Starting phenix.real_space_refine (version: 1.21rc1) on Mon Aug 21 18:51:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cam_16530/08_2023/8cam_16530_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cam_16530/08_2023/8cam_16530.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cam_16530/08_2023/8cam_16530_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cam_16530/08_2023/8cam_16530_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cam_16530/08_2023/8cam_16530_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cam_16530/08_2023/8cam_16530.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cam_16530/08_2023/8cam_16530.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cam_16530/08_2023/8cam_16530_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cam_16530/08_2023/8cam_16530_updated.pdb" } resolution = 1.86 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= 0.006 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: 9 Type Number sf(0) Gaussians K 72 8.98 5 Zn 1 6.06 5 P 2724 5.49 5 Mg 246 5.21 5 S 66 5.16 5 Cl 2 4.86 5 C 39719 2.51 5 N 14980 2.21 5 O 28838 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 44": "NH1" <-> "NH2" Residue "1 ARG 3": "NH1" <-> "NH2" Residue "1 ARG 12": "NH1" <-> "NH2" Residue "1 ARG 14": "NH1" <-> "NH2" Residue "1 ARG 21": "NH1" <-> "NH2" Residue "1 ARG 33": "NH1" <-> "NH2" Residue "1 ARG 41": "NH1" <-> "NH2" Residue "2 ARG 13": "NH1" <-> "NH2" Residue "2 ARG 30": "NH1" <-> "NH2" Residue "2 ARG 40": "NH1" <-> "NH2" Residue "3 ARG 24": "NH1" <-> "NH2" Residue "c GLU 23": "OE1" <-> "OE2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c ARG 63": "NH1" <-> "NH2" Residue "c ARG 80": "NH1" <-> "NH2" Residue "c TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 133": "NH1" <-> "NH2" Residue "c TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 167": "NH1" <-> "NH2" Residue "c ARG 177": "NH1" <-> "NH2" Residue "c ARG 182": "NH1" <-> "NH2" Residue "c ARG 189": "NH1" <-> "NH2" Residue "c ARG 203": "NH1" <-> "NH2" Residue "c ARG 212": "NH1" <-> "NH2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "d ASP 43": "OD1" <-> "OD2" Residue "d ARG 59": "NH1" <-> "NH2" Residue "d GLU 64": "OE1" <-> "OE2" Residue "d GLU 81": "OE1" <-> "OE2" Residue "d GLU 99": "OE1" <-> "OE2" Residue "d ARG 169": "NH1" <-> "NH2" Residue "e ARG 44": "NH1" <-> "NH2" Residue "e ARG 49": "NH1" <-> "NH2" Residue "e ARG 61": "NH1" <-> "NH2" Residue "e ARG 88": "NH1" <-> "NH2" Residue "e ARG 102": "NH1" <-> "NH2" Residue "e GLU 111": "OE1" <-> "OE2" Residue "e GLU 122": "OE1" <-> "OE2" Residue "e GLU 127": "OE1" <-> "OE2" Residue "e ASP 145": "OD1" <-> "OD2" Residue "e ARG 162": "NH1" <-> "NH2" Residue "e ARG 170": "NH1" <-> "NH2" Residue "g ARG 3": "NH1" <-> "NH2" Residue "g GLU 42": "OE1" <-> "OE2" Residue "g PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 81": "OE1" <-> "OE2" Residue "g ARG 95": "NH1" <-> "NH2" Residue "g ARG 153": "NH1" <-> "NH2" Residue "g GLU 155": "OE1" <-> "OE2" Residue "g ARG 163": "NH1" <-> "NH2" Residue "g GLU 167": "OE1" <-> "OE2" Residue "g ARG 170": "NH1" <-> "NH2" Residue "h ARG 27": "NH1" <-> "NH2" Residue "i ARG 13": "NH1" <-> "NH2" Residue "i ARG 37": "NH1" <-> "NH2" Residue "i GLU 43": "OE1" <-> "OE2" Residue "i TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 95": "NH1" <-> "NH2" Residue "i ARG 96": "NH1" <-> "NH2" Residue "k ARG 21": "NH1" <-> "NH2" Residue "k ARG 33": "NH1" <-> "NH2" Residue "k ARG 41": "NH1" <-> "NH2" Residue "k ARG 47": "NH1" <-> "NH2" Residue "k ARG 60": "NH1" <-> "NH2" Residue "k PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 78": "NH1" <-> "NH2" Residue "k ARG 126": "NH1" <-> "NH2" Residue "k GLU 143": "OE1" <-> "OE2" Residue "l ARG 6": "NH1" <-> "NH2" Residue "l ARG 10": "NH1" <-> "NH2" Residue "l ARG 18": "NH1" <-> "NH2" Residue "l ARG 40": "NH1" <-> "NH2" Residue "l ARG 44": "NH1" <-> "NH2" Residue "l ARG 50": "NH1" <-> "NH2" Residue "l ARG 55": "NH1" <-> "NH2" Residue "l GLU 90": "OE1" <-> "OE2" Residue "m ARG 12": "NH1" <-> "NH2" Residue "m ARG 17": "NH1" <-> "NH2" Residue "m ARG 22": "NH1" <-> "NH2" Residue "m ARG 46": "NH1" <-> "NH2" Residue "m ARG 63": "NH1" <-> "NH2" Residue "m ARG 64": "NH1" <-> "NH2" Residue "m ARG 69": "NH1" <-> "NH2" Residue "m ARG 71": "NH1" <-> "NH2" Residue "m GLU 82": "OE1" <-> "OE2" Residue "m ARG 96": "NH1" <-> "NH2" Residue "m ARG 118": "NH1" <-> "NH2" Residue "o PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 21": "NH1" <-> "NH2" Residue "o GLU 27": "OE1" <-> "OE2" Residue "o ARG 39": "NH1" <-> "NH2" Residue "o ARG 89": "NH1" <-> "NH2" Residue "o ARG 101": "NH1" <-> "NH2" Residue "o ARG 109": "NH1" <-> "NH2" Residue "p ARG 3": "NH1" <-> "NH2" Residue "p ARG 6": "NH1" <-> "NH2" Residue "p ARG 11": "NH1" <-> "NH2" Residue "p ARG 13": "NH1" <-> "NH2" Residue "p ARG 33": "NH1" <-> "NH2" Residue "p ARG 48": "NH1" <-> "NH2" Residue "p TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 111": "OE1" <-> "OE2" Residue "q GLU 16": "OE1" <-> "OE2" Residue "q ARG 21": "NH1" <-> "NH2" Residue "q GLU 34": "OE1" <-> "OE2" Residue "q ARG 68": "NH1" <-> "NH2" Residue "q GLU 70": "OE1" <-> "OE2" Residue "q PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 79": "NH1" <-> "NH2" Residue "q ARG 84": "NH1" <-> "NH2" Residue "r GLU 59": "OE1" <-> "OE2" Residue "r ARG 84": "NH1" <-> "NH2" Residue "r ARG 88": "NH1" <-> "NH2" Residue "r ARG 95": "NH1" <-> "NH2" Residue "s GLU 52": "OE1" <-> "OE2" Residue "s ARG 73": "NH1" <-> "NH2" Residue "t ARG 6": "NH1" <-> "NH2" Residue "t ARG 7": "NH1" <-> "NH2" Residue "t ARG 82": "NH1" <-> "NH2" Residue "t ARG 86": "NH1" <-> "NH2" Residue "t ARG 94": "NH1" <-> "NH2" Residue "u GLU 41": "OE1" <-> "OE2" Residue "u TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 70": "OE1" <-> "OE2" Residue "v GLU 83": "OE1" <-> "OE2" Residue "w ARG 3": "NH1" <-> "NH2" Residue "w ARG 11": "NH1" <-> "NH2" Residue "w ARG 37": "NH1" <-> "NH2" Residue "w GLU 43": "OE1" <-> "OE2" Residue "w ARG 50": "NH1" <-> "NH2" Residue "w ARG 57": "NH1" <-> "NH2" Residue "w ARG 74": "NH1" <-> "NH2" Residue "x GLU 5": "OE1" <-> "OE2" Residue "x GLU 17": "OE1" <-> "OE2" Residue "x ARG 29": "NH1" <-> "NH2" Residue "x ARG 47": "NH1" <-> "NH2" Residue "y ARG 11": "NH1" <-> "NH2" Residue "y ARG 30": "NH1" <-> "NH2" Residue "y GLU 37": "OE1" <-> "OE2" Residue "y GLU 39": "OE1" <-> "OE2" Residue "y ARG 45": "NH1" <-> "NH2" Residue "z ARG 10": "NH1" <-> "NH2" Residue "z ARG 16": "NH1" <-> "NH2" Residue "z GLU 36": "OE1" <-> "OE2" Residue "z ARG 52": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 86648 Number of models: 1 Model: "" Number of chains: 65 Chain: "0" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 413 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "1" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 367 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "2" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "3" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "a" Number of atoms: 57788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2690, 57788 Classifications: {'RNA': 2690} Modifications used: {'rna2p': 7, 'rna2p_pur': 263, 'rna2p_pyr': 140, 'rna3p': 14, 'rna3p_pur': 1290, 'rna3p_pyr': 976} Link IDs: {'rna2p': 410, 'rna3p': 2279} Chain breaks: 7 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 14 Chain: "b" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 734 Classifications: {'RNA': 34} Modifications used: {'rna2p_pyr': 3, 'rna3p_pur': 20, 'rna3p_pyr': 11} Link IDs: {'rna2p': 3, 'rna3p': 30} Chain: "c" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "d" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1552 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 200} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEQ:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 1524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1524 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 191} Chain breaks: 1 Chain: "g" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1304 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 8, 'TRANS': 165} Chain: "h" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 257 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 2, 'TRANS': 31} Chain breaks: 1 Chain: "i" Number of atoms: 1121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1121 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 134} Chain: "j" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "k" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "l" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1075 Unusual residues: {'MS6': 1} Classifications: {'peptide': 135, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126, None: 2} Not linked: pdbres="4D4 l 81 " pdbres="MS6 l 82 " Not linked: pdbres="MS6 l 82 " pdbres="GLY l 83 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4D4:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 945 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "o" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "p" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "q" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 803 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 99} Chain breaks: 1 Chain: "r" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 845 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 2, 'TRANS': 106} Chain: "s" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "t" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 724 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 1 Chain: "u" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 607 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 4, 'TRANS': 70} Chain breaks: 5 Chain: "v" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 559 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "w" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "x" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 491 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "y" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "z" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 429 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 420 Unusual residues: {' K': 68, ' MG': 237, '6O1': 1, 'ACT': 1} Classifications: {'undetermined': 307} Link IDs: {None: 306} Chain: "b" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "c" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' K': 2, ' MG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "1" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "2" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "3" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "a" Number of atoms: 5251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5251, 5251 Classifications: {'water': 5251} Link IDs: {None: 5250} Chain: "b" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Chain: "c" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 115 Classifications: {'water': 115} Link IDs: {None: 114} Chain: "d" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 74 Classifications: {'water': 74} Link IDs: {None: 73} Chain: "e" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "h" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "i" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "j" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "k" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "l" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "m" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "o" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "p" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "q" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "r" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "s" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "t" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "u" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "v" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "w" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "x" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "y" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "z" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1369 SG CYS 3 11 130.281 25.173 137.960 1.00 47.12 S ATOM 1394 SG CYS 3 14 129.864 29.255 138.464 1.00 46.76 S ATOM 1497 SG CYS 3 27 133.131 27.354 137.774 1.00 50.34 S Time building chain proxies: 33.24, per 1000 atoms: 0.38 Number of scatterers: 86648 At special positions: 0 Unit cell: (202.692, 200.406, 204.216, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 1 29.99 K 72 19.00 Cl 2 17.00 S 66 16.00 P 2724 15.00 Mg 246 11.99 O 28838 8.00 N 14980 7.00 C 39719 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 41.37 Conformation dependent library (CDL) restraints added in 2.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 3 101 " pdb="ZN ZN 3 101 " - pdb=" ND1 HIS 3 33 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 14 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 11 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 27 " Number of angles added : 3 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5038 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 79 helices and 47 sheets defined 25.3% alpha, 20.1% beta 937 base pairs and 1405 stacking pairs defined. Time for finding SS restraints: 41.61 Creating SS restraints... Processing helix chain '1' and resid 9 through 16 Processing helix chain '1' and resid 18 through 23 Processing helix chain '1' and resid 25 through 37 Processing helix chain '2' and resid 8 through 11 No H-bonds generated for 'chain '2' and resid 8 through 11' Processing helix chain '2' and resid 38 through 43 Processing helix chain '2' and resid 52 through 61 removed outlier: 4.484A pdb=" N GLY 2 56 " --> pdb=" O LYS 2 52 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N LEU 2 57 " --> pdb=" O GLY 2 53 " (cutoff:3.500A) Processing helix chain '3' and resid 31 through 33 No H-bonds generated for 'chain '3' and resid 31 through 33' Processing helix chain 'c' and resid 31 through 33 No H-bonds generated for 'chain 'c' and resid 31 through 33' Processing helix chain 'c' and resid 198 through 202 removed outlier: 3.897A pdb=" N MET c 201 " --> pdb=" O ALA c 198 " (cutoff:3.500A) Processing helix chain 'c' and resid 208 through 214 removed outlier: 3.619A pdb=" N ARG c 214 " --> pdb=" O ALA c 210 " (cutoff:3.500A) Processing helix chain 'c' and resid 222 through 224 No H-bonds generated for 'chain 'c' and resid 222 through 224' Processing helix chain 'c' and resid 264 through 266 No H-bonds generated for 'chain 'c' and resid 264 through 266' Processing helix chain 'd' and resid 62 through 71 removed outlier: 3.507A pdb=" N HIS d 67 " --> pdb=" O PRO d 63 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA d 71 " --> pdb=" O HIS d 67 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 101 Processing helix chain 'd' and resid 121 through 125 Processing helix chain 'e' and resid 16 through 19 No H-bonds generated for 'chain 'e' and resid 16 through 19' Processing helix chain 'e' and resid 25 through 38 Processing helix chain 'e' and resid 98 through 114 Processing helix chain 'e' and resid 131 through 141 Processing helix chain 'e' and resid 155 through 162 Processing helix chain 'e' and resid 172 through 174 No H-bonds generated for 'chain 'e' and resid 172 through 174' Processing helix chain 'e' and resid 177 through 182 Processing helix chain 'e' and resid 190 through 200 Processing helix chain 'g' and resid 3 through 6 No H-bonds generated for 'chain 'g' and resid 3 through 6' Processing helix chain 'g' and resid 60 through 76 removed outlier: 3.735A pdb=" N THR g 67 " --> pdb=" O GLN g 64 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG g 69 " --> pdb=" O GLY g 66 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN g 73 " --> pdb=" O ALA g 70 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER g 74 " --> pdb=" O LEU g 71 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL g 76 " --> pdb=" O ASN g 73 " (cutoff:3.500A) Processing helix chain 'g' and resid 138 through 151 removed outlier: 3.584A pdb=" N TYR g 151 " --> pdb=" O ASP g 147 " (cutoff:3.500A) Processing helix chain 'h' and resid 23 through 28 Processing helix chain 'h' and resid 30 through 33 No H-bonds generated for 'chain 'h' and resid 30 through 33' Processing helix chain 'i' and resid 25 through 37 removed outlier: 3.810A pdb=" N GLU i 31 " --> pdb=" O ARG i 27 " (cutoff:3.500A) Processing helix chain 'i' and resid 59 through 61 No H-bonds generated for 'chain 'i' and resid 59 through 61' Processing helix chain 'i' and resid 68 through 71 No H-bonds generated for 'chain 'i' and resid 68 through 71' Processing helix chain 'i' and resid 89 through 95 Processing helix chain 'i' and resid 97 through 108 removed outlier: 4.298A pdb=" N ILE i 101 " --> pdb=" O PRO i 97 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET i 108 " --> pdb=" O ALA i 104 " (cutoff:3.500A) Processing helix chain 'i' and resid 113 through 121 removed outlier: 3.980A pdb=" N LYS i 121 " --> pdb=" O ALA i 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 133 through 135 No H-bonds generated for 'chain 'i' and resid 133 through 135' Processing helix chain 'j' and resid 105 through 107 No H-bonds generated for 'chain 'j' and resid 105 through 107' Processing helix chain 'j' and resid 113 through 118 Processing helix chain 'k' and resid 38 through 40 No H-bonds generated for 'chain 'k' and resid 38 through 40' Processing helix chain 'k' and resid 57 through 60 No H-bonds generated for 'chain 'k' and resid 57 through 60' Processing helix chain 'k' and resid 69 through 72 No H-bonds generated for 'chain 'k' and resid 69 through 72' Processing helix chain 'k' and resid 79 through 81 No H-bonds generated for 'chain 'k' and resid 79 through 81' Processing helix chain 'k' and resid 92 through 97 Processing helix chain 'k' and resid 129 through 137 removed outlier: 3.515A pdb=" N ALA k 134 " --> pdb=" O GLY k 130 " (cutoff:3.500A) Processing helix chain 'l' and resid 43 through 57 Processing helix chain 'l' and resid 110 through 123 removed outlier: 3.881A pdb=" N LYS l 123 " --> pdb=" O LEU l 119 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 31 Processing helix chain 'm' and resid 38 through 56 removed outlier: 4.254A pdb=" N ARG m 46 " --> pdb=" O LYS m 42 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL m 47 " --> pdb=" O GLU m 43 " (cutoff:3.500A) Proline residue: m 50 - end of helix Processing helix chain 'm' and resid 60 through 70 Processing helix chain 'm' and resid 73 through 81 Processing helix chain 'm' and resid 83 through 86 No H-bonds generated for 'chain 'm' and resid 83 through 86' Processing helix chain 'o' and resid 3 through 12 removed outlier: 3.556A pdb=" N GLU o 11 " --> pdb=" O GLN o 7 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLN o 12 " --> pdb=" O LEU o 8 " (cutoff:3.500A) Processing helix chain 'o' and resid 54 through 56 No H-bonds generated for 'chain 'o' and resid 54 through 56' Processing helix chain 'o' and resid 98 through 102 Processing helix chain 'p' and resid 7 through 20 Processing helix chain 'p' and resid 26 through 29 Processing helix chain 'p' and resid 32 through 72 removed outlier: 3.547A pdb=" N GLN p 37 " --> pdb=" O ARG p 33 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG p 51 " --> pdb=" O TYR p 47 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS p 54 " --> pdb=" O ARG p 50 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG p 55 " --> pdb=" O ARG p 51 " (cutoff:3.500A) Processing helix chain 'p' and resid 76 through 85 Processing helix chain 'p' and resid 92 through 101 Processing helix chain 'p' and resid 103 through 117 Processing helix chain 'r' and resid 14 through 24 removed outlier: 4.089A pdb=" N VAL r 20 " --> pdb=" O LYS r 16 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU r 23 " --> pdb=" O LEU r 19 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE r 24 " --> pdb=" O VAL r 20 " (cutoff:3.500A) Processing helix chain 'r' and resid 29 through 37 Processing helix chain 'r' and resid 42 through 62 Processing helix chain 'r' and resid 66 through 68 No H-bonds generated for 'chain 'r' and resid 66 through 68' Processing helix chain 'r' and resid 89 through 91 No H-bonds generated for 'chain 'r' and resid 89 through 91' Processing helix chain 's' and resid 4 through 10 removed outlier: 3.802A pdb=" N LYS s 9 " --> pdb=" O GLU s 5 " (cutoff:3.500A) Processing helix chain 's' and resid 18 through 27 Processing helix chain 's' and resid 40 through 50 Processing helix chain 't' and resid 67 through 69 No H-bonds generated for 'chain 't' and resid 67 through 69' Processing helix chain 'u' and resid 14 through 23 Processing helix chain 'u' and resid 44 through 52 removed outlier: 3.919A pdb=" N ALA u 52 " --> pdb=" O MET u 48 " (cutoff:3.500A) Processing helix chain 'w' and resid 53 through 62 Processing helix chain 'w' and resid 64 through 74 Processing helix chain 'x' and resid 3 through 8 removed outlier: 4.386A pdb=" N GLU x 8 " --> pdb=" O LYS x 4 " (cutoff:3.500A) Processing helix chain 'x' and resid 11 through 34 Processing helix chain 'x' and resid 40 through 60 removed outlier: 3.529A pdb=" N LYS x 44 " --> pdb=" O HIS x 41 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL x 46 " --> pdb=" O LEU x 43 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR x 55 " --> pdb=" O ARG x 52 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU x 57 " --> pdb=" O LYS x 54 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS x 60 " --> pdb=" O LEU x 57 " (cutoff:3.500A) Processing helix chain 'y' and resid 18 through 27 Processing helix chain 'y' and resid 42 through 50 Processing helix chain 'y' and resid 52 through 54 No H-bonds generated for 'chain 'y' and resid 52 through 54' Processing helix chain 'z' and resid 10 through 19 removed outlier: 4.760A pdb=" N HIS z 19 " --> pdb=" O MET z 15 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain '0' and resid 20 through 25 Processing sheet with id= B, first strand: chain '2' and resid 14 through 16 Processing sheet with id= C, first strand: chain '3' and resid 2 through 4 Processing sheet with id= D, first strand: chain '3' and resid 14 through 19 Processing sheet with id= E, first strand: chain 'c' and resid 3 through 5 Processing sheet with id= F, first strand: chain 'c' and resid 34 through 36 Processing sheet with id= G, first strand: chain 'c' and resid 101 through 105 removed outlier: 6.280A pdb=" N LEU c 95 " --> pdb=" O VAL c 78 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL c 78 " --> pdb=" O LEU c 95 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'c' and resid 129 through 131 Processing sheet with id= I, first strand: chain 'c' and resid 181 through 185 removed outlier: 6.686A pdb=" N ARG c 175 " --> pdb=" O ILE c 164 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ILE c 164 " --> pdb=" O ARG c 175 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'd' and resid 169 through 172 removed outlier: 4.539A pdb=" N THR d 112 " --> pdb=" O ASP d 200 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ASP d 200 " --> pdb=" O THR d 112 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL d 26 " --> pdb=" O VAL d 9 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N MET d 11 " --> pdb=" O VAL d 24 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL d 24 " --> pdb=" O MET d 11 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG d 13 " --> pdb=" O ILE d 22 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE d 22 " --> pdb=" O ARG d 13 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LYS d 190 " --> pdb=" O VAL d 177 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL d 177 " --> pdb=" O LYS d 190 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'd' and resid 80 through 83 removed outlier: 6.350A pdb=" N THR d 51 " --> pdb=" O VAL d 34 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N VAL d 34 " --> pdb=" O THR d 51 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'd' and resid 115 through 119 removed outlier: 5.631A pdb=" N MET d 165 " --> pdb=" O LYS d 116 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N PHE d 118 " --> pdb=" O GLY d 163 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N GLY d 163 " --> pdb=" O PHE d 118 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'e' and resid 118 through 121 removed outlier: 6.197A pdb=" N VAL e 186 " --> pdb=" O ILE e 119 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL e 121 " --> pdb=" O VAL e 186 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N MET e 188 " --> pdb=" O VAL e 121 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'g' and resid 16 through 20 removed outlier: 3.892A pdb=" N VAL g 23 " --> pdb=" O ASN g 20 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'g' and resid 41 through 45 removed outlier: 3.508A pdb=" N GLU g 42 " --> pdb=" O GLY g 53 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY g 53 " --> pdb=" O GLU g 42 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'g' and resid 161 through 164 Processing sheet with id= Q, first strand: chain 'g' and resid 95 through 99 removed outlier: 3.688A pdb=" N VAL g 102 " --> pdb=" O LYS g 99 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'h' and resid 3 through 5 Processing sheet with id= S, first strand: chain 'i' and resid 15 through 19 removed outlier: 6.471A pdb=" N TYR i 53 " --> pdb=" O TYR i 16 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N VAL i 18 " --> pdb=" O TYR i 53 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE i 55 " --> pdb=" O VAL i 18 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'i' and resid 73 through 77 Processing sheet with id= U, first strand: chain 'j' and resid 7 through 9 removed outlier: 6.439A pdb=" N LYS j 40 " --> pdb=" O ILE j 22 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL j 24 " --> pdb=" O ILE j 38 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N ILE j 38 " --> pdb=" O VAL j 24 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA j 83 " --> pdb=" O VAL j 63 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'k' and resid 74 through 78 removed outlier: 6.833A pdb=" N PHE k 107 " --> pdb=" O ALA k 75 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ILE k 77 " --> pdb=" O PHE k 107 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LYS k 109 " --> pdb=" O ILE k 77 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'k' and resid 121 through 123 removed outlier: 6.573A pdb=" N LYS k 141 " --> pdb=" O VAL k 122 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'l' and resid 128 through 132 removed outlier: 6.555A pdb=" N ALA l 35 " --> pdb=" O VAL l 101 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL l 101 " --> pdb=" O ALA l 35 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'l' and resid 39 through 42 removed outlier: 7.001A pdb=" N ILE l 73 " --> pdb=" O GLU l 90 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TRP l 92 " --> pdb=" O LYS l 71 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LYS l 71 " --> pdb=" O TRP l 92 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'm' and resid 33 through 37 Processing sheet with id= AA, first strand: chain 'o' and resid 83 through 88 removed outlier: 6.592A pdb=" N THR o 25 " --> pdb=" O LYS o 87 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N GLU o 44 " --> pdb=" O ILE o 64 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ILE o 64 " --> pdb=" O GLU o 44 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N THR o 60 " --> pdb=" O ILE o 48 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ILE o 50 " --> pdb=" O ALA o 58 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA o 58 " --> pdb=" O ILE o 50 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'q' and resid 10 through 14 removed outlier: 3.617A pdb=" N MET q 40 " --> pdb=" O VAL q 4 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N GLN q 6 " --> pdb=" O VAL q 38 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N VAL q 38 " --> pdb=" O GLN q 6 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'q' and resid 19 through 23 Processing sheet with id= AD, first strand: chain 'q' and resid 32 through 35 removed outlier: 6.454A pdb=" N GLU q 62 " --> pdb=" O ILE q 98 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ILE q 98 " --> pdb=" O GLU q 62 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'q' and resid 72 through 78 removed outlier: 4.152A pdb=" N TYR q 83 " --> pdb=" O ARG q 78 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'r' and resid 2 through 7 removed outlier: 6.781A pdb=" N SER r 108 " --> pdb=" O VAL r 71 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N VAL r 71 " --> pdb=" O SER r 108 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'r' and resid 82 through 87 Processing sheet with id= AH, first strand: chain 's' and resid 11 through 14 removed outlier: 6.599A pdb=" N LYS s 33 " --> pdb=" O ARG s 12 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N VAL s 31 " --> pdb=" O PRO s 14 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS s 81 " --> pdb=" O VAL s 34 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL s 57 " --> pdb=" O THR s 86 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 's' and resid 67 through 69 Processing sheet with id= AJ, first strand: chain 't' and resid 22 through 24 Processing sheet with id= AK, first strand: chain 't' and resid 41 through 45 Processing sheet with id= AL, first strand: chain 't' and resid 83 through 88 Processing sheet with id= AM, first strand: chain 't' and resid 25 through 29 removed outlier: 6.723A pdb=" N ILE t 35 " --> pdb=" O LYS t 26 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N VAL t 28 " --> pdb=" O LYS t 33 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LYS t 33 " --> pdb=" O VAL t 28 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'u' and resid 3 through 5 removed outlier: 6.606A pdb=" N THR u 62 " --> pdb=" O ILE u 4 " (cutoff:3.500A) No H-bonds generated for sheet with id= AN Processing sheet with id= AO, first strand: chain 'u' and resid 25 through 30 Processing sheet with id= AP, first strand: chain 'u' and resid 76 through 79 removed outlier: 3.604A pdb=" N ASP u 76 " --> pdb=" O ASP u 90 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'v' and resid 45 through 47 removed outlier: 6.568A pdb=" N LYS v 78 " --> pdb=" O HIS v 46 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'v' and resid 51 through 53 Processing sheet with id= AS, first strand: chain 'w' and resid 13 through 18 Processing sheet with id= AT, first strand: chain 'w' and resid 33 through 40 Processing sheet with id= AU, first strand: chain 'y' and resid 35 through 39 677 hydrogen bonds defined for protein. 1851 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2349 hydrogen bonds 3628 hydrogen bond angles 0 basepair planarities 937 basepair parallelities 1405 stacking parallelities Total time for adding SS restraints: 429.45 Time building geometry restraints manager: 44.02 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: 9390 1.33 - 1.45: 40984 1.45 - 1.58: 31595 1.58 - 1.70: 5440 1.70 - 1.83: 120 Bond restraints: 87529 Sorted by residual: bond pdb=" C49 6O1 a3307 " pdb=" O47 6O1 a3307 " ideal model delta sigma weight residual 1.832 1.414 0.418 2.00e-02 2.50e+03 4.37e+02 bond pdb=" C49 6O1 a3307 " pdb=" O46 6O1 a3307 " ideal model delta sigma weight residual 1.013 1.416 -0.403 2.00e-02 2.50e+03 4.06e+02 bond pdb=" C49 6O1 a3307 " pdb=" C50 6O1 a3307 " ideal model delta sigma weight residual 1.176 1.534 -0.358 2.00e-02 2.50e+03 3.20e+02 bond pdb=" C4 5MU a 747 " pdb=" C5 5MU a 747 " ideal model delta sigma weight residual 1.802 1.449 0.353 2.00e-02 2.50e+03 3.11e+02 bond pdb=" C4 5MU a1939 " pdb=" C5 5MU a1939 " ideal model delta sigma weight residual 1.802 1.451 0.351 2.00e-02 2.50e+03 3.08e+02 ... (remaining 87524 not shown) Histogram of bond angle deviations from ideal: 90.77 - 99.55: 1051 99.55 - 108.33: 23763 108.33 - 117.11: 54597 117.11 - 125.88: 42449 125.88 - 134.66: 9830 Bond angle restraints: 131690 Sorted by residual: angle pdb=" C1' 6MZ a1618 " pdb=" N9 6MZ a1618 " pdb=" C8 6MZ a1618 " ideal model delta sigma weight residual 91.39 128.28 -36.89 3.00e+00 1.11e-01 1.51e+02 angle pdb=" C1' 6MZ a2030 " pdb=" N9 6MZ a2030 " pdb=" C8 6MZ a2030 " ideal model delta sigma weight residual 91.39 128.09 -36.70 3.00e+00 1.11e-01 1.50e+02 angle pdb=" C1' 6MZ a2030 " pdb=" N9 6MZ a2030 " pdb=" C4 6MZ a2030 " ideal model delta sigma weight residual 154.15 125.10 29.05 3.00e+00 1.11e-01 9.38e+01 angle pdb=" C1' 6MZ a1618 " pdb=" N9 6MZ a1618 " pdb=" C4 6MZ a1618 " ideal model delta sigma weight residual 154.15 125.37 28.78 3.00e+00 1.11e-01 9.21e+01 angle pdb=" C1' 1MG a 745 " pdb=" N9 1MG a 745 " pdb=" C8 1MG a 745 " ideal model delta sigma weight residual 100.16 128.25 -28.09 3.00e+00 1.11e-01 8.77e+01 ... (remaining 131685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.69: 44841 35.69 - 71.38: 1353 71.38 - 107.07: 145 107.07 - 142.76: 6 142.76 - 178.45: 6 Dihedral angle restraints: 46351 sinusoidal: 38534 harmonic: 7817 Sorted by residual: dihedral pdb=" O4' U a 99 " pdb=" C1' U a 99 " pdb=" N1 U a 99 " pdb=" C2 U a 99 " ideal model delta sinusoidal sigma weight residual 200.00 28.27 171.73 1 1.50e+01 4.44e-03 8.49e+01 dihedral pdb=" O4' U a2321 " pdb=" C1' U a2321 " pdb=" N1 U a2321 " pdb=" C2 U a2321 " ideal model delta sinusoidal sigma weight residual 200.00 52.41 147.59 1 1.50e+01 4.44e-03 7.87e+01 dihedral pdb=" O4' U a2192 " pdb=" C1' U a2192 " pdb=" N1 U a2192 " pdb=" C2 U a2192 " ideal model delta sinusoidal sigma weight residual 200.00 57.38 142.62 1 1.50e+01 4.44e-03 7.66e+01 ... (remaining 46348 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.089: 16840 1.089 - 2.178: 1 2.178 - 3.267: 0 3.267 - 4.355: 0 4.355 - 5.444: 1 Chirality restraints: 16842 Sorted by residual: chirality pdb=" C65 6O1 a3307 " pdb=" C64 6O1 a3307 " pdb=" C66 6O1 a3307 " pdb=" C68 6O1 a3307 " both_signs ideal model delta sigma weight residual False 2.65 -2.80 5.44 2.00e-01 2.50e+01 7.41e+02 chirality pdb=" C49 6O1 a3307 " pdb=" C50 6O1 a3307 " pdb=" O46 6O1 a3307 " pdb=" O53 6O1 a3307 " both_signs ideal model delta sigma weight residual False -1.08 -2.34 1.27 2.00e-01 2.50e+01 4.01e+01 chirality pdb=" C24 6O1 a3307 " pdb=" C23 6O1 a3307 " pdb=" C25 6O1 a3307 " pdb=" O24 6O1 a3307 " both_signs ideal model delta sigma weight residual False 2.06 2.76 -0.70 2.00e-01 2.50e+01 1.21e+01 ... (remaining 16839 not shown) Planarity restraints: 6493 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' G7M a2069 " 0.090 2.00e-02 2.50e+03 6.38e-01 9.15e+03 pdb=" C4' G7M a2069 " 0.477 2.00e-02 2.50e+03 pdb=" O4' G7M a2069 " 0.784 2.00e-02 2.50e+03 pdb=" C3' G7M a2069 " -0.614 2.00e-02 2.50e+03 pdb=" O3' G7M a2069 " -0.678 2.00e-02 2.50e+03 pdb=" C2' G7M a2069 " -0.165 2.00e-02 2.50e+03 pdb=" O2' G7M a2069 " 0.951 2.00e-02 2.50e+03 pdb=" C1' G7M a2069 " 0.164 2.00e-02 2.50e+03 pdb=" N9 G7M a2069 " -1.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 6MZ a1618 " -0.921 2.00e-02 2.50e+03 6.22e-01 8.69e+03 pdb=" C4' 6MZ a1618 " 0.202 2.00e-02 2.50e+03 pdb=" O4' 6MZ a1618 " 0.800 2.00e-02 2.50e+03 pdb=" C3' 6MZ a1618 " -0.192 2.00e-02 2.50e+03 pdb=" O3' 6MZ a1618 " 0.936 2.00e-02 2.50e+03 pdb=" C2' 6MZ a1618 " -0.650 2.00e-02 2.50e+03 pdb=" O2' 6MZ a1618 " -0.651 2.00e-02 2.50e+03 pdb=" C1' 6MZ a1618 " 0.435 2.00e-02 2.50e+03 pdb=" N9 6MZ a1618 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC a2498 " 0.059 2.00e-02 2.50e+03 6.06e-01 8.25e+03 pdb=" C4' OMC a2498 " 0.432 2.00e-02 2.50e+03 pdb=" O4' OMC a2498 " 0.685 2.00e-02 2.50e+03 pdb=" C3' OMC a2498 " -0.640 2.00e-02 2.50e+03 pdb=" O3' OMC a2498 " -0.641 2.00e-02 2.50e+03 pdb=" C2' OMC a2498 " -0.170 2.00e-02 2.50e+03 pdb=" O2' OMC a2498 " 0.961 2.00e-02 2.50e+03 pdb=" C1' OMC a2498 " 0.220 2.00e-02 2.50e+03 pdb=" N1 OMC a2498 " -0.907 2.00e-02 2.50e+03 ... (remaining 6490 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.48: 1302 2.48 - 3.15: 74805 3.15 - 3.81: 223583 3.81 - 4.48: 330566 4.48 - 5.14: 428895 Nonbonded interactions: 1059151 Sorted by model distance: nonbonded pdb=" OP2 A a 943 " pdb="MG MG a3099 " model vdw 1.821 2.170 nonbonded pdb=" OP2 C a1604 " pdb="MG MG a3002 " model vdw 1.829 2.170 nonbonded pdb=" O4 U a1263 " pdb="MG MG a3144 " model vdw 1.836 2.170 nonbonded pdb=" OP1 U a1313 " pdb="MG MG a3136 " model vdw 1.853 2.170 nonbonded pdb=" OP2 A a2821 " pdb="MG MG a3063 " model vdw 1.855 2.170 ... (remaining 1059146 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 8.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 30.930 Check model and map are aligned: 0.980 Set scattering table: 0.620 Process input model: 611.360 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 667.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.418 87529 Z= 0.620 Angle : 1.532 36.888 131690 Z= 0.939 Chirality : 0.113 5.444 16842 Planarity : 0.030 0.638 6493 Dihedral : 14.232 178.448 41313 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 0.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.05 % Favored : 96.84 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.14), residues: 2692 helix: -0.74 (0.17), residues: 695 sheet: -0.97 (0.19), residues: 605 loop : -0.72 (0.15), residues: 1392 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 2251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 598 time to evaluate : 3.834 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 0 residues processed: 601 average time/residue: 2.1014 time to fit residues: 1661.4112 Evaluate side-chains 479 residues out of total 2251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 479 time to evaluate : 3.819 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 453 optimal weight: 0.8980 chunk 407 optimal weight: 0.9980 chunk 225 optimal weight: 7.9990 chunk 139 optimal weight: 7.9990 chunk 274 optimal weight: 8.9990 chunk 217 optimal weight: 10.0000 chunk 420 optimal weight: 0.5980 chunk 162 optimal weight: 10.0000 chunk 255 optimal weight: 0.8980 chunk 313 optimal weight: 9.9990 chunk 487 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN 2 28 ASN c 90 ASN c 163 GLN d 185 ASN e 136 GLN g 104 ASN k 93 ASN k 104 GLN m 73 ASN o 115 ASN p 44 GLN p 71 GLN q 6 GLN q 86 GLN r 31 GLN s 28 ASN s 70 HIS v 46 HIS x 20 ASN x 58 ASN z 6 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 87529 Z= 0.163 Angle : 0.712 23.983 131690 Z= 0.394 Chirality : 0.040 1.983 16842 Planarity : 0.008 0.131 6493 Dihedral : 13.578 179.060 35885 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.52 % Favored : 98.44 % Rotamer Outliers : 1.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.15), residues: 2692 helix: 0.88 (0.19), residues: 692 sheet: -0.42 (0.20), residues: 562 loop : -0.23 (0.15), residues: 1438 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 481 time to evaluate : 4.154 Fit side-chains outliers start: 43 outliers final: 15 residues processed: 499 average time/residue: 2.1747 time to fit residues: 1427.6388 Evaluate side-chains 469 residues out of total 2251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 454 time to evaluate : 3.875 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 8 residues processed: 7 average time/residue: 1.1144 time to fit residues: 16.4370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 271 optimal weight: 9.9990 chunk 151 optimal weight: 10.0000 chunk 405 optimal weight: 6.9990 chunk 332 optimal weight: 0.2980 chunk 134 optimal weight: 10.0000 chunk 488 optimal weight: 7.9990 chunk 527 optimal weight: 9.9990 chunk 435 optimal weight: 10.0000 chunk 484 optimal weight: 3.9990 chunk 166 optimal weight: 9.9990 chunk 391 optimal weight: 5.9990 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN d 185 ASN g 38 ASN k 93 ASN k 104 GLN m 73 ASN q 86 GLN s 28 ASN s 91 GLN u 44 HIS v 46 HIS x 20 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.103 87529 Z= 0.419 Angle : 1.100 25.628 131690 Z= 0.551 Chirality : 0.054 2.099 16842 Planarity : 0.011 0.157 6493 Dihedral : 13.918 177.708 35885 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.75 % Favored : 97.21 % Rotamer Outliers : 3.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.15), residues: 2692 helix: 0.26 (0.19), residues: 693 sheet: -0.48 (0.20), residues: 571 loop : -0.31 (0.15), residues: 1428 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 446 time to evaluate : 3.851 Fit side-chains outliers start: 68 outliers final: 40 residues processed: 479 average time/residue: 2.1699 time to fit residues: 1359.9971 Evaluate side-chains 482 residues out of total 2251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 442 time to evaluate : 3.869 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 22 residues processed: 18 average time/residue: 1.4303 time to fit residues: 41.6173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 482 optimal weight: 4.9990 chunk 367 optimal weight: 6.9990 chunk 253 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 chunk 233 optimal weight: 8.9990 chunk 328 optimal weight: 3.9990 chunk 490 optimal weight: 4.9990 chunk 519 optimal weight: 5.9990 chunk 256 optimal weight: 7.9990 chunk 464 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN d 185 ASN g 143 GLN k 93 ASN k 104 GLN q 43 ASN q 86 GLN r 9 HIS s 28 ASN u 44 HIS v 46 HIS x 20 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.095 87529 Z= 0.415 Angle : 1.083 25.453 131690 Z= 0.545 Chirality : 0.053 2.071 16842 Planarity : 0.011 0.159 6493 Dihedral : 13.884 178.299 35885 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.75 % Favored : 97.21 % Rotamer Outliers : 2.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.15), residues: 2692 helix: 0.04 (0.19), residues: 697 sheet: -0.52 (0.21), residues: 549 loop : -0.34 (0.15), residues: 1446 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 442 time to evaluate : 3.953 Fit side-chains outliers start: 66 outliers final: 46 residues processed: 479 average time/residue: 2.1294 time to fit residues: 1343.4966 Evaluate side-chains 481 residues out of total 2251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 435 time to evaluate : 3.904 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 29 residues processed: 17 average time/residue: 1.6783 time to fit residues: 43.8393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 432 optimal weight: 0.7980 chunk 294 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 386 optimal weight: 0.0980 chunk 214 optimal weight: 3.9990 chunk 442 optimal weight: 3.9990 chunk 358 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 265 optimal weight: 7.9990 chunk 465 optimal weight: 0.7980 chunk 130 optimal weight: 9.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN c 134 ASN d 49 GLN d 185 ASN g 104 ASN g 143 GLN h 11 ASN k 93 ASN k 104 GLN o 7 GLN q 86 GLN s 28 ASN ** t 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 44 HIS u 80 HIS v 46 HIS x 20 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 87529 Z= 0.190 Angle : 0.742 24.561 131690 Z= 0.405 Chirality : 0.041 2.027 16842 Planarity : 0.008 0.139 6493 Dihedral : 13.593 178.921 35885 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.97 % Favored : 97.99 % Rotamer Outliers : 2.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.15), residues: 2692 helix: 0.73 (0.20), residues: 693 sheet: -0.29 (0.21), residues: 550 loop : -0.10 (0.15), residues: 1449 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 444 time to evaluate : 4.093 Fit side-chains outliers start: 54 outliers final: 29 residues processed: 482 average time/residue: 2.1901 time to fit residues: 1387.3401 Evaluate side-chains 456 residues out of total 2251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 427 time to evaluate : 3.859 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 24 residues processed: 5 average time/residue: 1.0142 time to fit residues: 12.4285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 174 optimal weight: 9.9990 chunk 467 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 304 optimal weight: 0.9980 chunk 128 optimal weight: 9.9990 chunk 519 optimal weight: 0.9990 chunk 431 optimal weight: 6.9990 chunk 240 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 171 optimal weight: 7.9990 chunk 272 optimal weight: 9.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN d 185 ASN g 143 GLN k 93 ASN k 104 GLN o 7 GLN q 86 GLN s 28 ASN u 80 HIS v 46 HIS x 20 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.087 87529 Z= 0.361 Angle : 1.000 25.332 131690 Z= 0.510 Chirality : 0.050 2.063 16842 Planarity : 0.010 0.156 6493 Dihedral : 13.806 179.434 35885 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.67 % Favored : 97.29 % Rotamer Outliers : 2.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.15), residues: 2692 helix: 0.31 (0.19), residues: 696 sheet: -0.38 (0.21), residues: 532 loop : -0.24 (0.15), residues: 1464 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 438 time to evaluate : 4.098 Fit side-chains outliers start: 63 outliers final: 37 residues processed: 476 average time/residue: 2.1574 time to fit residues: 1351.3255 Evaluate side-chains 465 residues out of total 2251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 428 time to evaluate : 3.853 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 26 residues processed: 11 average time/residue: 1.4009 time to fit residues: 26.7350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 500 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 296 optimal weight: 0.5980 chunk 379 optimal weight: 3.9990 chunk 293 optimal weight: 1.9990 chunk 437 optimal weight: 0.9990 chunk 290 optimal weight: 1.9990 chunk 517 optimal weight: 0.3980 chunk 323 optimal weight: 8.9990 chunk 315 optimal weight: 4.9990 chunk 238 optimal weight: 10.0000 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN c 134 ASN d 185 ASN g 143 GLN k 93 ASN k 104 GLN o 7 GLN q 86 GLN ** t 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 80 HIS v 46 HIS x 20 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 87529 Z= 0.154 Angle : 0.688 24.726 131690 Z= 0.382 Chirality : 0.039 1.996 16842 Planarity : 0.007 0.134 6493 Dihedral : 13.534 177.914 35885 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.89 % Favored : 98.07 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.16), residues: 2692 helix: 0.89 (0.20), residues: 694 sheet: -0.20 (0.21), residues: 551 loop : 0.02 (0.16), residues: 1447 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 445 time to evaluate : 3.978 Fit side-chains outliers start: 39 outliers final: 28 residues processed: 475 average time/residue: 2.1686 time to fit residues: 1355.3320 Evaluate side-chains 456 residues out of total 2251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 428 time to evaluate : 5.977 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 23 residues processed: 6 average time/residue: 0.7525 time to fit residues: 12.8700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 320 optimal weight: 9.9990 chunk 206 optimal weight: 9.9990 chunk 309 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 chunk 329 optimal weight: 2.9990 chunk 352 optimal weight: 9.9990 chunk 255 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 406 optimal weight: 0.9980 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN d 185 ASN g 143 GLN k 93 ASN k 104 GLN q 43 ASN q 66 HIS ** q 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 80 HIS v 46 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.117 87529 Z= 0.507 Angle : 1.224 25.649 131690 Z= 0.601 Chirality : 0.059 2.081 16842 Planarity : 0.011 0.163 6493 Dihedral : 13.961 179.954 35885 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.93 % Favored : 97.03 % Rotamer Outliers : 2.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.15), residues: 2692 helix: 0.05 (0.19), residues: 696 sheet: -0.42 (0.21), residues: 538 loop : -0.28 (0.15), residues: 1458 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 443 time to evaluate : 4.129 Fit side-chains outliers start: 61 outliers final: 37 residues processed: 479 average time/residue: 2.2319 time to fit residues: 1394.8051 Evaluate side-chains 475 residues out of total 2251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 438 time to evaluate : 3.915 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 28 residues processed: 9 average time/residue: 1.3759 time to fit residues: 22.4708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 470 optimal weight: 0.8980 chunk 495 optimal weight: 0.4980 chunk 452 optimal weight: 0.6980 chunk 482 optimal weight: 0.8980 chunk 290 optimal weight: 0.8980 chunk 210 optimal weight: 1.9990 chunk 378 optimal weight: 0.8980 chunk 148 optimal weight: 9.9990 chunk 435 optimal weight: 0.6980 chunk 456 optimal weight: 0.8980 chunk 480 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 134 ASN d 185 ASN g 143 GLN k 93 ASN k 104 GLN q 86 GLN ** t 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 80 HIS v 46 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 87529 Z= 0.130 Angle : 0.660 24.445 131690 Z= 0.370 Chirality : 0.038 1.994 16842 Planarity : 0.007 0.131 6493 Dihedral : 13.553 177.216 35885 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.60 % Favored : 98.37 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.16), residues: 2692 helix: 0.99 (0.20), residues: 688 sheet: -0.17 (0.21), residues: 543 loop : 0.08 (0.16), residues: 1461 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 442 time to evaluate : 5.014 Fit side-chains outliers start: 33 outliers final: 22 residues processed: 471 average time/residue: 2.1801 time to fit residues: 1350.7881 Evaluate side-chains 449 residues out of total 2251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 427 time to evaluate : 3.893 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 22 residues processed: 1 average time/residue: 0.8758 time to fit residues: 5.6695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 316 optimal weight: 6.9990 chunk 510 optimal weight: 0.0970 chunk 311 optimal weight: 0.8980 chunk 241 optimal weight: 5.9990 chunk 354 optimal weight: 0.8980 chunk 534 optimal weight: 20.0000 chunk 492 optimal weight: 9.9990 chunk 426 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 329 optimal weight: 3.9990 chunk 261 optimal weight: 10.0000 overall best weight: 2.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN c 134 ASN d 185 ASN g 143 GLN k 93 ASN k 104 GLN o 7 GLN ** q 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 28 ASN u 80 HIS v 46 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 87529 Z= 0.235 Angle : 0.806 24.813 131690 Z= 0.430 Chirality : 0.043 2.041 16842 Planarity : 0.008 0.143 6493 Dihedral : 13.615 177.150 35885 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.34 % Favored : 97.62 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.15), residues: 2692 helix: 0.71 (0.19), residues: 702 sheet: -0.20 (0.21), residues: 538 loop : -0.01 (0.16), residues: 1452 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 432 time to evaluate : 4.062 Fit side-chains outliers start: 29 outliers final: 21 residues processed: 456 average time/residue: 2.3057 time to fit residues: 1380.5526 Evaluate side-chains 449 residues out of total 2251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 428 time to evaluate : 4.069 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 20 residues processed: 1 average time/residue: 2.2128 time to fit residues: 7.1435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 338 optimal weight: 7.9990 chunk 453 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 392 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 chunk 426 optimal weight: 0.9980 chunk 178 optimal weight: 10.0000 chunk 438 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN c 134 ASN d 185 ASN g 143 GLN k 93 ASN k 104 GLN ** q 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 28 ASN u 80 HIS v 46 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.163937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.136090 restraints weight = 69440.873| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 0.33 r_work: 0.3409 rms_B_bonded: 1.09 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 1.92 restraints_weight: 0.2500 r_work: 0.3201 rms_B_bonded: 4.01 restraints_weight: 0.1250 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 87529 Z= 0.279 Angle : 0.874 24.863 131690 Z= 0.458 Chirality : 0.045 2.034 16842 Planarity : 0.009 0.147 6493 Dihedral : 13.646 177.612 35885 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.34 % Favored : 97.62 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.15), residues: 2692 helix: 0.57 (0.19), residues: 702 sheet: -0.23 (0.21), residues: 540 loop : -0.07 (0.16), residues: 1450 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25961.81 seconds wall clock time: 456 minutes 35.73 seconds (27395.73 seconds total)