Starting phenix.real_space_refine on Mon Nov 20 19:05:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7z_6057/11_2023/3j7z_6057_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7z_6057/11_2023/3j7z_6057.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7z_6057/11_2023/3j7z_6057_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7z_6057/11_2023/3j7z_6057_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7z_6057/11_2023/3j7z_6057_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7z_6057/11_2023/3j7z_6057.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7z_6057/11_2023/3j7z_6057.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7z_6057/11_2023/3j7z_6057_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7z_6057/11_2023/3j7z_6057_updated.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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 2974 5.49 5 S 90 5.16 5 C 45332 2.51 5 N 16874 2.21 5 O 25430 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 ARG 9": "NH1" <-> "NH2" Residue "0 ARG 15": "NH1" <-> "NH2" Residue "0 GLU 35": "OE1" <-> "OE2" Residue "0 ARG 51": "NH1" <-> "NH2" Residue "1 GLU 31": "OE1" <-> "OE2" Residue "1 GLU 34": "OE1" <-> "OE2" Residue "1 PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 43": "NH1" <-> "NH2" Residue "2 ARG 3": "NH1" <-> "NH2" Residue "2 ARG 12": "NH1" <-> "NH2" Residue "2 ARG 14": "NH1" <-> "NH2" Residue "2 PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 19": "NH1" <-> "NH2" Residue "2 ARG 21": "NH1" <-> "NH2" Residue "2 ARG 33": "NH1" <-> "NH2" Residue "2 ARG 41": "NH1" <-> "NH2" Residue "3 ARG 12": "NH1" <-> "NH2" Residue "3 ARG 29": "NH1" <-> "NH2" Residue "3 ARG 39": "NH1" <-> "NH2" Residue "3 ARG 41": "NH1" <-> "NH2" Residue "4 ARG 24": "NH1" <-> "NH2" Residue "5 GLU 17": "OE1" <-> "OE2" Residue "5 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 124": "OD1" <-> "OD2" Residue "6 ASP 5": "OD1" <-> "OD2" Residue "6 GLU 9": "OE1" <-> "OE2" Residue "C ARG 51": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C GLU 78": "OE1" <-> "OE2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C GLU 144": "OE1" <-> "OE2" Residue "C ARG 166": "NH1" <-> "NH2" Residue "C ARG 176": "NH1" <-> "NH2" Residue "C ARG 181": "NH1" <-> "NH2" Residue "C GLU 184": "OE1" <-> "OE2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C GLU 198": "OE1" <-> "OE2" Residue "C ARG 202": "NH1" <-> "NH2" Residue "C ARG 211": "NH1" <-> "NH2" Residue "C GLU 235": "OE1" <-> "OE2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D GLU 86": "OE1" <-> "OE2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "D GLU 168": "OE1" <-> "OE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E GLU 25": "OE1" <-> "OE2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E GLU 152": "OE1" <-> "OE2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "E PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 10": "OE1" <-> "OE2" Residue "F GLU 31": "OE1" <-> "OE2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F GLU 93": "OE1" <-> "OE2" Residue "F GLU 97": "OE1" <-> "OE2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 111": "NH1" <-> "NH2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "F GLU 133": "OE1" <-> "OE2" Residue "F PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 2": "NH1" <-> "NH2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G GLU 154": "OE1" <-> "OE2" Residue "G ARG 162": "NH1" <-> "NH2" Residue "G GLU 166": "OE1" <-> "OE2" Residue "G ARG 169": "NH1" <-> "NH2" Residue "H ARG 27": "NH1" <-> "NH2" Residue "I GLU 49": "OE1" <-> "OE2" Residue "I PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 9": "OE1" <-> "OE2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 91": "OE1" <-> "OE2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "K GLU 45": "OE1" <-> "OE2" Residue "K GLU 121": "OE1" <-> "OE2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L GLU 86": "OE1" <-> "OE2" Residue "L GLU 106": "OE1" <-> "OE2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M GLU 47": "OE1" <-> "OE2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 59": "NH1" <-> "NH2" Residue "M GLU 75": "OE1" <-> "OE2" Residue "M GLU 104": "OE1" <-> "OE2" Residue "M GLU 110": "OE1" <-> "OE2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "M PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N GLU 43": "OE1" <-> "OE2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 71": "NH1" <-> "NH2" Residue "N GLU 74": "OE1" <-> "OE2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N GLU 114": "OE1" <-> "OE2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O GLU 60": "OE1" <-> "OE2" Residue "O GLU 80": "OE1" <-> "OE2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "O GLU 112": "OE1" <-> "OE2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P GLU 33": "OE1" <-> "OE2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P GLU 43": "OE1" <-> "OE2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "P ARG 61": "NH1" <-> "NH2" Residue "P ARG 88": "NH1" <-> "NH2" Residue "P ARG 100": "NH1" <-> "NH2" Residue "P ARG 108": "NH1" <-> "NH2" Residue "Q ARG 2": "NH1" <-> "NH2" Residue "Q ARG 5": "NH1" <-> "NH2" Residue "Q ARG 12": "NH1" <-> "NH2" Residue "Q ARG 32": "NH1" <-> "NH2" Residue "Q ARG 47": "NH1" <-> "NH2" Residue "Q ARG 69": "NH1" <-> "NH2" Residue "Q GLU 88": "OE1" <-> "OE2" Residue "Q GLU 110": "OE1" <-> "OE2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R GLU 23": "OE1" <-> "OE2" Residue "R GLU 31": "OE1" <-> "OE2" Residue "R GLU 34": "OE1" <-> "OE2" Residue "R GLU 45": "OE1" <-> "OE2" Residue "R GLU 46": "OE1" <-> "OE2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R GLU 70": "OE1" <-> "OE2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "S GLU 59": "OE1" <-> "OE2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T GLU 18": "OE1" <-> "OE2" Residue "T GLU 42": "OE1" <-> "OE2" Residue "T ARG 73": "NH1" <-> "NH2" Residue "T GLU 89": "OE1" <-> "OE2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ASP 8": "OD1" <-> "OD2" Residue "U GLU 36": "OE1" <-> "OE2" Residue "U ARG 81": "NH1" <-> "NH2" Residue "U ARG 93": "NH1" <-> "NH2" Residue "V GLU 41": "OE1" <-> "OE2" Residue "V GLU 69": "OE1" <-> "OE2" Residue "W GLU 16": "OE1" <-> "OE2" Residue "W ARG 19": "NH1" <-> "NH2" Residue "W PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 69": "OE1" <-> "OE2" Residue "W ARG 76": "NH1" <-> "NH2" Residue "W GLU 84": "OE1" <-> "OE2" Residue "X ARG 2": "NH1" <-> "NH2" Residue "X ARG 10": "NH1" <-> "NH2" Residue "X ARG 17": "NH1" <-> "NH2" Residue "X ARG 36": "NH1" <-> "NH2" Residue "X GLU 40": "OE1" <-> "OE2" Residue "X ARG 49": "NH1" <-> "NH2" Residue "X ARG 56": "NH1" <-> "NH2" Residue "X ARG 73": "NH1" <-> "NH2" Residue "Y GLU 17": "OE1" <-> "OE2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Y GLU 59": "OE1" <-> "OE2" Residue "Z ARG 10": "NH1" <-> "NH2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z GLU 38": "OE1" <-> "OE2" Residue "Z ARG 44": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 90700 Number of models: 1 Model: "" Number of chains: 36 Chain: "0" 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: "1" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "2" 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: "3" 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: "4" 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: "5" Number of atoms: 1117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1117 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain: "6" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 227 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "7" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Classifications: {'RNA': 3} Modifications used: {'5*END': 1, 'rna3p_pyr': 2} Link IDs: {'rna3p': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 61274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2854, 61274 Classifications: {'RNA': 2854} Modifications used: {'rna2p_pur': 270, 'rna2p_pyr': 144, 'rna3p_pur': 1378, 'rna3p_pyr': 1062} Link IDs: {'rna2p': 414, 'rna3p': 2439} Chain breaks: 3 Chain: "B" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2529 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 56, 'rna3p_pyr': 48} Link IDs: {'rna2p': 14, 'rna3p': 103} Chain: "C" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'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: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 166} Chain: "H" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 384 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "I" 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: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} 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: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "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: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} 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: "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: "W" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 596 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" 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: "Z" 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: "a" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 36 Classifications: {'peptide': 7} Incomplete info: {'c_alpha_only': 3} Link IDs: {'TRANS': 6} Unresolved chain links: 4 Unresolved chain link angles: 12 Unresolved chain link dihedrals: 12 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'ERY': 1} Classifications: {'undetermined': 1} Time building chain proxies: 34.32, per 1000 atoms: 0.38 Number of scatterers: 90700 At special positions: 0 Unit cell: (202.764, 208.304, 261.488, 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 90 16.00 P 2974 15.00 O 25430 8.00 N 16874 7.00 C 45332 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS 4 11 " - pdb=" SG CYS 4 14 " distance=2.06 Simple disulfide: pdb=" SG CYS 4 11 " - pdb=" SG CYS 4 27 " distance=2.04 Simple disulfide: pdb=" SG CYS 4 14 " - pdb=" SG CYS 4 27 " distance=2.07 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 41.71 Conformation dependent library (CDL) restraints added in 4.0 seconds 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6302 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 106 helices and 41 sheets defined 24.5% alpha, 10.7% beta 965 base pairs and 1456 stacking pairs defined. Time for finding SS restraints: 46.19 Creating SS restraints... Processing helix chain '0' and resid 9 through 18 removed outlier: 4.721A pdb=" N HIS 0 18 " --> pdb=" O MET 0 14 " (cutoff:3.500A) Processing helix chain '2' and resid 9 through 16 Processing helix chain '2' and resid 18 through 23 Processing helix chain '2' and resid 25 through 36 Processing helix chain '3' and resid 7 through 10 No H-bonds generated for 'chain '3' and resid 7 through 10' Processing helix chain '3' and resid 37 through 43 Processing helix chain '3' and resid 54 through 60 Processing helix chain '4' and resid 31 through 33 No H-bonds generated for 'chain '4' and resid 31 through 33' Processing helix chain '5' and resid 4 through 7 No H-bonds generated for 'chain '5' and resid 4 through 7' Processing helix chain '5' and resid 9 through 18 removed outlier: 3.707A pdb=" N SER 5 16 " --> pdb=" O VAL 5 12 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU 5 17 " --> pdb=" O ALA 5 13 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL 5 18 " --> pdb=" O GLU 5 14 " (cutoff:3.500A) Processing helix chain '5' and resid 34 through 46 removed outlier: 3.584A pdb=" N GLU 5 40 " --> pdb=" O ASP 5 36 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG 5 42 " --> pdb=" O MET 5 38 " (cutoff:3.500A) Processing helix chain '5' and resid 60 through 63 No H-bonds generated for 'chain '5' and resid 60 through 63' Processing helix chain '5' and resid 95 through 103 removed outlier: 3.665A pdb=" N PHE 5 99 " --> pdb=" O LEU 5 95 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA 5 100 " --> pdb=" O PHE 5 96 " (cutoff:3.500A) Processing helix chain '5' and resid 134 through 137 Processing helix chain '5' and resid 140 through 147 removed outlier: 3.787A pdb=" N GLU 5 145 " --> pdb=" O ALA 5 141 " (cutoff:3.500A) Processing helix chain '6' and resid 4 through 6 No H-bonds generated for 'chain '6' and resid 4 through 6' Processing helix chain '6' and resid 16 through 19 No H-bonds generated for 'chain '6' and resid 16 through 19' Processing helix chain '6' and resid 25 through 28 No H-bonds generated for 'chain '6' and resid 25 through 28' Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 131 through 133 No H-bonds generated for 'chain 'C' and resid 131 through 133' Processing helix chain 'C' and resid 198 through 201 Processing helix chain 'C' and resid 207 through 213 removed outlier: 3.502A pdb=" N ARG C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 223 No H-bonds generated for 'chain 'C' and resid 221 through 223' Processing helix chain 'C' and resid 263 through 265 No H-bonds generated for 'chain 'C' and resid 263 through 265' Processing helix chain 'D' and resid 57 through 59 No H-bonds generated for 'chain 'D' and resid 57 through 59' Processing helix chain 'D' and resid 62 through 69 Processing helix chain 'D' and resid 98 through 101 Processing helix chain 'E' and resid 16 through 19 No H-bonds generated for 'chain 'E' and resid 16 through 19' Processing helix chain 'E' and resid 25 through 36 removed outlier: 3.591A pdb=" N VAL E 31 " --> pdb=" O LEU E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 112 Processing helix chain 'E' and resid 131 through 141 Processing helix chain 'E' and resid 155 through 159 Processing helix chain 'E' and resid 177 through 182 removed outlier: 3.547A pdb=" N ILE E 181 " --> pdb=" O PRO E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 199 removed outlier: 3.583A pdb=" N LYS E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 8 Processing helix chain 'F' and resid 12 through 19 removed outlier: 3.601A pdb=" N THR F 17 " --> pdb=" O LYS F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 26 No H-bonds generated for 'chain 'F' and resid 24 through 26' Processing helix chain 'F' and resid 41 through 43 No H-bonds generated for 'chain 'F' and resid 41 through 43' Processing helix chain 'F' and resid 47 through 59 removed outlier: 3.673A pdb=" N ASN F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA F 52 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 104 Processing helix chain 'F' and resid 142 through 144 No H-bonds generated for 'chain 'F' and resid 142 through 144' Processing helix chain 'F' and resid 162 through 171 Processing helix chain 'G' and resid 62 through 80 Processing helix chain 'G' and resid 137 through 151 removed outlier: 3.580A pdb=" N TYR G 150 " --> pdb=" O ASP G 146 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ARG G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 12 No H-bonds generated for 'chain 'H' and resid 10 through 12' Processing helix chain 'H' and resid 23 through 28 Processing helix chain 'H' and resid 43 through 46 No H-bonds generated for 'chain 'H' and resid 43 through 46' Processing helix chain 'I' and resid 24 through 27 removed outlier: 3.621A pdb=" N LEU I 27 " --> pdb=" O GLY I 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 24 through 27' Processing helix chain 'I' and resid 34 through 36 No H-bonds generated for 'chain 'I' and resid 34 through 36' Processing helix chain 'I' and resid 41 through 43 No H-bonds generated for 'chain 'I' and resid 41 through 43' Processing helix chain 'I' and resid 107 through 115 removed outlier: 4.481A pdb=" N LYS I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA I 113 " --> pdb=" O ALA I 109 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ALA I 114 " --> pdb=" O GLN I 110 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ASP I 115 " --> pdb=" O THR I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 132 removed outlier: 3.929A pdb=" N ILE I 128 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY I 130 " --> pdb=" O ARG I 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 10 No H-bonds generated for 'chain 'J' and resid 8 through 10' Processing helix chain 'J' and resid 27 through 37 removed outlier: 3.893A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 61 No H-bonds generated for 'chain 'J' and resid 59 through 61' Processing helix chain 'J' and resid 68 through 71 No H-bonds generated for 'chain 'J' and resid 68 through 71' Processing helix chain 'J' and resid 89 through 94 Processing helix chain 'J' and resid 97 through 106 removed outlier: 3.940A pdb=" N ILE J 103 " --> pdb=" O VAL J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 121 removed outlier: 3.573A pdb=" N ARG J 120 " --> pdb=" O ARG J 116 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 135 No H-bonds generated for 'chain 'J' and resid 133 through 135' Processing helix chain 'K' and resid 72 through 74 No H-bonds generated for 'chain 'K' and resid 72 through 74' Processing helix chain 'K' and resid 105 through 107 No H-bonds generated for 'chain 'K' and resid 105 through 107' Processing helix chain 'K' and resid 113 through 117 Processing helix chain 'L' and resid 57 through 60 No H-bonds generated for 'chain 'L' and resid 57 through 60' Processing helix chain 'L' and resid 71 through 73 No H-bonds generated for 'chain 'L' and resid 71 through 73' Processing helix chain 'L' and resid 129 through 138 Processing helix chain 'M' and resid 43 through 57 removed outlier: 3.874A pdb=" N ALA M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL M 57 " --> pdb=" O MET M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 123 removed outlier: 3.650A pdb=" N GLU M 115 " --> pdb=" O GLU M 111 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 31 Processing helix chain 'N' and resid 38 through 56 removed outlier: 3.526A pdb=" N ARG N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 60 through 68 Processing helix chain 'N' and resid 73 through 81 removed outlier: 4.465A pdb=" N PHE N 80 " --> pdb=" O VAL N 76 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN N 81 " --> pdb=" O ALA N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 87 Processing helix chain 'O' and resid 5 through 21 removed outlier: 4.275A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 56 through 59 No H-bonds generated for 'chain 'O' and resid 56 through 59' Processing helix chain 'O' and resid 68 through 85 removed outlier: 3.550A pdb=" N ALA O 79 " --> pdb=" O GLY O 75 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU O 80 " --> pdb=" O LYS O 76 " (cutoff:3.500A) Processing helix chain 'O' and resid 104 through 112 removed outlier: 5.067A pdb=" N ALA O 109 " --> pdb=" O ALA O 105 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 11 removed outlier: 3.688A pdb=" N LEU P 7 " --> pdb=" O ILE P 3 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N GLU P 8 " --> pdb=" O ILE P 4 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLN P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 55 No H-bonds generated for 'chain 'P' and resid 53 through 55' Processing helix chain 'P' and resid 78 through 80 No H-bonds generated for 'chain 'P' and resid 78 through 80' Processing helix chain 'P' and resid 97 through 101 Processing helix chain 'P' and resid 104 through 106 No H-bonds generated for 'chain 'P' and resid 104 through 106' Processing helix chain 'Q' and resid 7 through 20 removed outlier: 3.968A pdb=" N GLN Q 19 " --> pdb=" O LYS Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 29 Processing helix chain 'Q' and resid 31 through 70 removed outlier: 4.149A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 84 Processing helix chain 'Q' and resid 94 through 100 removed outlier: 3.591A pdb=" N PHE Q 100 " --> pdb=" O ILE Q 97 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 116 removed outlier: 3.602A pdb=" N ALA Q 115 " --> pdb=" O LYS Q 111 " (cutoff:3.500A) Processing helix chain 'S' and resid 21 through 23 No H-bonds generated for 'chain 'S' and resid 21 through 23' Processing helix chain 'S' and resid 29 through 38 removed outlier: 3.646A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 61 Processing helix chain 'S' and resid 89 through 91 No H-bonds generated for 'chain 'S' and resid 89 through 91' Processing helix chain 'T' and resid 18 through 23 Processing helix chain 'T' and resid 41 through 52 removed outlier: 3.599A pdb=" N ALA T 46 " --> pdb=" O GLU T 42 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N PHE T 51 " --> pdb=" O VAL T 47 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 68 No H-bonds generated for 'chain 'U' and resid 66 through 68' Processing helix chain 'V' and resid 14 through 23 Processing helix chain 'V' and resid 44 through 52 Processing helix chain 'V' and resid 54 through 58 Processing helix chain 'X' and resid 54 through 61 Processing helix chain 'X' and resid 63 through 71 removed outlier: 3.957A pdb=" N LEU X 70 " --> pdb=" O VAL X 66 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG X 71 " --> pdb=" O LEU X 67 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 22 removed outlier: 3.617A pdb=" N LEU Y 14 " --> pdb=" O SER Y 10 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASN Y 15 " --> pdb=" O VAL Y 11 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR Y 16 " --> pdb=" O GLU Y 12 " (cutoff:3.500A) Processing helix chain 'Y' and resid 24 through 33 Processing helix chain 'Y' and resid 40 through 58 removed outlier: 3.985A pdb=" N GLN Y 45 " --> pdb=" O LEU Y 42 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N VAL Y 46 " --> pdb=" O LEU Y 43 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG Y 47 " --> pdb=" O LYS Y 44 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG Y 48 " --> pdb=" O GLN Y 45 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU Y 56 " --> pdb=" O VAL Y 53 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LEU Y 57 " --> pdb=" O LYS Y 54 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN Y 58 " --> pdb=" O THR Y 55 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 26 Processing helix chain 'Z' and resid 41 through 49 Processing helix chain 'Z' and resid 51 through 53 No H-bonds generated for 'chain 'Z' and resid 51 through 53' Processing sheet with id= A, first strand: chain '0' and resid 27 through 29 Processing sheet with id= B, first strand: chain '1' and resid 6 through 11 Processing sheet with id= C, first strand: chain '1' and resid 35 through 39 Processing sheet with id= D, first strand: chain '4' and resid 17 through 19 Processing sheet with id= E, first strand: chain 'C' and resid 2 through 4 Processing sheet with id= F, first strand: chain 'C' and resid 79 through 81 removed outlier: 3.732A pdb=" N ARG C 79 " --> pdb=" O LEU C 92 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 180 through 183 removed outlier: 3.713A pdb=" N ALA C 165 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG C 174 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE C 163 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 3 through 7 Processing sheet with id= I, first strand: chain 'D' and resid 12 through 15 Processing sheet with id= J, first strand: chain 'D' and resid 25 through 28 Processing sheet with id= K, first strand: chain 'D' and resid 80 through 83 removed outlier: 6.355A pdb=" N THR D 51 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL D 34 " --> pdb=" O THR D 51 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 152 through 157 removed outlier: 6.828A pdb=" N THR F 67 " --> pdb=" O ILE F 84 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N CYS F 86 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU F 65 " --> pdb=" O CYS F 86 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 22 through 24 Processing sheet with id= N, first strand: chain 'G' and resid 40 through 43 Processing sheet with id= O, first strand: chain 'G' and resid 120 through 123 Processing sheet with id= P, first strand: chain 'J' and resid 17 through 19 removed outlier: 6.416A pdb=" N ILE J 55 " --> pdb=" O VAL J 18 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'J' and resid 75 through 77 Processing sheet with id= R, first strand: chain 'K' and resid 5 through 9 removed outlier: 3.509A pdb=" N CYS K 21 " --> pdb=" O GLN K 5 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N MET K 7 " --> pdb=" O VAL K 19 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL K 19 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N VAL K 24 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'L' and resid 74 through 76 removed outlier: 6.283A pdb=" N PHE L 107 " --> pdb=" O ALA L 75 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'L' and resid 89 through 91 removed outlier: 6.630A pdb=" N THR L 121 " --> pdb=" O VAL L 90 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS L 141 " --> pdb=" O VAL L 122 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'M' and resid 129 through 132 removed outlier: 3.693A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'M' and resid 39 through 42 Processing sheet with id= W, first strand: chain 'N' and resid 33 through 37 Processing sheet with id= X, first strand: chain 'O' and resid 91 through 93 removed outlier: 3.645A pdb=" N HIS O 29 " --> pdb=" O TYR O 36 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'P' and resid 37 through 43 removed outlier: 3.778A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'P' and resid 70 through 74 removed outlier: 3.772A pdb=" N ALA P 48 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARG P 61 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N VAL P 46 " --> pdb=" O ARG P 61 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'R' and resid 11 through 14 removed outlier: 3.685A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLN R 6 " --> pdb=" O VAL R 38 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL R 38 " --> pdb=" O GLN R 6 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'R' and resid 20 through 23 Processing sheet with id= AC, first strand: chain 'R' and resid 32 through 35 Processing sheet with id= AD, first strand: chain 'R' and resid 72 through 78 removed outlier: 4.213A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'S' and resid 4 through 7 removed outlier: 6.577A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'T' and resid 61 through 63 removed outlier: 3.837A pdb=" N LEU T 61 " --> pdb=" O LYS T 82 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'T' and resid 11 through 14 removed outlier: 6.626A pdb=" N LYS T 33 " --> pdb=" O ARG T 12 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'U' and resid 21 through 23 Processing sheet with id= AI, first strand: chain 'U' and resid 40 through 45 Processing sheet with id= AJ, first strand: chain 'U' and resid 82 through 84 Processing sheet with id= AK, first strand: chain 'U' and resid 24 through 27 removed outlier: 6.884A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'V' and resid 62 through 65 removed outlier: 7.995A pdb=" N ASN V 5 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ASP V 43 " --> pdb=" O ASN V 5 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL V 92 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ALA V 74 " --> pdb=" O VAL V 92 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'X' and resid 12 through 14 Processing sheet with id= AN, first strand: chain 'X' and resid 35 through 38 Processing sheet with id= AO, first strand: chain 'Z' and resid 35 through 37 607 hydrogen bonds defined for protein. 1635 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2429 hydrogen bonds 3876 hydrogen bond angles 0 basepair planarities 965 basepair parallelities 1456 stacking parallelities Total time for adding SS restraints: 139.72 Time building geometry restraints manager: 44.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 9888 1.32 - 1.46: 47551 1.46 - 1.59: 37719 1.59 - 1.73: 3393 1.73 - 1.87: 163 Bond restraints: 98714 Sorted by residual: bond pdb=" C1 ERY A9000 " pdb=" O2 ERY A9000 " ideal model delta sigma weight residual 1.490 1.334 0.156 2.00e-02 2.50e+03 6.05e+01 bond pdb=" CA ILE W 35 " pdb=" CB ILE W 35 " ideal model delta sigma weight residual 1.544 1.621 -0.077 1.19e-02 7.06e+03 4.16e+01 bond pdb=" CA VAL 4 3 " pdb=" CB VAL 4 3 " ideal model delta sigma weight residual 1.545 1.491 0.054 9.10e-03 1.21e+04 3.54e+01 bond pdb=" CA VAL W 50 " pdb=" CB VAL W 50 " ideal model delta sigma weight residual 1.540 1.616 -0.076 1.36e-02 5.41e+03 3.11e+01 bond pdb=" CA GLU J 43 " pdb=" C GLU J 43 " ideal model delta sigma weight residual 1.524 1.453 0.071 1.32e-02 5.74e+03 2.86e+01 ... (remaining 98709 not shown) Histogram of bond angle deviations from ideal: 95.12 - 105.24: 15561 105.24 - 115.36: 68437 115.36 - 125.47: 53388 125.47 - 135.59: 10617 135.59 - 145.71: 22 Bond angle restraints: 148025 Sorted by residual: angle pdb=" C THR D 151 " pdb=" N PRO D 152 " pdb=" CA PRO D 152 " ideal model delta sigma weight residual 119.19 103.98 15.21 1.06e+00 8.90e-01 2.06e+02 angle pdb=" N THR 5 131 " pdb=" CA THR 5 131 " pdb=" C THR 5 131 " ideal model delta sigma weight residual 111.28 96.67 14.61 1.09e+00 8.42e-01 1.80e+02 angle pdb=" C ALA 5 92 " pdb=" N ALA 5 93 " pdb=" CA ALA 5 93 " ideal model delta sigma weight residual 121.54 145.71 -24.17 1.91e+00 2.74e-01 1.60e+02 angle pdb=" C ALA 5 93 " pdb=" N ARG 5 94 " pdb=" CA ARG 5 94 " ideal model delta sigma weight residual 121.54 144.35 -22.81 1.91e+00 2.74e-01 1.43e+02 angle pdb=" C LEU 5 72 " pdb=" N LYS 5 73 " pdb=" CA LYS 5 73 " ideal model delta sigma weight residual 121.18 140.14 -18.96 1.64e+00 3.72e-01 1.34e+02 ... (remaining 148020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.26: 50293 35.26 - 70.52: 2060 70.52 - 105.78: 177 105.78 - 141.04: 54 141.04 - 176.30: 33 Dihedral angle restraints: 52617 sinusoidal: 42836 harmonic: 9781 Sorted by residual: dihedral pdb=" C4' A 7 76 " pdb=" C3' A 7 76 " pdb=" C2' A 7 76 " pdb=" C1' A 7 76 " ideal model delta sinusoidal sigma weight residual 36.35 -35.91 72.26 1 3.10e+00 1.04e-01 6.95e+02 dihedral pdb=" O4' A 7 76 " pdb=" C4' A 7 76 " pdb=" C3' A 7 76 " pdb=" C2' A 7 76 " ideal model delta sinusoidal sigma weight residual -35.15 27.03 -62.18 1 4.00e+00 6.25e-02 3.20e+02 dihedral pdb=" O4' A 7 76 " pdb=" C2' A 7 76 " pdb=" C1' A 7 76 " pdb=" C3' A 7 76 " ideal model delta sinusoidal sigma weight residual 25.59 -33.41 59.00 3 3.80e+00 6.93e-02 1.48e+02 ... (remaining 52614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.111: 18963 1.111 - 2.222: 7 2.222 - 3.333: 0 3.333 - 4.444: 0 4.444 - 5.556: 3 Chirality restraints: 18973 Sorted by residual: chirality pdb=" C6 ERY A9000 " pdb=" C32 ERY A9000 " pdb=" C5 ERY A9000 " pdb=" C7 ERY A9000 " both_signs ideal model delta sigma weight residual False -2.78 2.78 -5.56 2.00e-01 2.50e+01 7.72e+02 chirality pdb=" C12 ERY A9000 " pdb=" C11 ERY A9000 " pdb=" C13 ERY A9000 " pdb=" C35 ERY A9000 " both_signs ideal model delta sigma weight residual False -2.75 2.77 -5.52 2.00e-01 2.50e+01 7.62e+02 chirality pdb=" C16 ERY A9000 " pdb=" C15 ERY A9000 " pdb=" C17 ERY A9000 " pdb=" C19 ERY A9000 " both_signs ideal model delta sigma weight residual False 2.68 -2.61 5.29 2.00e-01 2.50e+01 6.99e+02 ... (remaining 18970 not shown) Planarity restraints: 7665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 ERY A9000 " 0.126 2.00e-02 2.50e+03 7.27e-02 5.29e+01 pdb=" C2 ERY A9000 " -0.037 2.00e-02 2.50e+03 pdb=" O1 ERY A9000 " -0.049 2.00e-02 2.50e+03 pdb=" O2 ERY A9000 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG K 71 " 0.070 5.00e-02 4.00e+02 1.06e-01 1.81e+01 pdb=" N PRO K 72 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO K 72 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO K 72 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A A1509 " 0.055 2.00e-02 2.50e+03 2.43e-02 1.63e+01 pdb=" N9 A A1509 " -0.055 2.00e-02 2.50e+03 pdb=" C8 A A1509 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A A1509 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A A1509 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A A1509 " 0.001 2.00e-02 2.50e+03 pdb=" N6 A A1509 " 0.018 2.00e-02 2.50e+03 pdb=" N1 A A1509 " 0.005 2.00e-02 2.50e+03 pdb=" C2 A A1509 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A A1509 " -0.010 2.00e-02 2.50e+03 pdb=" C4 A A1509 " -0.010 2.00e-02 2.50e+03 ... (remaining 7662 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.12: 23 2.12 - 2.82: 24399 2.82 - 3.51: 134016 3.51 - 4.21: 298887 4.21 - 4.90: 392909 Nonbonded interactions: 850234 Sorted by model distance: nonbonded pdb=" OP2 U A2506 " pdb=" N2 G A2576 " model vdw 1.426 2.520 nonbonded pdb=" C3' A 7 76 " pdb=" O ILE a 84 " model vdw 1.449 3.470 nonbonded pdb=" OP1 C A 912 " pdb=" NZ LYS M 8 " model vdw 1.791 2.520 nonbonded pdb=" O LEU 5 3 " pdb=" OD1 ASP 5 7 " model vdw 1.792 3.040 nonbonded pdb=" OP2 G A2061 " pdb=" NZ LYS E 63 " model vdw 1.881 2.520 ... (remaining 850229 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.89 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: 0.550 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: 0.060 Extract box with map and model: 5.780 Check model and map are aligned: 1.000 Set scattering table: 0.610 Process input model: 316.650 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 329.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 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 : 0.009 0.156 98714 Z= 0.568 Angle : 1.420 24.170 148025 Z= 0.747 Chirality : 0.095 5.556 18973 Planarity : 0.007 0.106 7665 Dihedral : 16.222 176.303 46306 Min Nonbonded Distance : 1.426 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 6.47 % Allowed : 16.34 % Favored : 77.19 % Rotamer: Outliers : 10.91 % Allowed : 12.70 % Favored : 76.39 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.89 % Twisted General : 0.12 % 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: -5.00 (0.12), residues: 3385 helix: -3.74 (0.11), residues: 854 sheet: -2.82 (0.21), residues: 534 loop : -3.41 (0.12), residues: 1997 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1266 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 304 poor density : 962 time to evaluate : 3.601 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 outliers start: 304 outliers final: 84 residues processed: 1139 average time/residue: 0.9998 time to fit residues: 1825.4712 Evaluate side-chains 787 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 703 time to evaluate : 3.653 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 84 outliers final: 3 residues processed: 84 average time/residue: 0.7720 time to fit residues: 119.8595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 530 optimal weight: 20.0000 chunk 475 optimal weight: 9.9990 chunk 264 optimal weight: 20.0000 chunk 162 optimal weight: 20.0000 chunk 321 optimal weight: 20.0000 chunk 254 optimal weight: 30.0000 chunk 492 optimal weight: 7.9990 chunk 190 optimal weight: 30.0000 chunk 299 optimal weight: 10.0000 chunk 366 optimal weight: 8.9990 chunk 570 optimal weight: 8.9990 overall best weight: 9.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 13 ASN C 69 ASN C 89 ASN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN D 130 GLN D 140 HIS E 163 ASN F 26 GLN F 62 GLN ** G 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 28 ASN J 40 HIS J 47 HIS J 58 ASN J 131 ASN L 99 ASN ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN Q 71 ASN R 18 GLN R 66 HIS S 9 HIS T 15 HIS V 44 HIS V 80 HIS Y 15 ASN Z 19 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.156 98714 Z= 0.369 Angle : 0.914 27.707 148025 Z= 0.454 Chirality : 0.052 2.073 18973 Planarity : 0.007 0.102 7665 Dihedral : 15.231 178.960 39594 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 2.92 % Allowed : 12.76 % Favored : 84.31 % Rotamer: Outliers : 7.25 % Allowed : 21.03 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -3.91 (0.12), residues: 3385 helix: -2.02 (0.15), residues: 867 sheet: -2.47 (0.20), residues: 543 loop : -3.01 (0.12), residues: 1975 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 985 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 783 time to evaluate : 3.735 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 outliers start: 202 outliers final: 105 residues processed: 904 average time/residue: 1.0059 time to fit residues: 1508.3636 Evaluate side-chains 793 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 688 time to evaluate : 3.670 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 105 outliers final: 2 residues processed: 105 average time/residue: 0.7527 time to fit residues: 151.3094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 316 optimal weight: 20.0000 chunk 176 optimal weight: 20.0000 chunk 474 optimal weight: 5.9990 chunk 388 optimal weight: 20.0000 chunk 157 optimal weight: 30.0000 chunk 571 optimal weight: 10.0000 chunk 617 optimal weight: 1.9990 chunk 508 optimal weight: 8.9990 chunk 566 optimal weight: 6.9990 chunk 194 optimal weight: 20.0000 chunk 458 optimal weight: 0.9980 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN C 133 ASN C 152 GLN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 GLN ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 GLN L 4 ASN ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 104 GLN P 76 HIS ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 71 ASN S 60 HIS T 15 HIS T 48 GLN ** X 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 22 ASN Y 15 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 98714 Z= 0.229 Angle : 0.721 27.894 148025 Z= 0.362 Chirality : 0.045 1.962 18973 Planarity : 0.006 0.109 7665 Dihedral : 14.846 176.896 39594 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 2.72 % Allowed : 11.91 % Favored : 85.38 % Rotamer: Outliers : 5.06 % Allowed : 24.04 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -3.21 (0.13), residues: 3385 helix: -1.06 (0.17), residues: 868 sheet: -2.20 (0.20), residues: 563 loop : -2.71 (0.13), residues: 1954 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 740 time to evaluate : 3.704 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 outliers start: 141 outliers final: 69 residues processed: 825 average time/residue: 0.9422 time to fit residues: 1292.9334 Evaluate side-chains 728 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 659 time to evaluate : 3.709 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 3 residues processed: 69 average time/residue: 0.7028 time to fit residues: 93.9879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 564 optimal weight: 20.0000 chunk 429 optimal weight: 40.0000 chunk 296 optimal weight: 20.0000 chunk 63 optimal weight: 30.0000 chunk 272 optimal weight: 20.0000 chunk 383 optimal weight: 50.0000 chunk 573 optimal weight: 8.9990 chunk 607 optimal weight: 20.0000 chunk 299 optimal weight: 20.0000 chunk 543 optimal weight: 7.9990 chunk 163 optimal weight: 20.0000 overall best weight: 15.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 35 GLN ** 5 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN C 57 HIS C 59 GLN C 152 GLN C 238 ASN C 250 GLN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN D 140 HIS D 150 GLN E 97 ASN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 28 ASN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 ASN ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 HIS O 38 GLN O 104 GLN ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN R 6 GLN R 66 HIS ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 15 HIS U 44 HIS W 75 ASN ** X 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 19 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.6805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.150 98714 Z= 0.524 Angle : 1.055 27.215 148025 Z= 0.513 Chirality : 0.057 2.017 18973 Planarity : 0.008 0.108 7665 Dihedral : 16.137 179.350 39594 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 22.16 Ramachandran Plot: Outliers : 2.45 % Allowed : 14.48 % Favored : 83.07 % Rotamer: Outliers : 7.46 % Allowed : 26.09 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -3.74 (0.12), residues: 3385 helix: -1.69 (0.16), residues: 855 sheet: -2.45 (0.20), residues: 550 loop : -2.97 (0.12), residues: 1980 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 948 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 740 time to evaluate : 3.751 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 outliers start: 208 outliers final: 116 residues processed: 861 average time/residue: 1.0132 time to fit residues: 1476.4434 Evaluate side-chains 794 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 678 time to evaluate : 3.712 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 116 outliers final: 2 residues processed: 116 average time/residue: 0.7865 time to fit residues: 174.2934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 505 optimal weight: 6.9990 chunk 344 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 451 optimal weight: 0.6980 chunk 250 optimal weight: 50.0000 chunk 518 optimal weight: 4.9990 chunk 419 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 309 optimal weight: 10.0000 chunk 544 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 57 ASN C 59 GLN C 152 GLN C 238 ASN D 49 GLN D 140 HIS ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN F 62 GLN ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 ASN ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 22 GLN ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 9 GLN ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN S 31 GLN T 15 HIS ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.7001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 98714 Z= 0.206 Angle : 0.718 27.772 148025 Z= 0.359 Chirality : 0.044 1.909 18973 Planarity : 0.005 0.109 7665 Dihedral : 15.238 178.753 39594 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 2.27 % Allowed : 11.85 % Favored : 85.88 % Rotamer: Outliers : 3.41 % Allowed : 28.78 % Favored : 67.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.31 (0.13), residues: 3385 helix: -1.26 (0.17), residues: 860 sheet: -2.19 (0.20), residues: 569 loop : -2.74 (0.12), residues: 1956 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 721 time to evaluate : 3.798 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 outliers start: 95 outliers final: 55 residues processed: 774 average time/residue: 0.9471 time to fit residues: 1221.9123 Evaluate side-chains 730 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 675 time to evaluate : 3.700 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 55 outliers final: 2 residues processed: 55 average time/residue: 0.7118 time to fit residues: 76.8507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 204 optimal weight: 10.0000 chunk 546 optimal weight: 10.0000 chunk 119 optimal weight: 20.0000 chunk 356 optimal weight: 9.9990 chunk 149 optimal weight: 50.0000 chunk 607 optimal weight: 20.0000 chunk 504 optimal weight: 9.9990 chunk 281 optimal weight: 20.0000 chunk 50 optimal weight: 30.0000 chunk 200 optimal weight: 20.0000 chunk 318 optimal weight: 20.0000 overall best weight: 11.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 HIS C 59 GLN C 152 GLN C 238 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 HIS ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 ASN ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 HIS ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN ** S 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN W 56 HIS ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.7370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.112 98714 Z= 0.410 Angle : 0.927 27.686 148025 Z= 0.450 Chirality : 0.051 1.971 18973 Planarity : 0.007 0.107 7665 Dihedral : 15.603 179.413 39594 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 2.22 % Allowed : 14.42 % Favored : 83.37 % Rotamer: Outliers : 6.21 % Allowed : 28.60 % Favored : 65.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.58 (0.13), residues: 3385 helix: -1.48 (0.17), residues: 851 sheet: -2.33 (0.20), residues: 579 loop : -2.92 (0.12), residues: 1955 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 706 time to evaluate : 3.527 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 outliers start: 173 outliers final: 101 residues processed: 793 average time/residue: 0.7862 time to fit residues: 1036.2201 Evaluate side-chains 782 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 681 time to evaluate : 3.525 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 101 outliers final: 2 residues processed: 101 average time/residue: 0.7042 time to fit residues: 135.4958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 585 optimal weight: 20.0000 chunk 68 optimal weight: 40.0000 chunk 346 optimal weight: 5.9990 chunk 443 optimal weight: 30.0000 chunk 343 optimal weight: 0.0570 chunk 511 optimal weight: 3.9990 chunk 339 optimal weight: 10.0000 chunk 605 optimal weight: 0.4980 chunk 378 optimal weight: 5.9990 chunk 369 optimal weight: 0.6980 chunk 279 optimal weight: 10.0000 overall best weight: 2.2502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 250 GLN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 ASN ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 9 GLN O 38 GLN ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN ** S 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN S 61 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.7507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 98714 Z= 0.157 Angle : 0.667 27.829 148025 Z= 0.332 Chirality : 0.042 1.904 18973 Planarity : 0.005 0.107 7665 Dihedral : 15.018 179.627 39594 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 2.10 % Allowed : 10.99 % Favored : 86.91 % Rotamer: Outliers : 2.01 % Allowed : 30.21 % Favored : 67.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.12 (0.13), residues: 3385 helix: -1.07 (0.17), residues: 864 sheet: -2.01 (0.22), residues: 549 loop : -2.66 (0.12), residues: 1972 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 729 time to evaluate : 3.742 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 outliers start: 56 outliers final: 30 residues processed: 761 average time/residue: 0.9375 time to fit residues: 1188.9894 Evaluate side-chains 718 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 688 time to evaluate : 3.631 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 30 outliers final: 2 residues processed: 30 average time/residue: 0.7208 time to fit residues: 43.9015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 374 optimal weight: 9.9990 chunk 241 optimal weight: 20.0000 chunk 361 optimal weight: 10.0000 chunk 182 optimal weight: 20.0000 chunk 118 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 384 optimal weight: 9.9990 chunk 412 optimal weight: 2.9990 chunk 299 optimal weight: 20.0000 chunk 56 optimal weight: 30.0000 chunk 475 optimal weight: 8.9990 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 ASN ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 9 GLN N 31 HIS Q 19 GLN ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.7727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 98714 Z= 0.304 Angle : 0.763 27.436 148025 Z= 0.375 Chirality : 0.046 1.932 18973 Planarity : 0.006 0.106 7665 Dihedral : 15.192 179.932 39594 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 2.16 % Allowed : 13.44 % Favored : 84.40 % Rotamer: Outliers : 2.55 % Allowed : 32.40 % Favored : 65.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.23 (0.13), residues: 3385 helix: -1.26 (0.17), residues: 876 sheet: -2.11 (0.21), residues: 563 loop : -2.68 (0.13), residues: 1946 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 702 time to evaluate : 3.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 47 residues processed: 731 average time/residue: 0.9317 time to fit residues: 1139.3706 Evaluate side-chains 730 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 683 time to evaluate : 3.712 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 47 outliers final: 2 residues processed: 47 average time/residue: 0.7035 time to fit residues: 65.7218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 550 optimal weight: 9.9990 chunk 579 optimal weight: 6.9990 chunk 529 optimal weight: 4.9990 chunk 564 optimal weight: 8.9990 chunk 339 optimal weight: 6.9990 chunk 245 optimal weight: 10.0000 chunk 442 optimal weight: 6.9990 chunk 173 optimal weight: 20.0000 chunk 509 optimal weight: 5.9990 chunk 533 optimal weight: 9.9990 chunk 562 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 250 GLN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 ASN ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN ** S 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.8057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 98714 Z= 0.245 Angle : 0.725 27.678 148025 Z= 0.358 Chirality : 0.045 1.921 18973 Planarity : 0.005 0.108 7665 Dihedral : 15.212 179.821 39594 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 2.07 % Allowed : 12.35 % Favored : 85.58 % Rotamer: Outliers : 1.79 % Allowed : 33.08 % Favored : 65.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.12 (0.13), residues: 3385 helix: -1.22 (0.17), residues: 871 sheet: -1.96 (0.22), residues: 554 loop : -2.60 (0.13), residues: 1960 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 721 time to evaluate : 3.813 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 outliers start: 50 outliers final: 28 residues processed: 745 average time/residue: 0.9409 time to fit residues: 1172.5167 Evaluate side-chains 719 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 691 time to evaluate : 3.670 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 28 outliers final: 2 residues processed: 28 average time/residue: 0.7000 time to fit residues: 40.9386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 370 optimal weight: 10.0000 chunk 596 optimal weight: 7.9990 chunk 364 optimal weight: 8.9990 chunk 282 optimal weight: 20.0000 chunk 414 optimal weight: 0.8980 chunk 625 optimal weight: 8.9990 chunk 575 optimal weight: 3.9990 chunk 498 optimal weight: 0.0970 chunk 51 optimal weight: 20.0000 chunk 384 optimal weight: 0.7980 chunk 305 optimal weight: 20.0000 overall best weight: 2.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 ASN C 250 GLN E 163 ASN F 62 GLN ** G 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 93 ASN L 4 ASN L 54 GLN N 9 GLN O 38 GLN P 65 ASN Q 19 GLN ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN ** S 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.8237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 98714 Z= 0.157 Angle : 0.654 27.983 148025 Z= 0.322 Chirality : 0.041 1.896 18973 Planarity : 0.005 0.110 7665 Dihedral : 14.925 179.705 39594 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 2.01 % Allowed : 11.88 % Favored : 86.12 % Rotamer: Outliers : 0.90 % Allowed : 34.45 % Favored : 64.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.14), residues: 3385 helix: -1.02 (0.18), residues: 855 sheet: -1.85 (0.23), residues: 527 loop : -2.46 (0.13), residues: 2003 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 717 time to evaluate : 5.342 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 outliers start: 25 outliers final: 18 residues processed: 724 average time/residue: 0.9382 time to fit residues: 1135.2504 Evaluate side-chains 709 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 691 time to evaluate : 3.851 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 18 outliers final: 1 residues processed: 18 average time/residue: 0.7573 time to fit residues: 28.8149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 395 optimal weight: 7.9990 chunk 530 optimal weight: 8.9990 chunk 152 optimal weight: 20.0000 chunk 459 optimal weight: 4.9990 chunk 73 optimal weight: 30.0000 chunk 138 optimal weight: 20.0000 chunk 498 optimal weight: 9.9990 chunk 208 optimal weight: 20.0000 chunk 512 optimal weight: 0.1980 chunk 63 optimal weight: 30.0000 chunk 91 optimal weight: 20.0000 overall best weight: 6.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 ASN P 65 ASN Q 19 GLN ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 HIS ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN ** S 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.158302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.130236 restraints weight = 156730.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.132423 restraints weight = 78372.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.132647 restraints weight = 48259.810| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3544 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3544 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.8304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 98714 Z= 0.242 Angle : 0.719 30.046 148025 Z= 0.350 Chirality : 0.043 1.911 18973 Planarity : 0.006 0.209 7665 Dihedral : 14.989 179.816 39594 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 1.98 % Allowed : 12.32 % Favored : 85.70 % Rotamer: Outliers : 1.15 % Allowed : 33.94 % Favored : 64.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.89 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.14), residues: 3385 helix: -1.08 (0.18), residues: 856 sheet: -1.92 (0.23), residues: 511 loop : -2.46 (0.13), residues: 2018 =============================================================================== Job complete usr+sys time: 19047.49 seconds wall clock time: 376 minutes 46.17 seconds (22606.17 seconds total)