Starting phenix.real_space_refine on Wed Mar 4 23:27:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ado_11732/03_2026/7ado_11732.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ado_11732/03_2026/7ado_11732.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ado_11732/03_2026/7ado_11732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ado_11732/03_2026/7ado_11732.map" model { file = "/net/cci-nas-00/data/ceres_data/7ado_11732/03_2026/7ado_11732.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ado_11732/03_2026/7ado_11732.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.055 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 65 5.16 5 C 10820 2.51 5 N 2863 2.21 5 O 3092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16845 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 7280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 915, 7280 Classifications: {'peptide': 915} Link IDs: {'PTRANS': 43, 'TRANS': 871} Chain breaks: 4 Chain: "B" Number of atoms: 2272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2272 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 4, 'TRANS': 270} Chain breaks: 1 Chain: "C" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1674 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 7, 'TRANS': 195} Chain breaks: 2 Chain: "D" Number of atoms: 509 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 64, 501 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 58} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 64, 501 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 58} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 504 Chain: "E" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 770 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "F" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 781 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "G" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 781 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 9, 'TRANS': 87} Chain breaks: 3 Chain: "H" Number of atoms: 1404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1404 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 7, 'TRANS': 168} Chain breaks: 3 Chain: "I" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1098 Classifications: {'peptide': 142} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 134} Chain breaks: 1 Chain: "K" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 80 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 93 Unusual residues: {'NAG': 3, 'PCW': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PCW:plan-2': 2, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'PCW': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'PCW': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCW': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.06, per 1000 atoms: 0.18 Number of scatterers: 16845 At special positions: 0 Unit cell: (157.472, 140.448, 177.901, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 65 16.00 P 5 15.00 O 3092 8.00 N 2863 7.00 C 10820 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 237 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM16689 O5 NAG A1003 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1001 " - " ASN A 818 " " NAG A1002 " - " ASN A 370 " " NAG A1003 " - " ASN A 913 " " NAG I 301 " - " ASN I 182 " Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 663.6 milliseconds 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3934 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 25 sheets defined 38.0% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 23 through 30 removed outlier: 3.962A pdb=" N PHE A 30 " --> pdb=" O GLN A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 450 removed outlier: 3.895A pdb=" N LEU A 449 " --> pdb=" O GLU A 446 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 450 " --> pdb=" O GLU A 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 446 through 450' Processing helix chain 'A' and resid 463 through 473 removed outlier: 3.900A pdb=" N PHE A 473 " --> pdb=" O LEU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 502 Processing helix chain 'A' and resid 655 through 666 Processing helix chain 'A' and resid 876 through 878 No H-bonds generated for 'chain 'A' and resid 876 through 878' Processing helix chain 'A' and resid 887 through 894 Processing helix chain 'A' and resid 961 through 967 removed outlier: 4.117A pdb=" N ILE A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER A 966 " --> pdb=" O TYR A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 982 Processing helix chain 'A' and resid 983 through 992 Processing helix chain 'B' and resid 13 through 25 Processing helix chain 'B' and resid 31 through 41 removed outlier: 3.728A pdb=" N GLU B 35 " --> pdb=" O GLU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 49 removed outlier: 3.602A pdb=" N LYS B 47 " --> pdb=" O GLU B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 67 removed outlier: 4.069A pdb=" N ILE B 55 " --> pdb=" O ASP B 51 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 83 removed outlier: 4.321A pdb=" N LEU B 73 " --> pdb=" O ASP B 69 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N PHE B 74 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 100 Processing helix chain 'B' and resid 102 through 116 removed outlier: 3.610A pdb=" N ALA B 106 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 134 removed outlier: 3.711A pdb=" N ALA B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 149 removed outlier: 3.626A pdb=" N ARG B 142 " --> pdb=" O VAL B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 168 removed outlier: 3.641A pdb=" N TRP B 158 " --> pdb=" O ASP B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 184 removed outlier: 3.749A pdb=" N PHE B 176 " --> pdb=" O ALA B 172 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 203 removed outlier: 4.327A pdb=" N CYS B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 223 removed outlier: 4.282A pdb=" N LEU B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS B 213 " --> pdb=" O GLU B 209 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU B 219 " --> pdb=" O PHE B 215 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ASN B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 240 Processing helix chain 'B' and resid 246 through 273 removed outlier: 3.639A pdb=" N LYS B 250 " --> pdb=" O SER B 246 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 255 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG B 273 " --> pdb=" O GLN B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 292 removed outlier: 4.460A pdb=" N LEU B 292 " --> pdb=" O MET B 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 17 removed outlier: 3.943A pdb=" N ARG C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 39 removed outlier: 4.324A pdb=" N THR C 24 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N PHE C 25 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS C 32 " --> pdb=" O GLY C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 65 removed outlier: 3.676A pdb=" N VAL C 49 " --> pdb=" O THR C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 82 Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.779A pdb=" N LYS C 90 " --> pdb=" O PHE C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 132 Proline residue: C 120 - end of helix removed outlier: 4.348A pdb=" N ILE C 124 " --> pdb=" O PRO C 120 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY C 125 " --> pdb=" O MET C 121 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY C 126 " --> pdb=" O ILE C 122 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP C 127 " --> pdb=" O LEU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 152 removed outlier: 3.711A pdb=" N MET C 151 " --> pdb=" O PHE C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 179 removed outlier: 3.971A pdb=" N TRP C 171 " --> pdb=" O SER C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 187 removed outlier: 3.829A pdb=" N TYR C 183 " --> pdb=" O ARG C 180 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N SER C 184 " --> pdb=" O SER C 181 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU C 185 " --> pdb=" O ILE C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 227 removed outlier: 4.015A pdb=" N LEU C 227 " --> pdb=" O GLU C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 242 Processing helix chain 'D' and resid 141 through 156 Processing helix chain 'D' and resid 160 through 165 Processing helix chain 'E' and resid 5 through 35 Processing helix chain 'E' and resid 42 through 64 removed outlier: 3.772A pdb=" N VAL E 46 " --> pdb=" O PRO E 42 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N HIS E 62 " --> pdb=" O TYR E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 77 removed outlier: 3.656A pdb=" N LYS E 77 " --> pdb=" O SER E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 85 removed outlier: 3.601A pdb=" N LEU E 84 " --> pdb=" O THR E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.545A pdb=" N TYR E 91 " --> pdb=" O PRO E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 100 Processing helix chain 'F' and resid 17 through 44 removed outlier: 4.020A pdb=" N CYS F 29 " --> pdb=" O VAL F 25 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER F 32 " --> pdb=" O TYR F 28 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA F 35 " --> pdb=" O THR F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 70 removed outlier: 3.758A pdb=" N PHE F 52 " --> pdb=" O GLY F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 74 Processing helix chain 'F' and resid 81 through 86 removed outlier: 3.534A pdb=" N PHE F 85 " --> pdb=" O ARG F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 108 removed outlier: 3.765A pdb=" N PHE F 94 " --> pdb=" O ILE F 90 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR F 95 " --> pdb=" O GLY F 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 65 removed outlier: 3.868A pdb=" N ASP G 60 " --> pdb=" O LYS G 57 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA G 65 " --> pdb=" O ILE G 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 21 removed outlier: 3.556A pdb=" N TYR H 21 " --> pdb=" O HIS H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 83 removed outlier: 4.337A pdb=" N LEU H 71 " --> pdb=" O LEU H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'H' and resid 105 through 116 Processing helix chain 'H' and resid 166 through 177 Processing helix chain 'H' and resid 179 through 183 Processing helix chain 'H' and resid 185 through 190 Processing helix chain 'H' and resid 199 through 209 removed outlier: 3.871A pdb=" N ASN H 203 " --> pdb=" O ASN H 199 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 103 Processing helix chain 'I' and resid 134 through 139 Processing helix chain 'I' and resid 197 through 203 removed outlier: 3.979A pdb=" N PHE I 201 " --> pdb=" O GLU I 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 16 Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 44 removed outlier: 3.601A pdb=" N ALA A 64 " --> pdb=" O VAL A 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 92 removed outlier: 6.778A pdb=" N VAL A 100 " --> pdb=" O ASP A 88 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N MET A 90 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE A 98 " --> pdb=" O MET A 90 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TRP A 119 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 130 through 134 removed outlier: 5.933A pdb=" N HIS A 155 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU A 161 " --> pdb=" O HIS A 155 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 175 through 179 removed outlier: 5.727A pdb=" N TYR A 175 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL A 191 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS A 196 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS A 201 " --> pdb=" O GLN A 211 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N GLN A 211 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ASN A 203 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ILE A 209 " --> pdb=" O ASN A 203 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 235 through 239 Processing sheet with id=AA6, first strand: chain 'A' and resid 275 through 277 removed outlier: 6.500A pdb=" N HIS A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS A 314 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLN A 304 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LEU A 312 " --> pdb=" O GLN A 304 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 322 through 326 removed outlier: 3.727A pdb=" N LEU A 377 " --> pdb=" O THR A 389 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N THR A 389 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 11.008A pdb=" N LEU A 379 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 10.651A pdb=" N LEU A 387 " --> pdb=" O LEU A 379 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 405 through 409 removed outlier: 3.567A pdb=" N TRP A 443 " --> pdb=" O PHE A 432 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 457 removed outlier: 3.914A pdb=" N CYS A 454 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 544 through 547 removed outlier: 3.840A pdb=" N TRP A 557 " --> pdb=" O GLY A 547 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 570 through 576 removed outlier: 6.043A pdb=" N GLN A 586 " --> pdb=" O GLN A 575 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS A 610 " --> pdb=" O ASN A 605 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 625 through 627 removed outlier: 4.081A pdb=" N GLN A 625 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 693 through 699 removed outlier: 5.766A pdb=" N LEU A 694 " --> pdb=" O ARG A 685 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG A 685 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR A 672 " --> pdb=" O GLY D 178 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 674 " --> pdb=" O GLY D 180 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 706 through 712 removed outlier: 7.271A pdb=" N VAL A 744 " --> pdb=" O VAL A 708 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N VAL A 710 " --> pdb=" O ALA A 742 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ALA A 742 " --> pdb=" O VAL A 710 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLY A 712 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N LEU A 740 " --> pdb=" O GLY A 712 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N HIS A 771 " --> pdb=" O LEU A 761 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ASP A 763 " --> pdb=" O ILE A 769 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE A 769 " --> pdb=" O ASP A 763 " (cutoff:3.500A) removed outlier: 9.052A pdb=" N THR I 191 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N SER A 772 " --> pdb=" O THR I 191 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 723 through 725 removed outlier: 3.682A pdb=" N GLY A 813 " --> pdb=" O TYR A 733 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 723 through 725 removed outlier: 3.682A pdb=" N GLY A 813 " --> pdb=" O TYR A 733 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASN A 803 " --> pdb=" O PHE A 840 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 840 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 845 through 849 removed outlier: 4.239A pdb=" N ALA A 846 " --> pdb=" O GLY A 864 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 921 through 926 Processing sheet with id=AC1, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.913A pdb=" N THR C 138 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 47 through 49 Processing sheet with id=AC3, first strand: chain 'G' and resid 93 through 96 Processing sheet with id=AC4, first strand: chain 'H' and resid 56 through 63 removed outlier: 3.728A pdb=" N LEU H 60 " --> pdb=" O ASN H 27 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ASN H 27 " --> pdb=" O LEU H 60 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N HIS H 62 " --> pdb=" O ALA H 25 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ALA H 25 " --> pdb=" O HIS H 62 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR H 93 " --> pdb=" O GLY H 28 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY H 91 " --> pdb=" O LEU H 30 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ILE H 89 " --> pdb=" O ALA H 32 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA H 123 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR H 92 " --> pdb=" O ALA H 123 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 144 through 145 Processing sheet with id=AC6, first strand: chain 'I' and resid 82 through 86 removed outlier: 3.787A pdb=" N THR I 82 " --> pdb=" O ASN I 77 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LYS I 70 " --> pdb=" O HIS I 58 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N HIS I 58 " --> pdb=" O LYS I 70 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY I 72 " --> pdb=" O LEU I 56 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU I 56 " --> pdb=" O GLY I 72 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 156 through 163 removed outlier: 8.765A pdb=" N GLN I 186 " --> pdb=" O ASP I 144 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU I 146 " --> pdb=" O GLN I 186 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N GLN I 188 " --> pdb=" O LEU I 146 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU I 148 " --> pdb=" O GLN I 188 " (cutoff:3.500A) 714 hydrogen bonds defined for protein. 2010 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.55 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2709 1.31 - 1.44: 4686 1.44 - 1.57: 9693 1.57 - 1.69: 13 1.69 - 1.82: 110 Bond restraints: 17211 Sorted by residual: bond pdb=" C11 PCW F 201 " pdb=" O3 PCW F 201 " ideal model delta sigma weight residual 1.326 1.435 -0.109 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C11 PCW C 301 " pdb=" O3 PCW C 301 " ideal model delta sigma weight residual 1.326 1.433 -0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" C11 PCW A1004 " pdb=" O3 PCW A1004 " ideal model delta sigma weight residual 1.326 1.431 -0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" C11 PCW E 201 " pdb=" O3 PCW E 201 " ideal model delta sigma weight residual 1.326 1.430 -0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" C11 PCW A1005 " pdb=" O3 PCW A1005 " ideal model delta sigma weight residual 1.326 1.429 -0.103 2.00e-02 2.50e+03 2.67e+01 ... (remaining 17206 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 22787 2.68 - 5.35: 461 5.35 - 8.03: 42 8.03 - 10.71: 11 10.71 - 13.38: 11 Bond angle restraints: 23312 Sorted by residual: angle pdb=" N GLY A 50 " pdb=" CA GLY A 50 " pdb=" C GLY A 50 " ideal model delta sigma weight residual 113.18 102.36 10.82 2.37e+00 1.78e-01 2.08e+01 angle pdb=" N LYS G 46 " pdb=" CA LYS G 46 " pdb=" C LYS G 46 " ideal model delta sigma weight residual 108.96 115.75 -6.79 1.49e+00 4.50e-01 2.07e+01 angle pdb=" O3P PCW A1004 " pdb=" P PCW A1004 " pdb=" O4P PCW A1004 " ideal model delta sigma weight residual 96.85 110.23 -13.38 3.00e+00 1.11e-01 1.99e+01 angle pdb=" O3P PCW F 201 " pdb=" P PCW F 201 " pdb=" O4P PCW F 201 " ideal model delta sigma weight residual 96.85 109.93 -13.08 3.00e+00 1.11e-01 1.90e+01 angle pdb=" O3P PCW A1005 " pdb=" P PCW A1005 " pdb=" O4P PCW A1005 " ideal model delta sigma weight residual 96.85 109.71 -12.86 3.00e+00 1.11e-01 1.84e+01 ... (remaining 23307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.49: 9631 24.49 - 48.98: 620 48.98 - 73.47: 68 73.47 - 97.95: 22 97.95 - 122.44: 2 Dihedral angle restraints: 10343 sinusoidal: 4265 harmonic: 6078 Sorted by residual: dihedral pdb=" CA TYR G 136 " pdb=" C TYR G 136 " pdb=" N PRO G 137 " pdb=" CA PRO G 137 " ideal model delta harmonic sigma weight residual -180.00 -128.26 -51.74 0 5.00e+00 4.00e-02 1.07e+02 dihedral pdb=" CA ASP A 427 " pdb=" C ASP A 427 " pdb=" N HIS A 428 " pdb=" CA HIS A 428 " ideal model delta harmonic sigma weight residual 180.00 129.04 50.96 0 5.00e+00 4.00e-02 1.04e+02 dihedral pdb=" CA GLU A 232 " pdb=" C GLU A 232 " pdb=" N ALA A 233 " pdb=" CA ALA A 233 " ideal model delta harmonic sigma weight residual 180.00 132.44 47.56 0 5.00e+00 4.00e-02 9.05e+01 ... (remaining 10340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 2578 0.125 - 0.250: 46 0.250 - 0.374: 0 0.374 - 0.499: 0 0.499 - 0.624: 1 Chirality restraints: 2625 Sorted by residual: chirality pdb=" C1 NAG I 301 " pdb=" ND2 ASN I 182 " pdb=" C2 NAG I 301 " pdb=" O5 NAG I 301 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.73e+00 chirality pdb=" CA PRO A 883 " pdb=" N PRO A 883 " pdb=" C PRO A 883 " pdb=" CB PRO A 883 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C2 PCW F 201 " pdb=" C1 PCW F 201 " pdb=" C3 PCW F 201 " pdb=" O2 PCW F 201 " both_signs ideal model delta sigma weight residual False -2.32 -2.54 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 2622 not shown) Planarity restraints: 2938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 913 " 0.005 2.00e-02 2.50e+03 2.67e-01 8.92e+02 pdb=" CG ASN A 913 " 0.050 2.00e-02 2.50e+03 pdb=" OD1 ASN A 913 " -0.206 2.00e-02 2.50e+03 pdb=" ND2 ASN A 913 " 0.463 2.00e-02 2.50e+03 pdb=" C1 NAG A1003 " -0.312 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN I 182 " -0.192 2.00e-02 2.50e+03 2.61e-01 8.50e+02 pdb=" CG ASN I 182 " 0.074 2.00e-02 2.50e+03 pdb=" OD1 ASN I 182 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN I 182 " 0.447 2.00e-02 2.50e+03 pdb=" C1 NAG I 301 " -0.313 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 370 " 0.159 2.00e-02 2.50e+03 1.94e-01 4.72e+02 pdb=" CG ASN A 370 " -0.051 2.00e-02 2.50e+03 pdb=" OD1 ASN A 370 " -0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN A 370 " -0.323 2.00e-02 2.50e+03 pdb=" C1 NAG A1002 " 0.238 2.00e-02 2.50e+03 ... (remaining 2935 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 108 2.49 - 3.09: 12966 3.09 - 3.70: 24595 3.70 - 4.30: 33704 4.30 - 4.90: 57914 Nonbonded interactions: 129287 Sorted by model distance: nonbonded pdb=" O GLN A 533 " pdb=" OG SER A 550 " model vdw 1.890 3.040 nonbonded pdb=" OD1 ASP A 459 " pdb=" OG1 THR A 578 " model vdw 2.003 3.040 nonbonded pdb=" O LEU H 174 " pdb=" OG SER H 177 " model vdw 2.105 3.040 nonbonded pdb=" OG SER I 136 " pdb=" O GLY I 166 " model vdw 2.120 3.040 nonbonded pdb=" O ASP C 85 " pdb=" NZ LYS C 90 " model vdw 2.139 3.120 ... (remaining 129282 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.880 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 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 : 0.008 0.109 17216 Z= 0.340 Angle : 1.028 50.437 23326 Z= 0.509 Chirality : 0.049 0.624 2625 Planarity : 0.008 0.116 2934 Dihedral : 16.076 122.442 6406 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.11 % Allowed : 4.26 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 3.53 % Twisted General : 0.41 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.86 (0.14), residues: 2020 helix: -2.40 (0.16), residues: 679 sheet: -2.32 (0.22), residues: 408 loop : -4.36 (0.14), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.003 ARG I 111 TYR 0.022 0.002 TYR A 938 PHE 0.031 0.002 PHE G 84 TRP 0.020 0.002 TRP A 696 HIS 0.007 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00786 (17211) covalent geometry : angle 0.96160 (23312) SS BOND : bond 0.00489 ( 1) SS BOND : angle 1.45504 ( 2) hydrogen bonds : bond 0.12025 ( 711) hydrogen bonds : angle 6.60790 ( 2010) link_NAG-ASN : bond 0.01646 ( 4) link_NAG-ASN : angle 16.06408 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 234 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLU cc_start: 0.7495 (pp20) cc_final: 0.7114 (pp20) REVERT: B 25 GLU cc_start: 0.7845 (pp20) cc_final: 0.7611 (pp20) REVERT: B 163 GLU cc_start: 0.7267 (tt0) cc_final: 0.6893 (tm-30) REVERT: C 59 ARG cc_start: 0.9086 (mtp-110) cc_final: 0.8852 (mtp-110) REVERT: C 63 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7578 (mt-10) REVERT: D 154 MET cc_start: 0.6963 (mmp) cc_final: 0.6523 (ptt) REVERT: E 70 MET cc_start: 0.8674 (ptt) cc_final: 0.8442 (ptt) REVERT: E 71 ASP cc_start: 0.8507 (t70) cc_final: 0.8007 (t0) REVERT: F 86 THR cc_start: 0.8780 (m) cc_final: 0.8477 (p) REVERT: G 45 PHE cc_start: 0.4701 (OUTLIER) cc_final: 0.4064 (m-80) REVERT: H 5 LYS cc_start: 0.7227 (mptt) cc_final: 0.6101 (tttp) REVERT: H 96 ASN cc_start: 0.8140 (m-40) cc_final: 0.7794 (t0) REVERT: H 109 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8526 (mt-10) REVERT: H 142 HIS cc_start: 0.7494 (t-90) cc_final: 0.6874 (t70) REVERT: H 181 GLU cc_start: 0.8011 (mp0) cc_final: 0.7630 (mp0) outliers start: 2 outliers final: 0 residues processed: 236 average time/residue: 0.1495 time to fit residues: 50.4102 Evaluate side-chains 165 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 45 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.0570 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 299 HIS A 376 ASN B 185 ASN B 263 GLN C 231 GLN I 79 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.102896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.072547 restraints weight = 43405.353| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 3.75 r_work: 0.3011 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17216 Z= 0.150 Angle : 0.745 16.431 23326 Z= 0.383 Chirality : 0.046 0.219 2625 Planarity : 0.005 0.085 2934 Dihedral : 10.120 104.125 2452 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 0.66 % Allowed : 10.90 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 2.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.17), residues: 2020 helix: -0.32 (0.19), residues: 689 sheet: -1.28 (0.24), residues: 420 loop : -3.68 (0.16), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 266 TYR 0.021 0.001 TYR H 93 PHE 0.019 0.001 PHE C 132 TRP 0.042 0.001 TRP A 219 HIS 0.006 0.001 HIS H 146 Details of bonding type rmsd covalent geometry : bond 0.00322 (17211) covalent geometry : angle 0.72180 (23312) SS BOND : bond 0.00102 ( 1) SS BOND : angle 6.78593 ( 2) hydrogen bonds : bond 0.04224 ( 711) hydrogen bonds : angle 4.94474 ( 2010) link_NAG-ASN : bond 0.00584 ( 4) link_NAG-ASN : angle 7.61110 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 195 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 759 ILE cc_start: 0.8843 (mm) cc_final: 0.8408 (tt) REVERT: B 25 GLU cc_start: 0.7869 (pp20) cc_final: 0.7623 (pp20) REVERT: B 100 MET cc_start: 0.7888 (mmp) cc_final: 0.7665 (mmp) REVERT: B 185 ASN cc_start: 0.8947 (OUTLIER) cc_final: 0.8397 (p0) REVERT: C 31 ARG cc_start: 0.8669 (mtm110) cc_final: 0.7954 (mmp-170) REVERT: C 59 ARG cc_start: 0.9163 (mtp-110) cc_final: 0.8754 (mtp-110) REVERT: C 92 LYS cc_start: 0.8279 (mmtt) cc_final: 0.7569 (mmtm) REVERT: C 236 ASP cc_start: 0.9023 (t0) cc_final: 0.8729 (t0) REVERT: D 16 LYS cc_start: 0.8161 (ttmt) cc_final: 0.7949 (ttpt) REVERT: E 69 ASP cc_start: 0.8070 (t0) cc_final: 0.7094 (t0) REVERT: E 70 MET cc_start: 0.8801 (ptt) cc_final: 0.8477 (ptt) REVERT: E 71 ASP cc_start: 0.8511 (t70) cc_final: 0.7142 (p0) REVERT: H 5 LYS cc_start: 0.7311 (mptt) cc_final: 0.5979 (tttp) REVERT: H 96 ASN cc_start: 0.8291 (m-40) cc_final: 0.7807 (t0) REVERT: H 109 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8728 (mt-10) REVERT: H 142 HIS cc_start: 0.6844 (t-90) cc_final: 0.6017 (t70) REVERT: H 181 GLU cc_start: 0.8300 (mp0) cc_final: 0.7835 (mp0) REVERT: H 188 ASN cc_start: 0.9102 (m-40) cc_final: 0.8695 (m-40) outliers start: 12 outliers final: 7 residues processed: 204 average time/residue: 0.1423 time to fit residues: 43.5020 Evaluate side-chains 168 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 160 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain H residue 12 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 41 optimal weight: 1.9990 chunk 84 optimal weight: 0.2980 chunk 180 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 148 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 178 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 ASN ** A 860 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 GLN B 185 ASN B 263 GLN ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 ASN I 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.098708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.067658 restraints weight = 43773.618| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.66 r_work: 0.2892 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2898 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2898 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 17216 Z= 0.268 Angle : 0.775 12.607 23326 Z= 0.400 Chirality : 0.048 0.180 2625 Planarity : 0.005 0.085 2934 Dihedral : 9.711 105.611 2450 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 1.66 % Allowed : 13.95 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 2.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.18), residues: 2020 helix: 0.16 (0.20), residues: 695 sheet: -1.02 (0.25), residues: 436 loop : -3.47 (0.17), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 169 TYR 0.017 0.002 TYR A 938 PHE 0.018 0.002 PHE A 128 TRP 0.012 0.002 TRP A 219 HIS 0.005 0.001 HIS I 141 Details of bonding type rmsd covalent geometry : bond 0.00634 (17211) covalent geometry : angle 0.76412 (23312) SS BOND : bond 0.00164 ( 1) SS BOND : angle 6.57773 ( 2) hydrogen bonds : bond 0.04600 ( 711) hydrogen bonds : angle 4.99255 ( 2010) link_NAG-ASN : bond 0.00360 ( 4) link_NAG-ASN : angle 5.09474 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8557 (tp30) REVERT: A 759 ILE cc_start: 0.8984 (mm) cc_final: 0.8629 (tt) REVERT: A 956 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7879 (tt) REVERT: B 25 GLU cc_start: 0.7998 (pp20) cc_final: 0.7732 (pp20) REVERT: C 92 LYS cc_start: 0.8284 (mmtt) cc_final: 0.7656 (mmtm) REVERT: C 154 GLN cc_start: 0.8871 (mm110) cc_final: 0.8631 (mm110) REVERT: C 236 ASP cc_start: 0.9181 (t0) cc_final: 0.8855 (t0) REVERT: D 154 MET cc_start: 0.7163 (mmp) cc_final: 0.6436 (ptt) REVERT: E 69 ASP cc_start: 0.8171 (t0) cc_final: 0.7416 (t0) REVERT: E 70 MET cc_start: 0.8931 (ptt) cc_final: 0.8212 (ptt) REVERT: E 71 ASP cc_start: 0.8731 (t70) cc_final: 0.7421 (p0) REVERT: H 5 LYS cc_start: 0.7397 (mptt) cc_final: 0.6026 (tttp) REVERT: H 14 MET cc_start: 0.7911 (tpp) cc_final: 0.7674 (tpp) REVERT: H 96 ASN cc_start: 0.8558 (m-40) cc_final: 0.7934 (t0) REVERT: H 109 GLU cc_start: 0.9270 (mt-10) cc_final: 0.8753 (mt-10) REVERT: H 142 HIS cc_start: 0.6910 (t-90) cc_final: 0.5682 (t-90) REVERT: H 181 GLU cc_start: 0.8318 (mp0) cc_final: 0.8106 (mp0) REVERT: H 188 ASN cc_start: 0.9116 (m110) cc_final: 0.8706 (m110) REVERT: I 151 ASP cc_start: 0.8012 (p0) cc_final: 0.7780 (p0) outliers start: 30 outliers final: 16 residues processed: 195 average time/residue: 0.1415 time to fit residues: 41.8492 Evaluate side-chains 179 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain I residue 161 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 11 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 175 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 199 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 169 optimal weight: 0.0370 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 860 HIS B 169 HIS B 193 GLN B 263 GLN C 46 GLN ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.101600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.070639 restraints weight = 43302.517| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 3.70 r_work: 0.2969 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17216 Z= 0.123 Angle : 0.658 13.870 23326 Z= 0.338 Chirality : 0.043 0.221 2625 Planarity : 0.004 0.083 2934 Dihedral : 8.957 104.326 2450 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 1.77 % Allowed : 15.77 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 2.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.18), residues: 2020 helix: 0.80 (0.20), residues: 690 sheet: -0.51 (0.26), residues: 431 loop : -3.26 (0.17), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 20 TYR 0.013 0.001 TYR H 93 PHE 0.020 0.001 PHE A 128 TRP 0.012 0.001 TRP A 219 HIS 0.004 0.001 HIS B 238 Details of bonding type rmsd covalent geometry : bond 0.00274 (17211) covalent geometry : angle 0.65031 (23312) SS BOND : bond 0.00076 ( 1) SS BOND : angle 5.03581 ( 2) hydrogen bonds : bond 0.03501 ( 711) hydrogen bonds : angle 4.46036 ( 2010) link_NAG-ASN : bond 0.00388 ( 4) link_NAG-ASN : angle 4.01560 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 193 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6727 (mtp) cc_final: 0.6366 (mtm) REVERT: A 759 ILE cc_start: 0.8954 (mm) cc_final: 0.8648 (tt) REVERT: B 25 GLU cc_start: 0.7771 (pp20) cc_final: 0.7530 (pp20) REVERT: B 100 MET cc_start: 0.7722 (mmp) cc_final: 0.7443 (mmp) REVERT: C 51 ASP cc_start: 0.8855 (m-30) cc_final: 0.8608 (m-30) REVERT: C 82 ASN cc_start: 0.7775 (t0) cc_final: 0.7529 (t0) REVERT: C 92 LYS cc_start: 0.8341 (mmtt) cc_final: 0.7649 (mmtm) REVERT: C 154 GLN cc_start: 0.8793 (mm110) cc_final: 0.8488 (mm110) REVERT: C 236 ASP cc_start: 0.9142 (t0) cc_final: 0.8809 (t0) REVERT: D 16 LYS cc_start: 0.8078 (ttmt) cc_final: 0.7846 (ttpt) REVERT: D 51 GLN cc_start: 0.9071 (mm110) cc_final: 0.8803 (mm-40) REVERT: D 172 GLU cc_start: 0.8572 (pp20) cc_final: 0.7983 (pp20) REVERT: E 69 ASP cc_start: 0.8103 (t0) cc_final: 0.7202 (t0) REVERT: E 70 MET cc_start: 0.8890 (ptt) cc_final: 0.8107 (ptt) REVERT: E 71 ASP cc_start: 0.8639 (t70) cc_final: 0.7369 (p0) REVERT: H 5 LYS cc_start: 0.7411 (mptt) cc_final: 0.5976 (tttp) REVERT: H 11 TYR cc_start: 0.6940 (t80) cc_final: 0.6684 (t80) REVERT: H 14 MET cc_start: 0.7933 (tpp) cc_final: 0.7555 (tpp) REVERT: H 96 ASN cc_start: 0.8524 (m-40) cc_final: 0.7925 (t0) REVERT: H 109 GLU cc_start: 0.9235 (mt-10) cc_final: 0.8703 (mt-10) REVERT: H 142 HIS cc_start: 0.6798 (t-90) cc_final: 0.5761 (t-90) REVERT: H 178 ARG cc_start: 0.8468 (tmm160) cc_final: 0.7984 (tpt90) REVERT: H 181 GLU cc_start: 0.8482 (mp0) cc_final: 0.7662 (mp0) REVERT: H 188 ASN cc_start: 0.9100 (m110) cc_final: 0.8631 (m110) REVERT: I 151 ASP cc_start: 0.8080 (p0) cc_final: 0.7794 (p0) outliers start: 32 outliers final: 20 residues processed: 215 average time/residue: 0.1433 time to fit residues: 45.9202 Evaluate side-chains 186 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 159 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 176 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 136 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 200 optimal weight: 7.9990 chunk 110 optimal weight: 0.9980 chunk 146 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 ASN C 247 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.100344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.069249 restraints weight = 43429.736| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.69 r_work: 0.2929 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17216 Z= 0.152 Angle : 0.660 13.171 23326 Z= 0.336 Chirality : 0.044 0.177 2625 Planarity : 0.004 0.081 2934 Dihedral : 8.573 102.866 2450 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 2.38 % Allowed : 16.99 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 2.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.19), residues: 2020 helix: 1.03 (0.21), residues: 693 sheet: -0.48 (0.25), residues: 444 loop : -3.11 (0.18), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 20 TYR 0.012 0.001 TYR E 58 PHE 0.019 0.001 PHE A 128 TRP 0.010 0.001 TRP G 61 HIS 0.003 0.001 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00355 (17211) covalent geometry : angle 0.65350 (23312) SS BOND : bond 0.00081 ( 1) SS BOND : angle 4.71569 ( 2) hydrogen bonds : bond 0.03539 ( 711) hydrogen bonds : angle 4.38341 ( 2010) link_NAG-ASN : bond 0.00313 ( 4) link_NAG-ASN : angle 3.54590 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 182 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6786 (mtp) cc_final: 0.6543 (mtm) REVERT: A 759 ILE cc_start: 0.8993 (mm) cc_final: 0.8677 (tt) REVERT: B 100 MET cc_start: 0.7673 (mmp) cc_final: 0.7326 (mmp) REVERT: C 51 ASP cc_start: 0.8890 (m-30) cc_final: 0.8628 (m-30) REVERT: C 82 ASN cc_start: 0.7934 (t0) cc_final: 0.7654 (t0) REVERT: C 92 LYS cc_start: 0.8332 (mmtt) cc_final: 0.7729 (mmtm) REVERT: C 151 MET cc_start: 0.8783 (ptp) cc_final: 0.8535 (mtt) REVERT: C 154 GLN cc_start: 0.8822 (mm110) cc_final: 0.8486 (mm110) REVERT: C 236 ASP cc_start: 0.9191 (t0) cc_final: 0.8819 (t0) REVERT: D 154 MET cc_start: 0.6790 (mmp) cc_final: 0.6163 (ptt) REVERT: D 172 GLU cc_start: 0.8586 (pp20) cc_final: 0.8000 (pp20) REVERT: E 69 ASP cc_start: 0.8221 (t0) cc_final: 0.7309 (t0) REVERT: E 70 MET cc_start: 0.8921 (ptt) cc_final: 0.8248 (ptt) REVERT: E 71 ASP cc_start: 0.8690 (t70) cc_final: 0.7427 (p0) REVERT: H 5 LYS cc_start: 0.7475 (mptt) cc_final: 0.6093 (tttp) REVERT: H 14 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7640 (tpp) REVERT: H 96 ASN cc_start: 0.8599 (m-40) cc_final: 0.7950 (t0) REVERT: H 109 GLU cc_start: 0.9262 (mt-10) cc_final: 0.8640 (mm-30) REVERT: H 142 HIS cc_start: 0.6731 (t-90) cc_final: 0.5923 (t-90) REVERT: H 188 ASN cc_start: 0.9162 (m110) cc_final: 0.8803 (m110) REVERT: I 151 ASP cc_start: 0.8103 (p0) cc_final: 0.7866 (p0) outliers start: 43 outliers final: 28 residues processed: 213 average time/residue: 0.1385 time to fit residues: 43.9695 Evaluate side-chains 192 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 14 MET Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 161 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 64 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 179 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 148 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 192 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 168 optimal weight: 9.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 GLN B 263 GLN C 247 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.096557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.065220 restraints weight = 43512.766| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.66 r_work: 0.2841 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2849 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 17216 Z= 0.298 Angle : 0.775 12.693 23326 Z= 0.396 Chirality : 0.048 0.222 2625 Planarity : 0.005 0.089 2934 Dihedral : 8.800 103.722 2450 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.70 % Favored : 89.30 % Rotamer: Outliers : 2.55 % Allowed : 17.87 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.18), residues: 2020 helix: 0.65 (0.20), residues: 718 sheet: -0.55 (0.25), residues: 453 loop : -3.21 (0.18), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 20 TYR 0.019 0.002 TYR G 136 PHE 0.022 0.002 PHE A 128 TRP 0.012 0.001 TRP G 61 HIS 0.006 0.001 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00706 (17211) covalent geometry : angle 0.76953 (23312) SS BOND : bond 0.00016 ( 1) SS BOND : angle 5.07321 ( 2) hydrogen bonds : bond 0.04490 ( 711) hydrogen bonds : angle 4.76262 ( 2010) link_NAG-ASN : bond 0.00425 ( 4) link_NAG-ASN : angle 3.67778 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 172 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8485 (tppt) REVERT: B 25 GLU cc_start: 0.8033 (pp20) cc_final: 0.7623 (pp20) REVERT: C 51 ASP cc_start: 0.8940 (m-30) cc_final: 0.8654 (m-30) REVERT: C 151 MET cc_start: 0.8825 (ptp) cc_final: 0.8557 (mtt) REVERT: C 154 GLN cc_start: 0.8878 (mm110) cc_final: 0.8519 (mm110) REVERT: C 236 ASP cc_start: 0.9291 (t0) cc_final: 0.8952 (t0) REVERT: D 154 MET cc_start: 0.6865 (mmp) cc_final: 0.6240 (ptt) REVERT: D 172 GLU cc_start: 0.8613 (pp20) cc_final: 0.7964 (pp20) REVERT: E 70 MET cc_start: 0.8934 (ptt) cc_final: 0.8508 (ptt) REVERT: E 71 ASP cc_start: 0.8786 (t70) cc_final: 0.8531 (t70) REVERT: H 5 LYS cc_start: 0.7522 (mptt) cc_final: 0.6142 (tttp) REVERT: H 96 ASN cc_start: 0.8606 (m-40) cc_final: 0.8120 (t0) REVERT: H 109 GLU cc_start: 0.9323 (mt-10) cc_final: 0.8797 (mm-30) REVERT: H 142 HIS cc_start: 0.6792 (t-90) cc_final: 0.5962 (t-90) REVERT: H 188 ASN cc_start: 0.9148 (m110) cc_final: 0.8779 (m110) REVERT: I 151 ASP cc_start: 0.8149 (p0) cc_final: 0.7924 (p0) outliers start: 46 outliers final: 31 residues processed: 206 average time/residue: 0.1425 time to fit residues: 43.6609 Evaluate side-chains 197 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 161 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.6980 chunk 116 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 49 optimal weight: 0.0870 chunk 176 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 127 optimal weight: 0.0030 chunk 2 optimal weight: 0.8980 overall best weight: 0.3968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 783 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.100615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.069641 restraints weight = 42674.163| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.65 r_work: 0.2942 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2947 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2947 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17216 Z= 0.120 Angle : 0.670 13.872 23326 Z= 0.340 Chirality : 0.043 0.184 2625 Planarity : 0.005 0.088 2934 Dihedral : 8.266 101.495 2450 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 1.60 % Allowed : 19.76 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 2.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.19), residues: 2020 helix: 1.05 (0.20), residues: 719 sheet: -0.14 (0.25), residues: 443 loop : -2.97 (0.19), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 20 TYR 0.020 0.001 TYR G 136 PHE 0.018 0.001 PHE A 128 TRP 0.014 0.001 TRP A 119 HIS 0.006 0.001 HIS A 783 Details of bonding type rmsd covalent geometry : bond 0.00266 (17211) covalent geometry : angle 0.66570 (23312) SS BOND : bond 0.00122 ( 1) SS BOND : angle 4.06297 ( 2) hydrogen bonds : bond 0.03142 ( 711) hydrogen bonds : angle 4.27520 ( 2010) link_NAG-ASN : bond 0.00364 ( 4) link_NAG-ASN : angle 2.92544 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.8187 (t70) cc_final: 0.7796 (t0) REVERT: A 759 ILE cc_start: 0.9094 (mm) cc_final: 0.8760 (tt) REVERT: C 51 ASP cc_start: 0.8841 (m-30) cc_final: 0.8633 (m-30) REVERT: C 82 ASN cc_start: 0.7999 (t0) cc_final: 0.7659 (t0) REVERT: C 236 ASP cc_start: 0.9237 (t0) cc_final: 0.8856 (t0) REVERT: D 154 MET cc_start: 0.6824 (mmp) cc_final: 0.6185 (ptt) REVERT: D 172 GLU cc_start: 0.8645 (pp20) cc_final: 0.8024 (pp20) REVERT: E 70 MET cc_start: 0.8847 (ptt) cc_final: 0.8403 (ptt) REVERT: H 5 LYS cc_start: 0.7541 (mptt) cc_final: 0.6134 (tttp) REVERT: H 14 MET cc_start: 0.7868 (tpp) cc_final: 0.7586 (tpp) REVERT: H 96 ASN cc_start: 0.8562 (m-40) cc_final: 0.8035 (t0) REVERT: H 109 GLU cc_start: 0.9257 (mt-10) cc_final: 0.8757 (mm-30) REVERT: H 142 HIS cc_start: 0.6655 (t-90) cc_final: 0.5841 (t-90) REVERT: H 178 ARG cc_start: 0.8556 (ttp80) cc_final: 0.8140 (ttp80) REVERT: H 188 ASN cc_start: 0.9123 (m110) cc_final: 0.8783 (m-40) REVERT: I 151 ASP cc_start: 0.8153 (p0) cc_final: 0.7913 (p0) outliers start: 29 outliers final: 22 residues processed: 206 average time/residue: 0.1326 time to fit residues: 41.8867 Evaluate side-chains 189 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain I residue 159 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 77 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 142 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN C 247 HIS ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.097968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.066926 restraints weight = 43200.523| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 3.63 r_work: 0.2883 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17216 Z= 0.207 Angle : 0.700 12.522 23326 Z= 0.356 Chirality : 0.045 0.212 2625 Planarity : 0.005 0.086 2934 Dihedral : 8.226 100.385 2450 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer: Outliers : 1.88 % Allowed : 19.70 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.19), residues: 2020 helix: 1.06 (0.20), residues: 715 sheet: -0.31 (0.25), residues: 455 loop : -2.97 (0.19), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 20 TYR 0.013 0.001 TYR E 58 PHE 0.019 0.001 PHE A 128 TRP 0.012 0.001 TRP G 61 HIS 0.004 0.001 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00494 (17211) covalent geometry : angle 0.69574 (23312) SS BOND : bond 0.00078 ( 1) SS BOND : angle 4.48471 ( 2) hydrogen bonds : bond 0.03741 ( 711) hydrogen bonds : angle 4.41056 ( 2010) link_NAG-ASN : bond 0.00291 ( 4) link_NAG-ASN : angle 3.03205 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.7185 (ttm) cc_final: 0.6884 (mtm) REVERT: A 231 ASP cc_start: 0.8276 (t70) cc_final: 0.7921 (t0) REVERT: A 759 ILE cc_start: 0.9115 (mm) cc_final: 0.8716 (tt) REVERT: B 25 GLU cc_start: 0.7862 (pp20) cc_final: 0.7622 (pp20) REVERT: C 51 ASP cc_start: 0.8880 (m-30) cc_final: 0.8661 (m-30) REVERT: C 82 ASN cc_start: 0.8003 (t0) cc_final: 0.7678 (t0) REVERT: C 154 GLN cc_start: 0.8975 (mm110) cc_final: 0.8713 (mm110) REVERT: C 236 ASP cc_start: 0.9301 (t0) cc_final: 0.8928 (t0) REVERT: D 149 TYR cc_start: 0.7377 (OUTLIER) cc_final: 0.6938 (t80) REVERT: D 154 MET cc_start: 0.6821 (mmp) cc_final: 0.6282 (ptt) REVERT: D 172 GLU cc_start: 0.8655 (pp20) cc_final: 0.8019 (pp20) REVERT: E 70 MET cc_start: 0.8890 (ptt) cc_final: 0.8468 (ptt) REVERT: H 5 LYS cc_start: 0.7500 (mptt) cc_final: 0.6070 (tttp) REVERT: H 96 ASN cc_start: 0.8578 (m-40) cc_final: 0.8095 (t0) REVERT: H 109 GLU cc_start: 0.9281 (mt-10) cc_final: 0.8808 (mm-30) REVERT: H 142 HIS cc_start: 0.6744 (t-90) cc_final: 0.6396 (t-90) REVERT: H 178 ARG cc_start: 0.8399 (ttp80) cc_final: 0.7922 (ttp80) REVERT: H 181 GLU cc_start: 0.8771 (mp0) cc_final: 0.8417 (mp0) REVERT: H 188 ASN cc_start: 0.9148 (m110) cc_final: 0.8817 (m110) REVERT: I 151 ASP cc_start: 0.8137 (p0) cc_final: 0.7911 (p0) outliers start: 34 outliers final: 27 residues processed: 196 average time/residue: 0.1293 time to fit residues: 38.5339 Evaluate side-chains 200 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain D residue 149 TYR Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 81 PHE Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 161 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 26 optimal weight: 7.9990 chunk 172 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 167 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 200 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 247 HIS ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.098502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.067279 restraints weight = 43437.457| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.67 r_work: 0.2884 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17216 Z= 0.174 Angle : 0.690 12.673 23326 Z= 0.351 Chirality : 0.044 0.209 2625 Planarity : 0.005 0.085 2934 Dihedral : 8.119 98.697 2450 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 1.88 % Allowed : 19.92 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.19), residues: 2020 helix: 1.15 (0.20), residues: 713 sheet: -0.23 (0.25), residues: 449 loop : -2.97 (0.19), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 20 TYR 0.011 0.001 TYR A 793 PHE 0.019 0.001 PHE A 128 TRP 0.013 0.001 TRP G 61 HIS 0.004 0.001 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00415 (17211) covalent geometry : angle 0.68546 (23312) SS BOND : bond 0.00628 ( 1) SS BOND : angle 5.07693 ( 2) hydrogen bonds : bond 0.03559 ( 711) hydrogen bonds : angle 4.36067 ( 2010) link_NAG-ASN : bond 0.00264 ( 4) link_NAG-ASN : angle 2.87565 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8642 (tptp) REVERT: A 177 MET cc_start: 0.7118 (ttm) cc_final: 0.6792 (mtm) REVERT: A 231 ASP cc_start: 0.8247 (t70) cc_final: 0.7909 (t0) REVERT: A 759 ILE cc_start: 0.9133 (mm) cc_final: 0.8735 (tt) REVERT: C 51 ASP cc_start: 0.8859 (m-30) cc_final: 0.8639 (m-30) REVERT: C 82 ASN cc_start: 0.7912 (t0) cc_final: 0.7582 (t0) REVERT: C 154 GLN cc_start: 0.8916 (mm110) cc_final: 0.8609 (mm110) REVERT: C 236 ASP cc_start: 0.9289 (t0) cc_final: 0.8909 (t0) REVERT: D 149 TYR cc_start: 0.7312 (OUTLIER) cc_final: 0.6830 (t80) REVERT: D 154 MET cc_start: 0.6786 (mmp) cc_final: 0.6295 (ptt) REVERT: D 172 GLU cc_start: 0.8660 (pp20) cc_final: 0.8017 (pp20) REVERT: E 70 MET cc_start: 0.8904 (ptt) cc_final: 0.8530 (ptt) REVERT: H 5 LYS cc_start: 0.7525 (mptt) cc_final: 0.6066 (tttp) REVERT: H 96 ASN cc_start: 0.8583 (m-40) cc_final: 0.8131 (t0) REVERT: H 109 GLU cc_start: 0.9270 (mt-10) cc_final: 0.8795 (mm-30) REVERT: H 142 HIS cc_start: 0.6741 (t-90) cc_final: 0.6414 (t-90) REVERT: H 178 ARG cc_start: 0.8419 (ttp80) cc_final: 0.7989 (ttp80) REVERT: H 181 GLU cc_start: 0.8732 (mp0) cc_final: 0.8329 (mp0) REVERT: H 188 ASN cc_start: 0.9139 (m110) cc_final: 0.8774 (m110) REVERT: I 151 ASP cc_start: 0.8189 (p0) cc_final: 0.7955 (p0) outliers start: 34 outliers final: 30 residues processed: 196 average time/residue: 0.1258 time to fit residues: 37.7119 Evaluate side-chains 203 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 171 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain D residue 149 TYR Chi-restraints excluded: chain E residue 81 PHE Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 161 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 9 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 202 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 187 optimal weight: 7.9990 chunk 161 optimal weight: 3.9990 chunk 182 optimal weight: 0.3980 chunk 30 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 199 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 247 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.099279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.068124 restraints weight = 43071.844| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 3.66 r_work: 0.2906 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17216 Z= 0.141 Angle : 0.674 12.433 23326 Z= 0.341 Chirality : 0.044 0.198 2625 Planarity : 0.005 0.083 2934 Dihedral : 7.888 95.842 2450 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 1.88 % Allowed : 19.87 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.19), residues: 2020 helix: 1.24 (0.20), residues: 709 sheet: -0.26 (0.25), residues: 459 loop : -2.92 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 20 TYR 0.014 0.001 TYR H 93 PHE 0.018 0.001 PHE A 128 TRP 0.012 0.001 TRP G 61 HIS 0.003 0.001 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00333 (17211) covalent geometry : angle 0.67015 (23312) SS BOND : bond 0.00163 ( 1) SS BOND : angle 4.88155 ( 2) hydrogen bonds : bond 0.03316 ( 711) hydrogen bonds : angle 4.28027 ( 2010) link_NAG-ASN : bond 0.00257 ( 4) link_NAG-ASN : angle 2.66473 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 176 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8393 (tppt) REVERT: A 177 MET cc_start: 0.7106 (ttm) cc_final: 0.6791 (mtm) REVERT: A 759 ILE cc_start: 0.9096 (mm) cc_final: 0.8727 (tt) REVERT: B 24 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8324 (mt-10) REVERT: B 288 MET cc_start: 0.8675 (tpt) cc_final: 0.8355 (tpt) REVERT: C 51 ASP cc_start: 0.8848 (m-30) cc_final: 0.8627 (m-30) REVERT: C 93 ARG cc_start: 0.6382 (mmm160) cc_final: 0.6150 (mmm160) REVERT: C 154 GLN cc_start: 0.8893 (mm110) cc_final: 0.8564 (mm110) REVERT: C 236 ASP cc_start: 0.9292 (t0) cc_final: 0.8905 (t0) REVERT: D 149 TYR cc_start: 0.7337 (OUTLIER) cc_final: 0.6796 (t80) REVERT: D 154 MET cc_start: 0.6606 (mmp) cc_final: 0.6173 (ptt) REVERT: D 172 GLU cc_start: 0.8665 (pp20) cc_final: 0.8032 (pp20) REVERT: E 70 MET cc_start: 0.8851 (ptt) cc_final: 0.8527 (ptt) REVERT: H 5 LYS cc_start: 0.7555 (mptt) cc_final: 0.6150 (tttp) REVERT: H 96 ASN cc_start: 0.8583 (m-40) cc_final: 0.8125 (t0) REVERT: H 109 GLU cc_start: 0.9275 (mt-10) cc_final: 0.8803 (mm-30) REVERT: H 117 GLU cc_start: 0.8651 (tt0) cc_final: 0.8302 (pp20) REVERT: H 142 HIS cc_start: 0.6724 (t-90) cc_final: 0.6390 (t-90) REVERT: H 188 ASN cc_start: 0.9141 (m110) cc_final: 0.8823 (m-40) REVERT: I 151 ASP cc_start: 0.8207 (p0) cc_final: 0.7964 (p0) outliers start: 34 outliers final: 29 residues processed: 201 average time/residue: 0.1268 time to fit residues: 39.2457 Evaluate side-chains 202 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain D residue 149 TYR Chi-restraints excluded: chain E residue 81 PHE Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 159 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 89 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 92 optimal weight: 0.0770 chunk 55 optimal weight: 0.0170 chunk 38 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 183 optimal weight: 10.0000 chunk 192 optimal weight: 1.9990 chunk 20 optimal weight: 0.0060 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 146 HIS H 188 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.100903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.069999 restraints weight = 43074.025| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 3.67 r_work: 0.2953 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17216 Z= 0.112 Angle : 0.664 11.902 23326 Z= 0.334 Chirality : 0.043 0.191 2625 Planarity : 0.005 0.082 2934 Dihedral : 7.566 92.035 2450 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 1.60 % Allowed : 20.25 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.19), residues: 2020 helix: 1.37 (0.21), residues: 708 sheet: -0.06 (0.25), residues: 448 loop : -2.82 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 20 TYR 0.016 0.001 TYR H 93 PHE 0.015 0.001 PHE A 128 TRP 0.013 0.001 TRP A 119 HIS 0.003 0.001 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00255 (17211) covalent geometry : angle 0.66039 (23312) SS BOND : bond 0.00107 ( 1) SS BOND : angle 4.38841 ( 2) hydrogen bonds : bond 0.02957 ( 711) hydrogen bonds : angle 4.13597 ( 2010) link_NAG-ASN : bond 0.00291 ( 4) link_NAG-ASN : angle 2.38585 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5285.04 seconds wall clock time: 90 minutes 49.84 seconds (5449.84 seconds total)