125 " --> pdb=" O THR W 105 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'X' and resid 82 through 86 removed outlier: 3.514A pdb=" N LYS X 126 " --> pdb=" O LEU X 103 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ALA X 105 " --> pdb=" O VAL X 124 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N VAL X 124 " --> pdb=" O ALA X 105 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'Y' and resid 55 through 58 removed outlier: 3.710A pdb=" N VAL Y 24 " --> pdb=" O LYS Y 11 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N LYS Y 11 " --> pdb=" O VAL Y 24 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASP Y 26 " --> pdb=" O THR Y 9 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N THR Y 9 " --> pdb=" O ASP Y 26 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU Y 28 " --> pdb=" O ILE Y 7 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ILE Y 7 " --> pdb=" O LEU Y 28 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'Z' and resid 89 through 91 Processing sheet with id= AP, first strand: chain 'a' and resid 20 through 22 Processing sheet with id= AQ, first strand: chain 'a' and resid 37 through 43 Processing sheet with id= AR, first strand: chain 'b' and resid 43 through 47 Processing sheet with id= AS, first strand: chain 'c' and resid 53 through 56 removed outlier: 3.733A pdb=" N ILE c 13 " --> pdb=" O ARG c 29 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ARG c 29 " --> pdb=" O ILE c 13 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N VAL c 15 " --> pdb=" O GLN c 27 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N GLN c 27 " --> pdb=" O VAL c 15 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'g' and resid 6 through 10 Processing sheet with id= AU, first strand: chain 'g' and resid 21 through 24 removed outlier: 6.853A pdb=" N GLY g 37 " --> pdb=" O THR g 22 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU g 24 " --> pdb=" O VAL g 35 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL g 35 " --> pdb=" O LEU g 24 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER g 38 " --> pdb=" O THR g 42 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR g 42 " --> pdb=" O SER g 38 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG g 60 " --> pdb=" O SER g 45 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ARG g 47 " --> pdb=" O PRO g 58 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'g' and resid 72 through 74 removed outlier: 3.570A pdb=" N ALA g 102 " --> pdb=" O LEU g 92 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASN g 94 " --> pdb=" O SER g 100 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N SER g 100 " --> pdb=" O ASN g 94 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'g' and resid 132 through 135 removed outlier: 3.720A pdb=" N ALA g 126 " --> pdb=" O SER g 113 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER g 113 " --> pdb=" O ALA g 126 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'g' and resid 198 through 200 removed outlier: 5.426A pdb=" N ILE g 182 " --> pdb=" O GLY g 178 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY g 178 " --> pdb=" O ILE g 182 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'g' and resid 208 through 211 Processing sheet with id= AZ, first strand: chain 'g' and resid 247 through 252 removed outlier: 6.678A pdb=" N ALA g 262 " --> pdb=" O PHE g 248 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU g 250 " --> pdb=" O THR g 260 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR g 260 " --> pdb=" O LEU g 250 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N PHE g 252 " --> pdb=" O TRP g 258 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N TRP g 258 " --> pdb=" O PHE g 252 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP g 279 " --> pdb=" O ILE g 269 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ASP g 271 " --> pdb=" O LEU g 277 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU g 277 " --> pdb=" O ASP g 271 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'i' and resid 76 through 80 removed outlier: 6.934A pdb=" N GLU i 48 " --> pdb=" O THR i 39 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N MET i 41 " --> pdb=" O ARG i 46 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N ARG i 46 " --> pdb=" O MET i 41 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU i 78 " --> pdb=" O VAL i 92 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'j' and resid 19 through 23 removed outlier: 6.772A pdb=" N ASP j 84 " --> pdb=" O LEU j 74 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE j 83 " --> pdb=" O GLU j 43 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU j 47 " --> pdb=" O LEU j 85 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'j' and resid 182 through 189 Processing sheet with id= BD, first strand: chain 'k' and resid 280 through 282 removed outlier: 8.443A pdb=" N VAL k 281 " --> pdb=" O VAL k 244 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE k 246 " --> pdb=" O VAL k 281 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ALA k 214 " --> pdb=" O ILE k 245 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N LEU k 247 " --> pdb=" O ALA k 214 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU k 216 " --> pdb=" O LEU k 247 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ILE k 103 " --> pdb=" O HIS k 188 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N SER k 190 " --> pdb=" O ILE k 103 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N THR k 105 " --> pdb=" O SER k 190 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL k 192 " --> pdb=" O THR k 105 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N GLY k 107 " --> pdb=" O VAL k 192 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE k 147 " --> pdb=" O VAL k 186 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N HIS k 188 " --> pdb=" O ALA k 145 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA k 145 " --> pdb=" O HIS k 188 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'k' and resid 373 through 376 removed outlier: 4.296A pdb=" N ASN k 344 " --> pdb=" O ARG k 314 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ILE k 316 " --> pdb=" O ILE k 342 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ILE k 342 " --> pdb=" O ILE k 316 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY k 394 " --> pdb=" O ILE k 342 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LEU k 380 " --> pdb=" O LEU k 387 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU k 387 " --> pdb=" O LEU k 380 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA k 382 " --> pdb=" O ASN k 385 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'k' and resid 319 through 322 Processing sheet with id= BG, first strand: chain 'k' and resid 425 through 427 Processing sheet with id= BH, first strand: chain 'k' and resid 482 through 486 removed outlier: 3.943A pdb=" N GLY k 513 " --> pdb=" O LEU k 501 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ARG k 484 " --> pdb=" O VAL k 476 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'k' and resid 502 through 504 Processing sheet with id= BJ, first strand: chain 'l' and resid 204 through 206 removed outlier: 3.573A pdb=" N VAL l 212 " --> pdb=" O SER l 204 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP l 206 " --> pdb=" O ARG l 210 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'm' and resid 103 through 106 removed outlier: 7.045A pdb=" N ILE m 26 " --> pdb=" O LYS m 104 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N HIS m 106 " --> pdb=" O ILE m 26 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE m 28 " --> pdb=" O HIS m 106 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR m 41 " --> pdb=" O ARG m 29 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN m 31 " --> pdb=" O LEU m 39 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'o' and resid 442 through 444 Processing sheet with id= BM, first strand: chain 'q' and resid 2 through 6 Processing sheet with id= BN, first strand: chain 'q' and resid 13 through 18 removed outlier: 6.923A pdb=" N CYS q 28 " --> pdb=" O THR q 14 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL q 16 " --> pdb=" O PHE q 26 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE q 26 " --> pdb=" O VAL q 16 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N TYR q 18 " --> pdb=" O LEU q 24 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LEU q 24 " --> pdb=" O TYR q 18 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N TYR q 38 " --> pdb=" O ARG q 44 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ARG q 44 " --> pdb=" O TYR q 38 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'q' and resid 55 through 60 removed outlier: 6.574A pdb=" N GLY q 70 " --> pdb=" O TRP q 56 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE q 58 " --> pdb=" O VAL q 68 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL q 68 " --> pdb=" O ILE q 58 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N VAL q 60 " --> pdb=" O TYR q 66 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N TYR q 66 " --> pdb=" O VAL q 60 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER q 71 " --> pdb=" O SER q 75 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N SER q 75 " --> pdb=" O SER q 71 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASP q 80 " --> pdb=" O CYS q 86 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N CYS q 86 " --> pdb=" O ASP q 80 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'q' and resid 145 through 148 removed outlier: 3.745A pdb=" N SER q 121 " --> pdb=" O LEU q 112 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG q 98 " --> pdb=" O ILE q 111 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'q' and resid 191 through 193 removed outlier: 5.020A pdb=" N LYS q 176 " --> pdb=" O HIS q 172 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS q 172 " --> pdb=" O LYS q 176 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'q' and resid 199 through 204 removed outlier: 6.812A pdb=" N SER q 214 " --> pdb=" O SER q 200 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N MET q 202 " --> pdb=" O ILE q 212 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE q 212 " --> pdb=" O MET q 202 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N PHE q 204 " --> pdb=" O TYR q 210 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N TYR q 210 " --> pdb=" O PHE q 204 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ASP q 224 " --> pdb=" O VAL q 230 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL q 230 " --> pdb=" O ASP q 224 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'q' and resid 240 through 245 removed outlier: 6.744A pdb=" N GLY q 255 " --> pdb=" O ASN q 241 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA q 243 " --> pdb=" O ILE q 253 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE q 253 " --> pdb=" O ALA q 243 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ILE q 245 " --> pdb=" O PHE q 251 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N PHE q 251 " --> pdb=" O ILE q 245 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N HIS q 279 " --> pdb=" O GLU q 285 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLU q 285 " --> pdb=" O HIS q 279 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'q' and resid 127 through 129 removed outlier: 3.530A pdb=" N LYS q 138 " --> pdb=" O GLU q 128 " (cutoff:3.500A) 2100 hydrogen bonds defined for protein. 6039 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1166 hydrogen bonds 2002 hydrogen bond angles 0 basepair planarities 473 basepair parallelities 892 stacking parallelities Total time for adding SS restraints: 65.58 Time building geometry restraints manager: 39.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 18803 1.33 - 1.46: 33483 1.46 - 1.58: 47652 1.58 - 1.70: 3741 1.70 - 1.83: 234 Bond restraints: 103913 Sorted by residual: bond pdb=" CA ILE p 630 " pdb=" CB ILE p 630 " ideal model delta sigma weight residual 1.539 1.570 -0.031 5.40e-03 3.43e+04 3.36e+01 bond pdb=" O2B GCP k 603 " pdb=" PB GCP k 603 " ideal model delta sigma weight residual 1.506 1.608 -0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" C4 GCP k 603 " pdb=" C5 GCP k 603 " ideal model delta sigma weight residual 1.382 1.479 -0.097 2.00e-02 2.50e+03 2.38e+01 bond pdb=" CA ILE p 300 " pdb=" CB ILE p 300 " ideal model delta sigma weight residual 1.534 1.567 -0.032 6.80e-03 2.16e+04 2.25e+01 bond pdb=" O3A GCP k 603 " pdb=" PB GCP k 603 " ideal model delta sigma weight residual 1.697 1.614 0.083 2.00e-02 2.50e+03 1.71e+01 ... (remaining 103908 not shown) Histogram of bond angle deviations from ideal: 95.81 - 103.91: 6882 103.91 - 112.01: 51761 112.01 - 120.11: 46789 120.11 - 128.21: 41052 128.21 - 136.31: 2856 Bond angle restraints: 149340 Sorted by residual: angle pdb=" C4' C 21157 " pdb=" C3' C 21157 " pdb=" O3' C 21157 " ideal model delta sigma weight residual 109.40 124.91 -15.51 1.50e+00 4.44e-01 1.07e+02 angle pdb=" O3' A 2 685 " pdb=" C3' A 2 685 " pdb=" C2' A 2 685 " ideal model delta sigma weight residual 113.70 127.30 -13.60 1.50e+00 4.44e-01 8.22e+01 angle pdb=" O3' U 2 279 " pdb=" C3' U 2 279 " pdb=" C2' U 2 279 " ideal model delta sigma weight residual 109.50 122.71 -13.21 1.50e+00 4.44e-01 7.75e+01 angle pdb=" O3' U 21430 " pdb=" C3' U 21430 " pdb=" C2' U 21430 " ideal model delta sigma weight residual 109.50 122.07 -12.57 1.50e+00 4.44e-01 7.02e+01 angle pdb=" C4' A 21080 " pdb=" C3' A 21080 " pdb=" O3' A 21080 " ideal model delta sigma weight residual 109.40 121.76 -12.36 1.50e+00 4.44e-01 6.79e+01 ... (remaining 149335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 54179 35.98 - 71.97: 4255 71.97 - 107.95: 398 107.95 - 143.93: 37 143.93 - 179.92: 71 Dihedral angle restraints: 58940 sinusoidal: 37381 harmonic: 21559 Sorted by residual: dihedral pdb=" CA PHE l 158 " pdb=" C PHE l 158 " pdb=" N ARG l 159 " pdb=" CA ARG l 159 " ideal model delta harmonic sigma weight residual 180.00 124.78 55.22 0 5.00e+00 4.00e-02 1.22e+02 dihedral pdb=" C5' U 2 279 " pdb=" C4' U 2 279 " pdb=" C3' U 2 279 " pdb=" O3' U 2 279 " ideal model delta sinusoidal sigma weight residual 147.00 70.49 76.51 1 8.00e+00 1.56e-02 1.15e+02 dihedral pdb=" C5' G 1 7 " pdb=" C4' G 1 7 " pdb=" C3' G 1 7 " pdb=" O3' G 1 7 " ideal model delta sinusoidal sigma weight residual 147.00 72.23 74.77 1 8.00e+00 1.56e-02 1.11e+02 ... (remaining 58937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.162: 15455 0.162 - 0.323: 2816 0.323 - 0.485: 109 0.485 - 0.646: 23 0.646 - 0.808: 6 Chirality restraints: 18409 Sorted by residual: chirality pdb=" CA TYR R 53 " pdb=" N TYR R 53 " pdb=" C TYR R 53 " pdb=" CB TYR R 53 " both_signs ideal model delta sigma weight residual False 2.51 1.70 0.81 2.00e-01 2.50e+01 1.63e+01 chirality pdb=" C3' A 21491 " pdb=" C4' A 21491 " pdb=" O3' A 21491 " pdb=" C2' A 21491 " both_signs ideal model delta sigma weight residual False -2.48 -1.75 -0.73 2.00e-01 2.50e+01 1.32e+01 chirality pdb=" C3' U 2 277 " pdb=" C4' U 2 277 " pdb=" O3' U 2 277 " pdb=" C2' U 2 277 " both_signs ideal model delta sigma weight residual False -2.74 -2.05 -0.69 2.00e-01 2.50e+01 1.20e+01 ... (remaining 18406 not shown) Planarity restraints: 12087 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C 21439 " 0.001 2.00e-02 2.50e+03 4.08e-02 3.75e+01 pdb=" N1 C 21439 " 0.002 2.00e-02 2.50e+03 pdb=" C2 C 21439 " 0.004 2.00e-02 2.50e+03 pdb=" O2 C 21439 " 0.046 2.00e-02 2.50e+03 pdb=" N3 C 21439 " -0.101 2.00e-02 2.50e+03 pdb=" C4 C 21439 " -0.001 2.00e-02 2.50e+03 pdb=" N4 C 21439 " 0.052 2.00e-02 2.50e+03 pdb=" C5 C 21439 " -0.003 2.00e-02 2.50e+03 pdb=" C6 C 21439 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 21269 " -0.012 2.00e-02 2.50e+03 3.45e-02 3.58e+01 pdb=" N9 G 21269 " 0.005 2.00e-02 2.50e+03 pdb=" C8 G 21269 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G 21269 " 0.003 2.00e-02 2.50e+03 pdb=" C5 G 21269 " 0.006 2.00e-02 2.50e+03 pdb=" C6 G 21269 " -0.002 2.00e-02 2.50e+03 pdb=" O6 G 21269 " -0.055 2.00e-02 2.50e+03 pdb=" N1 G 21269 " 0.096 2.00e-02 2.50e+03 pdb=" C2 G 21269 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G 21269 " -0.044 2.00e-02 2.50e+03 pdb=" N3 G 21269 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G 21269 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 21332 " 0.020 2.00e-02 2.50e+03 3.96e-02 3.53e+01 pdb=" N1 C 21332 " -0.017 2.00e-02 2.50e+03 pdb=" C2 C 21332 " 0.004 2.00e-02 2.50e+03 pdb=" O2 C 21332 " 0.040 2.00e-02 2.50e+03 pdb=" N3 C 21332 " -0.093 2.00e-02 2.50e+03 pdb=" C4 C 21332 " 0.001 2.00e-02 2.50e+03 pdb=" N4 C 21332 " 0.056 2.00e-02 2.50e+03 pdb=" C5 C 21332 " -0.003 2.00e-02 2.50e+03 pdb=" C6 C 21332 " -0.006 2.00e-02 2.50e+03 ... (remaining 12084 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.03: 44 2.03 - 2.74: 7564 2.74 - 3.46: 137702 3.46 - 4.18: 279251 4.18 - 4.90: 406789 Nonbonded interactions: 831350 Sorted by model distance: nonbonded pdb="MG MG 21876 " pdb="MG MG 21879 " model vdw 1.307 1.300 nonbonded pdb=" OP1 A 21761 " pdb="MG MG 21812 " model vdw 1.735 2.170 nonbonded pdb=" OP2 C 2 360 " pdb="MG MG 21828 " model vdw 1.755 2.170 nonbonded pdb=" OP1 G 21426 " pdb="MG MG 21876 " model vdw 1.818 2.170 nonbonded pdb=" OP2 G 21426 " pdb="MG MG 21876 " model vdw 1.827 2.170 ... (remaining 831345 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 9.920 Check model and map are aligned: 1.060 Set scattering table: 0.670 Process input model: 257.120 Find NCS groups from input model: 2.210 Set up NCS constraints: 0.250 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: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 275.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 103913 Z= 0.472 Angle : 1.392 15.700 149340 Z= 0.936 Chirality : 0.107 0.808 18409 Planarity : 0.006 0.123 12087 Dihedral : 22.424 179.918 44980 Min Nonbonded Distance : 1.307 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 3.36 % Allowed : 10.88 % Favored : 85.76 % Rotamer: Outliers : 13.17 % Allowed : 17.44 % Favored : 69.39 % Cbeta Deviations : 1.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.03 % 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: -1.68 (0.09), residues: 7149 helix: 1.34 (0.08), residues: 2541 sheet: -1.57 (0.15), residues: 1085 loop : -2.99 (0.09), residues: 3523 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14298 Ramachandran restraints generated. 7149 Oldfield, 0 Emsley, 7149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14298 Ramachandran restraints generated. 7149 Oldfield, 0 Emsley, 7149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2889 residues out of total 6271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 822 poor density : 2067 time to evaluate : 5.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 822 outliers final: 137 residues processed: 2559 average time/residue: 1.0223 time to fit residues: 4412.1092 Evaluate side-chains 1338 residues out of total 6271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1201 time to evaluate : 5.850 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 137 outliers final: 1 residues processed: 137 average time/residue: 0.9888 time to fit residues: 238.8997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 911 random chunks: chunk 769 optimal weight: 3.9990 chunk 690 optimal weight: 3.9990 chunk 383 optimal weight: 10.0000 chunk 235 optimal weight: 5.9990 chunk 465 optimal weight: 5.9990 chunk 368 optimal weight: 0.8980 chunk 714 optimal weight: 0.5980 chunk 276 optimal weight: 9.9990 chunk 434 optimal weight: 1.9990 chunk 531 optimal weight: 20.0000 chunk 827 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 ASN B 101 HIS B 178 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN E 258 GLN F 39 GLN F 81 ASN ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 GLN G 13 GLN G 210 GLN H 5 GLN H 155 ASN H 170 GLN ** J 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 GLN L 8 GLN L 22 ASN L 104 HIS L 127 GLN M 51 GLN N 123 HIS O 29 HIS O 99 GLN Q 83 GLN R 74 GLN S 44 ASN ** S 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 43 ASN T 64 HIS ** T 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 35 ASN W 80 ASN X 10 ASN X 65 ASN ** X 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 43 ASN b 49 HIS c 27 GLN d 5 ASN e 29 GLN f 133 HIS ** g 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 70 GLN ** g 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 226 GLN g 240 ASN i 44 ASN i 85 GLN ** j 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 109 HIS k 98 GLN k 102 ASN k 151 GLN k 221 ASN k 228 GLN k 422 HIS k 433 ASN k 508 HIS l 190 HIS l 243 ASN m 43 GLN m 67 ASN m 79 GLN m 81 GLN m 84 GLN o 32 HIS o 73 HIS o 108 GLN ** o 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 188 HIS o 209 HIS ** o 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 254 HIS o 265 HIS ** o 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 251 GLN p 313 GLN p 340 GLN p 495 ASN p 549 GLN p 564 HIS p 586 HIS p 613 ASN ** p 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 9 HIS ** q 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 705 HIS r 706 GLN r 722 GLN Total number of N/Q/H flips: 78 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.234 103913 Z= 0.235 Angle : 0.836 12.694 149340 Z= 0.433 Chirality : 0.048 0.392 18409 Planarity : 0.006 0.148 12087 Dihedral : 20.082 178.755 30540 Min Nonbonded Distance : 1.064 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 1.29 % Allowed : 8.95 % Favored : 89.76 % Rotamer: Outliers : 0.53 % Allowed : 6.28 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.75 % 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: -0.89 (0.10), residues: 7149 helix: 2.35 (0.10), residues: 2536 sheet: -1.38 (0.14), residues: 1186 loop : -2.76 (0.09), residues: 3427 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14298 Ramachandran restraints generated. 7149 Oldfield, 0 Emsley, 7149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14298 Ramachandran restraints generated. 7149 Oldfield, 0 Emsley, 7149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1668 residues out of total 6271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 1635 time to evaluate : 5.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 12 residues processed: 1652 average time/residue: 0.9619 time to fit residues: 2682.0536 Evaluate side-chains 1111 residues out of total 6271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1099 time to evaluate : 5.856 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.7324 time to fit residues: 23.9121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 911 random chunks: chunk 459 optimal weight: 7.9990 chunk 256 optimal weight: 9.9990 chunk 688 optimal weight: 8.9990 chunk 563 optimal weight: 0.1980 chunk 228 optimal weight: 3.9990 chunk 828 optimal weight: 6.9990 chunk 895 optimal weight: 0.0040 chunk 738 optimal weight: 6.9990 chunk 821 optimal weight: 20.0000 chunk 282 optimal weight: 30.0000 chunk 664 optimal weight: 5.9990 overall best weight: 3.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS B 74 GLN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 HIS E 142 HIS E 201 HIS F 102 ASN ** F 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 ASN J 74 ASN J 112 GLN L 127 GLN ** M 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 42 GLN T 43 ASN T 48 GLN T 93 HIS ** T 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 44 ASN ** U 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 33 GLN V 35 ASN V 74 GLN W 16 ASN ** W 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 48 HIS ** X 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 89 ASN ** X 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 72 HIS d 10 HIS f 93 HIS ** i 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 68 ASN ** k 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 102 ASN m 65 ASN ** o 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 194 GLN ** o 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 9 HIS ** q 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 269 ASN q 304 GLN q 320 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 103913 Z= 0.218 Angle : 0.741 13.144 149340 Z= 0.382 Chirality : 0.044 0.362 18409 Planarity : 0.006 0.149 12087 Dihedral : 19.733 179.622 30540 Min Nonbonded Distance : 0.984 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 1.11 % Allowed : 9.79 % Favored : 89.10 % Rotamer: Outliers : 0.21 % Allowed : 5.13 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.75 % 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: -1.01 (0.10), residues: 7149 helix: 1.88 (0.10), residues: 2513 sheet: -1.21 (0.14), residues: 1189 loop : -2.57 (0.10), residues: 3447 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14298 Ramachandran restraints generated. 7149 Oldfield, 0 Emsley, 7149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14298 Ramachandran restraints generated. 7149 Oldfield, 0 Emsley, 7149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1536 residues out of total 6271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1523 time to evaluate : 5.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 1530 average time/residue: 0.9384 time to fit residues: 2453.3317 Evaluate side-chains 1075 residues out of total 6271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1070 time to evaluate : 5.892 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.7527 time to fit residues: 14.6099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 911 random chunks: chunk 818 optimal weight: 30.0000 chunk 623 optimal weight: 9.9990 chunk 430 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 395 optimal weight: 7.9990 chunk 556 optimal weight: 6.9990 chunk 831 optimal weight: 30.0000 chunk 880 optimal weight: 1.9990 chunk 434 optimal weight: 0.0970 chunk 788 optimal weight: 0.1980 chunk 237 optimal weight: 3.9990 overall best weight: 2.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 ASN F 172 GLN H 30 ASN ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 112 GLN L 81 HIS L 127 GLN ** N 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 HIS ** O 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 74 HIS ** Q 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 20 HIS ** U 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 33 GLN V 35 ASN V 74 GLN W 16 ASN ** X 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 11 ASN f 93 HIS ** i 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 85 GLN j 68 ASN ** k 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 102 ASN k 508 HIS ** o 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 402 GLN ** o 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 506 ASN p 533 ASN p 595 ASN p 683 GLN ** q 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 103913 Z= 0.192 Angle : 0.702 13.194 149340 Z= 0.359 Chirality : 0.042 0.357 18409 Planarity : 0.005 0.151 12087 Dihedral : 19.497 179.901 30540 Min Nonbonded Distance : 1.061 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 1.08 % Allowed : 8.53 % Favored : 90.39 % Rotamer: Outliers : 0.11 % Allowed : 3.99 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.75 % 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: -1.04 (0.10), residues: 7149 helix: 1.73 (0.11), residues: 2482 sheet: -1.14 (0.14), residues: 1174 loop : -2.47 (0.10), residues: 3493 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14298 Ramachandran restraints generated. 7149 Oldfield, 0 Emsley, 7149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14298 Ramachandran restraints generated. 7149 Oldfield, 0 Emsley, 7149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1455 residues out of total 6271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1448 time to evaluate : 5.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 0 residues processed: 1451 average time/residue: 0.9242 time to fit residues: 2303.2977 Evaluate side-chains 1048 residues out of total 6271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1048 time to evaluate : 5.875 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.4914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 911 random chunks: chunk 733 optimal weight: 20.0000 chunk 499 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 655 optimal weight: 8.9990 chunk 363 optimal weight: 0.6980 chunk 751 optimal weight: 7.9990 chunk 608 optimal weight: 3.9990 chunk 1 optimal weight: 30.0000 chunk 449 optimal weight: 20.0000 chunk 790 optimal weight: 50.0000 chunk 222 optimal weight: 0.9980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 GLN H 30 ASN ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 ASN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 127 GLN ** N 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 HIS ** O 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 83 GLN R 74 GLN ** S 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 17 ASN ** T 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 33 GLN V 35 ASN V 74 GLN W 12 ASN ** W 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 27 GLN ** e 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 93 HIS g 53 GLN ** i 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 73 GLN j 243 GLN ** k 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 102 ASN l 243 ASN ** m 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 171 ASN ** o 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 223 ASN o 234 GLN ** o 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.5043 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: