Starting phenix.real_space_refine (version: dev) on Sat Dec 17 04:22:22 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gae_8001/12_2022/5gae_8001.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gae_8001/12_2022/5gae_8001.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gae_8001/12_2022/5gae_8001.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gae_8001/12_2022/5gae_8001.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gae_8001/12_2022/5gae_8001.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gae_8001/12_2022/5gae_8001.pdb" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.016 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "C GLU 23": "OE1" <-> "OE2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C ARG 52": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "C TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 133": "NH1" <-> "NH2" Residue "C GLU 145": "OE1" <-> "OE2" 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 GLU 199": "OE1" <-> "OE2" Residue "C ARG 203": "NH1" <-> "NH2" Residue "C ARG 212": "NH1" <-> "NH2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D GLU 30": "OE1" <-> "OE2" 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 ARG 77": "NH1" <-> "NH2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 168": "OE1" <-> "OE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E GLU 25": "OE1" <-> "OE2" 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 TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ASP 145": "OD1" <-> "OD2" Residue "E GLU 152": "OE1" <-> "OE2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "E ASP 176": "OD1" <-> "OD2" Residue "E ASP 191": "OD1" <-> "OD2" Residue "F GLU 19": "OE1" <-> "OE2" Residue "F GLU 32": "OE1" <-> "OE2" Residue "F ARG 71": "NH1" <-> "NH2" Residue "F ARG 80": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F GLU 98": "OE1" <-> "OE2" Residue "F ARG 102": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "F PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 133": "NH1" <-> "NH2" Residue "F PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G ASP 16": "OD1" <-> "OD2" Residue "G ASP 47": "OD1" <-> "OD2" Residue "G PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 124": "OE1" <-> "OE2" Residue "G ARG 153": "NH1" <-> "NH2" Residue "G TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 163": "NH1" <-> "NH2" Residue "G ASP 166": "OD1" <-> "OD2" Residue "G ARG 170": "NH1" <-> "NH2" Residue "H ARG 27": "NH1" <-> "NH2" Residue "H PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 86": "OD1" <-> "OD2" Residue "H GLU 114": "OE1" <-> "OE2" Residue "H GLU 137": "OE1" <-> "OE2" Residue "I GLU 87": "OE1" <-> "OE2" Residue "I GLU 114": "OE1" <-> "OE2" Residue "J ASP 121": "OD1" <-> "OD2" Residue "K PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 13": "NH1" <-> "NH2" Residue "K GLU 31": "OE1" <-> "OE2" Residue "K ARG 37": "NH1" <-> "NH2" Residue "K GLU 43": "OE1" <-> "OE2" Residue "K TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 90": "OE1" <-> "OE2" Residue "K GLU 91": "OE1" <-> "OE2" Residue "K ARG 96": "NH1" <-> "NH2" Residue "K ARG 120": "NH1" <-> "NH2" Residue "K TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 45": "OE1" <-> "OE2" Residue "L GLU 110": "OE1" <-> "OE2" Residue "L GLU 121": "OE1" <-> "OE2" Residue "M ARG 21": "NH1" <-> "NH2" Residue "M ARG 33": "NH1" <-> "NH2" Residue "M ARG 41": "NH1" <-> "NH2" Residue "M ARG 47": "NH1" <-> "NH2" Residue "M GLU 51": "OE1" <-> "OE2" Residue "M ARG 60": "NH1" <-> "NH2" Residue "M GLU 76": "OE1" <-> "OE2" Residue "M ARG 78": "NH1" <-> "NH2" Residue "M GLU 106": "OE1" <-> "OE2" Residue "M ARG 126": "NH1" <-> "NH2" Residue "M GLU 144": "OE1" <-> "OE2" Residue "N ARG 10": "NH1" <-> "NH2" Residue "N ARG 18": "NH1" <-> "NH2" Residue "N PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 40": "NH1" <-> "NH2" Residue "N ARG 44": "NH1" <-> "NH2" Residue "N GLU 47": "OE1" <-> "OE2" Residue "N ARG 50": "NH1" <-> "NH2" Residue "N ARG 55": "NH1" <-> "NH2" Residue "N ARG 59": "NH1" <-> "NH2" Residue "N PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 75": "OE1" <-> "OE2" Residue "N GLU 104": "OE1" <-> "OE2" Residue "N ARG 114": "NH1" <-> "NH2" Residue "O ARG 8": "NH1" <-> "NH2" Residue "O ARG 12": "NH1" <-> "NH2" Residue "O ARG 17": "NH1" <-> "NH2" Residue "O ARG 22": "NH1" <-> "NH2" Residue "O GLU 43": "OE1" <-> "OE2" Residue "O ARG 46": "NH1" <-> "NH2" Residue "O ARG 63": "NH1" <-> "NH2" Residue "O ARG 64": "NH1" <-> "NH2" Residue "O ARG 69": "NH1" <-> "NH2" Residue "O ARG 71": "NH1" <-> "NH2" Residue "O GLU 82": "OE1" <-> "OE2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 114": "OE1" <-> "OE2" Residue "P ARG 10": "NH1" <-> "NH2" Residue "P ARG 16": "NH1" <-> "NH2" Residue "P GLU 20": "OE1" <-> "OE2" Residue "P ARG 25": "NH1" <-> "NH2" Residue "P ARG 81": "NH1" <-> "NH2" Residue "P ARG 94": "NH1" <-> "NH2" Residue "P PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 102": "NH1" <-> "NH2" Residue "P ARG 111": "NH1" <-> "NH2" Residue "P PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 21": "NH1" <-> "NH2" Residue "Q ARG 39": "NH1" <-> "NH2" Residue "Q GLU 44": "OE1" <-> "OE2" Residue "Q ARG 62": "NH1" <-> "NH2" Residue "Q GLU 71": "OE1" <-> "OE2" Residue "Q ARG 89": "NH1" <-> "NH2" Residue "Q ARG 101": "NH1" <-> "NH2" Residue "Q ARG 109": "NH1" <-> "NH2" Residue "R ARG 3": "NH1" <-> "NH2" Residue "R ARG 6": "NH1" <-> "NH2" Residue "R ARG 13": "NH1" <-> "NH2" Residue "R ARG 33": "NH1" <-> "NH2" Residue "R TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 48": "NH1" <-> "NH2" Residue "R ARG 70": "NH1" <-> "NH2" Residue "R TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 111": "OE1" <-> "OE2" Residue "S TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 16": "OE1" <-> "OE2" Residue "S ARG 21": "NH1" <-> "NH2" Residue "S GLU 23": "OE1" <-> "OE2" Residue "S GLU 31": "OE1" <-> "OE2" Residue "S GLU 45": "OE1" <-> "OE2" Residue "S ARG 68": "NH1" <-> "NH2" Residue "S GLU 70": "OE1" <-> "OE2" Residue "S PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 78": "NH1" <-> "NH2" Residue "S ARG 79": "NH1" <-> "NH2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "T GLU 59": "OE1" <-> "OE2" Residue "T GLU 78": "OE1" <-> "OE2" Residue "T ARG 84": "NH1" <-> "NH2" Residue "T ARG 88": "NH1" <-> "NH2" Residue "T ARG 95": "NH1" <-> "NH2" Residue "T ARG 110": "NH1" <-> "NH2" Residue "U GLU 4": "OE1" <-> "OE2" Residue "U GLU 5": "OE1" <-> "OE2" Residue "U GLU 52": "OE1" <-> "OE2" Residue "U GLU 54": "OE1" <-> "OE2" Residue "U GLU 89": "OE1" <-> "OE2" Residue "V ARG 6": "NH1" <-> "NH2" Residue "V ARG 7": "NH1" <-> "NH2" Residue "V ARG 82": "NH1" <-> "NH2" Residue "V PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 86": "NH1" <-> "NH2" Residue "V PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 88": "OE1" <-> "OE2" Residue "V ARG 94": "NH1" <-> "NH2" Residue "W PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 11": "OE1" <-> "OE2" Residue "W PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 41": "OE1" <-> "OE2" Residue "W ASP 43": "OD1" <-> "OD2" Residue "W GLU 55": "OE1" <-> "OE2" Residue "W GLU 69": "OE1" <-> "OE2" Residue "W PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 17": "OE1" <-> "OE2" Residue "X PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 29": "OE1" <-> "OE2" Residue "X GLU 85": "OE1" <-> "OE2" Residue "Y ARG 3": "NH1" <-> "NH2" Residue "Y ARG 11": "NH1" <-> "NH2" Residue "Y ARG 18": "NH1" <-> "NH2" Residue "Y PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 37": "NH1" <-> "NH2" Residue "Y GLU 41": "OE1" <-> "OE2" Residue "Y GLU 43": "OE1" <-> "OE2" Residue "Y ARG 50": "NH1" <-> "NH2" Residue "Y ARG 57": "NH1" <-> "NH2" Residue "Y ARG 74": "NH1" <-> "NH2" Residue "Z GLU 12": "OE1" <-> "OE2" Residue "Z ARG 47": "NH1" <-> "NH2" Residue "Z ARG 52": "NH1" <-> "NH2" Residue "a ARG 11": "NH1" <-> "NH2" Residue "a ARG 30": "NH1" <-> "NH2" Residue "a GLU 37": "OE1" <-> "OE2" Residue "a ARG 45": "NH1" <-> "NH2" Residue "b ARG 10": "NH1" <-> "NH2" Residue "b ARG 16": "NH1" <-> "NH2" Residue "b ASP 31": "OD1" <-> "OD2" Residue "b ARG 52": "NH1" <-> "NH2" Residue "c GLU 32": "OE1" <-> "OE2" Residue "c ASP 40": "OD1" <-> "OD2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "d ARG 3": "NH1" <-> "NH2" Residue "d ARG 14": "NH1" <-> "NH2" Residue "d ARG 19": "NH1" <-> "NH2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "e ARG 13": "NH1" <-> "NH2" Residue "e ARG 30": "NH1" <-> "NH2" Residue "e ARG 40": "NH1" <-> "NH2" Residue "e ARG 42": "NH1" <-> "NH2" Residue "f ARG 24": "NH1" <-> "NH2" Residue "g PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 95192 Number of models: 1 Model: "" Number of chains: 41 Chain: "A" Number of atoms: 61923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2884, 61923 Classifications: {'RNA': 2884} Modifications used: {'rna2p_pur': 281, 'rna2p_pyr': 147, 'rna3p_pur': 1385, 'rna3p_pyr': 1071} Link IDs: {'rna2p': 428, 'rna3p': 2455} Chain breaks: 3 Chain: "B" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2569 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 50} Link IDs: {'rna2p': 13, 'rna3p': 106} Chain: "C" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 202} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "F" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "H" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1110 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "I" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 946 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 120} Chain: "J" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 502 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "K" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "L" 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: "M" 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: "N" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "O" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 993 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "P" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 900 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "Q" 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: "R" 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: "S" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 101} Chain: "T" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "U" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 756 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 1, 'TRANS': 93} Chain: "V" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "W" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "X" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 580 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Y" 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: "Z" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "a" 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: "b" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "c" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 414 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 48} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "e" 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: "f" 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: "g" Number of atoms: 3099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3099 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 17, 'TRANS': 381} Chain breaks: 2 Chain: "h" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 459 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "i" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 150 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 50 Planarities with less than four sites: {'UNK:plan-1': 25} Unresolved non-hydrogen planarities: 25 Chain: "x" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Classifications: {'RNA': 3} Modifications used: {'rna2p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna3p': 2} Chain: "A" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 313 Unusual residues: {' MG': 313} Classifications: {'undetermined': 313} Link IDs: {None: 312} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' MG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 90881 SG CYS f 11 73.380 81.676 179.446 1.00 95.35 S ATOM 91009 SG CYS f 27 76.470 79.625 180.542 1.00 84.14 S Time building chain proxies: 39.37, per 1000 atoms: 0.41 Number of scatterers: 95192 At special positions: 0 Unit cell: (267.305, 198.055, 243.76, 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 1 29.99 S 96 16.00 P 3007 15.00 Mg 323 11.99 O 26239 8.00 N 17599 7.00 C 47927 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: 37.64 Conformation dependent library (CDL) restraints added in 4.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN f 101 " pdb="ZN ZN f 101 " - pdb=" ND1 HIS f 33 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 27 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 11 " 7636 Ramachandran restraints generated. 3818 Oldfield, 0 Emsley, 3818 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7148 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 50 sheets defined 38.1% alpha, 19.7% beta 1036 base pairs and 1615 stacking pairs defined. Time for finding SS restraints: 34.21 Creating SS restraints... Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 197 through 203 removed outlier: 4.157A pdb=" N MET C 201 " --> pdb=" O ALA C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 214 removed outlier: 3.812A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 225 Processing helix chain 'C' and resid 263 through 265 No H-bonds generated for 'chain 'C' and resid 263 through 265' Processing helix chain 'D' and resid 61 through 72 removed outlier: 3.947A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 102 Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 39 Processing helix chain 'E' and resid 97 through 115 Processing helix chain 'E' and resid 130 through 141 Processing helix chain 'E' and resid 154 through 161 removed outlier: 3.623A pdb=" N PHE E 158 " --> pdb=" O ASP E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 175 No H-bonds generated for 'chain 'E' and resid 173 through 175' Processing helix chain 'E' and resid 176 through 183 removed outlier: 3.783A pdb=" N PHE E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 200 Processing helix chain 'F' and resid 3 through 11 Processing helix chain 'F' and resid 11 through 21 Processing helix chain 'F' and resid 24 through 28 Processing helix chain 'F' and resid 47 through 62 removed outlier: 3.514A pdb=" N GLY F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 105 Processing helix chain 'F' and resid 134 through 138 removed outlier: 3.896A pdb=" N ILE F 137 " --> pdb=" O GLU F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 173 Processing helix chain 'G' and resid 60 through 79 Processing helix chain 'G' and resid 137 through 152 removed outlier: 3.510A pdb=" N TYR G 151 " --> pdb=" O ASP G 147 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 29 Processing helix chain 'H' and resid 40 through 73 removed outlier: 6.140A pdb=" N ALA H 52 " --> pdb=" O GLU H 48 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N GLU H 53 " --> pdb=" O ALA H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 89 Processing helix chain 'H' and resid 95 through 105 removed outlier: 3.728A pdb=" N ALA H 105 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 113 No H-bonds generated for 'chain 'H' and resid 111 through 113' Processing helix chain 'I' and resid 4 through 20 Processing helix chain 'I' and resid 34 through 48 removed outlier: 3.516A pdb=" N ALA I 48 " --> pdb=" O ALA I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 65 removed outlier: 3.591A pdb=" N ARG I 62 " --> pdb=" O THR I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 75 removed outlier: 3.910A pdb=" N ASP I 74 " --> pdb=" O CYS I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 104 removed outlier: 3.666A pdb=" N LEU I 95 " --> pdb=" O ALA I 91 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS I 97 " --> pdb=" O ALA I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 125 removed outlier: 3.962A pdb=" N ASP I 124 " --> pdb=" O SER I 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 84 Processing helix chain 'J' and resid 102 through 117 Processing helix chain 'J' and resid 121 through 136 removed outlier: 3.626A pdb=" N MET J 125 " --> pdb=" O ASP J 121 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N MET J 136 " --> pdb=" O THR J 132 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 11 Processing helix chain 'K' and resid 24 through 38 removed outlier: 4.092A pdb=" N GLU K 31 " --> pdb=" O ARG K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 62 Processing helix chain 'K' and resid 67 through 72 Processing helix chain 'K' and resid 89 through 96 Processing helix chain 'K' and resid 97 through 109 removed outlier: 4.090A pdb=" N ILE K 101 " --> pdb=" O PRO K 97 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET K 108 " --> pdb=" O ALA K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 121 removed outlier: 3.652A pdb=" N LYS K 121 " --> pdb=" O ALA K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 131 through 136 removed outlier: 4.491A pdb=" N ALA K 134 " --> pdb=" O ASN K 131 " (cutoff:3.500A) Processing helix chain 'L' and resid 104 through 108 Processing helix chain 'L' and resid 112 through 119 Processing helix chain 'M' and resid 22 through 26 Processing helix chain 'M' and resid 56 through 61 Processing helix chain 'M' and resid 68 through 72 Processing helix chain 'M' and resid 78 through 85 removed outlier: 3.716A pdb=" N ALA M 83 " --> pdb=" O SER M 80 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL M 85 " --> pdb=" O LEU M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 98 Processing helix chain 'M' and resid 128 through 137 Processing helix chain 'N' and resid 43 through 57 removed outlier: 3.510A pdb=" N VAL N 57 " --> pdb=" O MET N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 109 through 122 Processing helix chain 'O' and resid 13 through 32 Processing helix chain 'O' and resid 38 through 56 removed outlier: 4.549A pdb=" N ARG O 46 " --> pdb=" O LYS O 42 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL O 47 " --> pdb=" O GLU O 43 " (cutoff:3.500A) Proline residue: O 50 - end of helix Processing helix chain 'O' and resid 59 through 71 Processing helix chain 'O' and resid 72 through 82 Processing helix chain 'O' and resid 82 through 87 Processing helix chain 'O' and resid 117 through 125 Processing helix chain 'P' and resid 2 through 22 removed outlier: 4.596A pdb=" N ARG P 13 " --> pdb=" O ARG P 9 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ALA P 14 " --> pdb=" O ARG P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 55 through 60 Processing helix chain 'P' and resid 67 through 85 Processing helix chain 'P' and resid 100 through 113 Processing helix chain 'Q' and resid 3 through 11 Processing helix chain 'Q' and resid 53 through 56 removed outlier: 4.007A pdb=" N HIS Q 56 " --> pdb=" O ARG Q 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 53 through 56' Processing helix chain 'Q' and resid 97 through 102 Processing helix chain 'Q' and resid 104 through 108 Processing helix chain 'R' and resid 6 through 21 removed outlier: 3.739A pdb=" N GLN R 20 " --> pdb=" O LYS R 16 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA R 21 " --> pdb=" O ILE R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 30 removed outlier: 3.726A pdb=" N ARG R 28 " --> pdb=" O TYR R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 72 removed outlier: 3.854A pdb=" N GLN R 37 " --> pdb=" O ARG R 33 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG R 51 " --> pdb=" O TYR R 47 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS R 54 " --> pdb=" O ARG R 50 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG R 55 " --> pdb=" O ARG R 51 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 86 Processing helix chain 'R' and resid 91 through 102 Processing helix chain 'R' and resid 102 through 118 removed outlier: 3.696A pdb=" N PHE R 106 " --> pdb=" O ASP R 102 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 22 removed outlier: 3.974A pdb=" N LEU T 19 " --> pdb=" O GLN T 15 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL T 20 " --> pdb=" O LYS T 16 " (cutoff:3.500A) Processing helix chain 'T' and resid 28 through 39 Processing helix chain 'T' and resid 41 through 62 removed outlier: 3.771A pdb=" N VAL T 45 " --> pdb=" O LYS T 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 65 through 69 Processing helix chain 'T' and resid 89 through 91 No H-bonds generated for 'chain 'T' and resid 89 through 91' Processing helix chain 'U' and resid 3 through 9 removed outlier: 3.527A pdb=" N LEU U 8 " --> pdb=" O GLU U 4 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS U 9 " --> pdb=" O GLU U 5 " (cutoff:3.500A) Processing helix chain 'U' and resid 17 through 27 Processing helix chain 'U' and resid 39 through 51 Processing helix chain 'V' and resid 50 through 54 removed outlier: 3.956A pdb=" N GLN V 54 " --> pdb=" O ALA V 51 " (cutoff:3.500A) Processing helix chain 'W' and resid 13 through 23 Processing helix chain 'W' and resid 44 through 51 Processing helix chain 'W' and resid 54 through 59 Processing helix chain 'Y' and resid 53 through 63 Processing helix chain 'Y' and resid 63 through 73 Processing helix chain 'Z' and resid 10 through 34 Processing helix chain 'Z' and resid 40 through 62 removed outlier: 4.304A pdb=" N LYS Z 44 " --> pdb=" O SER Z 40 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA Z 51 " --> pdb=" O ARG Z 47 " (cutoff:3.500A) Processing helix chain 'a' and resid 17 through 28 Processing helix chain 'a' and resid 41 through 52 removed outlier: 3.675A pdb=" N MET a 47 " --> pdb=" O ALA a 43 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 17 removed outlier: 3.554A pdb=" N ARG b 17 " --> pdb=" O ARG b 13 " (cutoff:3.500A) Processing helix chain 'b' and resid 18 through 20 No H-bonds generated for 'chain 'b' and resid 18 through 20' Processing helix chain 'd' and resid 8 through 17 Processing helix chain 'd' and resid 17 through 23 Processing helix chain 'd' and resid 24 through 37 Processing helix chain 'e' and resid 7 through 14 removed outlier: 3.587A pdb=" N LYS e 12 " --> pdb=" O ARG e 8 " (cutoff:3.500A) Processing helix chain 'e' and resid 37 through 45 removed outlier: 3.502A pdb=" N LEU e 44 " --> pdb=" O ARG e 40 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 62 Processing helix chain 'f' and resid 30 through 33 Processing helix chain 'g' and resid 16 through 37 removed outlier: 3.652A pdb=" N ARG g 22 " --> pdb=" O GLU g 18 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY g 28 " --> pdb=" O LEU g 24 " (cutoff:3.500A) Processing helix chain 'g' and resid 45 through 53 Processing helix chain 'g' and resid 58 through 66 Processing helix chain 'g' and resid 82 through 99 removed outlier: 3.630A pdb=" N ILE g 91 " --> pdb=" O SER g 87 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN g 93 " --> pdb=" O SER g 89 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL g 97 " --> pdb=" O GLN g 93 " (cutoff:3.500A) Processing helix chain 'g' and resid 99 through 107 removed outlier: 3.725A pdb=" N ILE g 105 " --> pdb=" O THR g 101 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS g 107 " --> pdb=" O ALA g 103 " (cutoff:3.500A) Processing helix chain 'g' and resid 109 through 139 removed outlier: 3.929A pdb=" N VAL g 126 " --> pdb=" O TYR g 122 " (cutoff:3.500A) Processing helix chain 'g' and resid 155 through 177 Processing helix chain 'g' and resid 185 through 197 Processing helix chain 'g' and resid 199 through 209 removed outlier: 3.895A pdb=" N ILE g 203 " --> pdb=" O LEU g 199 " (cutoff:3.500A) Processing helix chain 'g' and resid 216 through 240 removed outlier: 3.697A pdb=" N LEU g 220 " --> pdb=" O HIS g 216 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE g 228 " --> pdb=" O ALA g 224 " (cutoff:3.500A) Processing helix chain 'g' and resid 273 through 291 removed outlier: 3.909A pdb=" N ALA g 277 " --> pdb=" O GLY g 273 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE g 278 " --> pdb=" O VAL g 274 " (cutoff:3.500A) Proline residue: g 287 - end of helix Processing helix chain 'g' and resid 300 through 310 Processing helix chain 'g' and resid 314 through 337 removed outlier: 3.607A pdb=" N VAL g 318 " --> pdb=" O GLN g 314 " (cutoff:3.500A) Processing helix chain 'g' and resid 338 through 349 Processing helix chain 'g' and resid 359 through 395 removed outlier: 4.032A pdb=" N VAL g 376 " --> pdb=" O ARG g 372 " (cutoff:3.500A) Proline residue: g 388 - end of helix Processing helix chain 'g' and resid 403 through 427 removed outlier: 3.747A pdb=" N LEU g 407 " --> pdb=" O GLY g 403 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU g 423 " --> pdb=" O GLN g 419 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER g 426 " --> pdb=" O THR g 422 " (cutoff:3.500A) Processing helix chain 'h' and resid 61 through 80 Processing helix chain 'h' and resid 86 through 118 removed outlier: 4.410A pdb=" N ILE h 114 " --> pdb=" O GLY h 110 " (cutoff:3.500A) Processing helix chain 'i' and resid 29 through 50 removed outlier: 3.759A pdb=" N UNK i 33 " --> pdb=" O UNK i 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 35 Processing sheet with id=AA3, first strand: chain 'C' and resid 101 through 105 removed outlier: 3.567A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU C 95 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N VAL C 78 " --> pdb=" O LEU C 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 129 through 131 removed outlier: 6.392A pdb=" N THR C 173 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ARG C 167 " --> pdb=" O TYR C 171 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N TYR C 171 " --> pdb=" O ARG C 167 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LYS C 183 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ILE C 267 " --> pdb=" O LYS C 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 4 through 15 removed outlier: 5.655A pdb=" N LYS D 8 " --> pdb=" O GLU D 28 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLU D 28 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY D 10 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU D 186 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL D 180 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU D 188 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP D 176 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER D 174 " --> pdb=" O VAL D 107 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL D 107 " --> pdb=" O SER D 174 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 80 through 83 removed outlier: 6.730A pdb=" N ALA D 47 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N VAL D 37 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 117 through 119 removed outlier: 3.718A pdb=" N GLY D 117 " --> pdb=" O MET D 165 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 2 through 4 Processing sheet with id=AA9, first strand: chain 'E' and resid 118 through 121 Processing sheet with id=AB1, first strand: chain 'F' and resid 66 through 69 removed outlier: 3.612A pdb=" N GLY F 86 " --> pdb=" O THR F 68 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 16 through 20 Processing sheet with id=AB3, first strand: chain 'G' and resid 42 through 45 Processing sheet with id=AB4, first strand: chain 'G' and resid 122 through 124 Processing sheet with id=AB5, first strand: chain 'G' and resid 95 through 99 Processing sheet with id=AB6, first strand: chain 'H' and resid 18 through 20 Processing sheet with id=AB7, first strand: chain 'H' and resid 77 through 82 removed outlier: 3.745A pdb=" N SER H 131 " --> pdb=" O ARG H 116 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 50 through 54 removed outlier: 3.837A pdb=" N SER I 24 " --> pdb=" O VAL I 85 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 100 through 101 Processing sheet with id=AC1, first strand: chain 'K' and resid 122 through 124 removed outlier: 6.167A pdb=" N ILE K 54 " --> pdb=" O LYS K 123 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N TRP K 15 " --> pdb=" O GLN K 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 73 through 77 Processing sheet with id=AC3, first strand: chain 'L' and resid 7 through 10 removed outlier: 6.596A pdb=" N ARG L 17 " --> pdb=" O VAL L 10 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLU L 45 " --> pdb=" O ARG L 17 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL L 19 " --> pdb=" O ILE L 43 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE L 43 " --> pdb=" O VAL L 19 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N CYS L 21 " --> pdb=" O ILE L 41 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE L 41 " --> pdb=" O CYS L 21 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LYS L 23 " --> pdb=" O ILE L 39 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ILE L 39 " --> pdb=" O LYS L 23 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N CYS L 84 " --> pdb=" O MET L 7 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ASN L 9 " --> pdb=" O CYS L 84 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU L 86 " --> pdb=" O ASN L 9 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 69 through 70 removed outlier: 3.582A pdb=" N ALA Q 49 " --> pdb=" O THR Q 60 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG Q 62 " --> pdb=" O VAL Q 47 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N VAL Q 47 " --> pdb=" O ARG Q 62 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ILE Q 64 " --> pdb=" O GLY Q 45 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N GLY Q 45 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR Q 25 " --> pdb=" O LYS Q 87 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N TRP Q 31 " --> pdb=" O VAL Q 81 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL Q 81 " --> pdb=" O TRP Q 31 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 74 through 77 Processing sheet with id=AC6, first strand: chain 'M' and resid 89 through 90 removed outlier: 6.215A pdb=" N VAL M 90 " --> pdb=" O ARG M 123 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL M 122 " --> pdb=" O GLU M 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'N' and resid 62 through 65 removed outlier: 3.820A pdb=" N LYS N 100 " --> pdb=" O ALA N 35 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU N 33 " --> pdb=" O LEU N 102 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLU N 104 " --> pdb=" O PHE N 31 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N PHE N 31 " --> pdb=" O GLU N 104 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 39 through 42 removed outlier: 5.845A pdb=" N VAL N 89 " --> pdb=" O GLU N 75 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLU N 75 " --> pdb=" O VAL N 89 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR N 91 " --> pdb=" O ILE N 73 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 33 through 37 removed outlier: 4.405A pdb=" N MET O 110 " --> pdb=" O CYS O 100 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'P' and resid 47 through 52 removed outlier: 3.571A pdb=" N VAL P 49 " --> pdb=" O VAL P 39 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU P 26 " --> pdb=" O ASP P 93 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'S' and resid 10 through 15 removed outlier: 6.948A pdb=" N GLN S 6 " --> pdb=" O VAL S 38 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL S 38 " --> pdb=" O GLN S 6 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'S' and resid 19 through 23 removed outlier: 6.638A pdb=" N TRP S 92 " --> pdb=" O ARG S 68 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ARG S 68 " --> pdb=" O TRP S 92 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR S 94 " --> pdb=" O HIS S 66 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N HIS S 66 " --> pdb=" O THR S 94 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N VAL S 96 " --> pdb=" O VAL S 64 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N VAL S 64 " --> pdb=" O VAL S 96 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ILE S 98 " --> pdb=" O GLU S 62 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLU S 62 " --> pdb=" O ILE S 98 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'S' and resid 72 through 78 removed outlier: 4.083A pdb=" N TYR S 83 " --> pdb=" O ARG S 78 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'T' and resid 2 through 11 removed outlier: 3.747A pdb=" N HIS T 9 " --> pdb=" O SER T 101 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N SER T 101 " --> pdb=" O HIS T 9 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N SER T 108 " --> pdb=" O VAL T 71 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N VAL T 71 " --> pdb=" O SER T 108 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'T' and resid 82 through 87 Processing sheet with id=AD7, first strand: chain 'U' and resid 11 through 14 removed outlier: 3.706A pdb=" N LYS U 81 " --> pdb=" O VAL U 34 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N TRP U 80 " --> pdb=" O VAL U 62 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL U 62 " --> pdb=" O TRP U 80 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LYS U 82 " --> pdb=" O THR U 60 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N THR U 60 " --> pdb=" O LYS U 82 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TYR U 84 " --> pdb=" O VAL U 58 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N VAL U 58 " --> pdb=" O TYR U 84 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR U 86 " --> pdb=" O GLU U 56 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'U' and resid 67 through 70 Processing sheet with id=AD9, first strand: chain 'V' and resid 65 through 66 removed outlier: 6.759A pdb=" N LYS V 33 " --> pdb=" O VAL V 28 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N VAL V 28 " --> pdb=" O LYS V 33 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE V 35 " --> pdb=" O LYS V 26 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLU V 10 " --> pdb=" O PHE V 73 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE V 72 " --> pdb=" O ASP V 81 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'V' and resid 41 through 45 Processing sheet with id=AE2, first strand: chain 'V' and resid 83 through 88 removed outlier: 3.670A pdb=" N GLU V 101 " --> pdb=" O PHE V 96 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'W' and resid 3 through 8 removed outlier: 7.790A pdb=" N ASN W 5 " --> pdb=" O ASP W 43 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ASP W 43 " --> pdb=" O ASN W 5 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU W 7 " --> pdb=" O GLU W 41 " (cutoff:3.500A) removed outlier: 9.081A pdb=" N LYS W 25 " --> pdb=" O GLN W 87 " (cutoff:3.500A) removed outlier: 10.120A pdb=" N ILE W 89 " --> pdb=" O LYS W 25 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N PHE W 91 " --> pdb=" O PRO W 27 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE W 29 " --> pdb=" O PHE W 91 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ARG W 93 " --> pdb=" O ILE W 29 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N TYR W 31 " --> pdb=" O ARG W 93 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLN W 78 " --> pdb=" O GLN W 87 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE W 89 " --> pdb=" O ASP W 76 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ASP W 76 " --> pdb=" O ILE W 89 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N PHE W 91 " --> pdb=" O ALA W 74 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ALA W 74 " --> pdb=" O PHE W 91 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ARG W 93 " --> pdb=" O VAL W 72 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL W 72 " --> pdb=" O ARG W 93 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'X' and resid 22 through 23 removed outlier: 6.785A pdb=" N LEU X 59 " --> pdb=" O ILE X 37 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'X' and resid 30 through 31 Processing sheet with id=AE6, first strand: chain 'Y' and resid 13 through 18 Processing sheet with id=AE7, first strand: chain 'Y' and resid 33 through 40 Processing sheet with id=AE8, first strand: chain 'a' and resid 35 through 39 Processing sheet with id=AE9, first strand: chain 'b' and resid 28 through 30 Processing sheet with id=AF1, first strand: chain 'b' and resid 48 through 49 Processing sheet with id=AF2, first strand: chain 'c' and resid 20 through 25 Processing sheet with id=AF3, first strand: chain 'e' and resid 15 through 16 Processing sheet with id=AF4, first strand: chain 'f' and resid 2 through 4 removed outlier: 6.241A pdb=" N LYS f 2 " --> pdb=" O ARG f 36 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ILE f 23 " --> pdb=" O GLN f 37 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'g' and resid 258 through 267 1383 hydrogen bonds defined for protein. 3822 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2604 hydrogen bonds 4052 hydrogen bond angles 0 basepair planarities 1036 basepair parallelities 1615 stacking parallelities Total time for adding SS restraints: 189.58 Time building geometry restraints manager: 40.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.56: 96741 1.56 - 1.92: 6292 1.92 - 2.28: 0 2.28 - 2.64: 0 2.64 - 3.00: 1 Bond restraints: 103034 Sorted by residual: bond pdb=" O3' C A2789 " pdb=" P U A2790 " ideal model delta sigma weight residual 1.607 2.999 -1.392 1.50e-02 4.44e+03 8.61e+03 bond pdb=" CA UNK i 48 " pdb=" C UNK i 48 " ideal model delta sigma weight residual 1.525 1.640 -0.115 2.10e-02 2.27e+03 3.02e+01 bond pdb=" CA UNK i 47 " pdb=" C UNK i 47 " ideal model delta sigma weight residual 1.525 1.640 -0.115 2.10e-02 2.27e+03 3.01e+01 bond pdb=" CA UNK i 38 " pdb=" C UNK i 38 " ideal model delta sigma weight residual 1.525 1.638 -0.113 2.10e-02 2.27e+03 2.91e+01 bond pdb=" CA UNK i 40 " pdb=" C UNK i 40 " ideal model delta sigma weight residual 1.525 1.631 -0.106 2.10e-02 2.27e+03 2.54e+01 ... (remaining 103029 not shown) Histogram of bond angle deviations from ideal: 65.46 - 85.16: 2 85.16 - 104.86: 13754 104.86 - 124.56: 127696 124.56 - 144.26: 12584 144.26 - 163.97: 1 Bond angle restraints: 154037 Sorted by residual: angle pdb=" C3' C A2789 " pdb=" O3' C A2789 " pdb=" P U A2790 " ideal model delta sigma weight residual 120.20 90.98 29.22 1.50e+00 4.44e-01 3.79e+02 angle pdb=" O3' C A2789 " pdb=" P U A2790 " pdb=" OP2 U A2790 " ideal model delta sigma weight residual 108.00 163.97 -55.97 3.00e+00 1.11e-01 3.48e+02 angle pdb=" O3' C A2789 " pdb=" P U A2790 " pdb=" O5' U A2790 " ideal model delta sigma weight residual 104.00 81.88 22.12 1.50e+00 4.44e-01 2.17e+02 angle pdb=" O3' C A2789 " pdb=" P U A2790 " pdb=" OP1 U A2790 " ideal model delta sigma weight residual 108.00 65.46 42.54 3.00e+00 1.11e-01 2.01e+02 angle pdb=" N PRO g 200 " pdb=" CA PRO g 200 " pdb=" C PRO g 200 " ideal model delta sigma weight residual 110.70 121.26 -10.56 1.22e+00 6.72e-01 7.49e+01 ... (remaining 154032 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 52964 35.94 - 71.88: 1853 71.88 - 107.81: 153 107.81 - 143.75: 11 143.75 - 179.69: 13 Dihedral angle restraints: 54994 sinusoidal: 43898 harmonic: 11096 Sorted by residual: dihedral pdb=" O4' C A 898 " pdb=" C1' C A 898 " pdb=" N1 C A 898 " pdb=" C2 C A 898 " ideal model delta sinusoidal sigma weight residual 200.00 31.64 168.36 1 1.50e+01 4.44e-03 8.45e+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 41.15 158.85 1 1.50e+01 4.44e-03 8.25e+01 dihedral pdb=" O4' U A1779 " pdb=" C1' U A1779 " pdb=" N1 U A1779 " pdb=" C2 U A1779 " ideal model delta sinusoidal sigma weight residual 200.00 50.41 149.59 1 1.50e+01 4.44e-03 7.95e+01 ... (remaining 54991 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 17439 0.060 - 0.120: 2008 0.120 - 0.180: 247 0.180 - 0.240: 27 0.240 - 0.300: 6 Chirality restraints: 19727 Sorted by residual: chirality pdb=" C3' U A1344 " pdb=" C4' U A1344 " pdb=" O3' U A1344 " pdb=" C2' U A1344 " both_signs ideal model delta sigma weight residual False -2.74 -2.44 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" C1' G A 748 " pdb=" O4' G A 748 " pdb=" C2' G A 748 " pdb=" N9 G A 748 " both_signs ideal model delta sigma weight residual False 2.46 2.18 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C3' A A 613 " pdb=" C4' A A 613 " pdb=" O3' A A 613 " pdb=" C2' A A 613 " both_signs ideal model delta sigma weight residual False -2.74 -2.47 -0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 19724 not shown) Planarity restraints: 8295 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 13 " 0.057 2.00e-02 2.50e+03 2.18e-02 1.42e+01 pdb=" N9 G B 13 " -0.029 2.00e-02 2.50e+03 pdb=" C8 G B 13 " -0.017 2.00e-02 2.50e+03 pdb=" N7 G B 13 " -0.006 2.00e-02 2.50e+03 pdb=" C5 G B 13 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G B 13 " 0.012 2.00e-02 2.50e+03 pdb=" O6 G B 13 " 0.018 2.00e-02 2.50e+03 pdb=" N1 G B 13 " 0.007 2.00e-02 2.50e+03 pdb=" C2 G B 13 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G B 13 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G B 13 " -0.017 2.00e-02 2.50e+03 pdb=" C4 G B 13 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A1757 " -0.037 2.00e-02 2.50e+03 1.77e-02 8.65e+00 pdb=" N9 A A1757 " 0.044 2.00e-02 2.50e+03 pdb=" C8 A A1757 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A A1757 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A A1757 " -0.003 2.00e-02 2.50e+03 pdb=" C6 A A1757 " -0.005 2.00e-02 2.50e+03 pdb=" N6 A A1757 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A A1757 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A A1757 " 0.005 2.00e-02 2.50e+03 pdb=" N3 A A1757 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A A1757 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A1434 " 0.036 2.00e-02 2.50e+03 1.69e-02 7.88e+00 pdb=" N9 A A1434 " -0.041 2.00e-02 2.50e+03 pdb=" C8 A A1434 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A A1434 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A A1434 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A A1434 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A A1434 " 0.010 2.00e-02 2.50e+03 pdb=" N1 A A1434 " -0.000 2.00e-02 2.50e+03 pdb=" C2 A A1434 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A A1434 " -0.004 2.00e-02 2.50e+03 pdb=" C4 A A1434 " -0.004 2.00e-02 2.50e+03 ... (remaining 8292 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 434 2.49 - 3.09: 59813 3.09 - 3.69: 176746 3.69 - 4.30: 273435 4.30 - 4.90: 363178 Nonbonded interactions: 873606 Sorted by model distance: nonbonded pdb=" OP1 G A1235 " pdb="MG MG A3154 " model vdw 1.884 2.170 nonbonded pdb=" O4 U A1602 " pdb="MG MG A3093 " model vdw 1.893 2.170 nonbonded pdb=" OP1 U A1648 " pdb="MG MG A3035 " model vdw 1.901 2.170 nonbonded pdb=" OP2 G A1024 " pdb="MG MG A3142 " model vdw 1.903 2.170 nonbonded pdb=" OP1 A A1614 " pdb="MG MG A3020 " model vdw 1.920 2.170 ... (remaining 873601 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 Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 3007 5.49 5 Mg 323 5.21 5 S 96 5.16 5 C 47927 2.51 5 N 17599 2.21 5 O 26239 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 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: 13.270 Check model and map are aligned: 1.050 Convert atoms to be neutral: 0.610 Process input model: 383.040 Find NCS groups from input model: 1.640 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:2.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 403.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 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 1.392 103034 Z= 0.438 Angle : 0.937 55.965 154037 Z= 0.550 Chirality : 0.040 0.300 19727 Planarity : 0.004 0.067 8295 Dihedral : 14.776 179.689 47846 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.04 % Favored : 96.91 % Rotamer Outliers : 5.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.11), residues: 3818 helix: -2.84 (0.10), residues: 1304 sheet: -1.08 (0.16), residues: 708 loop : -1.17 (0.12), residues: 1806 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7636 Ramachandran restraints generated. 3818 Oldfield, 0 Emsley, 3818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7636 Ramachandran restraints generated. 3818 Oldfield, 0 Emsley, 3818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1207 residues out of total 3139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1039 time to evaluate : 4.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 168 outliers final: 51 residues processed: 1152 average time/residue: 0.9468 time to fit residues: 1815.9030 Evaluate side-chains 749 residues out of total 3139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 698 time to evaluate : 4.138 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.7898 time to fit residues: 76.4663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 675 random chunks: chunk 569 optimal weight: 9.9990 chunk 511 optimal weight: 4.9990 chunk 283 optimal weight: 10.0000 chunk 174 optimal weight: 10.0000 chunk 345 optimal weight: 0.9990 chunk 273 optimal weight: 20.0000 chunk 529 optimal weight: 0.1980 chunk 204 optimal weight: 10.0000 chunk 321 optimal weight: 4.9990 chunk 393 optimal weight: 3.9990 chunk 612 optimal weight: 7.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 153 GLN C 251 GLN F 27 GLN F 81 GLN G 139 GLN H 11 ASN H 33 GLN H 43 ASN H 66 ASN L 88 ASN O 3 HIS O 18 GLN O 62 ASN P 98 GLN Q 41 GLN R 44 GLN S 43 ASN T 7 HIS U 48 GLN ** U 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 40 ASN W 49 ASN X 76 ASN ** Y 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 15 ASN a 20 HIS ** d 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 92 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 103034 Z= 0.215 Angle : 0.586 9.054 154037 Z= 0.307 Chirality : 0.036 0.282 19727 Planarity : 0.005 0.059 8295 Dihedral : 13.829 178.420 40394 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.07 % Favored : 97.88 % Rotamer Outliers : 3.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.89 (0.12), residues: 3818 helix: -0.37 (0.13), residues: 1318 sheet: -0.51 (0.17), residues: 733 loop : -0.64 (0.13), residues: 1767 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7636 Ramachandran restraints generated. 3818 Oldfield, 0 Emsley, 3818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7636 Ramachandran restraints generated. 3818 Oldfield, 0 Emsley, 3818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 904 residues out of total 3139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 800 time to evaluate : 4.283 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 outliers start: 104 outliers final: 57 residues processed: 861 average time/residue: 0.9735 time to fit residues: 1427.6501 Evaluate side-chains 758 residues out of total 3139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 701 time to evaluate : 4.154 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 0 residues processed: 57 average time/residue: 0.7645 time to fit residues: 85.2066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 675 random chunks: chunk 340 optimal weight: 9.9990 chunk 190 optimal weight: 20.0000 chunk 510 optimal weight: 4.9990 chunk 417 optimal weight: 50.0000 chunk 169 optimal weight: 10.0000 chunk 614 optimal weight: 5.9990 chunk 663 optimal weight: 10.0000 chunk 546 optimal weight: 1.9990 chunk 608 optimal weight: 10.0000 chunk 209 optimal weight: 50.0000 chunk 492 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 140 HIS E 115 GLN H 33 GLN N 13 HIS P 38 GLN S 43 ASN T 15 GLN U 48 GLN V 54 GLN W 5 ASN Z 25 GLN Z 27 ASN c 19 HIS ** d 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 103034 Z= 0.303 Angle : 0.602 9.795 154037 Z= 0.312 Chirality : 0.036 0.249 19727 Planarity : 0.005 0.068 8295 Dihedral : 13.830 179.750 40394 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.62 % Favored : 97.33 % Rotamer Outliers : 3.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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: -0.29 (0.13), residues: 3818 helix: 0.43 (0.14), residues: 1327 sheet: -0.40 (0.18), residues: 727 loop : -0.45 (0.14), residues: 1764 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7636 Ramachandran restraints generated. 3818 Oldfield, 0 Emsley, 3818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7636 Ramachandran restraints generated. 3818 Oldfield, 0 Emsley, 3818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 849 residues out of total 3139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 744 time to evaluate : 4.168 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 outliers start: 105 outliers final: 54 residues processed: 807 average time/residue: 0.8899 time to fit residues: 1210.6163 Evaluate side-chains 733 residues out of total 3139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 679 time to evaluate : 4.108 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.6795 time to fit residues: 73.5634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 675 random chunks: chunk 606 optimal weight: 5.9990 chunk 461 optimal weight: 8.9990 chunk 318 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 293 optimal weight: 20.0000 chunk 412 optimal weight: 20.0000 chunk 616 optimal weight: 4.9990 chunk 652 optimal weight: 7.9990 chunk 321 optimal weight: 0.0980 chunk 584 optimal weight: 10.0000 chunk 175 optimal weight: 10.0000 overall best weight: 5.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 5 HIS ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 43 ASN W 5 ASN X 76 ASN Z 27 ASN b 42 HIS ** g 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 421 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 103034 Z= 0.327 Angle : 0.606 12.401 154037 Z= 0.313 Chirality : 0.037 0.253 19727 Planarity : 0.005 0.068 8295 Dihedral : 13.893 178.612 40394 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.83 % Favored : 97.09 % Rotamer Outliers : 2.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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: -0.17 (0.13), residues: 3818 helix: 0.69 (0.14), residues: 1321 sheet: -0.38 (0.18), residues: 725 loop : -0.50 (0.14), residues: 1772 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7636 Ramachandran restraints generated. 3818 Oldfield, 0 Emsley, 3818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7636 Ramachandran restraints generated. 3818 Oldfield, 0 Emsley, 3818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 3139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 716 time to evaluate : 4.231 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 outliers start: 78 outliers final: 43 residues processed: 758 average time/residue: 0.9050 time to fit residues: 1164.2673 Evaluate side-chains 714 residues out of total 3139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 671 time to evaluate : 4.352 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.6956 time to fit residues: 61.2630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 675 random chunks: chunk 543 optimal weight: 6.9990 chunk 370 optimal weight: 7.9990 chunk 9 optimal weight: 20.0000 chunk 485 optimal weight: 7.9990 chunk 269 optimal weight: 10.0000 chunk 556 optimal weight: 5.9990 chunk 451 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 333 optimal weight: 1.9990 chunk 585 optimal weight: 10.0000 chunk 164 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 142 HIS ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN H 135 HIS ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 43 ASN X 76 ASN Z 27 ASN g 93 GLN g 421 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.066 103034 Z= 0.349 Angle : 0.624 9.773 154037 Z= 0.321 Chirality : 0.038 0.345 19727 Planarity : 0.005 0.086 8295 Dihedral : 14.010 179.401 40394 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.35 % Favored : 96.57 % Rotamer Outliers : 2.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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: -0.19 (0.13), residues: 3818 helix: 0.76 (0.14), residues: 1315 sheet: -0.45 (0.18), residues: 735 loop : -0.55 (0.14), residues: 1768 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7636 Ramachandran restraints generated. 3818 Oldfield, 0 Emsley, 3818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7636 Ramachandran restraints generated. 3818 Oldfield, 0 Emsley, 3818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 3139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 703 time to evaluate : 4.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 84 outliers final: 46 residues processed: 751 average time/residue: 0.9085 time to fit residues: 1157.1511 Evaluate side-chains 708 residues out of total 3139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 662 time to evaluate : 4.233 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.6748 time to fit residues: 63.8162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 675 random chunks: chunk 219 optimal weight: 10.0000 chunk 587 optimal weight: 6.9990 chunk 128 optimal weight: 10.0000 chunk 383 optimal weight: 8.9990 chunk 161 optimal weight: 10.0000 chunk 653 optimal weight: 5.9990 chunk 542 optimal weight: 9.9990 chunk 302 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 216 optimal weight: 40.0000 chunk 342 optimal weight: 1.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 GLN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 10 GLN U 28 ASN U 92 ASN X 76 ASN Y 6 GLN Z 27 ASN g 247 ASN g 270 ASN g 421 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 103034 Z= 0.316 Angle : 0.600 9.363 154037 Z= 0.310 Chirality : 0.037 0.261 19727 Planarity : 0.005 0.051 8295 Dihedral : 13.983 179.515 40394 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.04 % Favored : 96.88 % Rotamer Outliers : 1.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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: -0.10 (0.13), residues: 3818 helix: 0.90 (0.14), residues: 1301 sheet: -0.48 (0.18), residues: 741 loop : -0.52 (0.14), residues: 1776 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7636 Ramachandran restraints generated. 3818 Oldfield, 0 Emsley, 3818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7636 Ramachandran restraints generated. 3818 Oldfield, 0 Emsley, 3818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 3139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 697 time to evaluate : 4.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 33 residues processed: 724 average time/residue: 0.9181 time to fit residues: 1124.0461 Evaluate side-chains 697 residues out of total 3139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 664 time to evaluate : 4.209 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.6903 time to fit residues: 47.6350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 675 random chunks: chunk 629 optimal weight: 0.6980 chunk 73 optimal weight: 10.0000 chunk 372 optimal weight: 5.9990 chunk 476 optimal weight: 7.9990 chunk 369 optimal weight: 0.0470 chunk 549 optimal weight: 0.7980 chunk 364 optimal weight: 2.9990 chunk 650 optimal weight: 0.8980 chunk 407 optimal weight: 8.9990 chunk 396 optimal weight: 30.0000 chunk 300 optimal weight: 20.0000 overall best weight: 1.0880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 10 GLN Z 27 ASN e 31 HIS g 247 ASN g 421 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.070 103034 Z= 0.130 Angle : 0.507 9.197 154037 Z= 0.264 Chirality : 0.031 0.264 19727 Planarity : 0.004 0.047 8295 Dihedral : 13.715 179.079 40394 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.85 % Favored : 97.04 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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: 0.34 (0.13), residues: 3818 helix: 1.25 (0.14), residues: 1316 sheet: -0.19 (0.19), residues: 740 loop : -0.27 (0.15), residues: 1762 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7636 Ramachandran restraints generated. 3818 Oldfield, 0 Emsley, 3818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7636 Ramachandran restraints generated. 3818 Oldfield, 0 Emsley, 3818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 765 residues out of total 3139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 730 time to evaluate : 4.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 21 residues processed: 752 average time/residue: 0.9649 time to fit residues: 1238.3614 Evaluate side-chains 686 residues out of total 3139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 665 time to evaluate : 4.132 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.7031 time to fit residues: 32.7429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 675 random chunks: chunk 402 optimal weight: 20.0000 chunk 259 optimal weight: 10.0000 chunk 388 optimal weight: 10.0000 chunk 195 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 413 optimal weight: 20.0000 chunk 443 optimal weight: 5.9990 chunk 321 optimal weight: 0.0570 chunk 60 optimal weight: 10.0000 chunk 511 optimal weight: 10.0000 overall best weight: 7.2112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 88 GLN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 10 GLN ** Q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 28 ASN W 49 ASN ** Z 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.076 103034 Z= 0.409 Angle : 0.654 9.922 154037 Z= 0.333 Chirality : 0.039 0.249 19727 Planarity : 0.005 0.063 8295 Dihedral : 13.961 179.058 40394 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.56 % Favored : 96.33 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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 (0.13), residues: 3818 helix: 1.00 (0.14), residues: 1303 sheet: -0.39 (0.18), residues: 741 loop : -0.48 (0.14), residues: 1774 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7636 Ramachandran restraints generated. 3818 Oldfield, 0 Emsley, 3818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7636 Ramachandran restraints generated. 3818 Oldfield, 0 Emsley, 3818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 3139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 662 time to evaluate : 5.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 30 residues processed: 677 average time/residue: 0.9181 time to fit residues: 1051.4900 Evaluate side-chains 669 residues out of total 3139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 639 time to evaluate : 4.158 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.6819 time to fit residues: 43.5996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 675 random chunks: chunk 591 optimal weight: 0.9990 chunk 623 optimal weight: 0.0000 chunk 568 optimal weight: 5.9990 chunk 606 optimal weight: 0.9980 chunk 364 optimal weight: 0.9980 chunk 264 optimal weight: 20.0000 chunk 476 optimal weight: 9.9990 chunk 186 optimal weight: 30.0000 chunk 547 optimal weight: 6.9990 chunk 573 optimal weight: 4.9990 chunk 604 optimal weight: 3.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 99 HIS g 247 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.059 103034 Z= 0.140 Angle : 0.516 9.748 154037 Z= 0.268 Chirality : 0.032 0.258 19727 Planarity : 0.004 0.048 8295 Dihedral : 13.705 179.003 40394 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.78 % Favored : 97.12 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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 (0.13), residues: 3818 helix: 1.24 (0.14), residues: 1311 sheet: -0.27 (0.19), residues: 740 loop : -0.30 (0.15), residues: 1767 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7636 Ramachandran restraints generated. 3818 Oldfield, 0 Emsley, 3818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7636 Ramachandran restraints generated. 3818 Oldfield, 0 Emsley, 3818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 3139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 701 time to evaluate : 4.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 707 average time/residue: 0.9008 time to fit residues: 1080.6455 Evaluate side-chains 668 residues out of total 3139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 661 time to evaluate : 4.210 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.6671 time to fit residues: 13.4902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 675 random chunks: chunk 398 optimal weight: 10.0000 chunk 641 optimal weight: 0.9980 chunk 391 optimal weight: 9.9990 chunk 304 optimal weight: 0.0020 chunk 445 optimal weight: 9.9990 chunk 672 optimal weight: 9.9990 chunk 618 optimal weight: 0.6980 chunk 535 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 413 optimal weight: 20.0000 chunk 328 optimal weight: 10.0000 overall best weight: 3.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 12 GLN ** Y 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 103034 Z= 0.223 Angle : 0.541 10.554 154037 Z= 0.279 Chirality : 0.033 0.247 19727 Planarity : 0.004 0.059 8295 Dihedral : 13.693 178.629 40394 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.30 % Favored : 96.60 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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: 0.26 (0.13), residues: 3818 helix: 1.23 (0.14), residues: 1312 sheet: -0.26 (0.19), residues: 742 loop : -0.34 (0.15), residues: 1764 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7636 Ramachandran restraints generated. 3818 Oldfield, 0 Emsley, 3818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7636 Ramachandran restraints generated. 3818 Oldfield, 0 Emsley, 3818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 3139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 663 time to evaluate : 4.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 668 average time/residue: 0.9330 time to fit residues: 1055.9423 Evaluate side-chains 651 residues out of total 3139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 644 time to evaluate : 4.278 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.6912 time to fit residues: 13.8281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 675 random chunks: chunk 425 optimal weight: 3.9990 chunk 570 optimal weight: 0.9980 chunk 164 optimal weight: 10.0000 chunk 493 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 148 optimal weight: 30.0000 chunk 536 optimal weight: 10.0000 chunk 224 optimal weight: 10.0000 chunk 550 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 27 GLN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 116 GLN Q 7 GLN ** Y 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 20 ASN ** Z 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 45 GLN g 247 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.087473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.061857 restraints weight = 286898.859| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.28 r_work: 0.2803 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.075 103034 Z= 0.370 Angle : 0.640 11.025 154037 Z= 0.328 Chirality : 0.038 0.251 19727 Planarity : 0.005 0.056 8295 Dihedral : 13.996 178.920 40394 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.95 % Favored : 95.91 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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 (0.13), residues: 3818 helix: 0.96 (0.14), residues: 1301 sheet: -0.44 (0.18), residues: 734 loop : -0.51 (0.14), residues: 1783 =============================================================================== Job complete usr+sys time: 20430.14 seconds wall clock time: 361 minutes 26.92 seconds (21686.92 seconds total)