Starting phenix.real_space_refine on Mon Mar 18 03:07:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syr_25538/03_2024/7syr_25538_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syr_25538/03_2024/7syr_25538.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syr_25538/03_2024/7syr_25538.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syr_25538/03_2024/7syr_25538.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syr_25538/03_2024/7syr_25538_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syr_25538/03_2024/7syr_25538_neut.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 1958 5.49 5 S 187 5.16 5 C 44687 2.51 5 N 15282 2.21 5 O 20890 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 53": "OD1" <-> "OD2" Residue "A TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 126": "OD1" <-> "OD2" Residue "B GLU 136": "OE1" <-> "OE2" Residue "B ASP 200": "OD1" <-> "OD2" Residue "C ASP 29": "OD1" <-> "OD2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C ASP 104": "OD1" <-> "OD2" Residue "C TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 175": "OE1" <-> "OE2" Residue "C ASP 196": "OD1" <-> "OD2" Residue "C ASP 209": "OD1" <-> "OD2" Residue "C PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 92": "OE1" <-> "OE2" Residue "D ASP 104": "OD1" <-> "OD2" Residue "D PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 23": "OE1" <-> "OE2" Residue "E PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 32": "OD1" <-> "OD2" Residue "E PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 81": "OE1" <-> "OE2" Residue "E GLU 103": "OE1" <-> "OE2" Residue "E TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 162": "OD1" <-> "OD2" Residue "E TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 206": "OD1" <-> "OD2" Residue "E GLU 212": "OE1" <-> "OE2" Residue "F TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 104": "OD1" <-> "OD2" Residue "F TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 199": "OE1" <-> "OE2" Residue "F GLU 251": "OE1" <-> "OE2" Residue "G ASP 16": "OD1" <-> "OD2" Residue "G TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 70": "OE1" <-> "OE2" Residue "G GLU 98": "OE1" <-> "OE2" Residue "G GLU 160": "OE1" <-> "OE2" Residue "G GLU 176": "OE1" <-> "OE2" Residue "G TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 197": "OE1" <-> "OE2" Residue "H GLU 29": "OE1" <-> "OE2" Residue "H GLU 91": "OE1" <-> "OE2" Residue "H GLU 150": "OE1" <-> "OE2" Residue "H TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 127": "OD1" <-> "OD2" Residue "I GLU 138": "OE1" <-> "OE2" Residue "I ASP 149": "OD1" <-> "OD2" Residue "I ASP 159": "OD1" <-> "OD2" Residue "I GLU 167": "OE1" <-> "OE2" Residue "J TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 196": "OE1" <-> "OE2" Residue "K PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 28": "OE1" <-> "OE2" Residue "K GLU 34": "OE1" <-> "OE2" Residue "K ASP 64": "OD1" <-> "OD2" Residue "K GLU 73": "OE1" <-> "OE2" Residue "K PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 152": "OD1" <-> "OD2" Residue "L GLU 13": "OE1" <-> "OE2" Residue "L GLU 18": "OE1" <-> "OE2" Residue "L GLU 60": "OE1" <-> "OE2" Residue "L TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 103": "OE1" <-> "OE2" Residue "N GLU 125": "OE1" <-> "OE2" Residue "N TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 87": "OD1" <-> "OD2" Residue "O ASP 108": "OD1" <-> "OD2" Residue "O GLU 119": "OE1" <-> "OE2" Residue "P ASP 39": "OD1" <-> "OD2" Residue "P ASP 67": "OD1" <-> "OD2" Residue "P ASP 131": "OD1" <-> "OD2" Residue "Q ASP 21": "OD1" <-> "OD2" Residue "Q TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 66": "OE1" <-> "OE2" Residue "Q GLU 74": "OE1" <-> "OE2" Residue "Q GLU 110": "OE1" <-> "OE2" Residue "R TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 53": "OE1" <-> "OE2" Residue "R ASP 67": "OD1" <-> "OD2" Residue "R TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 18": "OE1" <-> "OE2" Residue "S TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 75": "OE1" <-> "OE2" Residue "S GLU 79": "OE1" <-> "OE2" Residue "S PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 51": "OD1" <-> "OD2" Residue "T GLU 61": "OE1" <-> "OE2" Residue "T GLU 65": "OE1" <-> "OE2" Residue "T GLU 112": "OE1" <-> "OE2" Residue "U ASP 8": "OD1" <-> "OD2" Residue "U GLU 13": "OE1" <-> "OE2" Residue "U PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 32": "OE1" <-> "OE2" Residue "U TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 130": "OD1" <-> "OD2" Residue "V GLU 45": "OE1" <-> "OE2" Residue "V ASP 90": "OD1" <-> "OD2" Residue "V GLU 111": "OE1" <-> "OE2" Residue "W PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 38": "OE1" <-> "OE2" Residue "W PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 51": "OE1" <-> "OE2" Residue "X PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 87": "OE1" <-> "OE2" Residue "X PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 88": "OD1" <-> "OD2" Residue "Y GLU 99": "OE1" <-> "OE2" Residue "Z ASP 26": "OD1" <-> "OD2" Residue "Z ASP 53": "OD1" <-> "OD2" Residue "Z PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 77": "OD1" <-> "OD2" Residue "Z TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 33": "OD1" <-> "OD2" Residue "b GLU 55": "OE1" <-> "OE2" Residue "b ASP 60": "OD1" <-> "OD2" Residue "b ASP 94": "OD1" <-> "OD2" Residue "c GLU 15": "OE1" <-> "OE2" Residue "c TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 75": "OE1" <-> "OE2" Residue "d GLU 62": "OE1" <-> "OE2" Residue "e ASP 49": "OD1" <-> "OD2" Residue "f PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 124": "OD1" <-> "OD2" Residue "g TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 29": "OD1" <-> "OD2" Residue "h PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 126": "OD1" <-> "OD2" Residue "h TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 171": "OD1" <-> "OD2" Residue "h TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 268": "OD1" <-> "OD2" Residue "h GLU 269": "OE1" <-> "OE2" Residue "j GLU 38": "OE1" <-> "OE2" Residue "j GLU 117": "OE1" <-> "OE2" Residue "j PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 83005 Number of models: 1 Model: "" Number of chains: 40 Chain: "2" Number of atoms: 36227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1697, 36227 Classifications: {'RNA': 1697} Modifications used: {'5*END': 1, 'rna2p_pur': 144, 'rna2p_pyr': 112, 'rna3p_pur': 753, 'rna3p_pyr': 688} Link IDs: {'rna2p': 255, 'rna3p': 1441} Chain breaks: 11 Chain: "A" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 798 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "B" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1710 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 204} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1729 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "D" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1716 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 12, 'TRANS': 208} Chain: "E" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "F" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2076 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 247} Chain: "G" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1509 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 184} Chain: "H" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1923 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain: "I" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1488 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain breaks: 1 Chain: "J" Number of atoms: 1691 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 206, 1686 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Conformer: "B" Number of residues, atoms: 206, 1686 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} bond proxies already assigned to first conformer: 1709 Chain: "K" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1525 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "L" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 810 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 7, 'TRANS': 88} Chain: "M" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1233 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "N" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "O" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "P" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1016 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "Q" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 997 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "R" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1128 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 135} Chain: "S" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1068 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "T" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1190 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain: "U" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1097 Classifications: {'peptide': 141} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 136} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "V" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 795 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "W" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 636 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "X" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 125} Chain: "Y" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "Z" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1011 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "a" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "b" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 814 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "c" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "d" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 530 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "e" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 459 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "f" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 457 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "g" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 555 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "h" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2436 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "i" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1604 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 3, 'rna3p_pur': 32, 'rna3p_pyr': 30} Link IDs: {'rna2p': 12, 'rna3p': 62} Chain: "j" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1245 Classifications: {'peptide': 182} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 76} Link IDs: {'PTRANS': 4, 'TRANS': 177} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 259 Unresolved non-hydrogen angles: 338 Unresolved non-hydrogen dihedrals: 197 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 10, 'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 12, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 142 Chain: "n" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 239 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "z" Number of atoms: 4017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 4017 Classifications: {'RNA': 188} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 17, 'rna3p_pur': 80, 'rna3p_pyr': 74} Link IDs: {'rna2p': 34, 'rna3p': 153} Chain breaks: 1 Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 70175 SG CYS b 23 94.135 128.213 133.180 1.00 43.01 S ATOM 70196 SG CYS b 26 97.631 128.871 135.675 1.00 48.68 S ATOM 70579 SG CYS b 74 96.149 125.723 134.678 1.00 40.99 S ATOM 70598 SG CYS b 77 96.077 127.386 136.385 1.00 44.54 S Time building chain proxies: 33.40, per 1000 atoms: 0.40 Number of scatterers: 83005 At special positions: 0 Unit cell: (235.6, 209, 262.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 187 16.00 P 1958 15.00 O 20890 8.00 N 15282 7.00 C 44687 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS g 126 " - pdb=" SG CYS g 144 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 31.87 Conformation dependent library (CDL) restraints added in 6.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN b 201 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 77 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 74 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 23 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 26 " Number of angles added : 6 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9608 Finding SS restraints... Secondary structure from input PDB file: 161 helices and 63 sheets defined 34.8% alpha, 17.7% beta 527 base pairs and 1039 stacking pairs defined. Time for finding SS restraints: 28.57 Creating SS restraints... Processing helix chain 'A' and resid 97 through 107 removed outlier: 3.552A pdb=" N TYR A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 21 Processing helix chain 'B' and resid 31 through 36 removed outlier: 3.775A pdb=" N GLU B 35 " --> pdb=" O PHE B 32 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLN B 36 " --> pdb=" O GLN B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 68 removed outlier: 4.354A pdb=" N ILE B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 83 through 95 removed outlier: 3.701A pdb=" N VAL B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 88 " --> pdb=" O GLN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 137 removed outlier: 3.651A pdb=" N LEU B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 187 Processing helix chain 'B' and resid 198 through 203 removed outlier: 3.999A pdb=" N LEU B 201 " --> pdb=" O MET B 198 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N TYR B 202 " --> pdb=" O PRO B 199 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE B 203 " --> pdb=" O ASP B 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 198 through 203' Processing helix chain 'B' and resid 206 through 217 Processing helix chain 'C' and resid 23 through 26 removed outlier: 3.675A pdb=" N SER C 26 " --> pdb=" O ASP C 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 23 through 26' Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 106 through 114 removed outlier: 3.794A pdb=" N VAL C 114 " --> pdb=" O MET C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 178 removed outlier: 3.518A pdb=" N GLU C 175 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N VAL C 176 " --> pdb=" O MET C 172 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN C 177 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N THR C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 189 Processing helix chain 'C' and resid 191 through 201 Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 224 through 231 removed outlier: 4.385A pdb=" N LEU C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 72 removed outlier: 3.524A pdb=" N ARG D 68 " --> pdb=" O THR D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 84 Processing helix chain 'D' and resid 91 through 98 removed outlier: 3.710A pdb=" N ASP D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 161 Processing helix chain 'D' and resid 207 through 218 Processing helix chain 'D' and resid 232 through 246 Processing helix chain 'D' and resid 252 through 256 removed outlier: 3.901A pdb=" N TRP D 256 " --> pdb=" O PRO D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 269 Processing helix chain 'D' and resid 269 through 277 Processing helix chain 'E' and resid 6 through 29 removed outlier: 3.701A pdb=" N PHE E 11 " --> pdb=" O LYS E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 62 No H-bonds generated for 'chain 'E' and resid 60 through 62' Processing helix chain 'E' and resid 63 through 77 Processing helix chain 'E' and resid 93 through 96 Processing helix chain 'E' and resid 97 through 112 removed outlier: 3.559A pdb=" N GLN E 101 " --> pdb=" O CYS E 97 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY E 112 " --> pdb=" O LYS E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 129 Processing helix chain 'E' and resid 162 through 167 removed outlier: 3.515A pdb=" N TYR E 166 " --> pdb=" O ASP E 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 51 Processing helix chain 'F' and resid 57 through 67 removed outlier: 3.565A pdb=" N VAL F 61 " --> pdb=" O THR F 57 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS F 62 " --> pdb=" O GLY F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 263 Processing helix chain 'G' and resid 61 through 66 Processing helix chain 'G' and resid 67 through 77 removed outlier: 4.075A pdb=" N MET G 77 " --> pdb=" O THR G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 105 removed outlier: 3.576A pdb=" N THR G 104 " --> pdb=" O ILE G 100 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY G 105 " --> pdb=" O HIS G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 119 removed outlier: 3.503A pdb=" N VAL G 111 " --> pdb=" O ASN G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 162 Processing helix chain 'G' and resid 168 through 182 removed outlier: 3.763A pdb=" N ALA G 174 " --> pdb=" O ALA G 170 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU G 177 " --> pdb=" O LEU G 173 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE G 178 " --> pdb=" O ALA G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 203 removed outlier: 3.635A pdb=" N ASN G 203 " --> pdb=" O VAL G 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 42 removed outlier: 3.811A pdb=" N GLY H 42 " --> pdb=" O ASP H 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 39 through 42' Processing helix chain 'H' and resid 137 through 146 Processing helix chain 'H' and resid 181 through 237 removed outlier: 3.624A pdb=" N LEU H 185 " --> pdb=" O THR H 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 33 removed outlier: 3.680A pdb=" N SER I 21 " --> pdb=" O ASP I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 40 removed outlier: 3.725A pdb=" N LEU I 40 " --> pdb=" O LYS I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 67 No H-bonds generated for 'chain 'I' and resid 65 through 67' Processing helix chain 'I' and resid 68 through 74 removed outlier: 3.546A pdb=" N PHE I 72 " --> pdb=" O GLN I 68 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS I 74 " --> pdb=" O LYS I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 87 removed outlier: 4.742A pdb=" N ARG I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 120 Processing helix chain 'I' and resid 121 through 134 removed outlier: 4.194A pdb=" N VAL I 134 " --> pdb=" O LEU I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 168 No H-bonds generated for 'chain 'I' and resid 166 through 168' Processing helix chain 'I' and resid 169 through 181 Processing helix chain 'J' and resid 49 through 51 No H-bonds generated for 'chain 'J' and resid 49 through 51' Processing helix chain 'J' and resid 88 through 93 removed outlier: 4.230A pdb=" N ARG J 92 " --> pdb=" O ASN J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 117 Processing helix chain 'J' and resid 132 through 138 removed outlier: 4.004A pdb=" N ILE J 136 " --> pdb=" O GLU J 132 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU J 137 " --> pdb=" O GLU J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 153 Processing helix chain 'J' and resid 159 through 169 Processing helix chain 'J' and resid 178 through 183 Processing helix chain 'J' and resid 192 through 207 Processing helix chain 'K' and resid 21 through 36 removed outlier: 3.614A pdb=" N LEU K 25 " --> pdb=" O GLU K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 63 removed outlier: 4.156A pdb=" N VAL K 43 " --> pdb=" O ASN K 39 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU K 63 " --> pdb=" O GLU K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 84 Processing helix chain 'K' and resid 93 through 97 removed outlier: 3.809A pdb=" N TYR K 96 " --> pdb=" O LYS K 93 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE K 97 " --> pdb=" O LEU K 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 93 through 97' Processing helix chain 'K' and resid 101 through 108 removed outlier: 3.883A pdb=" N PHE K 105 " --> pdb=" O LYS K 101 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG K 108 " --> pdb=" O ASP K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 118 Processing helix chain 'K' and resid 122 through 131 Processing helix chain 'K' and resid 171 through 186 Processing helix chain 'L' and resid 4 through 18 removed outlier: 3.676A pdb=" N ARG L 8 " --> pdb=" O PRO L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 56 removed outlier: 3.819A pdb=" N VAL L 45 " --> pdb=" O PRO L 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 84 Processing helix chain 'N' and resid 15 through 28 Processing helix chain 'N' and resid 35 through 44 Processing helix chain 'N' and resid 60 through 70 Processing helix chain 'N' and resid 81 through 90 removed outlier: 3.526A pdb=" N LEU N 85 " --> pdb=" O ASP N 81 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU N 87 " --> pdb=" O LYS N 83 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TRP N 88 " --> pdb=" O LYS N 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 118 through 129 Processing helix chain 'O' and resid 29 through 43 removed outlier: 3.569A pdb=" N VAL O 33 " --> pdb=" O THR O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 58 Processing helix chain 'O' and resid 70 through 78 Processing helix chain 'O' and resid 85 through 105 removed outlier: 4.142A pdb=" N ARG O 104 " --> pdb=" O LYS O 100 " (cutoff:3.500A) Processing helix chain 'O' and resid 108 through 132 removed outlier: 3.649A pdb=" N TYR O 128 " --> pdb=" O ARG O 124 " (cutoff:3.500A) Processing helix chain 'O' and resid 143 through 149 removed outlier: 3.881A pdb=" N SER O 147 " --> pdb=" O SER O 143 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA O 148 " --> pdb=" O SER O 144 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 89 Processing helix chain 'P' and resid 111 through 122 removed outlier: 3.550A pdb=" N ARG P 117 " --> pdb=" O GLN P 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 21 through 27 Processing helix chain 'Q' and resid 29 through 37 removed outlier: 4.903A pdb=" N GLN Q 35 " --> pdb=" O GLU Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 46 Processing helix chain 'Q' and resid 54 through 66 Processing helix chain 'Q' and resid 86 through 90 removed outlier: 3.532A pdb=" N MET Q 89 " --> pdb=" O LEU Q 86 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL Q 90 " --> pdb=" O PRO Q 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 86 through 90' Processing helix chain 'Q' and resid 115 through 119 Processing helix chain 'R' and resid 47 through 59 Proline residue: R 54 - end of helix Processing helix chain 'R' and resid 77 through 99 removed outlier: 3.651A pdb=" N SER R 89 " --> pdb=" O ARG R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 116 removed outlier: 3.794A pdb=" N LYS R 105 " --> pdb=" O ASP R 101 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE R 111 " --> pdb=" O GLU R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 120 Processing helix chain 'S' and resid 6 through 20 Processing helix chain 'S' and resid 27 through 38 removed outlier: 3.509A pdb=" N ASN S 31 " --> pdb=" O ASP S 27 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 62 Processing helix chain 'S' and resid 76 through 83 Processing helix chain 'S' and resid 99 through 107 Processing helix chain 'T' and resid 25 through 30 removed outlier: 3.817A pdb=" N ILE T 30 " --> pdb=" O ILE T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 31 through 33 No H-bonds generated for 'chain 'T' and resid 31 through 33' Processing helix chain 'T' and resid 37 through 48 removed outlier: 3.506A pdb=" N ALA T 41 " --> pdb=" O GLY T 37 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS T 42 " --> pdb=" O ARG T 38 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL T 43 " --> pdb=" O ARG T 39 " (cutoff:3.500A) Processing helix chain 'T' and resid 55 through 59 removed outlier: 4.008A pdb=" N GLU T 58 " --> pdb=" O ARG T 55 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU T 59 " --> pdb=" O ALA T 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 55 through 59' Processing helix chain 'T' and resid 60 through 73 Processing helix chain 'T' and resid 74 through 78 removed outlier: 3.692A pdb=" N TYR T 77 " --> pdb=" O PRO T 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 80 through 84 removed outlier: 3.764A pdb=" N LEU T 84 " --> pdb=" O ASP T 81 " (cutoff:3.500A) Processing helix chain 'T' and resid 100 through 118 Processing helix chain 'T' and resid 119 through 128 Processing helix chain 'U' and resid 5 through 9 Processing helix chain 'U' and resid 10 through 26 removed outlier: 3.811A pdb=" N ARG U 16 " --> pdb=" O GLN U 12 " (cutoff:3.500A) Processing helix chain 'U' and resid 31 through 35 removed outlier: 3.640A pdb=" N VAL U 34 " --> pdb=" O PRO U 31 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASP U 35 " --> pdb=" O GLU U 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 31 through 35' Processing helix chain 'U' and resid 51 through 67 removed outlier: 4.378A pdb=" N THR U 55 " --> pdb=" O ASN U 51 " (cutoff:3.500A) Processing helix chain 'U' and resid 71 through 79 removed outlier: 3.504A pdb=" N LYS U 77 " --> pdb=" O GLY U 73 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR U 79 " --> pdb=" O MET U 75 " (cutoff:3.500A) Processing helix chain 'U' and resid 96 through 110 removed outlier: 3.858A pdb=" N ALA U 100 " --> pdb=" O SER U 96 " (cutoff:3.500A) Processing helix chain 'U' and resid 124 through 143 Processing helix chain 'V' and resid 29 through 46 Processing helix chain 'V' and resid 94 through 103 removed outlier: 3.799A pdb=" N VAL V 98 " --> pdb=" O PRO V 94 " (cutoff:3.500A) Processing helix chain 'W' and resid 56 through 63 removed outlier: 3.526A pdb=" N GLY W 63 " --> pdb=" O ILE W 59 " (cutoff:3.500A) Processing helix chain 'W' and resid 64 through 77 Processing helix chain 'X' and resid 5 through 21 removed outlier: 3.560A pdb=" N ASP X 9 " --> pdb=" O ASN X 5 " (cutoff:3.500A) Processing helix chain 'X' and resid 31 through 44 Processing helix chain 'X' and resid 85 through 94 removed outlier: 3.922A pdb=" N TRP X 89 " --> pdb=" O ASP X 85 " (cutoff:3.500A) Processing helix chain 'X' and resid 112 through 120 Processing helix chain 'Y' and resid 10 through 23 Processing helix chain 'Y' and resid 25 through 31 Processing helix chain 'Y' and resid 33 through 38 Processing helix chain 'Y' and resid 90 through 94 removed outlier: 3.503A pdb=" N PHE Y 93 " --> pdb=" O CYS Y 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 130 through 135 Processing helix chain 'Z' and resid 36 through 48 removed outlier: 3.590A pdb=" N ILE Z 40 " --> pdb=" O PRO Z 36 " (cutoff:3.500A) Processing helix chain 'Z' and resid 78 through 85 removed outlier: 3.877A pdb=" N ASN Z 85 " --> pdb=" O TYR Z 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 87 through 95 removed outlier: 3.610A pdb=" N LEU Z 91 " --> pdb=" O PRO Z 87 " (cutoff:3.500A) Processing helix chain 'Z' and resid 103 through 117 removed outlier: 3.839A pdb=" N VAL Z 117 " --> pdb=" O ARG Z 113 " (cutoff:3.500A) Processing helix chain 'Z' and resid 120 through 126 removed outlier: 3.707A pdb=" N ASN Z 124 " --> pdb=" O THR Z 120 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY Z 126 " --> pdb=" O LYS Z 122 " (cutoff:3.500A) Processing helix chain 'a' and resid 51 through 62 removed outlier: 3.773A pdb=" N TYR a 55 " --> pdb=" O ASP a 51 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP a 56 " --> pdb=" O LYS a 52 " (cutoff:3.500A) Processing helix chain 'a' and resid 63 through 65 No H-bonds generated for 'chain 'a' and resid 63 through 65' Processing helix chain 'a' and resid 69 through 78 Processing helix chain 'a' and resid 80 through 95 Processing helix chain 'b' and resid 49 through 55 Processing helix chain 'b' and resid 74 through 81 Processing helix chain 'c' and resid 11 through 18 removed outlier: 3.805A pdb=" N GLU c 15 " --> pdb=" O SER c 11 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS c 18 " --> pdb=" O GLU c 14 " (cutoff:3.500A) Processing helix chain 'e' and resid 3 through 7 Processing helix chain 'e' and resid 32 through 36 removed outlier: 3.598A pdb=" N LEU e 36 " --> pdb=" O LYS e 33 " (cutoff:3.500A) Processing helix chain 'e' and resid 40 through 46 Processing helix chain 'e' and resid 46 through 51 removed outlier: 3.738A pdb=" N ILE e 50 " --> pdb=" O TYR e 46 " (cutoff:3.500A) Processing helix chain 'f' and resid 83 through 89 Processing helix chain 'f' and resid 103 through 116 removed outlier: 3.932A pdb=" N ARG f 107 " --> pdb=" O GLY f 103 " (cutoff:3.500A) Processing helix chain 'g' and resid 101 through 105 Processing helix chain 'j' and resid 37 through 40 removed outlier: 4.170A pdb=" N ASN j 40 " --> pdb=" O LEU j 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 37 through 40' Processing helix chain 'j' and resid 58 through 62 removed outlier: 3.568A pdb=" N LEU j 62 " --> pdb=" O ILE j 59 " (cutoff:3.500A) Processing helix chain 'j' and resid 93 through 120 removed outlier: 4.244A pdb=" N LYS j 97 " --> pdb=" O GLU j 93 " (cutoff:3.500A) Processing helix chain 'j' and resid 123 through 135 Processing helix chain 'j' and resid 135 through 143 Processing helix chain 'j' and resid 146 through 157 removed outlier: 3.966A pdb=" N TYR j 150 " --> pdb=" O GLY j 146 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASP j 151 " --> pdb=" O TYR j 147 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA j 152 " --> pdb=" O GLY j 148 " (cutoff:3.500A) Processing helix chain 'j' and resid 159 through 164 Processing helix chain 'j' and resid 170 through 184 Processing helix chain 'n' and resid 2 through 24 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 60 removed outlier: 3.609A pdb=" N LEU A 47 " --> pdb=" O CYS A 59 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU A 34 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE A 77 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE A 76 " --> pdb=" O TYR A 95 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 38 through 42 removed outlier: 4.138A pdb=" N LYS B 40 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE B 48 " --> pdb=" O LYS B 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 100 removed outlier: 6.304A pdb=" N SER B 75 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE B 159 " --> pdb=" O THR B 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.801A pdb=" N VAL C 49 " --> pdb=" O ASP C 29 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 43 through 45 removed outlier: 7.192A pdb=" N VAL C 33 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR C 98 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N CYS C 96 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL C 91 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N THR C 98 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLU C 89 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N PHE C 100 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE C 87 " --> pdb=" O PHE C 100 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 43 through 45 removed outlier: 7.192A pdb=" N VAL C 33 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR C 98 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU C 105 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N ARG C 213 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASP C 209 " --> pdb=" O PHE C 142 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N PHE C 138 " --> pdb=" O ARG C 213 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 103 through 115 removed outlier: 6.024A pdb=" N ASP D 104 " --> pdb=" O GLY D 131 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N GLY D 131 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL D 106 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ALA D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LYS D 108 " --> pdb=" O PHE D 127 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL D 128 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY D 140 " --> pdb=" O VAL D 128 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 184 through 188 removed outlier: 3.584A pdb=" N VAL D 184 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS D 188 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL D 205 " --> pdb=" O CYS D 222 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR D 224 " --> pdb=" O VAL D 205 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 36 through 42 removed outlier: 3.789A pdb=" N GLU E 85 " --> pdb=" O THR E 46 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE E 48 " --> pdb=" O GLU E 85 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA E 52 " --> pdb=" O GLU E 89 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 148 through 155 removed outlier: 3.885A pdb=" N GLY E 133 " --> pdb=" O MET E 189 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER E 139 " --> pdb=" O GLY E 183 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE E 188 " --> pdb=" O ASP E 169 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 209 through 210 removed outlier: 3.502A pdb=" N SER E 209 " --> pdb=" O ILE S 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 224 through 226 removed outlier: 3.940A pdb=" N GLU E 225 " --> pdb=" O ASN h 187 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN h 187 " --> pdb=" O GLU E 225 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL h 176 " --> pdb=" O LYS h 185 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ASN h 187 " --> pdb=" O VAL h 174 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL h 174 " --> pdb=" O ASN h 187 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AB5, first strand: chain 'F' and resid 75 through 76 removed outlier: 3.824A pdb=" N GLU F 97 " --> pdb=" O ILE F 92 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASN F 98 " --> pdb=" O ILE F 114 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 102 through 103 removed outlier: 4.109A pdb=" N ILE F 102 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA F 110 " --> pdb=" O ILE F 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'F' and resid 137 through 141 removed outlier: 6.716A pdb=" N HIS F 138 " --> pdb=" O ILE F 129 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ILE F 129 " --> pdb=" O HIS F 138 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL F 140 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS F 122 " --> pdb=" O ILE F 162 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N THR F 159 " --> pdb=" O PHE F 172 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N PHE F 172 " --> pdb=" O THR F 159 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N GLN F 161 " --> pdb=" O THR F 170 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 217 through 221 removed outlier: 7.530A pdb=" N VAL F 207 " --> pdb=" O ARG F 198 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ARG F 198 " --> pdb=" O VAL F 207 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N HIS F 209 " --> pdb=" O THR F 196 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY F 193 " --> pdb=" O CYS F 181 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU F 180 " --> pdb=" O ILE F 228 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE F 228 " --> pdb=" O LEU F 180 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 19 through 20 Processing sheet with id=AC1, first strand: chain 'G' and resid 123 through 127 removed outlier: 17.986A pdb=" N ARG G 136 " --> pdb=" O ILE d 43 " (cutoff:3.500A) removed outlier: 12.862A pdb=" N ASN d 45 " --> pdb=" O ARG G 136 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ALA G 138 " --> pdb=" O ASN d 45 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N LYS d 47 " --> pdb=" O ALA G 138 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASP G 140 " --> pdb=" O LYS d 47 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLN d 29 " --> pdb=" O VAL d 17 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N VAL d 17 " --> pdb=" O GLN d 29 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ARG d 31 " --> pdb=" O THR d 15 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 12 through 17 removed outlier: 6.548A pdb=" N LYS H 2 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEU H 111 " --> pdb=" O LYS H 2 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ASN H 4 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE H 113 " --> pdb=" O ASN H 4 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N SER H 6 " --> pdb=" O ILE H 113 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N LYS H 115 " --> pdb=" O SER H 6 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY H 54 " --> pdb=" O ASN H 110 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL H 112 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ILE H 52 " --> pdb=" O VAL H 112 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL H 114 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N VAL H 50 " --> pdb=" O VAL H 114 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 72 through 77 Processing sheet with id=AC4, first strand: chain 'I' and resid 48 through 52 removed outlier: 3.958A pdb=" N ILE I 61 " --> pdb=" O LYS I 49 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE I 51 " --> pdb=" O ALA I 59 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA I 59 " --> pdb=" O ILE I 51 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N LYS I 58 " --> pdb=" O HIS I 91 " (cutoff:3.500A) removed outlier: 8.939A pdb=" N VAL I 93 " --> pdb=" O LYS I 58 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE I 60 " --> pdb=" O VAL I 93 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ILE I 95 " --> pdb=" O ILE I 60 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ILE I 62 " --> pdb=" O ILE I 95 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 184 through 188 removed outlier: 4.525A pdb=" N ASP I 184 " --> pdb=" O ARG I 152 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 37 through 38 removed outlier: 6.149A pdb=" N LYS J 37 " --> pdb=" O LEU J 60 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'J' and resid 45 through 47 Processing sheet with id=AC8, first strand: chain 'J' and resid 64 through 67 removed outlier: 3.658A pdb=" N PHE J 65 " --> pdb=" O ARG J 74 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG J 74 " --> pdb=" O PHE J 65 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 78 through 84 removed outlier: 7.749A pdb=" N ILE J 78 " --> pdb=" O ASP J 105 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ASP J 105 " --> pdb=" O ILE J 78 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ILE J 101 " --> pdb=" O VAL J 82 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N CYS J 100 " --> pdb=" O ILE J 175 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 135 through 137 Processing sheet with id=AD2, first strand: chain 'L' and resid 20 through 24 removed outlier: 3.581A pdb=" N MET L 21 " --> pdb=" O TRP L 69 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA L 23 " --> pdb=" O PHE L 67 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 72 through 79 removed outlier: 17.528A pdb=" N ILE M 72 " --> pdb=" O LEU M 93 " (cutoff:3.500A) removed outlier: 14.469A pdb=" N LEU M 93 " --> pdb=" O ILE M 72 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N SER M 74 " --> pdb=" O ASP M 91 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASP M 91 " --> pdb=" O SER M 74 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N VAL M 87 " --> pdb=" O THR M 78 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG M 90 " --> pdb=" O LYS M 107 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS M 107 " --> pdb=" O ARG M 90 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE M 96 " --> pdb=" O ARG M 101 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG M 101 " --> pdb=" O ILE M 96 " (cutoff:3.500A) removed outlier: 9.641A pdb=" N VAL M 138 " --> pdb=" O ASN M 108 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N SER M 110 " --> pdb=" O VAL M 138 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N PHE M 140 " --> pdb=" O SER M 110 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N THR M 127 " --> pdb=" O LEU M 143 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL M 145 " --> pdb=" O ILE M 125 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ILE M 125 " --> pdb=" O VAL M 145 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 31 through 33 removed outlier: 3.823A pdb=" N VAL N 109 " --> pdb=" O VAL N 51 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N VAL N 79 " --> pdb=" O CYS N 50 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU N 52 " --> pdb=" O VAL N 79 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 52 through 57 removed outlier: 7.220A pdb=" N VAL P 44 " --> pdb=" O ILE P 53 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ARG P 55 " --> pdb=" O VAL P 42 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N VAL P 42 " --> pdb=" O ARG P 55 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N THR P 57 " --> pdb=" O THR P 40 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N THR P 40 " --> pdb=" O THR P 57 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'P' and resid 52 through 57 removed outlier: 7.220A pdb=" N VAL P 44 " --> pdb=" O ILE P 53 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ARG P 55 " --> pdb=" O VAL P 42 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N VAL P 42 " --> pdb=" O ARG P 55 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N THR P 57 " --> pdb=" O THR P 40 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N THR P 40 " --> pdb=" O THR P 57 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Q' and resid 76 through 78 removed outlier: 6.682A pdb=" N VAL Q 76 " --> pdb=" O GLY Q 95 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N TYR Q 97 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N THR Q 78 " --> pdb=" O TYR Q 97 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL Q 96 " --> pdb=" O ASN Q 103 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN Q 103 " --> pdb=" O VAL Q 96 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 9 through 10 removed outlier: 3.509A pdb=" N VAL R 10 " --> pdb=" O CYS R 25 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'R' and resid 9 through 10 removed outlier: 3.509A pdb=" N VAL R 10 " --> pdb=" O CYS R 25 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU R 31 " --> pdb=" O VAL R 66 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'S' and resid 96 through 98 Processing sheet with id=AE2, first strand: chain 'T' and resid 12 through 15 removed outlier: 3.656A pdb=" N VAL T 15 " --> pdb=" O THR T 18 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'U' and resid 81 through 83 removed outlier: 3.518A pdb=" N HIS U 91 " --> pdb=" O GLN U 83 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'U' and resid 113 through 115 Processing sheet with id=AE5, first strand: chain 'V' and resid 54 through 55 removed outlier: 3.642A pdb=" N PHE V 80 " --> pdb=" O ILE V 63 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE V 63 " --> pdb=" O PHE V 80 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS V 59 " --> pdb=" O ILE V 84 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'V' and resid 54 through 55 Processing sheet with id=AE7, first strand: chain 'W' and resid 32 through 34 removed outlier: 3.593A pdb=" N ILE W 55 " --> pdb=" O ILE W 32 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'W' and resid 37 through 39 removed outlier: 4.783A pdb=" N GLN W 49 " --> pdb=" O GLU W 38 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'X' and resid 24 through 27 removed outlier: 3.580A pdb=" N VAL X 25 " --> pdb=" O VAL X 63 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL X 63 " --> pdb=" O VAL X 25 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'X' and resid 71 through 74 removed outlier: 3.556A pdb=" N LYS X 71 " --> pdb=" O PHE X 130 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'X' and resid 71 through 74 removed outlier: 3.556A pdb=" N LYS X 71 " --> pdb=" O PHE X 130 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL X 103 " --> pdb=" O LEU X 126 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE X 128 " --> pdb=" O PHE X 101 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE X 101 " --> pdb=" O PHE X 128 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET X 111 " --> pdb=" O LEU X 104 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Y' and resid 80 through 82 removed outlier: 3.885A pdb=" N GLU Y 53 " --> pdb=" O ARG Y 71 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLN Y 73 " --> pdb=" O VAL Y 51 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N VAL Y 51 " --> pdb=" O GLN Y 73 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N GLU Y 99 " --> pdb=" O VAL Y 125 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL Y 125 " --> pdb=" O GLU Y 99 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU Y 101 " --> pdb=" O VAL Y 123 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Z' and resid 6 through 15 removed outlier: 4.393A pdb=" N PHE Z 12 " --> pdb=" O GLN Z 22 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N GLN Z 22 " --> pdb=" O PHE Z 12 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N THR Z 14 " --> pdb=" O ARG Z 20 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ARG Z 20 " --> pdb=" O THR Z 14 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N MET Z 23 " --> pdb=" O GLY Z 73 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LYS Z 68 " --> pdb=" O THR Z 62 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N THR Z 62 " --> pdb=" O LYS Z 68 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR Z 70 " --> pdb=" O PHE Z 60 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N PHE Z 60 " --> pdb=" O THR Z 70 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'a' and resid 67 through 68 removed outlier: 3.987A pdb=" N SER a 101 " --> pdb=" O ILE a 108 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N THR a 110 " --> pdb=" O LEU a 99 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU a 99 " --> pdb=" O THR a 110 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'b' and resid 20 through 22 Processing sheet with id=AF7, first strand: chain 'b' and resid 36 through 43 removed outlier: 3.508A pdb=" N VAL b 40 " --> pdb=" O VAL b 69 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL b 69 " --> pdb=" O VAL b 40 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG b 42 " --> pdb=" O LEU b 67 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'c' and resid 32 through 34 removed outlier: 3.539A pdb=" N MET c 33 " --> pdb=" O VAL c 46 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'c' and resid 54 through 55 removed outlier: 6.422A pdb=" N VAL c 54 " --> pdb=" O LEU c 63 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN c 65 " --> pdb=" O ARG c 72 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG c 72 " --> pdb=" O GLN c 65 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'e' and resid 30 through 31 removed outlier: 3.536A pdb=" N MET e 38 " --> pdb=" O ILE e 31 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'g' and resid 138 through 140 Processing sheet with id=AG3, first strand: chain 'h' and resid 5 through 11 removed outlier: 5.331A pdb=" N LEU h 7 " --> pdb=" O GLN h 311 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N GLN h 311 " --> pdb=" O LEU h 7 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLY h 9 " --> pdb=" O VAL h 309 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR h 297 " --> pdb=" O TRP h 291 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N TRP h 291 " --> pdb=" O THR h 297 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N PHE h 299 " --> pdb=" O LEU h 289 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU h 289 " --> pdb=" O PHE h 299 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLY h 301 " --> pdb=" O THR h 287 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'h' and resid 18 through 23 removed outlier: 3.580A pdb=" N GLN h 20 " --> pdb=" O ALA h 34 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER h 33 " --> pdb=" O ILE h 41 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG h 57 " --> pdb=" O MET h 42 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N LYS h 44 " --> pdb=" O PRO h 55 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'h' and resid 66 through 71 removed outlier: 6.587A pdb=" N GLY h 81 " --> pdb=" O SER h 67 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL h 69 " --> pdb=" O LEU h 79 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU h 79 " --> pdb=" O VAL h 69 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ILE h 71 " --> pdb=" O PHE h 77 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N PHE h 77 " --> pdb=" O ILE h 71 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG h 88 " --> pdb=" O SER h 80 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU h 87 " --> pdb=" O ARG h 100 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ARG h 100 " --> pdb=" O LEU h 87 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LEU h 89 " --> pdb=" O THR h 98 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'h' and resid 108 through 113 removed outlier: 3.614A pdb=" N ILE h 120 " --> pdb=" O TRP h 132 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS h 130 " --> pdb=" O SER h 122 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE h 129 " --> pdb=" O THR h 141 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR h 141 " --> pdb=" O ILE h 129 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU h 131 " --> pdb=" O LYS h 139 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'h' and resid 195 through 200 removed outlier: 3.570A pdb=" N SER h 209 " --> pdb=" O MET h 217 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLY h 211 " --> pdb=" O GLN h 215 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N GLN h 215 " --> pdb=" O GLY h 211 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR h 228 " --> pdb=" O LEU h 218 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ASP h 220 " --> pdb=" O HIS h 226 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N HIS h 226 " --> pdb=" O ASP h 220 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'h' and resid 236 through 241 removed outlier: 4.279A pdb=" N ALA h 238 " --> pdb=" O ALA h 251 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS h 257 " --> pdb=" O ALA h 250 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE h 258 " --> pdb=" O ASP h 268 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP h 268 " --> pdb=" O ILE h 258 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ASP h 260 " --> pdb=" O ILE h 266 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE h 266 " --> pdb=" O ASP h 260 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'j' and resid 19 through 27 removed outlier: 6.803A pdb=" N TYR j 33 " --> pdb=" O ARG j 25 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE j 46 " --> pdb=" O ALA j 32 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL j 34 " --> pdb=" O GLY j 44 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY j 44 " --> pdb=" O VAL j 34 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N GLU j 43 " --> pdb=" O ILE j 83 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N LEU j 85 " --> pdb=" O GLU j 43 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N MET j 45 " --> pdb=" O LEU j 85 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG j 75 " --> pdb=" O ASP j 84 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N SER j 86 " --> pdb=" O VAL j 73 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL j 73 " --> pdb=" O SER j 86 " (cutoff:3.500A) 1512 hydrogen bonds defined for protein. 4347 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1325 hydrogen bonds 2212 hydrogen bond angles 0 basepair planarities 527 basepair parallelities 1039 stacking parallelities Total time for adding SS restraints: 69.49 Time building geometry restraints manager: 34.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 14022 1.33 - 1.45: 32702 1.45 - 1.58: 37723 1.58 - 1.70: 3906 1.70 - 1.82: 285 Bond restraints: 88638 Sorted by residual: bond pdb=" C THR J 130 " pdb=" N PRO J 131 " ideal model delta sigma weight residual 1.334 1.387 -0.054 8.40e-03 1.42e+04 4.08e+01 bond pdb=" CD2 TRP j 136 " pdb=" CE2 TRP j 136 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.70e-02 3.46e+03 1.86e+01 bond pdb=" CA LEU F 23 " pdb=" CB LEU F 23 " ideal model delta sigma weight residual 1.527 1.622 -0.095 2.48e-02 1.63e+03 1.47e+01 bond pdb=" C GLU R 53 " pdb=" N PRO R 54 " ideal model delta sigma weight residual 1.336 1.381 -0.045 1.20e-02 6.94e+03 1.42e+01 bond pdb=" CD2 TRP j 136 " pdb=" CE3 TRP j 136 " ideal model delta sigma weight residual 1.398 1.457 -0.059 1.60e-02 3.91e+03 1.36e+01 ... (remaining 88633 not shown) Histogram of bond angle deviations from ideal: 96.34 - 104.43: 8724 104.43 - 112.52: 49186 112.52 - 120.62: 41321 120.62 - 128.71: 28015 128.71 - 136.80: 1820 Bond angle restraints: 129066 Sorted by residual: angle pdb=" CD2 TRP j 136 " pdb=" CE3 TRP j 136 " pdb=" CZ3 TRP j 136 " ideal model delta sigma weight residual 118.60 129.36 -10.76 1.30e+00 5.92e-01 6.85e+01 angle pdb=" CE2 TRP j 136 " pdb=" CD2 TRP j 136 " pdb=" CE3 TRP j 136 " ideal model delta sigma weight residual 118.80 124.89 -6.09 1.00e+00 1.00e+00 3.71e+01 angle pdb=" C GLU S 75 " pdb=" N GLU S 76 " pdb=" CA GLU S 76 " ideal model delta sigma weight residual 121.54 131.93 -10.39 1.91e+00 2.74e-01 2.96e+01 angle pdb=" N GLU H 208 " pdb=" CA GLU H 208 " pdb=" CB GLU H 208 " ideal model delta sigma weight residual 110.28 118.11 -7.83 1.55e+00 4.16e-01 2.55e+01 angle pdb=" C3' U 2 688 " pdb=" O3' U 2 688 " pdb=" P U 2 689 " ideal model delta sigma weight residual 120.20 127.77 -7.57 1.50e+00 4.44e-01 2.54e+01 ... (remaining 129061 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 51225 35.84 - 71.69: 4679 71.69 - 107.53: 617 107.53 - 143.38: 14 143.38 - 179.22: 32 Dihedral angle restraints: 56567 sinusoidal: 41679 harmonic: 14888 Sorted by residual: dihedral pdb=" O4' C 21206 " pdb=" C1' C 21206 " pdb=" N1 C 21206 " pdb=" C2 C 21206 " ideal model delta sinusoidal sigma weight residual -160.00 18.58 -178.58 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C 21303 " pdb=" C1' C 21303 " pdb=" N1 C 21303 " pdb=" C2 C 21303 " ideal model delta sinusoidal sigma weight residual 200.00 29.00 171.00 1 1.50e+01 4.44e-03 8.48e+01 dihedral pdb=" O4' C 21139 " pdb=" C1' C 21139 " pdb=" N1 C 21139 " pdb=" C2 C 21139 " ideal model delta sinusoidal sigma weight residual -160.00 3.38 -163.38 1 1.50e+01 4.44e-03 8.36e+01 ... (remaining 56564 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 14775 0.077 - 0.153: 1123 0.153 - 0.230: 100 0.230 - 0.306: 20 0.306 - 0.383: 3 Chirality restraints: 16021 Sorted by residual: chirality pdb=" CB ILE H 52 " pdb=" CA ILE H 52 " pdb=" CG1 ILE H 52 " pdb=" CG2 ILE H 52 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" C3' G 2 895 " pdb=" C4' G 2 895 " pdb=" O3' G 2 895 " pdb=" C2' G 2 895 " both_signs ideal model delta sigma weight residual False -2.48 -2.13 -0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CB THR X 105 " pdb=" CA THR X 105 " pdb=" OG1 THR X 105 " pdb=" CG2 THR X 105 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.33 2.00e-01 2.50e+01 2.68e+00 ... (remaining 16018 not shown) Planarity restraints: 9109 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C 21852 " 0.003 2.00e-02 2.50e+03 2.95e-02 1.95e+01 pdb=" N1 C 21852 " -0.004 2.00e-02 2.50e+03 pdb=" C2 C 21852 " -0.071 2.00e-02 2.50e+03 pdb=" O2 C 21852 " 0.050 2.00e-02 2.50e+03 pdb=" N3 C 21852 " -0.005 2.00e-02 2.50e+03 pdb=" C4 C 21852 " 0.002 2.00e-02 2.50e+03 pdb=" N4 C 21852 " 0.004 2.00e-02 2.50e+03 pdb=" C5 C 21852 " 0.014 2.00e-02 2.50e+03 pdb=" C6 C 21852 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA Q 67 " -0.066 5.00e-02 4.00e+02 1.00e-01 1.60e+01 pdb=" N PRO Q 68 " 0.173 5.00e-02 4.00e+02 pdb=" CA PRO Q 68 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO Q 68 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 32 " -0.024 2.00e-02 2.50e+03 2.80e-02 1.37e+01 pdb=" CG PHE B 32 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 PHE B 32 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE B 32 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE B 32 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE B 32 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 32 " 0.001 2.00e-02 2.50e+03 ... (remaining 9106 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 19748 2.80 - 3.33: 66891 3.33 - 3.85: 158130 3.85 - 4.38: 180546 4.38 - 4.90: 264606 Nonbonded interactions: 689921 Sorted by model distance: nonbonded pdb=" O2' U 2 375 " pdb=" OE2 GLU M 7 " model vdw 2.281 2.440 nonbonded pdb=" O PHE J 65 " pdb=" OH TYR J 109 " model vdw 2.281 2.440 nonbonded pdb=" O MET C 169 " pdb=" OG1 THR C 173 " model vdw 2.282 2.440 nonbonded pdb=" OG1 THR h 24 " pdb=" O PHE h 27 " model vdw 2.287 2.440 nonbonded pdb=" OE2 GLU B 56 " pdb=" OG SER W 80 " model vdw 2.292 2.440 ... (remaining 689916 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 16.300 Check model and map are aligned: 0.940 Set scattering table: 0.550 Process input model: 241.910 Find NCS groups from input model: 2.010 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 267.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 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 : 0.003 0.095 88638 Z= 0.216 Angle : 0.812 12.958 129066 Z= 0.410 Chirality : 0.042 0.383 16021 Planarity : 0.006 0.100 9109 Dihedral : 22.022 179.220 46956 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.14 % Allowed : 0.61 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.10), residues: 5104 helix: -1.46 (0.11), residues: 1583 sheet: -0.69 (0.18), residues: 836 loop : -1.74 (0.11), residues: 2685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP e 8 HIS 0.008 0.001 HIS X 120 PHE 0.065 0.002 PHE B 32 TYR 0.041 0.002 TYR G 188 ARG 0.017 0.001 ARG L 8 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1669 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1664 time to evaluate : 4.722 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: A 46 ARG cc_start: 0.3474 (mtm180) cc_final: 0.2958 (mtt180) REVERT: B 15 VAL cc_start: 0.8396 (t) cc_final: 0.8052 (t) REVERT: B 78 SER cc_start: 0.7968 (t) cc_final: 0.7588 (m) REVERT: C 73 ASP cc_start: 0.7553 (m-30) cc_final: 0.7302 (t0) REVERT: C 90 ASP cc_start: 0.4399 (p0) cc_final: 0.4145 (m-30) REVERT: D 105 GLU cc_start: 0.7209 (pm20) cc_final: 0.6903 (mt-10) REVERT: D 108 LYS cc_start: 0.7817 (tttt) cc_final: 0.7591 (tttp) REVERT: E 59 LEU cc_start: 0.6135 (mt) cc_final: 0.5725 (tp) REVERT: E 77 PHE cc_start: 0.5069 (m-80) cc_final: 0.4838 (m-80) REVERT: E 143 ARG cc_start: 0.5491 (mtm-85) cc_final: 0.5290 (mmm160) REVERT: E 152 PHE cc_start: 0.6366 (m-80) cc_final: 0.6037 (m-10) REVERT: E 198 ILE cc_start: 0.6367 (mp) cc_final: 0.6056 (mm) REVERT: F 95 THR cc_start: 0.6493 (p) cc_final: 0.6261 (t) REVERT: F 256 LEU cc_start: 0.5800 (mt) cc_final: 0.5360 (tt) REVERT: G 48 TYR cc_start: 0.5630 (m-80) cc_final: 0.5115 (m-80) REVERT: G 134 VAL cc_start: 0.7232 (t) cc_final: 0.6977 (p) REVERT: G 137 GLN cc_start: 0.7605 (tp-100) cc_final: 0.7227 (tp-100) REVERT: G 156 THR cc_start: 0.8701 (t) cc_final: 0.8478 (t) REVERT: G 192 LYS cc_start: 0.6847 (mttt) cc_final: 0.6558 (mtpp) REVERT: H 61 PHE cc_start: 0.6071 (m-80) cc_final: 0.5858 (m-80) REVERT: H 65 GLN cc_start: 0.6221 (tp40) cc_final: 0.4344 (mp10) REVERT: I 91 HIS cc_start: 0.4816 (m170) cc_final: 0.4093 (m90) REVERT: I 179 LYS cc_start: 0.7065 (tptt) cc_final: 0.6809 (tttt) REVERT: J 189 VAL cc_start: 0.8126 (p) cc_final: 0.7350 (p) REVERT: J 194 GLU cc_start: 0.6807 (mm-30) cc_final: 0.6213 (mm-30) REVERT: J 205 ARG cc_start: 0.4650 (tpt170) cc_final: 0.3731 (tpt170) REVERT: K 64 ASP cc_start: 0.6369 (t70) cc_final: 0.5398 (m-30) REVERT: K 92 MET cc_start: 0.5144 (tpt) cc_final: 0.4659 (ptt) REVERT: L 16 PHE cc_start: 0.6845 (t80) cc_final: 0.6619 (t80) REVERT: L 78 TYR cc_start: 0.6241 (t80) cc_final: 0.5790 (t80) REVERT: M 7 GLU cc_start: 0.5675 (tt0) cc_final: 0.5055 (mt-10) REVERT: O 32 ASP cc_start: 0.4602 (t0) cc_final: 0.4322 (t0) REVERT: Q 111 MET cc_start: 0.5461 (mmp) cc_final: 0.4677 (mmp) REVERT: R 100 VAL cc_start: 0.5808 (t) cc_final: 0.5535 (t) REVERT: S 22 THR cc_start: 0.7344 (p) cc_final: 0.6945 (t) REVERT: S 59 LYS cc_start: 0.7870 (mttp) cc_final: 0.7489 (mtmt) REVERT: S 126 MET cc_start: 0.5598 (mtm) cc_final: 0.5178 (mmt) REVERT: U 88 MET cc_start: 0.4203 (mmp) cc_final: 0.2512 (tpp) REVERT: V 110 VAL cc_start: 0.6272 (t) cc_final: 0.6019 (t) REVERT: X 61 ILE cc_start: 0.8902 (mp) cc_final: 0.8433 (mt) REVERT: Z 48 TYR cc_start: 0.5722 (m-80) cc_final: 0.5496 (m-80) REVERT: Z 81 TYR cc_start: 0.5279 (m-10) cc_final: 0.4863 (m-10) REVERT: a 57 LYS cc_start: 0.7832 (tttp) cc_final: 0.7621 (mtpp) REVERT: d 11 LEU cc_start: 0.7936 (pp) cc_final: 0.7721 (mp) REVERT: e 13 LYS cc_start: 0.6232 (tptp) cc_final: 0.5205 (tptp) REVERT: g 139 HIS cc_start: 0.4837 (m-70) cc_final: 0.4582 (m-70) REVERT: h 171 ASP cc_start: 0.6820 (m-30) cc_final: 0.6095 (m-30) outliers start: 5 outliers final: 1 residues processed: 1667 average time/residue: 0.8898 time to fit residues: 2394.7787 Evaluate side-chains 839 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 838 time to evaluate : 4.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain j residue 147 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 587 optimal weight: 8.9990 chunk 527 optimal weight: 7.9990 chunk 292 optimal weight: 8.9990 chunk 180 optimal weight: 8.9990 chunk 355 optimal weight: 9.9990 chunk 281 optimal weight: 3.9990 chunk 545 optimal weight: 9.9990 chunk 211 optimal weight: 9.9990 chunk 331 optimal weight: 5.9990 chunk 406 optimal weight: 6.9990 chunk 632 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 HIS B 33 GLN B 164 ASN C 147 ASN D 235 ASN E 57 ASN ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 73 GLN ** I 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 146 GLN K 124 HIS ** L 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 13 GLN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 83 GLN M 94 HIS O 5 HIS O 49 GLN O 123 HIS ** P 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 GLN S 83 ASN T 125 HIS ** V 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 21 ASN Y 87 ASN ** c 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 51 GLN e 5 GLN e 28 HIS h 64 HIS h 159 ASN j 11 HIS j 114 HIS n 22 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.5012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.123 88638 Z= 0.384 Angle : 0.813 12.390 129066 Z= 0.410 Chirality : 0.045 0.434 16021 Planarity : 0.007 0.075 9109 Dihedral : 23.191 179.486 36412 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.10 % Allowed : 16.31 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.11), residues: 5104 helix: -0.38 (0.12), residues: 1608 sheet: -1.01 (0.17), residues: 933 loop : -1.57 (0.11), residues: 2563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP h 43 HIS 0.011 0.002 HIS h 191 PHE 0.042 0.003 PHE F 69 TYR 0.031 0.003 TYR B 156 ARG 0.024 0.001 ARG h 99 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1057 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 878 time to evaluate : 4.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.2826 (mtp) cc_final: 0.1959 (ptt) REVERT: B 31 ASP cc_start: 0.6676 (t0) cc_final: 0.6373 (t0) REVERT: B 78 SER cc_start: 0.8084 (t) cc_final: 0.7863 (m) REVERT: B 196 GLU cc_start: 0.4941 (mp0) cc_final: 0.4442 (mt-10) REVERT: C 76 ASN cc_start: 0.6130 (m-40) cc_final: 0.5928 (m-40) REVERT: C 178 THR cc_start: 0.6730 (p) cc_final: 0.6459 (p) REVERT: C 225 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7680 (mp) REVERT: D 220 ASP cc_start: 0.8414 (p0) cc_final: 0.8068 (p0) REVERT: E 40 ARG cc_start: 0.4411 (ptp-110) cc_final: 0.3845 (ttp80) REVERT: E 143 ARG cc_start: 0.5607 (mtm-85) cc_final: 0.5208 (mmm160) REVERT: F 19 MET cc_start: 0.8540 (ptm) cc_final: 0.8143 (ptm) REVERT: F 104 ASP cc_start: 0.6730 (p0) cc_final: 0.6502 (p0) REVERT: F 252 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.7145 (ttm-80) REVERT: G 26 ASP cc_start: 0.6774 (OUTLIER) cc_final: 0.6301 (m-30) REVERT: G 43 GLU cc_start: 0.6061 (mm-30) cc_final: 0.5740 (mm-30) REVERT: G 88 MET cc_start: 0.8755 (ttp) cc_final: 0.8412 (ttp) REVERT: I 60 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.7388 (mt) REVERT: I 72 PHE cc_start: 0.6956 (m-10) cc_final: 0.6651 (m-10) REVERT: I 131 GLU cc_start: 0.7236 (tm-30) cc_final: 0.7033 (tm-30) REVERT: J 129 LEU cc_start: 0.3308 (tp) cc_final: 0.2855 (pp) REVERT: J 148 LYS cc_start: 0.7050 (ttpp) cc_final: 0.6830 (ttmm) REVERT: K 104 ASP cc_start: 0.6614 (OUTLIER) cc_final: 0.6333 (m-30) REVERT: L 24 LYS cc_start: 0.7836 (tmtt) cc_final: 0.7480 (ttmt) REVERT: L 96 ARG cc_start: 0.5129 (ptp-170) cc_final: 0.4600 (ptm160) REVERT: M 49 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7439 (mp0) REVERT: M 108 ASN cc_start: 0.8203 (p0) cc_final: 0.7880 (p0) REVERT: P 26 ASN cc_start: 0.7843 (OUTLIER) cc_final: 0.7295 (m-40) REVERT: P 90 ILE cc_start: 0.8500 (mm) cc_final: 0.8174 (mt) REVERT: Q 93 MET cc_start: 0.8083 (tpt) cc_final: 0.7736 (mmm) REVERT: Q 111 MET cc_start: 0.7265 (mmp) cc_final: 0.6832 (mmp) REVERT: R 53 GLU cc_start: 0.6547 (mt-10) cc_final: 0.6318 (mt-10) REVERT: S 126 MET cc_start: 0.7157 (mtm) cc_final: 0.6903 (mtp) REVERT: T 73 ASN cc_start: 0.7608 (t0) cc_final: 0.7095 (t0) REVERT: U 93 SER cc_start: 0.8552 (t) cc_final: 0.8168 (m) REVERT: W 43 THR cc_start: 0.8230 (t) cc_final: 0.7694 (m) REVERT: W 49 GLN cc_start: 0.6735 (mm-40) cc_final: 0.6357 (mm110) REVERT: W 74 LYS cc_start: 0.7960 (mmtm) cc_final: 0.7747 (mttm) REVERT: X 61 ILE cc_start: 0.9056 (mp) cc_final: 0.8732 (mt) REVERT: Y 48 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.6754 (mttt) REVERT: Y 80 LYS cc_start: 0.6528 (mmmt) cc_final: 0.6074 (mmtp) REVERT: Z 47 MET cc_start: 0.5935 (OUTLIER) cc_final: 0.5645 (ttm) REVERT: Z 48 TYR cc_start: 0.6278 (m-80) cc_final: 0.5924 (m-80) REVERT: c 26 GLN cc_start: 0.8659 (tt0) cc_final: 0.7941 (pt0) REVERT: d 11 LEU cc_start: 0.8363 (pp) cc_final: 0.7809 (mp) REVERT: e 13 LYS cc_start: 0.6019 (tptp) cc_final: 0.5622 (tptp) REVERT: h 171 ASP cc_start: 0.6780 (m-30) cc_final: 0.6495 (m-30) REVERT: h 213 ASP cc_start: 0.5673 (p0) cc_final: 0.4996 (m-30) REVERT: h 225 LYS cc_start: 0.7379 (pttp) cc_final: 0.7002 (mmtm) REVERT: j 21 MET cc_start: 0.6291 (ttm) cc_final: 0.5986 (mtp) REVERT: j 97 LYS cc_start: 0.7574 (mtmm) cc_final: 0.7335 (mtmm) outliers start: 179 outliers final: 109 residues processed: 1007 average time/residue: 0.8029 time to fit residues: 1367.0574 Evaluate side-chains 802 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 685 time to evaluate : 4.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 236 ILE Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 252 ARG Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain J residue 49 ARG Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain K residue 104 ASP Chi-restraints excluded: chain K residue 107 GLU Chi-restraints excluded: chain K residue 132 GLN Chi-restraints excluded: chain K residue 149 VAL Chi-restraints excluded: chain L residue 73 ASN Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain N residue 57 ASP Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 75 ASN Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 131 THR Chi-restraints excluded: chain P residue 26 ASN Chi-restraints excluded: chain P residue 68 GLU Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 140 THR Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain Q residue 105 VAL Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain S residue 71 ILE Chi-restraints excluded: chain T residue 43 VAL Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 35 ASP Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 11 LEU Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 17 CYS Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 76 SER Chi-restraints excluded: chain X residue 104 LEU Chi-restraints excluded: chain X residue 105 THR Chi-restraints excluded: chain Y residue 48 LYS Chi-restraints excluded: chain Z residue 25 ILE Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 47 MET Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain b residue 40 VAL Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain c residue 40 CYS Chi-restraints excluded: chain d residue 33 GLU Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain d residue 57 THR Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 14 PHE Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain h residue 50 THR Chi-restraints excluded: chain h residue 94 THR Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 145 GLU Chi-restraints excluded: chain h residue 198 VAL Chi-restraints excluded: chain h residue 306 LEU Chi-restraints excluded: chain j residue 11 HIS Chi-restraints excluded: chain j residue 24 VAL Chi-restraints excluded: chain j residue 46 ILE Chi-restraints excluded: chain j residue 60 ASN Chi-restraints excluded: chain j residue 110 SER Chi-restraints excluded: chain j residue 131 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 351 optimal weight: 0.0020 chunk 196 optimal weight: 6.9990 chunk 526 optimal weight: 7.9990 chunk 430 optimal weight: 0.6980 chunk 174 optimal weight: 0.9980 chunk 633 optimal weight: 4.9990 chunk 684 optimal weight: 20.0000 chunk 563 optimal weight: 9.9990 chunk 627 optimal weight: 20.0000 chunk 215 optimal weight: 6.9990 chunk 507 optimal weight: 4.9990 overall best weight: 2.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 HIS ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 GLN J 181 GLN L 66 HIS O 58 HIS O 62 GLN O 69 ASN ** P 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 104 GLN S 62 GLN T 73 ASN X 90 GLN Y 87 ASN ** c 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 28 HIS g 93 HIS j 11 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.5244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 88638 Z= 0.163 Angle : 0.547 9.977 129066 Z= 0.281 Chirality : 0.035 0.226 16021 Planarity : 0.004 0.054 9109 Dihedral : 22.966 179.983 36410 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.73 % Allowed : 19.61 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.11), residues: 5104 helix: 0.41 (0.13), residues: 1623 sheet: -0.75 (0.17), residues: 912 loop : -1.39 (0.12), residues: 2569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 195 HIS 0.019 0.001 HIS j 11 PHE 0.020 0.001 PHE F 47 TYR 0.022 0.001 TYR h 140 ARG 0.008 0.000 ARG f 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 955 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 792 time to evaluate : 6.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.2943 (mtp) cc_final: 0.2026 (ptt) REVERT: B 31 ASP cc_start: 0.6671 (t0) cc_final: 0.6393 (t0) REVERT: B 52 LYS cc_start: 0.8043 (ttmt) cc_final: 0.7668 (mttt) REVERT: B 188 THR cc_start: 0.6649 (p) cc_final: 0.6383 (m) REVERT: C 157 GLN cc_start: 0.7371 (OUTLIER) cc_final: 0.7111 (mm-40) REVERT: C 227 LYS cc_start: 0.6922 (mmtm) cc_final: 0.6361 (mmtm) REVERT: E 40 ARG cc_start: 0.4361 (ptp-110) cc_final: 0.4033 (ttp80) REVERT: E 74 GLN cc_start: 0.7104 (OUTLIER) cc_final: 0.6853 (pt0) REVERT: E 143 ARG cc_start: 0.5389 (mtm-85) cc_final: 0.5132 (mmm160) REVERT: F 44 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7374 (tt) REVERT: F 52 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7654 (mp) REVERT: F 87 MET cc_start: 0.8178 (tpp) cc_final: 0.7814 (tpp) REVERT: F 104 ASP cc_start: 0.6702 (p0) cc_final: 0.6492 (p0) REVERT: G 76 MET cc_start: 0.7765 (tpp) cc_final: 0.7416 (tpt) REVERT: G 88 MET cc_start: 0.8524 (ttp) cc_final: 0.8225 (ttp) REVERT: G 182 LYS cc_start: 0.8854 (ptpp) cc_final: 0.8626 (ptmt) REVERT: H 65 GLN cc_start: 0.8262 (tp-100) cc_final: 0.8053 (tp-100) REVERT: I 60 ILE cc_start: 0.7775 (OUTLIER) cc_final: 0.7371 (mt) REVERT: I 131 GLU cc_start: 0.7336 (tm-30) cc_final: 0.7082 (tm-30) REVERT: J 205 ARG cc_start: 0.4262 (ttt180) cc_final: 0.3692 (tpt90) REVERT: K 104 ASP cc_start: 0.6464 (OUTLIER) cc_final: 0.6145 (m-30) REVERT: L 24 LYS cc_start: 0.7976 (tmtt) cc_final: 0.7502 (ttmt) REVERT: L 53 LYS cc_start: 0.8342 (tttp) cc_final: 0.7978 (ptmm) REVERT: M 18 GLN cc_start: 0.6970 (tm-30) cc_final: 0.6273 (pt0) REVERT: M 49 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7431 (mp0) REVERT: P 26 ASN cc_start: 0.7865 (OUTLIER) cc_final: 0.7319 (m-40) REVERT: Q 111 MET cc_start: 0.7392 (mmp) cc_final: 0.6902 (mmp) REVERT: R 107 GLU cc_start: 0.7259 (tm-30) cc_final: 0.6876 (tp30) REVERT: U 93 SER cc_start: 0.8506 (t) cc_final: 0.8147 (m) REVERT: V 49 LYS cc_start: 0.7099 (ptpt) cc_final: 0.6869 (pttp) REVERT: W 43 THR cc_start: 0.8273 (t) cc_final: 0.7881 (m) REVERT: Y 80 LYS cc_start: 0.6511 (mmmt) cc_final: 0.6088 (mmtp) REVERT: Z 48 TYR cc_start: 0.6261 (m-80) cc_final: 0.5907 (m-80) REVERT: d 11 LEU cc_start: 0.8401 (pp) cc_final: 0.7927 (mp) REVERT: e 13 LYS cc_start: 0.6195 (tptp) cc_final: 0.5920 (tptp) REVERT: h 171 ASP cc_start: 0.6891 (m-30) cc_final: 0.5471 (m-30) REVERT: h 225 LYS cc_start: 0.7235 (pttp) cc_final: 0.6968 (mmtm) REVERT: j 46 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.8029 (mt) REVERT: j 88 ARG cc_start: 0.7192 (OUTLIER) cc_final: 0.6817 (mtm180) REVERT: n 6 ARG cc_start: 0.7756 (mtp85) cc_final: 0.7343 (mtp-110) outliers start: 163 outliers final: 96 residues processed: 897 average time/residue: 0.8308 time to fit residues: 1277.2593 Evaluate side-chains 807 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 702 time to evaluate : 4.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 157 GLN Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 236 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 77 MET Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 70 LYS Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain J residue 49 ARG Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain K residue 104 ASP Chi-restraints excluded: chain K residue 107 GLU Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 149 VAL Chi-restraints excluded: chain L residue 73 ASN Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain N residue 58 GLU Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 87 ASP Chi-restraints excluded: chain P residue 26 ASN Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 126 ILE Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 84 ILE Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain S residue 8 THR Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 71 ILE Chi-restraints excluded: chain S residue 110 ASP Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 43 VAL Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 35 ASP Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain V residue 114 VAL Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 17 CYS Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain Z residue 25 ILE Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain a residue 89 GLN Chi-restraints excluded: chain b residue 40 VAL Chi-restraints excluded: chain c residue 40 CYS Chi-restraints excluded: chain d residue 39 SER Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain d residue 57 THR Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain f residue 92 VAL Chi-restraints excluded: chain g residue 93 HIS Chi-restraints excluded: chain h residue 54 ILE Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 107 ASP Chi-restraints excluded: chain h residue 145 GLU Chi-restraints excluded: chain h residue 199 THR Chi-restraints excluded: chain h residue 203 ASP Chi-restraints excluded: chain j residue 11 HIS Chi-restraints excluded: chain j residue 42 ILE Chi-restraints excluded: chain j residue 46 ILE Chi-restraints excluded: chain j residue 60 ASN Chi-restraints excluded: chain j residue 77 ASP Chi-restraints excluded: chain j residue 88 ARG Chi-restraints excluded: chain j residue 110 SER Chi-restraints excluded: chain j residue 131 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 625 optimal weight: 2.9990 chunk 476 optimal weight: 9.9990 chunk 328 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 302 optimal weight: 2.9990 chunk 425 optimal weight: 0.0270 chunk 635 optimal weight: 0.9990 chunk 672 optimal weight: 20.0000 chunk 331 optimal weight: 6.9990 chunk 602 optimal weight: 0.6980 chunk 181 optimal weight: 7.9990 overall best weight: 1.5444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 136 HIS ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 203 ASN ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 GLN J 146 GLN ** J 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 181 GLN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 132 GLN M 106 HIS O 49 GLN P 32 HIS R 114 GLN S 62 GLN U 11 GLN Y 87 ASN ** c 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 37 ASN g 93 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.5518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 88638 Z= 0.134 Angle : 0.505 8.796 129066 Z= 0.260 Chirality : 0.033 0.196 16021 Planarity : 0.004 0.060 9109 Dihedral : 22.795 179.389 36410 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.80 % Allowed : 20.59 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.12), residues: 5104 helix: 0.94 (0.13), residues: 1625 sheet: -0.49 (0.18), residues: 886 loop : -1.23 (0.12), residues: 2593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 8 HIS 0.039 0.001 HIS g 93 PHE 0.032 0.001 PHE C 211 TYR 0.019 0.001 TYR H 84 ARG 0.009 0.000 ARG Z 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 929 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 763 time to evaluate : 4.793 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: A 50 MET cc_start: 0.2645 (mtp) cc_final: 0.1675 (ptt) REVERT: B 31 ASP cc_start: 0.6752 (t0) cc_final: 0.6376 (t0) REVERT: B 52 LYS cc_start: 0.8134 (ttmt) cc_final: 0.7728 (mttt) REVERT: B 73 ASP cc_start: 0.7251 (m-30) cc_final: 0.6985 (m-30) REVERT: B 188 THR cc_start: 0.6706 (p) cc_final: 0.6456 (m) REVERT: C 157 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.7084 (mm-40) REVERT: C 196 ASP cc_start: 0.7241 (OUTLIER) cc_final: 0.6690 (t70) REVERT: D 268 GLU cc_start: 0.6976 (tp30) cc_final: 0.6669 (tp30) REVERT: E 59 LEU cc_start: 0.6573 (mt) cc_final: 0.5600 (tp) REVERT: E 74 GLN cc_start: 0.7097 (OUTLIER) cc_final: 0.6887 (pt0) REVERT: E 81 GLU cc_start: 0.6373 (tp30) cc_final: 0.6139 (tp30) REVERT: E 143 ARG cc_start: 0.5234 (mtm-85) cc_final: 0.5000 (mmm160) REVERT: G 36 GLN cc_start: 0.7693 (tp-100) cc_final: 0.7470 (mm110) REVERT: G 76 MET cc_start: 0.7519 (tpp) cc_final: 0.7309 (tpt) REVERT: G 88 MET cc_start: 0.8416 (ttp) cc_final: 0.8207 (ttp) REVERT: I 60 ILE cc_start: 0.7777 (OUTLIER) cc_final: 0.7321 (mt) REVERT: I 84 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.6374 (mt-10) REVERT: I 131 GLU cc_start: 0.7394 (tm-30) cc_final: 0.7123 (tm-30) REVERT: J 80 ASP cc_start: 0.6572 (p0) cc_final: 0.5273 (t0) REVERT: J 205 ARG cc_start: 0.4369 (ttt180) cc_final: 0.3845 (tpt90) REVERT: K 63 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.6947 (mp) REVERT: L 24 LYS cc_start: 0.8017 (tmtt) cc_final: 0.7610 (ttmt) REVERT: L 53 LYS cc_start: 0.8369 (tttp) cc_final: 0.8070 (ptmm) REVERT: M 18 GLN cc_start: 0.6869 (tm-30) cc_final: 0.6312 (pt0) REVERT: M 103 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7109 (tt0) REVERT: P 26 ASN cc_start: 0.7789 (OUTLIER) cc_final: 0.7253 (m-40) REVERT: P 51 GLU cc_start: 0.6760 (tp30) cc_final: 0.6559 (tp30) REVERT: Q 111 MET cc_start: 0.7318 (mmp) cc_final: 0.6817 (mmp) REVERT: R 107 GLU cc_start: 0.7255 (tm-30) cc_final: 0.7013 (tp30) REVERT: S 47 ARG cc_start: 0.7072 (OUTLIER) cc_final: 0.6792 (ptt-90) REVERT: T 40 TYR cc_start: 0.8111 (t80) cc_final: 0.7822 (t80) REVERT: U 93 SER cc_start: 0.8491 (t) cc_final: 0.8104 (m) REVERT: W 43 THR cc_start: 0.8187 (t) cc_final: 0.7829 (m) REVERT: Y 80 LYS cc_start: 0.6627 (mmmt) cc_final: 0.6178 (mmtp) REVERT: Z 81 TYR cc_start: 0.6467 (OUTLIER) cc_final: 0.5878 (m-10) REVERT: d 11 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8124 (mp) REVERT: e 13 LYS cc_start: 0.6258 (tptp) cc_final: 0.5970 (tptp) REVERT: f 96 GLU cc_start: 0.6171 (mm-30) cc_final: 0.5949 (tt0) REVERT: h 171 ASP cc_start: 0.6513 (m-30) cc_final: 0.6021 (m-30) REVERT: h 213 ASP cc_start: 0.5918 (OUTLIER) cc_final: 0.5433 (m-30) REVERT: h 225 LYS cc_start: 0.7503 (pttp) cc_final: 0.7159 (mmtm) REVERT: j 45 MET cc_start: 0.6399 (OUTLIER) cc_final: 0.6038 (tpp) REVERT: j 46 ILE cc_start: 0.8398 (pt) cc_final: 0.8038 (mt) REVERT: j 88 ARG cc_start: 0.7176 (OUTLIER) cc_final: 0.6830 (mtm180) outliers start: 166 outliers final: 106 residues processed: 871 average time/residue: 0.8616 time to fit residues: 1302.1237 Evaluate side-chains 817 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 697 time to evaluate : 4.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 157 GLN Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 216 MET Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 236 ILE Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 70 LYS Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain J residue 49 ARG Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 73 ASN Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 103 GLU Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain N residue 75 ASN Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 87 ASP Chi-restraints excluded: chain O residue 131 THR Chi-restraints excluded: chain P residue 26 ASN Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 126 ILE Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 84 ILE Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain S residue 47 ARG Chi-restraints excluded: chain S residue 110 ASP Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 43 VAL Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 35 ASP Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 17 CYS Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain Y residue 115 ILE Chi-restraints excluded: chain Z residue 7 ILE Chi-restraints excluded: chain Z residue 25 ILE Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 81 TYR Chi-restraints excluded: chain Z residue 96 LEU Chi-restraints excluded: chain Z residue 114 MET Chi-restraints excluded: chain a residue 89 GLN Chi-restraints excluded: chain b residue 2 THR Chi-restraints excluded: chain b residue 40 VAL Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain c residue 40 CYS Chi-restraints excluded: chain c residue 64 CYS Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 39 SER Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain d residue 57 THR Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain f residue 92 VAL Chi-restraints excluded: chain h residue 60 ARG Chi-restraints excluded: chain h residue 94 THR Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 107 ASP Chi-restraints excluded: chain h residue 142 VAL Chi-restraints excluded: chain h residue 143 GLN Chi-restraints excluded: chain h residue 145 GLU Chi-restraints excluded: chain h residue 199 THR Chi-restraints excluded: chain h residue 213 ASP Chi-restraints excluded: chain h residue 309 VAL Chi-restraints excluded: chain j residue 24 VAL Chi-restraints excluded: chain j residue 45 MET Chi-restraints excluded: chain j residue 60 ASN Chi-restraints excluded: chain j residue 77 ASP Chi-restraints excluded: chain j residue 88 ARG Chi-restraints excluded: chain j residue 110 SER Chi-restraints excluded: chain j residue 131 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 560 optimal weight: 7.9990 chunk 381 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 500 optimal weight: 2.9990 chunk 277 optimal weight: 0.0670 chunk 574 optimal weight: 0.9980 chunk 465 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 343 optimal weight: 6.9990 chunk 603 optimal weight: 9.9990 chunk 169 optimal weight: 0.9980 overall best weight: 1.1720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN F 98 ASN ** G 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 GLN ** J 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 132 GLN K 177 ASN M 106 HIS O 69 ASN S 62 GLN S 93 GLN T 11 HIS Y 87 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.5692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 88638 Z= 0.120 Angle : 0.487 12.288 129066 Z= 0.249 Chirality : 0.032 0.193 16021 Planarity : 0.004 0.049 9109 Dihedral : 22.718 179.885 36410 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.98 % Favored : 96.00 % Rotamer: Outliers : 3.39 % Allowed : 21.98 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.12), residues: 5104 helix: 1.21 (0.13), residues: 1628 sheet: -0.44 (0.18), residues: 872 loop : -1.13 (0.12), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 8 HIS 0.021 0.001 HIS D 136 PHE 0.016 0.001 PHE F 226 TYR 0.023 0.001 TYR L 78 ARG 0.008 0.000 ARG T 142 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 886 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 738 time to evaluate : 4.917 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: A 50 MET cc_start: 0.2600 (mtp) cc_final: 0.1564 (ptt) REVERT: B 31 ASP cc_start: 0.6514 (t0) cc_final: 0.6171 (t0) REVERT: B 52 LYS cc_start: 0.8164 (ttmt) cc_final: 0.7742 (mttt) REVERT: B 73 ASP cc_start: 0.7216 (m-30) cc_final: 0.6921 (m-30) REVERT: B 188 THR cc_start: 0.6638 (p) cc_final: 0.6404 (m) REVERT: C 62 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.8008 (mp) REVERT: C 157 GLN cc_start: 0.7241 (OUTLIER) cc_final: 0.6998 (mm-40) REVERT: C 196 ASP cc_start: 0.7172 (OUTLIER) cc_final: 0.6585 (t70) REVERT: D 268 GLU cc_start: 0.6969 (tp30) cc_final: 0.6703 (tp30) REVERT: E 74 GLN cc_start: 0.7288 (OUTLIER) cc_final: 0.7081 (pt0) REVERT: I 60 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.7324 (mt) REVERT: I 84 GLU cc_start: 0.6769 (OUTLIER) cc_final: 0.6439 (mt-10) REVERT: I 131 GLU cc_start: 0.7403 (tm-30) cc_final: 0.7067 (tm-30) REVERT: J 80 ASP cc_start: 0.6712 (p0) cc_final: 0.5482 (t0) REVERT: J 205 ARG cc_start: 0.4327 (ttt180) cc_final: 0.3888 (tpt90) REVERT: K 63 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.6994 (mp) REVERT: L 24 LYS cc_start: 0.8069 (tmtt) cc_final: 0.7712 (ttmt) REVERT: L 53 LYS cc_start: 0.8359 (tttp) cc_final: 0.8094 (ptmm) REVERT: L 84 HIS cc_start: 0.4340 (m170) cc_final: 0.3606 (m90) REVERT: M 18 GLN cc_start: 0.6790 (tm-30) cc_final: 0.6183 (pt0) REVERT: N 63 LYS cc_start: 0.2127 (pttm) cc_final: 0.1105 (ptpp) REVERT: P 26 ASN cc_start: 0.7798 (OUTLIER) cc_final: 0.7230 (m-40) REVERT: Q 111 MET cc_start: 0.7371 (mmp) cc_final: 0.6816 (mmp) REVERT: R 107 GLU cc_start: 0.7260 (tm-30) cc_final: 0.7028 (tp30) REVERT: S 47 ARG cc_start: 0.7082 (OUTLIER) cc_final: 0.6793 (ptt-90) REVERT: U 93 SER cc_start: 0.8506 (t) cc_final: 0.8099 (m) REVERT: U 114 GLU cc_start: 0.6774 (pm20) cc_final: 0.6488 (pm20) REVERT: W 43 THR cc_start: 0.8188 (t) cc_final: 0.7839 (m) REVERT: Y 80 LYS cc_start: 0.6628 (mmmt) cc_final: 0.6141 (mmtp) REVERT: Z 64 PHE cc_start: 0.6166 (t80) cc_final: 0.5925 (t80) REVERT: Z 81 TYR cc_start: 0.6525 (OUTLIER) cc_final: 0.5887 (m-10) REVERT: b 51 ARG cc_start: 0.7525 (mtp180) cc_final: 0.7318 (mmm-85) REVERT: d 11 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8176 (mp) REVERT: e 13 LYS cc_start: 0.6307 (tptp) cc_final: 0.5923 (tptp) REVERT: h 171 ASP cc_start: 0.6542 (m-30) cc_final: 0.6059 (m-30) REVERT: h 225 LYS cc_start: 0.7639 (pttp) cc_final: 0.7278 (mmtt) REVERT: h 269 GLU cc_start: 0.6016 (tp30) cc_final: 0.5803 (tp30) REVERT: j 46 ILE cc_start: 0.8480 (pt) cc_final: 0.8080 (mt) REVERT: n 6 ARG cc_start: 0.7819 (mtp85) cc_final: 0.7532 (mtp-110) outliers start: 148 outliers final: 105 residues processed: 835 average time/residue: 0.7732 time to fit residues: 1109.8717 Evaluate side-chains 803 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 687 time to evaluate : 4.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 157 GLN Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 216 MET Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain J residue 49 ARG Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 149 VAL Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 48 LYS Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain N residue 75 ASN Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 87 ASP Chi-restraints excluded: chain P residue 26 ASN Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 68 GLU Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 126 ILE Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 84 ILE Chi-restraints excluded: chain R residue 68 ILE Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain S residue 8 THR Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 47 ARG Chi-restraints excluded: chain S residue 93 GLN Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 35 ASP Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain V residue 114 VAL Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 76 SER Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain Y residue 115 ILE Chi-restraints excluded: chain Z residue 25 ILE Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 81 TYR Chi-restraints excluded: chain Z residue 114 MET Chi-restraints excluded: chain a residue 89 GLN Chi-restraints excluded: chain b residue 40 VAL Chi-restraints excluded: chain b residue 58 VAL Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain c residue 26 GLN Chi-restraints excluded: chain c residue 40 CYS Chi-restraints excluded: chain c residue 62 VAL Chi-restraints excluded: chain c residue 64 CYS Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 39 SER Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain d residue 57 THR Chi-restraints excluded: chain f residue 92 VAL Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain h residue 60 ARG Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 107 ASP Chi-restraints excluded: chain h residue 198 VAL Chi-restraints excluded: chain h residue 199 THR Chi-restraints excluded: chain h residue 203 ASP Chi-restraints excluded: chain h residue 213 ASP Chi-restraints excluded: chain j residue 11 HIS Chi-restraints excluded: chain j residue 24 VAL Chi-restraints excluded: chain j residue 60 ASN Chi-restraints excluded: chain j residue 77 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 226 optimal weight: 20.0000 chunk 605 optimal weight: 20.0000 chunk 132 optimal weight: 10.0000 chunk 394 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 673 optimal weight: 9.9990 chunk 559 optimal weight: 8.9990 chunk 311 optimal weight: 9.9990 chunk 55 optimal weight: 20.0000 chunk 222 optimal weight: 0.7980 chunk 353 optimal weight: 7.9990 overall best weight: 7.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 232 HIS G 36 GLN I 114 GLN ** I 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 84 ASN J 99 ASN J 146 GLN J 165 GLN ** O 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 24 GLN R 86 GLN S 62 GLN S 127 ASN ** U 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 92 HIS Y 87 ASN ** Z 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 63 HIS b 43 ASN g 93 HIS g 135 HIS h 51 ASN h 117 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.6889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.114 88638 Z= 0.378 Angle : 0.738 14.117 129066 Z= 0.371 Chirality : 0.042 0.267 16021 Planarity : 0.006 0.058 9109 Dihedral : 23.028 179.986 36410 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 5.28 % Allowed : 21.91 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.11), residues: 5104 helix: 0.46 (0.12), residues: 1629 sheet: -0.65 (0.18), residues: 884 loop : -1.34 (0.12), residues: 2591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 30 HIS 0.009 0.002 HIS L 84 PHE 0.027 0.003 PHE P 34 TYR 0.024 0.002 TYR L 78 ARG 0.016 0.001 ARG Y 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 940 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 709 time to evaluate : 5.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.2407 (mtp) cc_final: 0.1382 (ptt) REVERT: A 84 TYR cc_start: 0.2959 (OUTLIER) cc_final: -0.1064 (p90) REVERT: B 31 ASP cc_start: 0.6642 (t0) cc_final: 0.6199 (t0) REVERT: B 52 LYS cc_start: 0.8404 (ttmt) cc_final: 0.7803 (mttt) REVERT: C 62 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8065 (mp) REVERT: C 196 ASP cc_start: 0.7304 (OUTLIER) cc_final: 0.6796 (t70) REVERT: D 268 GLU cc_start: 0.7423 (tp30) cc_final: 0.7122 (tp30) REVERT: F 104 ASP cc_start: 0.7057 (p0) cc_final: 0.6727 (p0) REVERT: F 182 MET cc_start: 0.7724 (tpt) cc_final: 0.7188 (tpt) REVERT: I 60 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7362 (mt) REVERT: I 63 PHE cc_start: 0.7320 (m-10) cc_final: 0.7091 (m-80) REVERT: I 84 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6581 (mt-10) REVERT: I 91 HIS cc_start: 0.4640 (OUTLIER) cc_final: 0.4053 (m90) REVERT: J 205 ARG cc_start: 0.4505 (ttt180) cc_final: 0.3874 (tpt90) REVERT: K 63 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.6973 (mp) REVERT: L 24 LYS cc_start: 0.8291 (tmtt) cc_final: 0.7885 (ttmt) REVERT: L 53 LYS cc_start: 0.8394 (tttp) cc_final: 0.8014 (ptmm) REVERT: L 60 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.5862 (tp30) REVERT: M 103 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7254 (tt0) REVERT: Q 28 MET cc_start: 0.6628 (mtm) cc_final: 0.6240 (mtt) REVERT: U 93 SER cc_start: 0.8495 (t) cc_final: 0.8246 (p) REVERT: Y 80 LYS cc_start: 0.6488 (mmmt) cc_final: 0.6048 (mmtp) REVERT: Z 81 TYR cc_start: 0.7024 (OUTLIER) cc_final: 0.6788 (m-10) REVERT: d 11 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8180 (mp) REVERT: f 113 ARG cc_start: 0.7757 (mtp180) cc_final: 0.7373 (ttm-80) REVERT: h 171 ASP cc_start: 0.6494 (OUTLIER) cc_final: 0.6291 (m-30) REVERT: n 6 ARG cc_start: 0.7818 (mtp85) cc_final: 0.7517 (mtp-110) outliers start: 231 outliers final: 162 residues processed: 869 average time/residue: 0.8500 time to fit residues: 1263.3878 Evaluate side-chains 821 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 647 time to evaluate : 4.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 131 HIS Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 216 MET Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 236 ILE Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 77 MET Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain I residue 7 LYS Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain I residue 91 HIS Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain J residue 49 ARG Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 149 VAL Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 48 LYS Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 103 GLU Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain N residue 57 ASP Chi-restraints excluded: chain N residue 75 ASN Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 131 THR Chi-restraints excluded: chain P residue 26 ASN Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 68 GLU Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 90 ILE Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 84 ILE Chi-restraints excluded: chain Q residue 96 VAL Chi-restraints excluded: chain R residue 25 CYS Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain S residue 8 THR Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 93 GLN Chi-restraints excluded: chain S residue 110 ASP Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 35 ASP Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain V residue 114 VAL Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 17 CYS Chi-restraints excluded: chain W residue 50 PHE Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 26 LEU Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 76 SER Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain X residue 105 THR Chi-restraints excluded: chain Y residue 85 VAL Chi-restraints excluded: chain Z residue 7 ILE Chi-restraints excluded: chain Z residue 26 ASP Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 81 TYR Chi-restraints excluded: chain a residue 44 LEU Chi-restraints excluded: chain a residue 68 ILE Chi-restraints excluded: chain a residue 89 GLN Chi-restraints excluded: chain b residue 2 THR Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 40 VAL Chi-restraints excluded: chain b residue 43 ASN Chi-restraints excluded: chain b residue 58 VAL Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain c residue 26 GLN Chi-restraints excluded: chain c residue 40 CYS Chi-restraints excluded: chain c residue 45 THR Chi-restraints excluded: chain c residue 62 VAL Chi-restraints excluded: chain c residue 64 CYS Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 33 GLU Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain d residue 57 THR Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain f residue 92 VAL Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain g residue 93 HIS Chi-restraints excluded: chain h residue 50 THR Chi-restraints excluded: chain h residue 60 ARG Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 107 ASP Chi-restraints excluded: chain h residue 142 VAL Chi-restraints excluded: chain h residue 143 GLN Chi-restraints excluded: chain h residue 144 ASP Chi-restraints excluded: chain h residue 171 ASP Chi-restraints excluded: chain h residue 198 VAL Chi-restraints excluded: chain h residue 199 THR Chi-restraints excluded: chain h residue 213 ASP Chi-restraints excluded: chain j residue 24 VAL Chi-restraints excluded: chain j residue 42 ILE Chi-restraints excluded: chain j residue 60 ASN Chi-restraints excluded: chain j residue 77 ASP Chi-restraints excluded: chain j residue 110 SER Chi-restraints excluded: chain j residue 112 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 649 optimal weight: 7.9990 chunk 75 optimal weight: 30.0000 chunk 383 optimal weight: 5.9990 chunk 491 optimal weight: 6.9990 chunk 381 optimal weight: 2.9990 chunk 566 optimal weight: 8.9990 chunk 376 optimal weight: 0.5980 chunk 670 optimal weight: 0.0670 chunk 419 optimal weight: 2.9990 chunk 408 optimal weight: 5.9990 chunk 309 optimal weight: 9.9990 overall best weight: 2.5324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 53 GLN E 56 GLN ** I 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 146 GLN J 165 GLN ** O 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 24 GLN ** Q 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN S 116 ASN S 127 ASN ** Z 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 43 ASN g 93 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.6914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 88638 Z= 0.162 Angle : 0.544 10.066 129066 Z= 0.280 Chirality : 0.035 0.212 16021 Planarity : 0.004 0.071 9109 Dihedral : 22.840 179.247 36410 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.05 % Allowed : 23.53 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.12), residues: 5104 helix: 0.89 (0.13), residues: 1634 sheet: -0.57 (0.18), residues: 892 loop : -1.21 (0.12), residues: 2578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 8 HIS 0.025 0.001 HIS g 93 PHE 0.019 0.001 PHE b 101 TYR 0.020 0.001 TYR L 78 ARG 0.019 0.000 ARG b 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 898 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 721 time to evaluate : 4.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.2361 (mtp) cc_final: 0.1392 (ptt) REVERT: B 52 LYS cc_start: 0.8336 (ttmt) cc_final: 0.7829 (mttt) REVERT: C 62 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8096 (mp) REVERT: C 196 ASP cc_start: 0.7298 (OUTLIER) cc_final: 0.6742 (t70) REVERT: D 248 TYR cc_start: 0.7703 (OUTLIER) cc_final: 0.7131 (m-10) REVERT: D 268 GLU cc_start: 0.7317 (tp30) cc_final: 0.7110 (tp30) REVERT: F 182 MET cc_start: 0.7618 (tpt) cc_final: 0.7142 (tpt) REVERT: G 18 LYS cc_start: 0.7184 (OUTLIER) cc_final: 0.6910 (mppt) REVERT: G 197 GLU cc_start: 0.7047 (mm-30) cc_final: 0.6789 (mt-10) REVERT: I 41 ARG cc_start: 0.6365 (tpt170) cc_final: 0.5470 (tpt170) REVERT: I 60 ILE cc_start: 0.7816 (OUTLIER) cc_final: 0.7336 (mt) REVERT: I 72 PHE cc_start: 0.7270 (m-10) cc_final: 0.7066 (m-10) REVERT: I 84 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6488 (mt-10) REVERT: I 131 GLU cc_start: 0.7278 (tm-30) cc_final: 0.6873 (tm-30) REVERT: J 80 ASP cc_start: 0.6994 (p0) cc_final: 0.6191 (t0) REVERT: J 205 ARG cc_start: 0.4500 (ttt180) cc_final: 0.4028 (tpt90) REVERT: K 92 MET cc_start: 0.7131 (tpp) cc_final: 0.6882 (tpp) REVERT: L 24 LYS cc_start: 0.8108 (tmtt) cc_final: 0.7858 (ttmt) REVERT: L 53 LYS cc_start: 0.8400 (tttp) cc_final: 0.8107 (ptmm) REVERT: M 103 GLU cc_start: 0.7999 (tp30) cc_final: 0.7337 (tt0) REVERT: U 93 SER cc_start: 0.8627 (t) cc_final: 0.8291 (m) REVERT: V 97 ILE cc_start: 0.5150 (tp) cc_final: 0.4729 (mp) REVERT: W 43 THR cc_start: 0.8242 (t) cc_final: 0.7994 (m) REVERT: Y 80 LYS cc_start: 0.6574 (mmmt) cc_final: 0.6124 (mmtp) REVERT: Z 72 PHE cc_start: 0.6913 (OUTLIER) cc_final: 0.6677 (t80) REVERT: Z 81 TYR cc_start: 0.6783 (OUTLIER) cc_final: 0.6442 (m-10) REVERT: a 91 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8100 (mm) REVERT: d 11 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8175 (mp) REVERT: e 13 LYS cc_start: 0.6645 (tmtt) cc_final: 0.6191 (tptp) REVERT: f 113 ARG cc_start: 0.7586 (mtp180) cc_final: 0.7244 (ttm-80) REVERT: h 171 ASP cc_start: 0.6493 (OUTLIER) cc_final: 0.6241 (m-30) REVERT: j 99 GLU cc_start: 0.7364 (mm-30) cc_final: 0.7138 (mm-30) REVERT: n 1 MET cc_start: 0.7579 (mtp) cc_final: 0.7316 (mtm) REVERT: n 6 ARG cc_start: 0.7805 (mtp85) cc_final: 0.7604 (mtp-110) outliers start: 177 outliers final: 129 residues processed: 842 average time/residue: 0.7765 time to fit residues: 1123.2259 Evaluate side-chains 808 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 668 time to evaluate : 4.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 216 MET Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 250 TYR Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 236 ILE Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain G residue 18 LYS Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 77 MET Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain I residue 7 LYS Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain J residue 49 ARG Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain K residue 149 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain N residue 75 ASN Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 87 ASP Chi-restraints excluded: chain P residue 26 ASN Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 68 GLU Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 84 ILE Chi-restraints excluded: chain R residue 25 CYS Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain S residue 8 THR Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 110 ASP Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 35 ASP Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain V residue 114 VAL Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 26 LEU Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 76 SER Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain Y residue 85 VAL Chi-restraints excluded: chain Y residue 115 ILE Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 72 PHE Chi-restraints excluded: chain Z residue 81 TYR Chi-restraints excluded: chain a residue 89 GLN Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain b residue 2 THR Chi-restraints excluded: chain b residue 40 VAL Chi-restraints excluded: chain b residue 58 VAL Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain c residue 34 ASP Chi-restraints excluded: chain c residue 40 CYS Chi-restraints excluded: chain c residue 62 VAL Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain d residue 57 THR Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain f residue 92 VAL Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain h residue 42 MET Chi-restraints excluded: chain h residue 60 ARG Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 107 ASP Chi-restraints excluded: chain h residue 142 VAL Chi-restraints excluded: chain h residue 143 GLN Chi-restraints excluded: chain h residue 165 ILE Chi-restraints excluded: chain h residue 171 ASP Chi-restraints excluded: chain h residue 198 VAL Chi-restraints excluded: chain h residue 199 THR Chi-restraints excluded: chain h residue 213 ASP Chi-restraints excluded: chain h residue 248 LEU Chi-restraints excluded: chain j residue 42 ILE Chi-restraints excluded: chain j residue 60 ASN Chi-restraints excluded: chain j residue 68 ASN Chi-restraints excluded: chain j residue 77 ASP Chi-restraints excluded: chain j residue 110 SER Chi-restraints excluded: chain j residue 112 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 415 optimal weight: 7.9990 chunk 267 optimal weight: 3.9990 chunk 400 optimal weight: 8.9990 chunk 202 optimal weight: 0.0870 chunk 131 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 426 optimal weight: 6.9990 chunk 457 optimal weight: 6.9990 chunk 331 optimal weight: 3.9990 chunk 62 optimal weight: 30.0000 chunk 527 optimal weight: 0.0170 overall best weight: 3.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 GLN J 165 GLN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 GLN ** O 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 74 GLN S 93 GLN S 127 ASN ** U 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 65 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.7079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 88638 Z= 0.184 Angle : 0.546 10.497 129066 Z= 0.280 Chirality : 0.035 0.207 16021 Planarity : 0.004 0.062 9109 Dihedral : 22.793 179.761 36410 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.23 % Allowed : 23.59 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.12), residues: 5104 helix: 0.98 (0.13), residues: 1631 sheet: -0.49 (0.18), residues: 873 loop : -1.18 (0.12), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 69 HIS 0.004 0.001 HIS L 84 PHE 0.021 0.001 PHE b 101 TYR 0.026 0.001 TYR L 78 ARG 0.012 0.000 ARG j 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 688 time to evaluate : 4.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.2343 (mtp) cc_final: 0.1385 (ptt) REVERT: B 31 ASP cc_start: 0.6615 (t0) cc_final: 0.6200 (t0) REVERT: B 52 LYS cc_start: 0.8336 (ttmt) cc_final: 0.7771 (mttt) REVERT: C 62 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8111 (mp) REVERT: C 196 ASP cc_start: 0.7297 (OUTLIER) cc_final: 0.6743 (t70) REVERT: D 248 TYR cc_start: 0.7749 (OUTLIER) cc_final: 0.7203 (m-10) REVERT: E 107 TYR cc_start: 0.7029 (m-80) cc_final: 0.6823 (m-80) REVERT: I 41 ARG cc_start: 0.6477 (tpt170) cc_final: 0.5526 (tpt170) REVERT: I 60 ILE cc_start: 0.7817 (OUTLIER) cc_final: 0.7341 (mt) REVERT: I 84 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.6552 (mt-10) REVERT: I 91 HIS cc_start: 0.4646 (OUTLIER) cc_final: 0.4125 (m90) REVERT: J 80 ASP cc_start: 0.7047 (p0) cc_final: 0.6229 (t0) REVERT: J 205 ARG cc_start: 0.4535 (ttt180) cc_final: 0.4064 (tpt90) REVERT: K 63 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6995 (mp) REVERT: K 92 MET cc_start: 0.7165 (tpp) cc_final: 0.6938 (tpp) REVERT: L 24 LYS cc_start: 0.8105 (tmtt) cc_final: 0.7879 (ttmt) REVERT: L 53 LYS cc_start: 0.8382 (tttp) cc_final: 0.8067 (ptmm) REVERT: M 103 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7214 (tt0) REVERT: P 26 ASN cc_start: 0.8229 (OUTLIER) cc_final: 0.7430 (m-40) REVERT: R 116 ASP cc_start: 0.6196 (p0) cc_final: 0.5941 (p0) REVERT: S 93 GLN cc_start: 0.6294 (OUTLIER) cc_final: 0.6038 (pm20) REVERT: U 93 SER cc_start: 0.8660 (t) cc_final: 0.8315 (m) REVERT: V 97 ILE cc_start: 0.5255 (tp) cc_final: 0.4847 (mp) REVERT: W 43 THR cc_start: 0.8243 (t) cc_final: 0.8021 (m) REVERT: X 51 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6706 (tp30) REVERT: Y 80 LYS cc_start: 0.6510 (mmmt) cc_final: 0.6055 (mmtp) REVERT: Z 72 PHE cc_start: 0.6922 (OUTLIER) cc_final: 0.6700 (t80) REVERT: Z 81 TYR cc_start: 0.6767 (OUTLIER) cc_final: 0.6453 (m-10) REVERT: a 91 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8115 (mm) REVERT: d 11 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8214 (mp) REVERT: f 113 ARG cc_start: 0.7571 (mtp180) cc_final: 0.7266 (ttm-80) REVERT: h 269 GLU cc_start: 0.5852 (tp30) cc_final: 0.5515 (tp30) REVERT: j 88 ARG cc_start: 0.7100 (OUTLIER) cc_final: 0.6748 (mtm180) outliers start: 185 outliers final: 143 residues processed: 814 average time/residue: 0.7739 time to fit residues: 1078.0278 Evaluate side-chains 826 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 667 time to evaluate : 4.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 216 MET Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 250 TYR Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 236 ILE Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 77 MET Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain I residue 7 LYS Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain I residue 91 HIS Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain J residue 49 ARG Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 149 VAL Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 103 GLU Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain N residue 75 ASN Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain O residue 87 ASP Chi-restraints excluded: chain O residue 131 THR Chi-restraints excluded: chain P residue 26 ASN Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 68 GLU Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 84 ILE Chi-restraints excluded: chain R residue 25 CYS Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain S residue 8 THR Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 92 ASP Chi-restraints excluded: chain S residue 93 GLN Chi-restraints excluded: chain S residue 110 ASP Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 35 ASP Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain V residue 114 VAL Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 26 LEU Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 51 GLU Chi-restraints excluded: chain X residue 76 SER Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain X residue 105 THR Chi-restraints excluded: chain Y residue 85 VAL Chi-restraints excluded: chain Y residue 115 ILE Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 72 PHE Chi-restraints excluded: chain Z residue 81 TYR Chi-restraints excluded: chain a residue 89 GLN Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain b residue 2 THR Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 40 VAL Chi-restraints excluded: chain b residue 58 VAL Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain c residue 34 ASP Chi-restraints excluded: chain c residue 40 CYS Chi-restraints excluded: chain c residue 62 VAL Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 33 GLU Chi-restraints excluded: chain d residue 41 SER Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain d residue 57 THR Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain f residue 92 VAL Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain h residue 42 MET Chi-restraints excluded: chain h residue 60 ARG Chi-restraints excluded: chain h residue 94 THR Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 107 ASP Chi-restraints excluded: chain h residue 142 VAL Chi-restraints excluded: chain h residue 143 GLN Chi-restraints excluded: chain h residue 165 ILE Chi-restraints excluded: chain h residue 198 VAL Chi-restraints excluded: chain h residue 199 THR Chi-restraints excluded: chain h residue 213 ASP Chi-restraints excluded: chain h residue 248 LEU Chi-restraints excluded: chain j residue 60 ASN Chi-restraints excluded: chain j residue 68 ASN Chi-restraints excluded: chain j residue 77 ASP Chi-restraints excluded: chain j residue 88 ARG Chi-restraints excluded: chain j residue 110 SER Chi-restraints excluded: chain j residue 112 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 610 optimal weight: 9.9990 chunk 642 optimal weight: 10.0000 chunk 586 optimal weight: 9.9990 chunk 625 optimal weight: 20.0000 chunk 376 optimal weight: 8.9990 chunk 272 optimal weight: 2.9990 chunk 490 optimal weight: 8.9990 chunk 191 optimal weight: 5.9990 chunk 564 optimal weight: 6.9990 chunk 591 optimal weight: 6.9990 chunk 622 optimal weight: 0.3980 overall best weight: 4.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 161 GLN ** I 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 146 GLN J 165 GLN ** O 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 93 GLN S 127 ASN ** Z 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.7405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.142 88638 Z= 0.252 Angle : 0.607 11.978 129066 Z= 0.310 Chirality : 0.037 0.226 16021 Planarity : 0.005 0.076 9109 Dihedral : 22.868 179.877 36410 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.48 % Allowed : 23.69 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.12), residues: 5104 helix: 0.77 (0.13), residues: 1640 sheet: -0.57 (0.18), residues: 880 loop : -1.24 (0.12), residues: 2584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP h 132 HIS 0.005 0.001 HIS a 103 PHE 0.021 0.002 PHE b 101 TYR 0.023 0.002 TYR L 78 ARG 0.014 0.001 ARG j 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 669 time to evaluate : 4.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.2209 (mtp) cc_final: 0.1245 (ptt) REVERT: A 84 TYR cc_start: 0.2941 (OUTLIER) cc_final: -0.1047 (p90) REVERT: B 31 ASP cc_start: 0.6811 (t0) cc_final: 0.6543 (t0) REVERT: B 52 LYS cc_start: 0.8370 (ttmt) cc_final: 0.7816 (mttt) REVERT: C 62 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8239 (mp) REVERT: C 196 ASP cc_start: 0.7302 (OUTLIER) cc_final: 0.6732 (t70) REVERT: D 248 TYR cc_start: 0.7898 (OUTLIER) cc_final: 0.7437 (m-10) REVERT: I 41 ARG cc_start: 0.6398 (tpt170) cc_final: 0.5553 (tpt170) REVERT: I 60 ILE cc_start: 0.7867 (OUTLIER) cc_final: 0.7399 (mt) REVERT: I 84 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6321 (mt-10) REVERT: I 91 HIS cc_start: 0.4701 (OUTLIER) cc_final: 0.4084 (m-70) REVERT: J 205 ARG cc_start: 0.4596 (ttt180) cc_final: 0.4069 (tpt90) REVERT: K 63 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6971 (mp) REVERT: K 92 MET cc_start: 0.7341 (tpp) cc_final: 0.7045 (tpp) REVERT: L 24 LYS cc_start: 0.8155 (tmtt) cc_final: 0.7884 (ttmt) REVERT: L 53 LYS cc_start: 0.8373 (tttp) cc_final: 0.8013 (ptmm) REVERT: M 103 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7382 (tt0) REVERT: N 60 MET cc_start: 0.6008 (mtm) cc_final: 0.5403 (mtm) REVERT: U 93 SER cc_start: 0.8551 (t) cc_final: 0.8327 (p) REVERT: V 97 ILE cc_start: 0.5461 (tp) cc_final: 0.5056 (mp) REVERT: X 51 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6701 (tp30) REVERT: Y 80 LYS cc_start: 0.6472 (mmmt) cc_final: 0.6057 (mmtp) REVERT: Z 72 PHE cc_start: 0.6902 (OUTLIER) cc_final: 0.6634 (t80) REVERT: Z 81 TYR cc_start: 0.6965 (OUTLIER) cc_final: 0.6568 (m-10) REVERT: d 11 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8209 (mp) REVERT: f 113 ARG cc_start: 0.7575 (mtp180) cc_final: 0.7315 (ttm-80) REVERT: h 269 GLU cc_start: 0.5840 (tp30) cc_final: 0.5639 (tp30) REVERT: j 88 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6877 (mtm180) outliers start: 196 outliers final: 160 residues processed: 816 average time/residue: 0.7704 time to fit residues: 1079.4103 Evaluate side-chains 814 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 640 time to evaluate : 4.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 216 MET Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 77 MET Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain I residue 91 HIS Chi-restraints excluded: chain I residue 103 LYS Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain J residue 49 ARG Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 149 VAL Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 103 GLU Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain N residue 57 ASP Chi-restraints excluded: chain N residue 75 ASN Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 29 THR Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain O residue 131 THR Chi-restraints excluded: chain P residue 26 ASN Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 68 GLU Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 90 ILE Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain R residue 25 CYS Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain S residue 8 THR Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 71 ILE Chi-restraints excluded: chain S residue 110 ASP Chi-restraints excluded: chain S residue 127 ASN Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 35 ASP Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain V residue 114 VAL Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 17 CYS Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 26 LEU Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 51 GLU Chi-restraints excluded: chain X residue 76 SER Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain X residue 105 THR Chi-restraints excluded: chain Y residue 85 VAL Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 72 PHE Chi-restraints excluded: chain Z residue 81 TYR Chi-restraints excluded: chain a residue 89 GLN Chi-restraints excluded: chain b residue 2 THR Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 40 VAL Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain c residue 26 GLN Chi-restraints excluded: chain c residue 34 ASP Chi-restraints excluded: chain c residue 45 THR Chi-restraints excluded: chain c residue 62 VAL Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 33 GLU Chi-restraints excluded: chain d residue 41 SER Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain d residue 57 THR Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain f residue 92 VAL Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain h residue 42 MET Chi-restraints excluded: chain h residue 60 ARG Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 107 ASP Chi-restraints excluded: chain h residue 142 VAL Chi-restraints excluded: chain h residue 143 GLN Chi-restraints excluded: chain h residue 165 ILE Chi-restraints excluded: chain h residue 198 VAL Chi-restraints excluded: chain h residue 199 THR Chi-restraints excluded: chain h residue 213 ASP Chi-restraints excluded: chain h residue 248 LEU Chi-restraints excluded: chain h residue 274 VAL Chi-restraints excluded: chain j residue 42 ILE Chi-restraints excluded: chain j residue 60 ASN Chi-restraints excluded: chain j residue 68 ASN Chi-restraints excluded: chain j residue 77 ASP Chi-restraints excluded: chain j residue 88 ARG Chi-restraints excluded: chain j residue 110 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 410 optimal weight: 5.9990 chunk 661 optimal weight: 5.9990 chunk 403 optimal weight: 1.9990 chunk 313 optimal weight: 7.9990 chunk 459 optimal weight: 0.9990 chunk 693 optimal weight: 40.0000 chunk 638 optimal weight: 7.9990 chunk 552 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 426 optimal weight: 10.0000 chunk 338 optimal weight: 0.0170 overall best weight: 3.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 138 HIS ** I 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 ASN ** O 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.7449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 88638 Z= 0.181 Angle : 0.553 11.563 129066 Z= 0.283 Chirality : 0.035 0.217 16021 Planarity : 0.004 0.063 9109 Dihedral : 22.815 179.688 36410 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.96 % Allowed : 24.41 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.12), residues: 5104 helix: 0.96 (0.13), residues: 1632 sheet: -0.53 (0.18), residues: 883 loop : -1.16 (0.12), residues: 2589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP L 69 HIS 0.006 0.001 HIS B 193 PHE 0.038 0.001 PHE S 128 TYR 0.036 0.001 TYR h 228 ARG 0.014 0.000 ARG j 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10208 Ramachandran restraints generated. 5104 Oldfield, 0 Emsley, 5104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 668 time to evaluate : 4.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.2293 (mtp) cc_final: 0.1355 (ptt) REVERT: A 84 TYR cc_start: 0.2885 (OUTLIER) cc_final: -0.0923 (p90) REVERT: B 31 ASP cc_start: 0.6828 (t0) cc_final: 0.6556 (t0) REVERT: B 52 LYS cc_start: 0.8291 (ttmt) cc_final: 0.7731 (mttt) REVERT: B 118 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7444 (pm20) REVERT: C 62 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8203 (mp) REVERT: C 196 ASP cc_start: 0.7270 (OUTLIER) cc_final: 0.6694 (t70) REVERT: D 248 TYR cc_start: 0.7829 (OUTLIER) cc_final: 0.7410 (m-10) REVERT: E 107 TYR cc_start: 0.7027 (m-80) cc_final: 0.6631 (m-80) REVERT: I 41 ARG cc_start: 0.6316 (tpt170) cc_final: 0.5520 (tpt170) REVERT: I 60 ILE cc_start: 0.7821 (OUTLIER) cc_final: 0.7385 (mt) REVERT: I 84 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6469 (mt-10) REVERT: I 91 HIS cc_start: 0.4523 (OUTLIER) cc_final: 0.4157 (m-70) REVERT: K 63 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6993 (mp) REVERT: K 92 MET cc_start: 0.7277 (tpp) cc_final: 0.7056 (tpp) REVERT: L 53 LYS cc_start: 0.8296 (tttp) cc_final: 0.8001 (ptmm) REVERT: M 103 GLU cc_start: 0.7997 (tp30) cc_final: 0.7217 (tt0) REVERT: N 85 LEU cc_start: 0.3517 (pp) cc_final: 0.3157 (tt) REVERT: P 26 ASN cc_start: 0.8321 (OUTLIER) cc_final: 0.7498 (m-40) REVERT: P 131 ASP cc_start: 0.7860 (t0) cc_final: 0.7626 (t0) REVERT: T 142 ARG cc_start: 0.6564 (mmp80) cc_final: 0.5828 (mmt180) REVERT: U 93 SER cc_start: 0.8655 (t) cc_final: 0.8306 (m) REVERT: V 97 ILE cc_start: 0.5349 (tp) cc_final: 0.4971 (mp) REVERT: X 51 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6685 (tp30) REVERT: X 93 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8249 (mp) REVERT: Y 80 LYS cc_start: 0.6452 (mmmt) cc_final: 0.6027 (mmtp) REVERT: Z 72 PHE cc_start: 0.6892 (OUTLIER) cc_final: 0.6677 (t80) REVERT: Z 81 TYR cc_start: 0.6849 (OUTLIER) cc_final: 0.6521 (m-10) REVERT: d 11 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8260 (mp) REVERT: f 113 ARG cc_start: 0.7548 (mtp180) cc_final: 0.7303 (ttm-80) REVERT: h 269 GLU cc_start: 0.5902 (tp30) cc_final: 0.5602 (tp30) REVERT: j 88 ARG cc_start: 0.7184 (OUTLIER) cc_final: 0.6852 (mtm180) outliers start: 173 outliers final: 145 residues processed: 793 average time/residue: 0.7778 time to fit residues: 1060.0576 Evaluate side-chains 812 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 651 time to evaluate : 4.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 216 MET Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 77 MET Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain I residue 91 HIS Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain J residue 49 ARG Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 104 ASP Chi-restraints excluded: chain K residue 149 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain N residue 75 ASN Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 29 THR Chi-restraints excluded: chain O residue 131 THR Chi-restraints excluded: chain P residue 26 ASN Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 68 GLU Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 90 ILE Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain S residue 8 THR Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 35 ASP Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain V residue 114 VAL Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 17 CYS Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 26 LEU Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 51 GLU Chi-restraints excluded: chain X residue 76 SER Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain X residue 105 THR Chi-restraints excluded: chain Y residue 85 VAL Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 72 PHE Chi-restraints excluded: chain Z residue 81 TYR Chi-restraints excluded: chain a residue 89 GLN Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain b residue 2 THR Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 40 VAL Chi-restraints excluded: chain b residue 52 ASP Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain c residue 26 GLN Chi-restraints excluded: chain c residue 34 ASP Chi-restraints excluded: chain c residue 62 VAL Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 33 GLU Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain d residue 57 THR Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain f residue 92 VAL Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain h residue 42 MET Chi-restraints excluded: chain h residue 60 ARG Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 107 ASP Chi-restraints excluded: chain h residue 142 VAL Chi-restraints excluded: chain h residue 143 GLN Chi-restraints excluded: chain h residue 165 ILE Chi-restraints excluded: chain h residue 198 VAL Chi-restraints excluded: chain h residue 199 THR Chi-restraints excluded: chain h residue 213 ASP Chi-restraints excluded: chain h residue 248 LEU Chi-restraints excluded: chain h residue 274 VAL Chi-restraints excluded: chain j residue 24 VAL Chi-restraints excluded: chain j residue 42 ILE Chi-restraints excluded: chain j residue 60 ASN Chi-restraints excluded: chain j residue 68 ASN Chi-restraints excluded: chain j residue 77 ASP Chi-restraints excluded: chain j residue 88 ARG Chi-restraints excluded: chain j residue 110 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 438 optimal weight: 9.9990 chunk 588 optimal weight: 6.9990 chunk 169 optimal weight: 0.1980 chunk 509 optimal weight: 9.9990 chunk 81 optimal weight: 20.0000 chunk 153 optimal weight: 10.0000 chunk 553 optimal weight: 10.0000 chunk 231 optimal weight: 0.9980 chunk 567 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 overall best weight: 5.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 216 ASN ** I 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 22 HIS J 111 GLN J 138 ASN J 165 GLN ** O 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 74 GLN S 127 ASN T 42 HIS ** Z 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 29 ASN n 22 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.101227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.080287 restraints weight = 230667.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.080517 restraints weight = 166277.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.080722 restraints weight = 149322.491| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3297 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.7739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 88638 Z= 0.289 Angle : 0.644 12.353 129066 Z= 0.328 Chirality : 0.039 0.233 16021 Planarity : 0.005 0.077 9109 Dihedral : 22.951 179.859 36410 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 4.28 % Allowed : 24.25 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.12), residues: 5104 helix: 0.64 (0.13), residues: 1633 sheet: -0.59 (0.18), residues: 870 loop : -1.30 (0.12), residues: 2601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 45 HIS 0.006 0.001 HIS B 193 PHE 0.020 0.002 PHE b 101 TYR 0.028 0.002 TYR h 228 ARG 0.011 0.001 ARG e 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18880.07 seconds wall clock time: 333 minutes 26.01 seconds (20006.01 seconds total)