Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 17 22:20:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o9j_0661/10_2023/6o9j_0661.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o9j_0661/10_2023/6o9j_0661.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o9j_0661/10_2023/6o9j_0661.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o9j_0661/10_2023/6o9j_0661.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o9j_0661/10_2023/6o9j_0661.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o9j_0661/10_2023/6o9j_0661.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4564 5.49 5 S 149 5.16 5 C 71705 2.51 5 N 26586 2.21 5 O 39678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "V PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 7": "OE1" <-> "OE2" Residue "V GLU 35": "OE1" <-> "OE2" Residue "V GLU 41": "OE1" <-> "OE2" Residue "V PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 34": "OE1" <-> "OE2" Residue "C PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C GLU 99": "OE1" <-> "OE2" Residue "C TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C GLU 144": "OE1" <-> "OE2" Residue "C ARG 155": "NH1" <-> "NH2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "C ARG 181": "NH1" <-> "NH2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C ARG 269": "NH1" <-> "NH2" Residue "D PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 108": "OD1" <-> "OD2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 51": "OE1" <-> "OE2" Residue "E PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 122": "OE1" <-> "OE2" Residue "E ASP 140": "OD1" <-> "OD2" Residue "E ASP 145": "OD1" <-> "OD2" Residue "F TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 18": "OE1" <-> "OE2" Residue "F ASP 50": "OD1" <-> "OD2" Residue "F PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 93": "OE1" <-> "OE2" Residue "F GLU 100": "OE1" <-> "OE2" Residue "F ASP 122": "OD1" <-> "OD2" Residue "F GLU 139": "OE1" <-> "OE2" Residue "F ASP 146": "OD1" <-> "OD2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 48": "OE1" <-> "OE2" Residue "H GLU 53": "OE1" <-> "OE2" Residue "J TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 110": "OE1" <-> "OE2" Residue "K PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 10": "OE1" <-> "OE2" Residue "L PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 143": "OE1" <-> "OE2" Residue "M PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 104": "OE1" <-> "OE2" Residue "M PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 43": "OE1" <-> "OE2" Residue "N PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 127": "OE1" <-> "OE2" Residue "O GLU 46": "OE1" <-> "OE2" Residue "O TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 93": "OD1" <-> "OD2" Residue "O GLU 112": "OE1" <-> "OE2" Residue "P GLU 10": "OE1" <-> "OE2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 70": "OE1" <-> "OE2" Residue "P PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 90": "OD1" <-> "OD2" Residue "Q PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 34": "OE1" <-> "OE2" Residue "R PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 5": "OE1" <-> "OE2" Residue "T ASP 37": "OD1" <-> "OD2" Residue "T PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 79": "OD1" <-> "OD2" Residue "T PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 9": "OE1" <-> "OE2" Residue "U ASP 17": "OD1" <-> "OD2" Residue "U PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 14": "OD1" <-> "OD2" Residue "W ASP 55": "OD1" <-> "OD2" Residue "W PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 17": "OE1" <-> "OE2" Residue "Z PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 35": "OE1" <-> "OE2" Residue "1 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 20": "OD1" <-> "OD2" Residue "6 ASP 141": "OD1" <-> "OD2" Residue "c GLU 27": "OE1" <-> "OE2" Residue "c PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 109": "OE1" <-> "OE2" Residue "c GLU 165": "OE1" <-> "OE2" Residue "c ASP 182": "OD1" <-> "OD2" Residue "c GLU 187": "OE1" <-> "OE2" Residue "d GLU 56": "OE1" <-> "OE2" Residue "d GLU 68": "OE1" <-> "OE2" Residue "d TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 94": "OE1" <-> "OE2" Residue "d ASP 98": "OD1" <-> "OD2" Residue "d TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 173": "OD1" <-> "OD2" Residue "d ASP 193": "OD1" <-> "OD2" Residue "d GLU 201": "OE1" <-> "OE2" Residue "d TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 9": "OE1" <-> "OE2" Residue "e GLU 12": "OE1" <-> "OE2" Residue "e PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 40": "OD1" <-> "OD2" Residue "e GLU 54": "OE1" <-> "OE2" Residue "e GLU 64": "OE1" <-> "OE2" Residue "e PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 141": "OD1" <-> "OD2" Residue "f ASP 13": "OD1" <-> "OD2" Residue "f GLU 16": "OE1" <-> "OE2" Residue "f GLU 23": "OE1" <-> "OE2" Residue "f TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 40": "OE1" <-> "OE2" Residue "f PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 98": "OE1" <-> "OE2" Residue "g ASP 14": "OD1" <-> "OD2" Residue "g GLU 20": "OE1" <-> "OE2" Residue "g ASP 32": "OD1" <-> "OD2" Residue "g GLU 62": "OE1" <-> "OE2" Residue "g GLU 66": "OE1" <-> "OE2" Residue "g TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 89": "OE1" <-> "OE2" Residue "g GLU 128": "OE1" <-> "OE2" Residue "g ASP 139": "OD1" <-> "OD2" Residue "g PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 41": "OE1" <-> "OE2" Residue "h GLU 59": "OE1" <-> "OE2" Residue "h GLU 90": "OE1" <-> "OE2" Residue "h ASP 112": "OD1" <-> "OD2" Residue "h GLU 123": "OE1" <-> "OE2" Residue "i TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 35": "OE1" <-> "OE2" Residue "i PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 52": "OE1" <-> "OE2" Residue "i ASP 55": "OD1" <-> "OD2" Residue "i GLU 88": "OE1" <-> "OE2" Residue "i ASP 90": "OD1" <-> "OD2" Residue "i GLU 96": "OE1" <-> "OE2" Residue "i PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 106": "OD1" <-> "OD2" Residue "j PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 19": "OD1" <-> "OD2" Residue "j GLU 24": "OE1" <-> "OE2" Residue "j GLU 47": "OE1" <-> "OE2" Residue "j TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 81": "OE1" <-> "OE2" Residue "j ASP 91": "OD1" <-> "OD2" Residue "j ASP 97": "OD1" <-> "OD2" Residue "k GLU 67": "OE1" <-> "OE2" Residue "k ASP 71": "OD1" <-> "OD2" Residue "k TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 93": "OE1" <-> "OE2" Residue "l GLU 24": "OE1" <-> "OE2" Residue "l GLU 69": "OE1" <-> "OE2" Residue "l ASP 88": "OD1" <-> "OD2" Residue "m TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 49": "OE1" <-> "OE2" Residue "m GLU 71": "OE1" <-> "OE2" Residue "n GLU 9": "OE1" <-> "OE2" Residue "n TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 13": "OE1" <-> "OE2" Residue "o PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 17": "OD1" <-> "OD2" Residue "o GLU 25": "OE1" <-> "OE2" Residue "o PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 45": "OE1" <-> "OE2" Residue "p GLU 47": "OE1" <-> "OE2" Residue "p ASP 53": "OD1" <-> "OD2" Residue "q ASP 14": "OD1" <-> "OD2" Residue "q TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 48": "OE1" <-> "OE2" Residue "r TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 24": "OD1" <-> "OD2" Residue "r TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 71": "OD1" <-> "OD2" Residue "s PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 63": "OD1" <-> "OD2" Residue "s GLU 64": "OE1" <-> "OE2" Residue "t GLU 14": "OE1" <-> "OE2" Residue "t GLU 39": "OE1" <-> "OE2" Residue "7 PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 55": "OE1" <-> "OE2" Residue "7 GLU 77": "OE1" <-> "OE2" Residue "7 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 132": "OE1" <-> "OE2" Residue "7 ASP 158": "OD1" <-> "OD2" Residue "7 PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ASP 12": "OD1" <-> "OD2" Residue "u GLU 35": "OE1" <-> "OE2" Residue "u PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 142682 Number of models: 1 Model: "" Number of chains: 53 Chain: "A" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2507 Classifications: {'RNA': 117} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 2, 'rna3p_pur': 58, 'rna3p_pyr': 52} Link IDs: {'rna2p': 7, 'rna3p': 109} Chain: "B" Number of atoms: 60995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2841, 60995 Classifications: {'RNA': 2841} Modifications used: {'rna2p_pur': 250, 'rna2p_pyr': 135, 'rna3p_pur': 1391, 'rna3p_pyr': 1065} Link IDs: {'rna2p': 385, 'rna3p': 2455} Chain breaks: 3 Chain: "V" 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: "C" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2053 Classifications: {'peptide': 267} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 249} 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: {'PTRANS': 6, '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: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1420 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 171} 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: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 144} Chain: "J" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1112 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "K" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 930 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "L" 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: "M" 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: "N" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1008 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "O" 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: "P" 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: "Q" 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: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" 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: "T" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 777 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "U" 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: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 634 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "X" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "Y" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "Z" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 549 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "1" 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: "2" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 441 Classifications: {'peptide': 54} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "3" 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: "4" 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: "5" 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: "6" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "a" Number of atoms: 32831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1530, 32831 Classifications: {'RNA': 1530} Modifications used: {'rna2p_pur': 108, 'rna2p_pyr': 77, 'rna3p_pur': 764, 'rna3p_pyr': 581} Link IDs: {'rna2p': 185, 'rna3p': 1344} Chain: "c" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "d" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "e" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1105 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "f" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 817 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "g" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1174 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "h" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "i" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "j" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "k" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "l" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "m" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "n" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 774 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Chain: "o" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 716 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "p" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "r" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 455 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "s" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "t" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "7" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1704 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "u" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "v" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1623 Classifications: {'RNA': 76} Modifications used: {'p5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 2, 'rna3p_pur': 32, 'rna3p_pyr': 35} Link IDs: {'rna2p': 9, 'rna3p': 66} Time building chain proxies: 51.46, per 1000 atoms: 0.36 Number of scatterers: 142682 At special positions: 0 Unit cell: (232.4, 250.66, 273.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 149 16.00 P 4564 15.00 O 39678 8.00 N 26586 7.00 C 71705 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 Atom "ATOM A0D5Q O4' G a1279 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DZ4 O5' A a1329 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DMC O4' U a1307 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0D6A O5' A a1280 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0CFV O4' A a1236 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DMC O4' U a1307 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0AM7 O4' U a1126 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0D80 O5' U a1283 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0D6A O5' A a1280 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0CR9 O4' G a1255 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0D5N O5' G a1279 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0AMR O4' G a1127 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DZ7 O4' A a1329 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0WLF O4' C v 56 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DJT O5' C a1303 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0CQK O5' A a1254 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0C55 O5' C a1218 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0EH4 O4' C a1359 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0ALN O4' U a1125 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0D5Q O4' G a1279 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0AM7 O4' U a1126 .*. O " rejected from bonding due to valence issues. Atom "ATOM A08D8 O4' U a 989 .*. O " rejected from bonding due to valence issues. Atom "ATOM A088K O4' U a 981 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DZ7 O4' A a1329 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0C6E O4' G a1220 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DTZ O5' C a1320 .*. O " rejected from bonding due to valence issues. Atom "ATOM A08TQ O4' U a1017 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0E2S O5' U a1335 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0D80 O5' U a1283 .*. O " rejected from bonding due to valence issues. Atom "ATOM A08D8 O4' U a 989 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0ALN O4' U a1125 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0C55 O5' C a1218 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0WLF O4' C v 56 .*. O " rejected from bonding due to valence issues. Atom "ATOM A085I O5' G a 976 .*. O " rejected from bonding due to valence issues. Atom "ATOM A088H O5' U a 981 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0AZT O5' C a1149 .*. O " rejected from bonding due to valence issues. Atom "ATOM A08RS O5' A a1014 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0EH1 O5' C a1359 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0CFV O4' A a1236 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0D53 O4' G a1278 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0CRT O5' A a1256 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0AZW O4' C a1149 .*. O " rejected from bonding due to valence issues. Atom "ATOM A08T1 O5' A a1016 .*. O " rejected from bonding due to valence issues. Atom "ATOM A07OD O4' G a 947 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DM9 O5' U a1307 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DU2 O4' C a1320 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0AM7 O4' U a1126 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DMW O4' U a1308 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0WLF O4' C v 56 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0C6E O4' G a1220 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0D5Q O4' G a1279 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0AZW O4' C a1149 .*. O " rejected from bonding due to valence issues. Atom "ATOM A08D8 O4' U a 989 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DL0 O5' G a1305 .*. O " rejected from bonding due to valence issues. Atom "ATOM A07OA O5' G a 947 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0B1O O4' A a1152 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0D5N O5' G a1279 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0CR9 O4' G a1255 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DZ7 O4' A a1329 .*. O " rejected from bonding due to valence issues. Atom "ATOM A07OA O5' G a 947 .*. O " rejected from bonding due to valence issues. Atom "ATOM A088H O5' U a 981 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0E25 O5' G a1334 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0AM4 O5' U a1126 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0EGH O5' U a1358 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0E2S O5' U a1335 .*. O " rejected from bonding due to valence issues. Atom "ATOM 93743 O4' C a 193 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0B0G O4' A a1150 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DSR O5' A a1318 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DKD O5' G a1304 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0D53 O4' G a1278 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0CF8 O5' U a1235 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0CRT O5' A a1256 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0C4O O4' C a1217 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0ALN O4' U a1125 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0D6D O4' A a1280 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DZQ O5' U a1330 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0C55 O5' C a1218 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0AMR O4' G a1127 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DZ4 O5' A a1329 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0E1M O4' A a1333 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0ALN O4' U a1125 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DJW O4' C a1303 .*. O " rejected from bonding due to valence issues. Atom "ATOM A08RV O4' A a1014 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0EFV O5' A a1357 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DKD O5' G a1304 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0AM7 O4' U a1126 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0CQN O4' A a1254 .*. O " rejected from bonding due to valence issues. Atom "ATOM A088K O4' U a 981 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DKD O5' G a1304 .*. O " rejected from bonding due to valence issues. Atom "ATOM A08D8 O4' U a 989 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0AZT O5' C a1149 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0CTO O5' C a1259 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DSR O5' A a1318 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DMC O4' U a1307 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0C6E O4' G a1220 .*. O " rejected from bonding due to valence issues. Atom "ATOM A08G3 O4' A a 994 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0CR9 O4' G a1255 .*. O " rejected from bonding due to valence issues. Atom "ATOM A07OX O5' C a 948 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0D3W O4' G a1276 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0B0Z O5' A a1151 .*. O " rejected from bonding due to valence issues. Atom "ATOM A08TN O5' U a1017 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0EGH O5' U a1358 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0AM4 O5' U a1126 .*. O " rejected from bonding due to valence issues. Atom "ATOM A08TQ O4' U a1017 .*. O " rejected from bonding due to valence issues. Atom "ATOM A07OA O5' G a 947 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0D53 O4' G a1278 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0AKD O5' U a1123 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0AKG O4' U a1123 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0D6A O5' A a1280 .*. O " rejected from bonding due to valence issues. Atom "ATOM A07NR O4' A a 946 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0EH4 O4' C a1359 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DLQ O4' A a1306 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0E25 O5' G a1334 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0E28 O4' G a1334 .*. O " rejected from bonding due to valence issues. Atom "ATOM A08TQ O4' U a1017 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0AOF O5' A a1130 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 65.92 Conformation dependent library (CDL) restraints added in 5.9 seconds 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10516 Finding SS restraints... Secondary structure from input PDB file: 157 helices and 37 sheets defined 27.4% alpha, 4.8% beta 1590 base pairs and 2207 stacking pairs defined. Time for finding SS restraints: 49.30 Creating SS restraints... Processing helix chain 'V' and resid 13 through 23 removed outlier: 3.891A pdb=" N ARG V 19 " --> pdb=" O GLY V 15 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 48 Processing helix chain 'V' and resid 53 through 57 Processing helix chain 'C' and resid 130 through 134 Processing helix chain 'C' and resid 197 through 201 Processing helix chain 'D' and resid 61 through 67 Processing helix chain 'E' and resid 24 through 36 removed outlier: 4.038A pdb=" N VAL E 28 " --> pdb=" O ASN E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 103 Processing helix chain 'E' and resid 107 through 112 Processing helix chain 'E' and resid 133 through 139 removed outlier: 4.192A pdb=" N LYS E 137 " --> pdb=" O LEU E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 161 removed outlier: 4.129A pdb=" N LEU E 159 " --> pdb=" O ASN E 156 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA E 161 " --> pdb=" O PHE E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 181 Processing helix chain 'F' and resid 3 through 9 removed outlier: 4.124A pdb=" N LYS F 8 " --> pdb=" O HIS F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 61 removed outlier: 3.924A pdb=" N ALA F 54 " --> pdb=" O ASP F 50 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP F 55 " --> pdb=" O ASN F 51 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU F 56 " --> pdb=" O ALA F 52 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA F 58 " --> pdb=" O ALA F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 101 removed outlier: 3.513A pdb=" N GLU F 97 " --> pdb=" O GLU F 93 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE F 98 " --> pdb=" O ARG F 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 81 removed outlier: 4.502A pdb=" N TRP G 61 " --> pdb=" O TYR G 57 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ALA G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N GLN G 63 " --> pdb=" O ASP G 59 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA G 64 " --> pdb=" O GLY G 60 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET G 74 " --> pdb=" O LEU G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 150 removed outlier: 3.583A pdb=" N GLN G 142 " --> pdb=" O GLN G 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 46 Processing helix chain 'H' and resid 51 through 60 removed outlier: 4.239A pdb=" N GLU H 55 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS H 57 " --> pdb=" O GLU H 53 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N LEU H 58 " --> pdb=" O LEU H 54 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA H 59 " --> pdb=" O GLU H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 67 removed outlier: 3.938A pdb=" N ALA H 67 " --> pdb=" O ALA H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 72 Processing helix chain 'H' and resid 96 through 101 Processing helix chain 'H' and resid 102 through 104 No H-bonds generated for 'chain 'H' and resid 102 through 104' Processing helix chain 'H' and resid 111 through 115 removed outlier: 3.929A pdb=" N VAL H 115 " --> pdb=" O LYS H 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 28 Processing helix chain 'J' and resid 29 through 34 Processing helix chain 'J' and resid 66 through 71 removed outlier: 3.997A pdb=" N ARG J 69 " --> pdb=" O GLY J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 94 Processing helix chain 'J' and resid 100 through 109 removed outlier: 4.153A pdb=" N VAL J 105 " --> pdb=" O GLU J 102 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY J 107 " --> pdb=" O ALA J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 removed outlier: 3.897A pdb=" N MET J 118 " --> pdb=" O LEU J 114 " (cutoff:3.500A) Processing helix chain 'K' and resid 114 through 118 Processing helix chain 'L' and resid 128 through 133 Processing helix chain 'M' and resid 43 through 52 Processing helix chain 'M' and resid 109 through 118 removed outlier: 3.776A pdb=" N GLU M 115 " --> pdb=" O GLU M 111 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA M 116 " --> pdb=" O LEU M 112 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS M 118 " --> pdb=" O ARG M 114 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 31 removed outlier: 5.047A pdb=" N MET N 24 " --> pdb=" O MET N 20 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU N 28 " --> pdb=" O MET N 24 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL N 29 " --> pdb=" O ALA N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 53 removed outlier: 3.674A pdb=" N ARG N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL N 48 " --> pdb=" O LEU N 44 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 61 through 65 removed outlier: 3.934A pdb=" N LEU N 65 " --> pdb=" O ASN N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 73 through 82 Processing helix chain 'N' and resid 82 through 87 removed outlier: 3.771A pdb=" N PHE N 87 " --> pdb=" O LEU N 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 8 through 12 Processing helix chain 'O' and resid 14 through 18 removed outlier: 4.061A pdb=" N LYS O 17 " --> pdb=" O ALA O 14 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU O 18 " --> pdb=" O ARG O 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 14 through 18' Processing helix chain 'O' and resid 68 through 83 removed outlier: 3.577A pdb=" N ALA O 73 " --> pdb=" O ASP O 69 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL O 74 " --> pdb=" O ALA O 70 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL O 78 " --> pdb=" O VAL O 74 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ALA O 79 " --> pdb=" O GLY O 75 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 112 removed outlier: 3.600A pdb=" N ALA O 110 " --> pdb=" O LEU O 106 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 18 removed outlier: 5.216A pdb=" N ALA Q 11 " --> pdb=" O VAL Q 7 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS Q 13 " --> pdb=" O ALA Q 9 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 removed outlier: 3.664A pdb=" N ARG Q 29 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 68 removed outlier: 4.574A pdb=" N ILE Q 39 " --> pdb=" O PHE Q 35 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS Q 40 " --> pdb=" O GLN Q 36 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN Q 55 " --> pdb=" O GLN Q 51 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG Q 57 " --> pdb=" O LYS Q 53 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU Q 59 " --> pdb=" O GLN Q 55 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 72 Processing helix chain 'Q' and resid 74 through 84 removed outlier: 3.601A pdb=" N ILE Q 79 " --> pdb=" O TYR Q 75 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASN Q 80 " --> pdb=" O SER Q 76 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS Q 84 " --> pdb=" O ASN Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 93 through 95 No H-bonds generated for 'chain 'Q' and resid 93 through 95' Processing helix chain 'Q' and resid 96 through 101 removed outlier: 4.046A pdb=" N PHE Q 100 " --> pdb=" O ASP Q 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 114 removed outlier: 3.631A pdb=" N GLU Q 110 " --> pdb=" O THR Q 106 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS Q 111 " --> pdb=" O ALA Q 107 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA Q 112 " --> pdb=" O LEU Q 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 24 removed outlier: 3.776A pdb=" N VAL S 17 " --> pdb=" O SER S 13 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP S 22 " --> pdb=" O ARG S 18 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 57 removed outlier: 3.548A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS S 49 " --> pdb=" O VAL S 45 " (cutoff:3.500A) Processing helix chain 'T' and resid 6 through 10 removed outlier: 4.181A pdb=" N VAL T 10 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 40 through 50 removed outlier: 3.636A pdb=" N GLN T 48 " --> pdb=" O LYS T 44 " (cutoff:3.500A) Processing helix chain 'X' and resid 18 through 21 Processing helix chain 'X' and resid 22 through 27 Processing helix chain 'X' and resid 42 through 48 removed outlier: 5.749A pdb=" N ARG X 47 " --> pdb=" O LYS X 44 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ARG X 48 " --> pdb=" O GLN X 45 " (cutoff:3.500A) Processing helix chain 'X' and resid 49 through 60 Processing helix chain 'Y' and resid 17 through 22 removed outlier: 3.981A pdb=" N ALA Y 21 " --> pdb=" O PRO Y 17 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 42 No H-bonds generated for 'chain 'Y' and resid 40 through 42' Processing helix chain 'Y' and resid 43 through 50 removed outlier: 3.831A pdb=" N ILE Y 47 " --> pdb=" O ILE Y 43 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA Y 49 " --> pdb=" O GLY Y 45 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL Y 50 " --> pdb=" O MET Y 46 " (cutoff:3.500A) Processing helix chain 'Z' and resid 53 through 58 removed outlier: 3.935A pdb=" N VAL Z 57 " --> pdb=" O THR Z 53 " (cutoff:3.500A) Processing helix chain '1' and resid 14 through 20 removed outlier: 3.656A pdb=" N ALA 1 20 " --> pdb=" O SER 1 17 " (cutoff:3.500A) Processing helix chain '3' and resid 8 through 13 removed outlier: 3.839A pdb=" N ASN 3 13 " --> pdb=" O LEU 3 10 " (cutoff:3.500A) Processing helix chain '3' and resid 19 through 23 Processing helix chain '3' and resid 24 through 35 removed outlier: 3.815A pdb=" N LEU 3 31 " --> pdb=" O GLY 3 27 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA 3 32 " --> pdb=" O ARG 3 28 " (cutoff:3.500A) Processing helix chain '4' and resid 5 through 13 removed outlier: 3.778A pdb=" N ALA 4 9 " --> pdb=" O THR 4 5 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA 4 10 " --> pdb=" O VAL 4 6 " (cutoff:3.500A) Processing helix chain '4' and resid 51 through 56 Processing helix chain '6' and resid 24 through 29 Processing helix chain '6' and resid 33 through 49 removed outlier: 3.701A pdb=" N LYS 6 44 " --> pdb=" O ALA 6 40 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER 6 47 " --> pdb=" O ALA 6 43 " (cutoff:3.500A) Processing helix chain '6' and resid 74 through 84 Processing helix chain '6' and resid 102 through 113 Processing helix chain '6' and resid 120 through 136 removed outlier: 3.581A pdb=" N THR 6 131 " --> pdb=" O SER 6 127 " (cutoff:3.500A) Processing helix chain 'c' and resid 7 through 11 Processing helix chain 'c' and resid 24 through 45 removed outlier: 3.749A pdb=" N ALA c 29 " --> pdb=" O THR c 25 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ASP c 30 " --> pdb=" O LYS c 26 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP c 33 " --> pdb=" O ALA c 29 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR c 43 " --> pdb=" O ARG c 39 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS c 44 " --> pdb=" O GLN c 40 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 77 removed outlier: 3.537A pdb=" N VAL c 75 " --> pdb=" O ARG c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 90 Processing helix chain 'c' and resid 111 through 124 removed outlier: 3.775A pdb=" N ILE c 119 " --> pdb=" O VAL c 115 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 139 removed outlier: 3.513A pdb=" N ALA c 132 " --> pdb=" O MET c 128 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL c 137 " --> pdb=" O MET c 133 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN c 139 " --> pdb=" O ARG c 135 " (cutoff:3.500A) Processing helix chain 'c' and resid 140 through 142 No H-bonds generated for 'chain 'c' and resid 140 through 142' Processing helix chain 'c' and resid 176 through 180 removed outlier: 3.742A pdb=" N ASP c 180 " --> pdb=" O LEU c 177 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 14 removed outlier: 4.039A pdb=" N SER d 11 " --> pdb=" O LYS d 7 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU d 14 " --> pdb=" O LEU d 10 " (cutoff:3.500A) Processing helix chain 'd' and resid 50 through 65 removed outlier: 3.886A pdb=" N GLU d 56 " --> pdb=" O VAL d 52 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS d 57 " --> pdb=" O GLN d 53 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N TYR d 64 " --> pdb=" O VAL d 60 " (cutoff:3.500A) Processing helix chain 'd' and resid 67 through 81 removed outlier: 3.981A pdb=" N ARG d 80 " --> pdb=" O LYS d 76 " (cutoff:3.500A) Processing helix chain 'd' and resid 84 through 95 removed outlier: 3.519A pdb=" N LEU d 89 " --> pdb=" O THR d 85 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU d 90 " --> pdb=" O GLY d 86 " (cutoff:3.500A) Processing helix chain 'd' and resid 96 through 103 removed outlier: 3.746A pdb=" N TYR d 102 " --> pdb=" O ASP d 98 " (cutoff:3.500A) Processing helix chain 'd' and resid 109 through 119 removed outlier: 3.788A pdb=" N GLN d 115 " --> pdb=" O ALA d 111 " (cutoff:3.500A) Processing helix chain 'd' and resid 152 through 158 removed outlier: 3.531A pdb=" N LEU d 158 " --> pdb=" O VAL d 154 " (cutoff:3.500A) Processing helix chain 'd' and resid 159 through 163 Processing helix chain 'd' and resid 186 through 190 Processing helix chain 'd' and resid 195 through 203 removed outlier: 3.891A pdb=" N ILE d 199 " --> pdb=" O ASN d 195 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 68 removed outlier: 3.752A pdb=" N ILE e 59 " --> pdb=" O VAL e 55 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 115 Processing helix chain 'e' and resid 131 through 146 removed outlier: 4.484A pdb=" N ARG e 137 " --> pdb=" O ILE e 133 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE e 140 " --> pdb=" O VAL e 136 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY e 142 " --> pdb=" O ALA e 138 " (cutoff:3.500A) Processing helix chain 'e' and resid 151 through 156 Processing helix chain 'f' and resid 12 through 16 removed outlier: 3.723A pdb=" N SER f 15 " --> pdb=" O PRO f 12 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLU f 16 " --> pdb=" O ASP f 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 12 through 16' Processing helix chain 'f' and resid 17 through 31 removed outlier: 3.537A pdb=" N GLU f 23 " --> pdb=" O PRO f 19 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 80 removed outlier: 3.518A pdb=" N GLU f 73 " --> pdb=" O GLU f 69 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU f 74 " --> pdb=" O VAL f 70 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU f 75 " --> pdb=" O ILE f 71 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR f 76 " --> pdb=" O ASP f 72 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR f 77 " --> pdb=" O GLU f 73 " (cutoff:3.500A) Processing helix chain 'g' and resid 19 through 30 removed outlier: 3.958A pdb=" N PHE g 25 " --> pdb=" O LEU g 21 " (cutoff:3.500A) Processing helix chain 'g' and resid 34 through 48 removed outlier: 3.568A pdb=" N ALA g 38 " --> pdb=" O LYS g 34 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER g 44 " --> pdb=" O SER g 40 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA g 45 " --> pdb=" O ILE g 41 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU g 47 " --> pdb=" O TYR g 43 " (cutoff:3.500A) Processing helix chain 'g' and resid 48 through 53 removed outlier: 3.579A pdb=" N ARG g 52 " --> pdb=" O THR g 48 " (cutoff:3.500A) Processing helix chain 'g' and resid 58 through 67 removed outlier: 4.572A pdb=" N GLU g 62 " --> pdb=" O LEU g 58 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASN g 67 " --> pdb=" O VAL g 63 " (cutoff:3.500A) Processing helix chain 'g' and resid 91 through 106 removed outlier: 4.176A pdb=" N ALA g 97 " --> pdb=" O VAL g 93 " (cutoff:3.500A) Processing helix chain 'g' and resid 114 through 128 removed outlier: 3.770A pdb=" N ALA g 120 " --> pdb=" O ALA g 116 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU g 122 " --> pdb=" O ARG g 118 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER g 124 " --> pdb=" O ALA g 120 " (cutoff:3.500A) Processing helix chain 'g' and resid 130 through 142 removed outlier: 3.775A pdb=" N VAL g 134 " --> pdb=" O LYS g 130 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG g 137 " --> pdb=" O ALA g 133 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU g 138 " --> pdb=" O VAL g 134 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 19 removed outlier: 3.546A pdb=" N MET h 9 " --> pdb=" O PRO h 5 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU h 10 " --> pdb=" O ILE h 6 " (cutoff:3.500A) Processing helix chain 'h' and resid 29 through 42 removed outlier: 3.534A pdb=" N VAL h 38 " --> pdb=" O ALA h 34 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU h 41 " --> pdb=" O ASN h 37 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 98 Processing helix chain 'h' and resid 112 through 119 Processing helix chain 'i' and resid 48 through 53 Processing helix chain 'i' and resid 70 through 90 removed outlier: 3.709A pdb=" N ILE i 78 " --> pdb=" O GLN i 74 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET i 87 " --> pdb=" O THR i 83 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU i 88 " --> pdb=" O ARG i 84 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR i 89 " --> pdb=" O ALA i 85 " (cutoff:3.500A) Processing helix chain 'i' and resid 93 through 101 removed outlier: 3.521A pdb=" N ALA i 100 " --> pdb=" O GLU i 96 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 28 removed outlier: 5.283A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE j 25 " --> pdb=" O ALA j 21 " (cutoff:3.500A) Processing helix chain 'k' and resid 58 through 67 removed outlier: 4.382A pdb=" N VAL k 64 " --> pdb=" O PHE k 60 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA k 65 " --> pdb=" O ALA k 61 " (cutoff:3.500A) Processing helix chain 'k' and resid 68 through 72 Processing helix chain 'k' and resid 93 through 103 removed outlier: 3.826A pdb=" N GLY k 103 " --> pdb=" O LEU k 99 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 9 removed outlier: 3.581A pdb=" N LYS l 9 " --> pdb=" O GLN l 5 " (cutoff:3.500A) Processing helix chain 'm' and resid 13 through 19 Processing helix chain 'm' and resid 27 through 35 removed outlier: 3.987A pdb=" N LEU m 33 " --> pdb=" O SER m 29 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA m 34 " --> pdb=" O LYS m 30 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA m 35 " --> pdb=" O ALA m 31 " (cutoff:3.500A) Processing helix chain 'm' and resid 43 through 47 Processing helix chain 'm' and resid 48 through 56 removed outlier: 5.464A pdb=" N THR m 54 " --> pdb=" O GLY m 50 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU m 55 " --> pdb=" O GLN m 51 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG m 56 " --> pdb=" O ILE m 52 " (cutoff:3.500A) Processing helix chain 'm' and resid 64 through 81 Processing helix chain 'm' and resid 84 through 91 Processing helix chain 'm' and resid 105 through 110 Processing helix chain 'n' and resid 4 through 19 removed outlier: 3.607A pdb=" N GLU n 9 " --> pdb=" O MET n 5 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL n 10 " --> pdb=" O LYS n 6 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA n 14 " --> pdb=" O VAL n 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 19 through 31 removed outlier: 5.783A pdb=" N GLU n 25 " --> pdb=" O ALA n 21 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU n 26 " --> pdb=" O LYS n 22 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS n 27 " --> pdb=" O ARG n 23 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE n 30 " --> pdb=" O LEU n 26 " (cutoff:3.500A) Processing helix chain 'n' and resid 41 through 48 Processing helix chain 'n' and resid 80 through 89 Processing helix chain 'o' and resid 3 through 15 removed outlier: 4.153A pdb=" N LYS o 9 " --> pdb=" O GLU o 5 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N SER o 12 " --> pdb=" O ALA o 8 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU o 13 " --> pdb=" O LYS o 9 " (cutoff:3.500A) Processing helix chain 'o' and resid 23 through 44 removed outlier: 3.545A pdb=" N ALA o 29 " --> pdb=" O GLU o 25 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA o 33 " --> pdb=" O ALA o 29 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN o 34 " --> pdb=" O LEU o 30 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY o 40 " --> pdb=" O ASN o 36 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N HIS o 41 " --> pdb=" O HIS o 37 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU o 44 " --> pdb=" O GLY o 40 " (cutoff:3.500A) Processing helix chain 'o' and resid 51 through 71 removed outlier: 3.641A pdb=" N TYR o 68 " --> pdb=" O LYS o 64 " (cutoff:3.500A) Processing helix chain 'o' and resid 73 through 81 removed outlier: 3.540A pdb=" N TYR o 77 " --> pdb=" O ASP o 73 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR o 78 " --> pdb=" O VAL o 74 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 62 removed outlier: 4.111A pdb=" N HIS p 59 " --> pdb=" O ASP p 55 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TRP p 60 " --> pdb=" O ARG p 56 " (cutoff:3.500A) Processing helix chain 'p' and resid 68 through 78 Processing helix chain 'r' and resid 24 through 28 Processing helix chain 'r' and resid 48 through 64 removed outlier: 3.780A pdb=" N GLN r 53 " --> pdb=" O LYS r 49 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE r 58 " --> pdb=" O LEU r 54 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR r 63 " --> pdb=" O LYS r 59 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU r 64 " --> pdb=" O ARG r 60 " (cutoff:3.500A) Processing helix chain 's' and resid 11 through 24 removed outlier: 4.001A pdb=" N LYS s 17 " --> pdb=" O HIS s 13 " (cutoff:3.500A) Processing helix chain 's' and resid 69 through 74 Processing helix chain 't' and resid 5 through 40 removed outlier: 3.648A pdb=" N ARG t 9 " --> pdb=" O SER t 5 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE t 11 " --> pdb=" O LYS t 7 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA t 16 " --> pdb=" O GLN t 12 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER t 22 " --> pdb=" O LYS t 18 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG t 28 " --> pdb=" O ARG t 24 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE t 30 " --> pdb=" O MET t 26 " (cutoff:3.500A) Processing helix chain 't' and resid 42 through 58 removed outlier: 3.575A pdb=" N GLN t 47 " --> pdb=" O LYS t 43 " (cutoff:3.500A) Proline residue: t 55 - end of helix removed outlier: 3.567A pdb=" N ASP t 58 " --> pdb=" O GLN t 54 " (cutoff:3.500A) Processing helix chain 't' and resid 59 through 63 Processing helix chain 't' and resid 69 through 84 removed outlier: 3.519A pdb=" N ARG t 73 " --> pdb=" O ASN t 69 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N HIS t 74 " --> pdb=" O LYS t 70 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS t 75 " --> pdb=" O ALA t 71 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU t 78 " --> pdb=" O HIS t 74 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN t 81 " --> pdb=" O ASN t 77 " (cutoff:3.500A) Processing helix chain '7' and resid 41 through 44 Processing helix chain '7' and resid 45 through 61 removed outlier: 3.584A pdb=" N ASN 7 50 " --> pdb=" O VAL 7 46 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA 7 52 " --> pdb=" O MET 7 48 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LEU 7 53 " --> pdb=" O PHE 7 49 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU 7 55 " --> pdb=" O GLU 7 51 " (cutoff:3.500A) Processing helix chain '7' and resid 72 through 77 removed outlier: 4.279A pdb=" N GLU 7 77 " --> pdb=" O ARG 7 73 " (cutoff:3.500A) Processing helix chain '7' and resid 79 through 83 Processing helix chain '7' and resid 102 through 122 removed outlier: 4.276A pdb=" N GLN 7 108 " --> pdb=" O LYS 7 104 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER 7 109 " --> pdb=" O THR 7 105 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE 7 110 " --> pdb=" O VAL 7 106 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG 7 112 " --> pdb=" O GLN 7 108 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN 7 119 " --> pdb=" O ASP 7 115 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER 7 120 " --> pdb=" O LEU 7 116 " (cutoff:3.500A) Processing helix chain '7' and resid 123 through 126 Processing helix chain '7' and resid 129 through 147 removed outlier: 3.638A pdb=" N LEU 7 134 " --> pdb=" O LYS 7 130 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLU 7 139 " --> pdb=" O MET 7 135 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU 7 140 " --> pdb=" O ARG 7 136 " (cutoff:3.500A) Processing helix chain '7' and resid 168 through 179 removed outlier: 3.534A pdb=" N ALA 7 175 " --> pdb=" O ALA 7 171 " (cutoff:3.500A) Processing helix chain '7' and resid 191 through 195 removed outlier: 3.574A pdb=" N GLY 7 194 " --> pdb=" O ASP 7 191 " (cutoff:3.500A) Processing helix chain '7' and resid 205 through 222 removed outlier: 3.572A pdb=" N THR 7 210 " --> pdb=" O ILE 7 206 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR 7 219 " --> pdb=" O ALA 7 215 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU 7 222 " --> pdb=" O ALA 7 218 " (cutoff:3.500A) Processing helix chain 'u' and resid 15 through 19 Processing helix chain 'u' and resid 28 through 33 removed outlier: 4.538A pdb=" N ARG u 33 " --> pdb=" O ALA u 29 " (cutoff:3.500A) Processing helix chain 'u' and resid 37 through 44 removed outlier: 4.036A pdb=" N THR u 41 " --> pdb=" O TYR u 37 " (cutoff:3.500A) Processing helix chain 'u' and resid 46 through 51 Processing sheet with id=AA1, first strand: chain 'V' and resid 28 through 31 removed outlier: 6.082A pdb=" N ILE V 29 " --> pdb=" O PHE V 91 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLN V 78 " --> pdb=" O GLN V 87 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ILE V 89 " --> pdb=" O ASP V 76 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ASP V 76 " --> pdb=" O ILE V 89 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N PHE V 91 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA V 74 " --> pdb=" O PHE V 91 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 127 through 128 Processing sheet with id=AA3, first strand: chain 'G' and resid 15 through 19 removed outlier: 3.811A pdb=" N LYS G 17 " --> pdb=" O THR G 24 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.790A pdb=" N LYS G 84 " --> pdb=" O LEU G 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 95 through 96 removed outlier: 3.691A pdb=" N ILE G 102 " --> pdb=" O HIS G 114 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 84 through 85 Processing sheet with id=AA7, first strand: chain 'H' and resid 128 through 130 Processing sheet with id=AA8, first strand: chain 'K' and resid 7 through 9 Processing sheet with id=AA9, first strand: chain 'K' and resid 39 through 42 removed outlier: 4.816A pdb=" N LYS K 59 " --> pdb=" O LEU K 87 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 69 through 70 Processing sheet with id=AB2, first strand: chain 'M' and resid 39 through 41 Processing sheet with id=AB3, first strand: chain 'M' and resid 62 through 63 Processing sheet with id=AB4, first strand: chain 'P' and resid 62 through 63 Processing sheet with id=AB5, first strand: chain 'Y' and resid 6 through 7 Processing sheet with id=AB6, first strand: chain '2' and resid 9 through 10 Processing sheet with id=AB7, first strand: chain '6' and resid 8 through 12 Processing sheet with id=AB8, first strand: chain '6' and resid 98 through 101 Processing sheet with id=AB9, first strand: chain 'c' and resid 51 through 55 removed outlier: 6.392A pdb=" N HIS c 68 " --> pdb=" O SER c 52 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE c 54 " --> pdb=" O THR c 66 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N THR c 66 " --> pdb=" O ILE c 54 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'c' and resid 168 through 169 Processing sheet with id=AC2, first strand: chain 'd' and resid 127 through 128 Processing sheet with id=AC3, first strand: chain 'e' and resid 11 through 16 removed outlier: 6.683A pdb=" N LEU e 35 " --> pdb=" O ILE e 15 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL e 38 " --> pdb=" O GLY e 46 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG e 44 " --> pdb=" O ASP e 40 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'e' and resid 21 through 23 Processing sheet with id=AC5, first strand: chain 'e' and resid 85 through 88 Processing sheet with id=AC6, first strand: chain 'e' and resid 104 through 105 Processing sheet with id=AC7, first strand: chain 'f' and resid 4 through 6 removed outlier: 3.613A pdb=" N GLU f 5 " --> pdb=" O MET f 90 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'f' and resid 41 through 46 removed outlier: 7.097A pdb=" N MET f 9 " --> pdb=" O ILE f 85 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'h' and resid 23 through 27 Processing sheet with id=AD1, first strand: chain 'h' and resid 73 through 76 removed outlier: 3.556A pdb=" N SER h 73 " --> pdb=" O ALA h 129 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS h 86 " --> pdb=" O GLY h 122 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'h' and resid 73 through 76 removed outlier: 3.556A pdb=" N SER h 73 " --> pdb=" O ALA h 129 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ILE h 124 " --> pdb=" O SER h 104 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N SER h 104 " --> pdb=" O ILE h 124 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'i' and resid 5 through 7 removed outlier: 3.518A pdb=" N GLY i 7 " --> pdb=" O VAL i 18 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL i 18 " --> pdb=" O GLY i 7 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N VAL i 28 " --> pdb=" O ILE i 64 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'j' and resid 10 through 12 removed outlier: 3.983A pdb=" N GLU j 47 " --> pdb=" O ILE j 67 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR j 69 " --> pdb=" O ARG j 45 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG j 45 " --> pdb=" O THR j 69 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'k' and resid 29 through 32 Processing sheet with id=AD6, first strand: chain 'l' and resid 29 through 30 Processing sheet with id=AD7, first strand: chain 'l' and resid 51 through 55 Processing sheet with id=AD8, first strand: chain 'p' and resid 2 through 3 Processing sheet with id=AD9, first strand: chain 'q' and resid 19 through 22 removed outlier: 3.971A pdb=" N ILE q 20 " --> pdb=" O VAL q 45 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain '7' and resid 89 through 91 928 hydrogen bonds defined for protein. 2484 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3997 hydrogen bonds 6248 hydrogen bond angles 0 basepair planarities 1590 basepair parallelities 2207 stacking parallelities Total time for adding SS restraints: 213.59 Time building geometry restraints manager: 70.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.99 - 1.19: 4 1.19 - 1.39: 55497 1.39 - 1.59: 90612 1.59 - 1.79: 8726 1.79 - 1.99: 198 Bond restraints: 155037 Sorted by residual: bond pdb=" C LEU u 15 " pdb=" N ARG u 16 " ideal model delta sigma weight residual 1.333 0.989 0.343 1.45e-02 4.76e+03 5.61e+02 bond pdb=" N VAL R 54 " pdb=" CA VAL R 54 " ideal model delta sigma weight residual 1.459 1.226 0.233 1.25e-02 6.40e+03 3.47e+02 bond pdb=" CA VAL R 54 " pdb=" CB VAL R 54 " ideal model delta sigma weight residual 1.540 1.776 -0.236 1.36e-02 5.41e+03 3.01e+02 bond pdb=" CA VAL R 54 " pdb=" C VAL R 54 " ideal model delta sigma weight residual 1.523 1.713 -0.190 1.27e-02 6.20e+03 2.23e+02 bond pdb=" CB PHE R 53 " pdb=" CG PHE R 53 " ideal model delta sigma weight residual 1.502 1.813 -0.311 2.30e-02 1.89e+03 1.82e+02 ... (remaining 155032 not shown) Histogram of bond angle deviations from ideal: 74.98 - 88.01: 4 88.01 - 101.04: 328 101.04 - 114.07: 125163 114.07 - 127.10: 95689 127.10 - 140.13: 10744 Bond angle restraints: 231928 Sorted by residual: angle pdb=" CA PHE R 53 " pdb=" C PHE R 53 " pdb=" N VAL R 54 " ideal model delta sigma weight residual 115.51 79.08 36.43 1.24e+00 6.50e-01 8.63e+02 angle pdb=" N ILE E 73 " pdb=" CA ILE E 73 " pdb=" C ILE E 73 " ideal model delta sigma weight residual 112.43 131.70 -19.27 9.20e-01 1.18e+00 4.39e+02 angle pdb=" N LYS E 74 " pdb=" CA LYS E 74 " pdb=" C LYS E 74 " ideal model delta sigma weight residual 112.72 90.85 21.87 1.14e+00 7.69e-01 3.68e+02 angle pdb=" C VAL R 54 " pdb=" CA VAL R 54 " pdb=" CB VAL R 54 " ideal model delta sigma weight residual 111.29 140.13 -28.84 1.64e+00 3.72e-01 3.09e+02 angle pdb=" N LEU L 6 " pdb=" CA LEU L 6 " pdb=" C LEU L 6 " ideal model delta sigma weight residual 111.90 134.26 -22.36 1.32e+00 5.74e-01 2.87e+02 ... (remaining 231923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 78286 35.79 - 71.58: 4176 71.58 - 107.36: 330 107.36 - 143.15: 35 143.15 - 178.94: 44 Dihedral angle restraints: 82871 sinusoidal: 66564 harmonic: 16307 Sorted by residual: dihedral pdb=" N VAL R 54 " pdb=" C VAL R 54 " pdb=" CA VAL R 54 " pdb=" CB VAL R 54 " ideal model delta harmonic sigma weight residual 123.40 70.08 53.32 0 2.50e+00 1.60e-01 4.55e+02 dihedral pdb=" C5' C a1397 " pdb=" C4' C a1397 " pdb=" C3' C a1397 " pdb=" O3' C a1397 " ideal model delta sinusoidal sigma weight residual 147.00 73.27 73.73 1 8.00e+00 1.56e-02 1.08e+02 dihedral pdb=" C LYS 1 52 " pdb=" N LYS 1 52 " pdb=" CA LYS 1 52 " pdb=" CB LYS 1 52 " ideal model delta harmonic sigma weight residual -122.60 -96.65 -25.95 0 2.50e+00 1.60e-01 1.08e+02 ... (remaining 82868 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.183: 28348 0.183 - 0.367: 1155 0.367 - 0.550: 92 0.550 - 0.734: 31 0.734 - 0.917: 13 Chirality restraints: 29639 Sorted by residual: chirality pdb=" CA PRO C 28 " pdb=" N PRO C 28 " pdb=" C PRO C 28 " pdb=" CB PRO C 28 " both_signs ideal model delta sigma weight residual False 2.72 1.80 0.92 2.00e-01 2.50e+01 2.10e+01 chirality pdb=" CB VAL R 54 " pdb=" CA VAL R 54 " pdb=" CG1 VAL R 54 " pdb=" CG2 VAL R 54 " both_signs ideal model delta sigma weight residual False -2.63 -3.54 0.91 2.00e-01 2.50e+01 2.09e+01 chirality pdb=" C3' G B1250 " pdb=" C4' G B1250 " pdb=" O3' G B1250 " pdb=" C2' G B1250 " both_signs ideal model delta sigma weight residual False -2.74 -1.83 -0.91 2.00e-01 2.50e+01 2.08e+01 ... (remaining 29636 not shown) Planarity restraints: 12421 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR J 75 " -0.307 2.00e-02 2.50e+03 1.69e-01 5.69e+02 pdb=" CG TYR J 75 " 0.110 2.00e-02 2.50e+03 pdb=" CD1 TYR J 75 " 0.123 2.00e-02 2.50e+03 pdb=" CD2 TYR J 75 " 0.127 2.00e-02 2.50e+03 pdb=" CE1 TYR J 75 " 0.083 2.00e-02 2.50e+03 pdb=" CE2 TYR J 75 " 0.091 2.00e-02 2.50e+03 pdb=" CZ TYR J 75 " 0.042 2.00e-02 2.50e+03 pdb=" OH TYR J 75 " -0.269 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B2272 " -0.068 2.00e-02 2.50e+03 1.57e-01 5.55e+02 pdb=" N1 U B2272 " -0.066 2.00e-02 2.50e+03 pdb=" C2 U B2272 " 0.017 2.00e-02 2.50e+03 pdb=" O2 U B2272 " -0.035 2.00e-02 2.50e+03 pdb=" N3 U B2272 " 0.172 2.00e-02 2.50e+03 pdb=" C4 U B2272 " 0.213 2.00e-02 2.50e+03 pdb=" O4 U B2272 " -0.338 2.00e-02 2.50e+03 pdb=" C5 U B2272 " 0.145 2.00e-02 2.50e+03 pdb=" C6 U B2272 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B1060 " -0.149 2.00e-02 2.50e+03 1.51e-01 5.10e+02 pdb=" N1 U B1060 " -0.034 2.00e-02 2.50e+03 pdb=" C2 U B1060 " 0.031 2.00e-02 2.50e+03 pdb=" O2 U B1060 " 0.007 2.00e-02 2.50e+03 pdb=" N3 U B1060 " 0.135 2.00e-02 2.50e+03 pdb=" C4 U B1060 " 0.168 2.00e-02 2.50e+03 pdb=" O4 U B1060 " -0.331 2.00e-02 2.50e+03 pdb=" C5 U B1060 " 0.150 2.00e-02 2.50e+03 pdb=" C6 U B1060 " 0.023 2.00e-02 2.50e+03 ... (remaining 12418 not shown) Histogram of nonbonded interaction distances: 0.15 - 1.10: 496 1.10 - 2.05: 2629 2.05 - 3.00: 85479 3.00 - 3.95: 488095 3.95 - 4.90: 790612 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1367311 Sorted by model distance: nonbonded pdb=" C VAL c 75 " pdb=" CA SER j 54 " model vdw 0.154 3.700 nonbonded pdb=" N4 C a1262 " pdb=" CZ2 TRP n 100 " model vdw 0.199 3.420 nonbonded pdb=" CA PHE F 137 " pdb=" CB ARG m 112 " model vdw 0.257 3.870 nonbonded pdb=" N1 C a1359 " pdb=" CA PRO n 69 " model vdw 0.309 3.550 nonbonded pdb=" N6 A a1012 " pdb=" CA VAL n 33 " model vdw 0.335 3.550 ... (remaining 1367306 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 9.290 Check model and map are aligned: 1.500 Set scattering table: 0.920 Process input model: 475.440 Find NCS groups from input model: 2.720 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 494.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6419 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 : 0.006 0.343 155037 Z= 0.358 Angle : 1.253 36.427 231928 Z= 0.798 Chirality : 0.096 0.917 29639 Planarity : 0.014 0.188 12421 Dihedral : 17.385 178.941 72355 Min Nonbonded Distance : 0.154 Molprobity Statistics. All-atom Clashscore : 55.29 Ramachandran Plot: Outliers : 14.74 % Allowed : 26.57 % Favored : 58.69 % Rotamer: Outliers : 23.17 % Allowed : 18.21 % Favored : 58.62 % Cbeta Deviations : 0.48 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -7.10 (0.07), residues: 5631 helix: -4.33 (0.08), residues: 1315 sheet: -4.73 (0.15), residues: 646 loop : -5.23 (0.07), residues: 3670 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3148 residues out of total 4669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1082 poor density : 2066 time to evaluate : 5.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1082 outliers final: 294 residues processed: 2663 average time/residue: 1.4226 time to fit residues: 6291.6456 Evaluate side-chains 1580 residues out of total 4669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 294 poor density : 1286 time to evaluate : 5.745 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 294 outliers final: 38 residues processed: 294 average time/residue: 1.2765 time to fit residues: 663.0966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1005 random chunks: chunk 848 optimal weight: 7.9990 chunk 761 optimal weight: 9.9990 chunk 422 optimal weight: 8.9990 chunk 260 optimal weight: 10.0000 chunk 513 optimal weight: 7.9990 chunk 406 optimal weight: 2.9990 chunk 787 optimal weight: 0.0770 chunk 304 optimal weight: 0.8980 chunk 478 optimal weight: 0.0980 chunk 586 optimal weight: 1.9990 chunk 912 optimal weight: 20.0000 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 88 HIS C 14 HIS C 133 ASN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN D 32 ASN ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN ** D 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN E 97 ASN E 136 GLN E 156 ASN E 195 GLN F 26 GLN F 36 ASN ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 HIS G 138 GLN J 128 ASN J 131 ASN J 135 GLN K 5 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 17 ASN M 88 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 HIS ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 104 GLN P 2 ASN ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 GLN Q 55 GLN Q 58 GLN R 12 HIS R 18 GLN S 7 HIS ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 59 ASN U 26 ASN U 39 ASN ** W 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 39 GLN Y 8 GLN Z 30 HIS ** 4 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 13 ASN 6 11 GLN 6 29 GLN 6 93 ASN c 31 ASN ** c 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 70 GLN d 99 ASN d 151 GLN ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 147 ASN g 27 ASN g 67 ASN g 85 GLN h 15 ASN ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 74 GLN i 109 GLN ** i 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 20 GLN ** j 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 99 GLN k 23 HIS k 27 ASN k 37 GLN l 45 ASN ** l 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 13 HIS ** m 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 61 ASN n 65 GLN o 36 ASN o 39 GLN ** p 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 13 HIS ** s 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 51 HIS s 55 GLN t 12 GLN ** t 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 23 ASN 7 38 HIS 7 119 GLN 7 169 HIS ** 7 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6607 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.016 155037 Z= 0.670 Angle : 1.347 73.376 231928 Z= 0.657 Chirality : 0.067 3.841 29639 Planarity : 0.011 0.274 12421 Dihedral : 15.801 178.205 61107 Min Nonbonded Distance : 1.298 Molprobity Statistics. All-atom Clashscore : 33.81 Ramachandran Plot: Outliers : 4.67 % Allowed : 24.81 % Favored : 70.52 % Rotamer: Outliers : 9.79 % Allowed : 27.48 % Favored : 62.73 % Cbeta Deviations : 0.72 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 2.60 % Twisted General : 0.93 % 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: -6.07 (0.08), residues: 5631 helix: -3.12 (0.11), residues: 1381 sheet: -4.02 (0.17), residues: 625 loop : -4.74 (0.08), residues: 3625 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1888 residues out of total 4669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 457 poor density : 1431 time to evaluate : 5.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 457 outliers final: 183 residues processed: 1744 average time/residue: 1.3314 time to fit residues: 3988.0231 Evaluate side-chains 1383 residues out of total 4669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 1200 time to evaluate : 5.771 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 183 outliers final: 5 residues processed: 183 average time/residue: 1.1459 time to fit residues: 387.8926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1005 random chunks: chunk 507 optimal weight: 0.9980 chunk 283 optimal weight: 10.0000 chunk 759 optimal weight: 10.0000 chunk 621 optimal weight: 10.0000 chunk 251 optimal weight: 10.0000 chunk 914 optimal weight: 7.9990 chunk 987 optimal weight: 8.9990 chunk 814 optimal weight: 10.0000 chunk 906 optimal weight: 20.0000 chunk 311 optimal weight: 2.9990 chunk 733 optimal weight: 9.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 88 HIS ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 GLN D 167 ASN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 GLN F 80 GLN ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 28 ASN ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN L 54 GLN O 38 GLN O 98 GLN P 6 GLN ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN Q 51 GLN ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 58 ASN Y 48 ASN Z 30 HIS 1 4 GLN 1 40 HIS ** 4 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 25 HIS 6 33 ASN 6 93 ASN c 5 HIS ** c 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 ASN d 119 HIS d 135 GLN e 121 ASN e 134 ASN f 14 GLN ** f 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 67 ASN h 15 ASN ** i 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 20 GLN ** j 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 23 HIS k 27 ASN k 80 ASN l 5 GLN m 13 HIS m 90 HIS n 42 ASN o 39 GLN p 18 GLN ** p 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 79 ASN ** s 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 17 HIS ** 7 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.6146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.962 155037 Z= 0.702 Angle : 1.268 60.967 231928 Z= 0.623 Chirality : 0.059 1.356 29639 Planarity : 0.011 0.449 12421 Dihedral : 16.119 177.821 61107 Min Nonbonded Distance : 1.351 Molprobity Statistics. All-atom Clashscore : 36.02 Ramachandran Plot: Outliers : 3.98 % Allowed : 25.00 % Favored : 71.02 % Rotamer: Outliers : 11.27 % Allowed : 28.83 % Favored : 59.91 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 2.60 % Twisted General : 0.87 % 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: -5.51 (0.09), residues: 5631 helix: -2.72 (0.11), residues: 1382 sheet: -3.45 (0.18), residues: 572 loop : -4.39 (0.08), residues: 3677 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1905 residues out of total 4669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 526 poor density : 1379 time to evaluate : 6.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 526 outliers final: 247 residues processed: 1736 average time/residue: 1.3836 time to fit residues: 4146.2783 Evaluate side-chains 1410 residues out of total 4669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 1163 time to evaluate : 5.803 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 247 outliers final: 5 residues processed: 247 average time/residue: 1.1955 time to fit residues: 549.8123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1005 random chunks: chunk 903 optimal weight: 7.9990 chunk 687 optimal weight: 10.0000 chunk 474 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 436 optimal weight: 3.9990 chunk 613 optimal weight: 7.9990 chunk 917 optimal weight: 6.9990 chunk 971 optimal weight: 1.9990 chunk 479 optimal weight: 0.9980 chunk 869 optimal weight: 7.9990 chunk 261 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 GLN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 ASN E 94 GLN E 97 ASN ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 6 GLN Q 43 GLN ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 59 ASN ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 45 GLN ** W 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 58 ASN Y 48 ASN ** Z 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 53 GLN ** e 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 96 GLN e 134 ASN ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 125 GLN ** j 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 27 ASN k 80 ASN n 3 GLN ** n 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 27 GLN ** p 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 83 ASN 7 14 HIS ** 7 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.6747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.943 155037 Z= 0.596 Angle : 1.032 60.681 231928 Z= 0.510 Chirality : 0.048 1.328 29639 Planarity : 0.008 0.302 12421 Dihedral : 15.670 179.889 61107 Min Nonbonded Distance : 1.343 Molprobity Statistics. All-atom Clashscore : 27.58 Ramachandran Plot: Outliers : 3.52 % Allowed : 21.97 % Favored : 74.52 % Rotamer: Outliers : 6.28 % Allowed : 32.47 % Favored : 61.26 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 3.12 % Twisted General : 0.73 % 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: -5.06 (0.09), residues: 5631 helix: -2.21 (0.12), residues: 1361 sheet: -3.17 (0.19), residues: 588 loop : -4.15 (0.09), residues: 3682 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1594 residues out of total 4669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 293 poor density : 1301 time to evaluate : 5.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 293 outliers final: 139 residues processed: 1493 average time/residue: 1.2751 time to fit residues: 3263.1971 Evaluate side-chains 1259 residues out of total 4669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 1120 time to evaluate : 5.937 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 139 outliers final: 5 residues processed: 139 average time/residue: 1.2251 time to fit residues: 319.6107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1005 random chunks: chunk 809 optimal weight: 9.9990 chunk 551 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 chunk 723 optimal weight: 9.9990 chunk 400 optimal weight: 3.9990 chunk 828 optimal weight: 2.9990 chunk 671 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 496 optimal weight: 2.9990 chunk 871 optimal weight: 0.7980 chunk 245 optimal weight: 10.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS G 63 GLN G 114 HIS ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN P 74 GLN ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 88 ASN d 135 GLN ** e 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 15 HIS j 20 GLN k 27 ASN k 80 ASN ** m 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 70 HIS p 18 GLN q 50 ASN r 51 GLN ** s 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 83 ASN 7 35 ASN ** 7 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.7522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.874 155037 Z= 0.599 Angle : 0.998 59.853 231928 Z= 0.497 Chirality : 0.046 1.171 29639 Planarity : 0.008 0.148 12421 Dihedral : 15.721 179.687 61107 Min Nonbonded Distance : 1.304 Molprobity Statistics. All-atom Clashscore : 28.60 Ramachandran Plot: Outliers : 3.20 % Allowed : 23.19 % Favored : 73.61 % Rotamer: Outliers : 6.15 % Allowed : 33.24 % Favored : 60.61 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 3.12 % Twisted General : 0.66 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.92 (0.10), residues: 5631 helix: -2.13 (0.12), residues: 1407 sheet: -2.94 (0.20), residues: 554 loop : -4.08 (0.09), residues: 3670 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1538 residues out of total 4669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 287 poor density : 1251 time to evaluate : 6.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 287 outliers final: 171 residues processed: 1448 average time/residue: 1.3482 time to fit residues: 3384.1061 Evaluate side-chains 1306 residues out of total 4669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 1135 time to evaluate : 5.824 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 171 outliers final: 4 residues processed: 171 average time/residue: 1.1267 time to fit residues: 367.4174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1005 random chunks: chunk 326 optimal weight: 6.9990 chunk 874 optimal weight: 0.5980 chunk 192 optimal weight: 9.9990 chunk 570 optimal weight: 8.9990 chunk 239 optimal weight: 10.0000 chunk 972 optimal weight: 5.9990 chunk 807 optimal weight: 2.9990 chunk 450 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 321 optimal weight: 0.0870 chunk 510 optimal weight: 8.9990 overall best weight: 2.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN ** E 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 ASN ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 17 ASN P 9 GLN Q 43 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 39 ASN ** U 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 63 ASN ** h 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 27 ASN k 80 ASN m 11 HIS ** m 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 18 GLN q 50 ASN ** s 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 83 ASN ** 7 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.7871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.868 155037 Z= 0.564 Angle : 0.925 59.548 231928 Z= 0.459 Chirality : 0.042 0.943 29639 Planarity : 0.007 0.152 12421 Dihedral : 15.562 179.709 61107 Min Nonbonded Distance : 1.288 Molprobity Statistics. All-atom Clashscore : 25.29 Ramachandran Plot: Outliers : 3.05 % Allowed : 21.33 % Favored : 75.62 % Rotamer: Outliers : 3.94 % Allowed : 34.98 % Favored : 61.08 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 3.12 % Twisted General : 0.71 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.77 (0.10), residues: 5631 helix: -1.98 (0.12), residues: 1411 sheet: -2.73 (0.20), residues: 579 loop : -4.02 (0.09), residues: 3641 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1425 residues out of total 4669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1241 time to evaluate : 5.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 184 outliers final: 82 residues processed: 1359 average time/residue: 1.3163 time to fit residues: 3070.0546 Evaluate side-chains 1227 residues out of total 4669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 1145 time to evaluate : 5.260 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 4 residues processed: 82 average time/residue: 1.1565 time to fit residues: 179.3970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1005 random chunks: chunk 937 optimal weight: 0.0470 chunk 109 optimal weight: 10.0000 chunk 554 optimal weight: 0.8980 chunk 710 optimal weight: 10.0000 chunk 550 optimal weight: 4.9990 chunk 818 optimal weight: 0.4980 chunk 542 optimal weight: 1.9990 chunk 968 optimal weight: 5.9990 chunk 606 optimal weight: 0.3980 chunk 590 optimal weight: 0.9990 chunk 447 optimal weight: 9.9990 overall best weight: 0.5680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 ASN G 114 HIS M 17 ASN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 6 HIS ** 4 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 122 GLN ** e 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 3 HIS ** f 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 125 GLN ** j 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 80 ASN ** l 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 34 ASN p 18 GLN ** p 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 50 ASN ** s 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 83 ASN ** 7 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.8106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.891 155037 Z= 0.551 Angle : 0.866 39.899 231928 Z= 0.433 Chirality : 0.039 0.898 29639 Planarity : 0.007 0.163 12421 Dihedral : 15.334 179.121 61107 Min Nonbonded Distance : 1.299 Molprobity Statistics. All-atom Clashscore : 22.68 Ramachandran Plot: Outliers : 2.97 % Allowed : 20.32 % Favored : 76.72 % Rotamer: Outliers : 3.41 % Allowed : 36.28 % Favored : 60.31 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 3.12 % Twisted General : 0.66 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.50 (0.10), residues: 5631 helix: -1.74 (0.13), residues: 1387 sheet: -2.37 (0.22), residues: 539 loop : -3.88 (0.09), residues: 3705 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1420 residues out of total 4669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1261 time to evaluate : 5.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 159 outliers final: 69 residues processed: 1367 average time/residue: 1.3433 time to fit residues: 3144.7326 Evaluate side-chains 1201 residues out of total 4669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 1132 time to evaluate : 5.750 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 3 residues processed: 69 average time/residue: 1.0862 time to fit residues: 147.5449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1005 random chunks: chunk 599 optimal weight: 4.9990 chunk 386 optimal weight: 8.9990 chunk 578 optimal weight: 6.9990 chunk 291 optimal weight: 10.0000 chunk 190 optimal weight: 10.0000 chunk 187 optimal weight: 10.0000 chunk 615 optimal weight: 10.0000 chunk 659 optimal weight: 9.9990 chunk 478 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 761 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 HIS ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN ** S 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 15 HIS ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN ** W 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 122 GLN d 88 ASN d 135 GLN e 11 GLN ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 125 GLN k 80 ASN ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 18 GLN ** q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 50 ASN ** 7 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.8733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.863 155037 Z= 0.659 Angle : 1.055 40.126 231928 Z= 0.521 Chirality : 0.049 0.984 29639 Planarity : 0.008 0.168 12421 Dihedral : 15.862 179.875 61107 Min Nonbonded Distance : 1.262 Molprobity Statistics. All-atom Clashscore : 30.97 Ramachandran Plot: Outliers : 3.07 % Allowed : 22.66 % Favored : 74.27 % Rotamer: Outliers : 4.22 % Allowed : 36.43 % Favored : 59.35 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 3.12 % Twisted General : 0.84 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.75 (0.10), residues: 5631 helix: -2.04 (0.12), residues: 1396 sheet: -2.56 (0.21), residues: 581 loop : -4.00 (0.09), residues: 3654 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1374 residues out of total 4669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 1177 time to evaluate : 5.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 197 outliers final: 127 residues processed: 1275 average time/residue: 1.3743 time to fit residues: 3027.3606 Evaluate side-chains 1236 residues out of total 4669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 1109 time to evaluate : 5.764 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 127 outliers final: 3 residues processed: 127 average time/residue: 1.1125 time to fit residues: 268.2869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1005 random chunks: chunk 881 optimal weight: 4.9990 chunk 927 optimal weight: 6.9990 chunk 846 optimal weight: 1.9990 chunk 902 optimal weight: 5.9990 chunk 543 optimal weight: 1.9990 chunk 393 optimal weight: 5.9990 chunk 708 optimal weight: 10.0000 chunk 277 optimal weight: 10.0000 chunk 815 optimal weight: 6.9990 chunk 853 optimal weight: 5.9990 chunk 899 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 GLN ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 41 HIS ** Z 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 68 HIS c 122 GLN ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 27 ASN h 15 ASN i 125 GLN k 80 ASN ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 18 GLN ** q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 14 HIS ** 7 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.9054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.862 155037 Z= 0.580 Angle : 0.935 40.283 231928 Z= 0.467 Chirality : 0.043 0.987 29639 Planarity : 0.007 0.152 12421 Dihedral : 15.733 179.536 61107 Min Nonbonded Distance : 1.289 Molprobity Statistics. All-atom Clashscore : 27.08 Ramachandran Plot: Outliers : 2.88 % Allowed : 21.22 % Favored : 75.90 % Rotamer: Outliers : 2.18 % Allowed : 37.80 % Favored : 60.01 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 2.08 % Twisted General : 0.73 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.65 (0.10), residues: 5631 helix: -1.96 (0.13), residues: 1391 sheet: -2.43 (0.22), residues: 548 loop : -3.93 (0.09), residues: 3692 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1297 residues out of total 4669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1195 time to evaluate : 5.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 102 outliers final: 54 residues processed: 1248 average time/residue: 1.3463 time to fit residues: 2869.1712 Evaluate side-chains 1173 residues out of total 4669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 1119 time to evaluate : 5.791 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 2 residues processed: 54 average time/residue: 1.1517 time to fit residues: 119.1526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1005 random chunks: chunk 592 optimal weight: 10.0000 chunk 954 optimal weight: 8.9990 chunk 582 optimal weight: 0.9990 chunk 452 optimal weight: 7.9990 chunk 663 optimal weight: 10.0000 chunk 1001 optimal weight: 10.0000 chunk 921 optimal weight: 6.9990 chunk 797 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 615 optimal weight: 9.9990 chunk 488 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 HIS ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN K 89 ASN ** M 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 15 HIS ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 25 GLN ** X 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 42 ASN c 68 HIS c 122 GLN ** d 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 3 GLN h 15 ASN i 125 GLN k 80 ASN ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 18 GLN ** q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 73 HIS ** s 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.9614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.852 155037 Z= 0.635 Angle : 1.035 40.361 231928 Z= 0.515 Chirality : 0.048 1.039 29639 Planarity : 0.008 0.155 12421 Dihedral : 16.176 179.255 61107 Min Nonbonded Distance : 1.284 Molprobity Statistics. All-atom Clashscore : 32.27 Ramachandran Plot: Outliers : 2.93 % Allowed : 23.99 % Favored : 73.08 % Rotamer: Outliers : 1.97 % Allowed : 38.87 % Favored : 59.16 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 2.08 % Twisted General : 0.89 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.79 (0.10), residues: 5631 helix: -2.10 (0.12), residues: 1404 sheet: -2.44 (0.21), residues: 574 loop : -4.05 (0.09), residues: 3653 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1261 residues out of total 4669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 1169 time to evaluate : 5.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 92 outliers final: 56 residues processed: 1206 average time/residue: 1.3206 time to fit residues: 2732.6537 Evaluate side-chains 1166 residues out of total 4669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 1110 time to evaluate : 5.750 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 2 residues processed: 56 average time/residue: 1.2089 time to fit residues: 126.7535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1005 random chunks: chunk 633 optimal weight: 10.0000 chunk 849 optimal weight: 5.9990 chunk 244 optimal weight: 10.0000 chunk 735 optimal weight: 10.0000 chunk 117 optimal weight: 30.0000 chunk 221 optimal weight: 20.0000 chunk 798 optimal weight: 6.9990 chunk 334 optimal weight: 1.9990 chunk 819 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 overall best weight: 6.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 GLN K 89 ASN ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 9 HIS S 57 ASN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 ASN ** W 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 41 HIS ** 3 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 122 GLN ** d 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 15 ASN i 125 GLN j 35 GLN ** j 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 80 ASN ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 18 GLN ** q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 83 ASN ** 7 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.128456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.111808 restraints weight = 398093.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.114271 restraints weight = 158405.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.115714 restraints weight = 86025.740| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 1.0041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.862 155037 Z= 0.645 Angle : 1.059 40.301 231928 Z= 0.526 Chirality : 0.050 1.011 29639 Planarity : 0.008 0.167 12421 Dihedral : 16.404 179.812 61107 Min Nonbonded Distance : 1.283 Molprobity Statistics. All-atom Clashscore : 32.80 Ramachandran Plot: Outliers : 2.84 % Allowed : 23.30 % Favored : 73.86 % Rotamer: Outliers : 2.06 % Allowed : 39.11 % Favored : 58.83 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 2.60 % Twisted General : 0.87 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.93 (0.10), residues: 5631 helix: -2.19 (0.12), residues: 1419 sheet: -2.85 (0.19), residues: 635 loop : -4.08 (0.09), residues: 3577 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 46969.14 seconds wall clock time: 817 minutes 37.23 seconds (49057.23 seconds total)