Starting phenix.real_space_refine on Sat Jul 4 00:46:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ado_11732/07_2026/7ado_11732.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ado_11732/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7ado_11732/07_2026/7ado_11732.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ado_11732/07_2026/7ado_11732.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ado_11732/07_2026/7ado_11732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ado_11732/07_2026/7ado_11732.map" model { file = "/net/cci-nas-00/data/ceres_data/7ado_11732/07_2026/7ado_11732.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ado_11732/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 53 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: 27 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 chiralities: 1 Time building chain proxies: 3.49, per 1000 atoms: 0.21 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: 1.89 Conformation dependent library (CDL) restraints added in 577.7 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: 0.55 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: 3.16 Time building geometry restraints manager: 2.34 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: 9537 24.49 - 48.98: 597 48.98 - 73.47: 61 73.47 - 97.95: 20 97.95 - 122.44: 2 Dihedral angle restraints: 10217 sinusoidal: 4139 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 10214 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: 4.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.510 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 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 : 15.849 122.442 6280 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/Z covalent geometry : bond 0.00786 / 0.34 (17211) covalent geometry : angle 0.96160 / 0.49 (23312) SS BOND : bond 0.00489 / 0.26 ( 1) SS BOND : angle 1.45504 / 0.81 ( 2) hydrogen bonds : bond 0.12025 / 8.18 ( 711) hydrogen bonds : angle 6.60790 / 4.53 ( 2010) link_NAG-ASN : bond 0.01646 / 0.83 ( 4) link_NAG-ASN : angle 16.06408 / 10.49 ( 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 : 0.685 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: 0.1602 time to fit residues: 54.4117 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 : 0.708 ------------------------------------------------------------------------------- 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... A 26 GLN A 299 HIS A 376 ASN B 169 HIS B 185 ASN B 263 GLN C 231 GLN I 79 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.102911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.072541 restraints weight = 43414.715| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 3.74 r_work: 0.3012 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 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 = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1871 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= 0.145 Angle : 0.740 15.830 23326 Z= 0.381 Chirality : 0.046 0.229 2625 Planarity : 0.005 0.085 2934 Dihedral : 9.060 104.756 2326 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.10 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: -2.85 (0.17), residues: 2020 helix: -0.25 (0.19), residues: 689 sheet: -1.23 (0.24), residues: 420 loop : -3.64 (0.16), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 266 TYR 0.027 0.002 TYR H 93 PHE 0.020 0.001 PHE C 132 TRP 0.046 0.002 TRP A 219 HIS 0.006 0.001 HIS H 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (17211) covalent geometry : angle 0.72164 / 0.38 (23312) SS BOND : bond 0.01495 / 0.79 ( 1) SS BOND : angle 5.76890 / 3.22 ( 2) hydrogen bonds : bond 0.04109 / 2.70 ( 711) hydrogen bonds : angle 4.89228 / 3.38 ( 2010) link_NAG-ASN : bond 0.00621 / 0.31 ( 4) link_NAG-ASN : angle 6.78660 / 4.08 ( 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 209 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 197 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 759 ILE cc_start: 0.8844 (mm) cc_final: 0.8398 (tt) REVERT: B 25 GLU cc_start: 0.7879 (pp20) cc_final: 0.7633 (pp20) REVERT: B 100 MET cc_start: 0.7786 (mmp) cc_final: 0.7462 (mmp) REVERT: B 185 ASN cc_start: 0.8966 (OUTLIER) cc_final: 0.8591 (p0) REVERT: C 59 ARG cc_start: 0.9168 (mtp-110) cc_final: 0.8764 (mtp-110) REVERT: C 92 LYS cc_start: 0.8280 (mmtt) cc_final: 0.7567 (mmtm) REVERT: C 236 ASP cc_start: 0.9016 (t0) cc_final: 0.8708 (t0) REVERT: D 16 LYS cc_start: 0.8154 (ttmt) cc_final: 0.7939 (ttpt) REVERT: D 51 GLN cc_start: 0.9099 (mm-40) cc_final: 0.8883 (mm-40) REVERT: E 69 ASP cc_start: 0.8069 (t0) cc_final: 0.7162 (t0) REVERT: E 70 MET cc_start: 0.8811 (ptt) cc_final: 0.8503 (ptt) REVERT: E 71 ASP cc_start: 0.8493 (t70) cc_final: 0.7116 (p0) REVERT: H 5 LYS cc_start: 0.7339 (mptt) cc_final: 0.5983 (tttp) REVERT: H 96 ASN cc_start: 0.8335 (m-40) cc_final: 0.7840 (t0) REVERT: H 109 GLU cc_start: 0.9165 (mt-10) cc_final: 0.8726 (mt-10) REVERT: H 142 HIS cc_start: 0.6777 (t-90) cc_final: 0.5965 (t70) REVERT: H 181 GLU cc_start: 0.8356 (mp0) cc_final: 0.7862 (mp0) REVERT: H 188 ASN cc_start: 0.9103 (m-40) cc_final: 0.8695 (m-40) outliers start: 12 outliers final: 7 residues processed: 206 average time/residue: 0.1282 time to fit residues: 39.9997 Evaluate side-chains 167 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 159 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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: 2.9990 chunk 84 optimal weight: 0.6980 chunk 180 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 178 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 chunk 116 optimal weight: 7.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 860 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 GLN B 185 ASN B 263 GLN C 129 ASN C 247 HIS H 188 ASN I 79 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.097411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.066260 restraints weight = 44001.976| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.65 r_work: 0.2866 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2657 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= 0.314 Angle : 0.819 12.530 23326 Z= 0.422 Chirality : 0.049 0.179 2625 Planarity : 0.005 0.086 2934 Dihedral : 8.762 105.435 2324 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 2.27 % Allowed : 14.33 % Favored : 83.40 % 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: -2.43 (0.18), residues: 2020 helix: 0.15 (0.20), residues: 692 sheet: -1.01 (0.25), residues: 441 loop : -3.49 (0.17), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 62 TYR 0.019 0.002 TYR A 938 PHE 0.026 0.002 PHE A 128 TRP 0.035 0.002 TRP A 219 HIS 0.006 0.001 HIS A 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00744 / 0.31 (17211) covalent geometry : angle 0.80988 / 0.42 (23312) SS BOND : bond 0.00526 / 0.28 ( 1) SS BOND : angle 6.68395 / 3.85 ( 2) hydrogen bonds : bond 0.04931 / 3.26 ( 711) hydrogen bonds : angle 5.09752 / 3.52 ( 2010) link_NAG-ASN : bond 0.00439 / 0.22 ( 4) link_NAG-ASN : angle 4.69793 / 2.77 ( 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 215 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 174 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.7057 (mtp) cc_final: 0.6760 (mtp) REVERT: A 759 ILE cc_start: 0.9027 (mm) cc_final: 0.8666 (tt) REVERT: A 956 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7986 (tt) REVERT: B 25 GLU cc_start: 0.8059 (pp20) cc_final: 0.7790 (pp20) REVERT: C 51 ASP cc_start: 0.8907 (m-30) cc_final: 0.8699 (m-30) REVERT: C 92 LYS cc_start: 0.8241 (mmtt) cc_final: 0.7622 (mmtm) REVERT: C 154 GLN cc_start: 0.8876 (mm110) cc_final: 0.8638 (mm110) REVERT: C 236 ASP cc_start: 0.9226 (t0) cc_final: 0.8914 (t0) REVERT: D 154 MET cc_start: 0.7114 (mmp) cc_final: 0.6431 (ptt) REVERT: E 69 ASP cc_start: 0.8204 (t0) cc_final: 0.7436 (t0) REVERT: E 70 MET cc_start: 0.8942 (ptt) cc_final: 0.8183 (ptt) REVERT: E 71 ASP cc_start: 0.8773 (t70) cc_final: 0.7429 (p0) REVERT: H 5 LYS cc_start: 0.7405 (mptt) cc_final: 0.6028 (tttp) REVERT: H 14 MET cc_start: 0.7952 (tpp) cc_final: 0.7676 (tpp) REVERT: H 96 ASN cc_start: 0.8575 (m-40) cc_final: 0.8054 (t0) REVERT: H 109 GLU cc_start: 0.9298 (mt-10) cc_final: 0.8784 (mt-10) REVERT: H 142 HIS cc_start: 0.6908 (t-90) cc_final: 0.5765 (t-90) REVERT: H 181 GLU cc_start: 0.8360 (mp0) cc_final: 0.8126 (mp0) REVERT: H 188 ASN cc_start: 0.9141 (m110) cc_final: 0.8751 (m110) REVERT: I 151 ASP cc_start: 0.8035 (p0) cc_final: 0.7793 (p0) outliers start: 41 outliers final: 21 residues processed: 205 average time/residue: 0.1403 time to fit residues: 43.5773 Evaluate side-chains 184 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 335 VAL 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 941 ASP Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain B residue 205 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 G residue 63 SER Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain I residue 159 VAL 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: 5.9990 chunk 3 optimal weight: 0.9990 chunk 175 optimal weight: 0.7980 chunk 138 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 199 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 169 optimal weight: 0.0770 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 860 HIS B 193 GLN C 129 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.100550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.069525 restraints weight = 43159.894| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.68 r_work: 0.2941 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 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 = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2911 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= 0.122 Angle : 0.659 13.953 23326 Z= 0.339 Chirality : 0.043 0.212 2625 Planarity : 0.004 0.083 2934 Dihedral : 8.008 102.482 2324 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 1.72 % Allowed : 16.33 % Favored : 81.96 % 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: -1.75 (0.18), residues: 2020 helix: 0.83 (0.20), residues: 689 sheet: -0.50 (0.26), residues: 431 loop : -3.25 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 20 TYR 0.013 0.001 TYR A 793 PHE 0.021 0.001 PHE A 128 TRP 0.021 0.001 TRP A 219 HIS 0.004 0.001 HIS H 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (17211) covalent geometry : angle 0.65227 / 0.34 (23312) SS BOND : bond 0.00129 / 0.07 ( 1) SS BOND : angle 5.03069 / 2.85 ( 2) hydrogen bonds : bond 0.03531 / 2.31 ( 711) hydrogen bonds : angle 4.49213 / 3.10 ( 2010) link_NAG-ASN : bond 0.00442 / 0.22 ( 4) link_NAG-ASN : angle 3.75244 / 2.27 ( 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 218 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 187 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6881 (mtp) cc_final: 0.6457 (mtm) REVERT: A 759 ILE cc_start: 0.8975 (mm) cc_final: 0.8655 (tt) REVERT: B 25 GLU cc_start: 0.7783 (pp20) cc_final: 0.7550 (pp20) REVERT: B 100 MET cc_start: 0.7683 (mmp) cc_final: 0.7392 (mmp) REVERT: C 31 ARG cc_start: 0.8694 (mtm110) cc_final: 0.8490 (ttp80) REVERT: C 51 ASP cc_start: 0.8909 (m-30) cc_final: 0.8658 (m-30) REVERT: C 82 ASN cc_start: 0.7801 (t0) cc_final: 0.7544 (t0) REVERT: C 92 LYS cc_start: 0.8338 (mmtt) cc_final: 0.7741 (mmtm) REVERT: C 236 ASP cc_start: 0.9178 (t0) cc_final: 0.8827 (t0) REVERT: D 51 GLN cc_start: 0.9140 (mm-40) cc_final: 0.8771 (mm110) REVERT: D 172 GLU cc_start: 0.8653 (pp20) cc_final: 0.7987 (pp20) REVERT: E 69 ASP cc_start: 0.8137 (t0) cc_final: 0.7238 (t0) REVERT: E 70 MET cc_start: 0.8880 (ptt) cc_final: 0.8190 (ptt) REVERT: E 71 ASP cc_start: 0.8622 (t70) cc_final: 0.7289 (p0) REVERT: F 85 PHE cc_start: 0.9032 (m-10) cc_final: 0.8768 (m-10) REVERT: H 5 LYS cc_start: 0.7449 (mptt) cc_final: 0.6089 (tttp) REVERT: H 11 TYR cc_start: 0.6978 (t80) cc_final: 0.6732 (t80) REVERT: H 14 MET cc_start: 0.7926 (tpp) cc_final: 0.7604 (tpp) REVERT: H 96 ASN cc_start: 0.8565 (m-40) cc_final: 0.7949 (t0) REVERT: H 109 GLU cc_start: 0.9247 (mt-10) cc_final: 0.8596 (mm-30) REVERT: H 142 HIS cc_start: 0.6812 (t-90) cc_final: 0.5808 (t-90) REVERT: H 188 ASN cc_start: 0.9125 (m110) cc_final: 0.8707 (m110) REVERT: I 151 ASP cc_start: 0.8078 (p0) cc_final: 0.7835 (p0) outliers start: 31 outliers final: 19 residues processed: 211 average time/residue: 0.1327 time to fit residues: 42.4676 Evaluate side-chains 181 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 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 538 MET 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 A residue 988 LEU Chi-restraints excluded: chain B residue 183 MET 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 34 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 176 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 136 optimal weight: 0.5980 chunk 109 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 29 optimal weight: 0.0370 chunk 200 optimal weight: 6.9990 chunk 110 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 GLN C 129 ASN C 154 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.101473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.070509 restraints weight = 43410.255| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.70 r_work: 0.2963 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 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 = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17216 Z= 0.120 Angle : 0.640 13.555 23326 Z= 0.326 Chirality : 0.043 0.183 2625 Planarity : 0.004 0.080 2934 Dihedral : 7.491 100.739 2324 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 1.94 % Allowed : 17.27 % Favored : 80.80 % 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: -1.38 (0.19), residues: 2020 helix: 1.18 (0.21), residues: 691 sheet: -0.35 (0.25), residues: 450 loop : -3.10 (0.18), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 20 TYR 0.013 0.001 TYR E 58 PHE 0.018 0.001 PHE A 128 TRP 0.017 0.001 TRP A 219 HIS 0.004 0.001 HIS A 783 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (17211) covalent geometry : angle 0.63494 / 0.32 (23312) SS BOND : bond 0.00192 / 0.10 ( 1) SS BOND : angle 4.39859 / 2.49 ( 2) hydrogen bonds : bond 0.03197 / 2.10 ( 711) hydrogen bonds : angle 4.26812 / 2.94 ( 2010) link_NAG-ASN : bond 0.00321 / 0.16 ( 4) link_NAG-ASN : angle 3.11781 / 1.93 ( 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 221 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 186 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6872 (mtp) cc_final: 0.6306 (mtm) REVERT: A 759 ILE cc_start: 0.8985 (mm) cc_final: 0.8658 (tt) REVERT: B 100 MET cc_start: 0.7647 (mmp) cc_final: 0.7272 (mmp) REVERT: C 31 ARG cc_start: 0.8682 (mtm110) cc_final: 0.8476 (ttp80) REVERT: C 51 ASP cc_start: 0.8918 (m-30) cc_final: 0.8690 (m-30) REVERT: C 82 ASN cc_start: 0.7939 (t0) cc_final: 0.7637 (t0) REVERT: C 151 MET cc_start: 0.8783 (ptp) cc_final: 0.8581 (mtt) REVERT: C 154 GLN cc_start: 0.8897 (mm110) cc_final: 0.8643 (mm110) REVERT: C 236 ASP cc_start: 0.9190 (t0) cc_final: 0.8800 (t0) REVERT: D 17 TRP cc_start: 0.8910 (m100) cc_final: 0.8673 (m100) REVERT: D 154 MET cc_start: 0.6843 (mmp) cc_final: 0.6231 (ptt) REVERT: D 172 GLU cc_start: 0.8640 (pp20) cc_final: 0.8024 (pp20) REVERT: E 70 MET cc_start: 0.8896 (ptt) cc_final: 0.8252 (ptt) REVERT: E 71 ASP cc_start: 0.8654 (t70) cc_final: 0.8405 (t70) REVERT: H 5 LYS cc_start: 0.7451 (mptt) cc_final: 0.6080 (tttp) REVERT: H 14 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.7547 (tpp) REVERT: H 96 ASN cc_start: 0.8554 (m-40) cc_final: 0.7876 (t0) REVERT: H 109 GLU cc_start: 0.9244 (mt-10) cc_final: 0.8647 (mm-30) REVERT: H 142 HIS cc_start: 0.6690 (t-90) cc_final: 0.5910 (t-90) REVERT: H 188 ASN cc_start: 0.9131 (m110) cc_final: 0.8797 (m-40) REVERT: I 151 ASP cc_start: 0.8085 (p0) cc_final: 0.7847 (p0) outliers start: 35 outliers final: 26 residues processed: 211 average time/residue: 0.1154 time to fit residues: 36.9396 Evaluate side-chains 199 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 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 538 MET 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 B residue 183 MET 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 33 VAL 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 H residue 14 MET Chi-restraints excluded: chain I residue 137 LEU 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: 8.9990 chunk 99 optimal weight: 4.9990 chunk 179 optimal weight: 3.9990 chunk 183 optimal weight: 8.9990 chunk 148 optimal weight: 4.9990 chunk 108 optimal weight: 0.3980 chunk 192 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 168 optimal weight: 9.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 193 GLN C 129 ASN C 247 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.097537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.066221 restraints weight = 43433.518| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.68 r_work: 0.2867 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 17216 Z= 0.265 Angle : 0.720 12.633 23326 Z= 0.369 Chirality : 0.046 0.204 2625 Planarity : 0.005 0.086 2934 Dihedral : 7.660 100.787 2324 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.70 % Favored : 89.30 % Rotamer: Outliers : 2.43 % Allowed : 18.21 % Favored : 79.36 % 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: 0.89 (0.20), residues: 716 sheet: -0.46 (0.25), residues: 455 loop : -3.12 (0.18), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 20 TYR 0.017 0.001 TYR A 938 PHE 0.022 0.002 PHE A 128 TRP 0.013 0.001 TRP A 254 HIS 0.005 0.001 HIS A 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00628 / 0.26 (17211) covalent geometry : angle 0.71554 / 0.37 (23312) SS BOND : bond 0.00176 / 0.09 ( 1) SS BOND : angle 4.82236 / 2.75 ( 2) hydrogen bonds : bond 0.04086 / 2.69 ( 711) hydrogen bonds : angle 4.55266 / 3.13 ( 2010) link_NAG-ASN : bond 0.00348 / 0.17 ( 4) link_NAG-ASN : angle 3.22128 / 1.94 ( 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 223 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 179 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.7018 (mtp) cc_final: 0.6808 (ttm) REVERT: A 550 SER cc_start: 0.9326 (OUTLIER) cc_final: 0.9051 (p) REVERT: A 759 ILE cc_start: 0.9069 (mm) cc_final: 0.8696 (tt) REVERT: B 25 GLU cc_start: 0.7933 (pp20) cc_final: 0.7675 (pp20) REVERT: C 51 ASP cc_start: 0.8959 (m-30) cc_final: 0.8699 (m-30) REVERT: C 82 ASN cc_start: 0.7925 (t0) cc_final: 0.7611 (t0) REVERT: C 236 ASP cc_start: 0.9261 (t0) cc_final: 0.8905 (t0) REVERT: D 17 TRP cc_start: 0.9032 (m100) cc_final: 0.8729 (m100) REVERT: D 154 MET cc_start: 0.6840 (mmp) cc_final: 0.6239 (ptt) REVERT: D 172 GLU cc_start: 0.8683 (pp20) cc_final: 0.8005 (pp20) REVERT: E 70 MET cc_start: 0.8967 (ptt) cc_final: 0.8514 (ptt) REVERT: H 5 LYS cc_start: 0.7535 (mptt) cc_final: 0.6119 (tttp) REVERT: H 96 ASN cc_start: 0.8619 (m-40) cc_final: 0.8131 (t0) REVERT: H 109 GLU cc_start: 0.9301 (mt-10) cc_final: 0.8797 (mm-30) REVERT: H 142 HIS cc_start: 0.6817 (t-90) cc_final: 0.6103 (t-90) REVERT: H 188 ASN cc_start: 0.9180 (m110) cc_final: 0.8839 (m110) REVERT: I 151 ASP cc_start: 0.8144 (p0) cc_final: 0.7892 (p0) outliers start: 44 outliers final: 34 residues processed: 211 average time/residue: 0.1341 time to fit residues: 42.3848 Evaluate side-chains 202 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 167 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 139 SER 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 550 SER 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 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 B residue 183 MET 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 80 THR Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 40 THR 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 176 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 154 GLN C 247 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.099630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.068536 restraints weight = 42825.514| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.66 r_work: 0.2919 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2925 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 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 = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2925 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 17216 Z= 0.130 Angle : 0.655 13.388 23326 Z= 0.335 Chirality : 0.043 0.212 2625 Planarity : 0.004 0.088 2934 Dihedral : 7.377 97.582 2324 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 2.10 % Allowed : 19.04 % Favored : 78.86 % 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: -1.22 (0.19), residues: 2020 helix: 1.12 (0.20), residues: 716 sheet: -0.19 (0.25), residues: 449 loop : -2.99 (0.19), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 20 TYR 0.016 0.001 TYR G 136 PHE 0.018 0.001 PHE A 128 TRP 0.012 0.001 TRP A 219 HIS 0.005 0.001 HIS H 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (17211) covalent geometry : angle 0.65133 / 0.33 (23312) SS BOND : bond 0.00082 / 0.04 ( 1) SS BOND : angle 4.17709 / 2.37 ( 2) hydrogen bonds : bond 0.03304 / 2.17 ( 711) hydrogen bonds : angle 4.27949 / 2.95 ( 2010) link_NAG-ASN : bond 0.00321 / 0.16 ( 4) link_NAG-ASN : angle 2.81871 / 1.73 ( 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 220 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 182 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8470 (tppt) REVERT: A 231 ASP cc_start: 0.8220 (t70) cc_final: 0.7874 (t0) REVERT: A 550 SER cc_start: 0.9056 (OUTLIER) cc_final: 0.8717 (p) REVERT: A 759 ILE cc_start: 0.9034 (mm) cc_final: 0.8711 (tt) REVERT: B 24 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8387 (mt-10) REVERT: C 51 ASP cc_start: 0.8949 (m-30) cc_final: 0.8665 (m-30) REVERT: C 82 ASN cc_start: 0.7980 (t0) cc_final: 0.7636 (t0) REVERT: C 236 ASP cc_start: 0.9237 (t0) cc_final: 0.8863 (t0) REVERT: D 154 MET cc_start: 0.6843 (mmp) cc_final: 0.6261 (ptt) REVERT: D 172 GLU cc_start: 0.8687 (pp20) cc_final: 0.8018 (pp20) REVERT: E 39 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6827 (pp20) REVERT: E 70 MET cc_start: 0.8864 (ptt) cc_final: 0.8444 (ptt) REVERT: H 5 LYS cc_start: 0.7520 (mptt) cc_final: 0.6120 (tttp) REVERT: H 96 ASN cc_start: 0.8566 (m-40) cc_final: 0.8048 (t0) REVERT: H 109 GLU cc_start: 0.9248 (mt-10) cc_final: 0.8751 (mm-30) REVERT: H 142 HIS cc_start: 0.6692 (t-90) cc_final: 0.5904 (t-90) REVERT: H 181 GLU cc_start: 0.8712 (mp0) cc_final: 0.8333 (mp0) REVERT: H 188 ASN cc_start: 0.9152 (m110) cc_final: 0.8846 (m-40) REVERT: I 151 ASP cc_start: 0.8128 (p0) cc_final: 0.7849 (p0) outliers start: 38 outliers final: 29 residues processed: 208 average time/residue: 0.1270 time to fit residues: 39.6993 Evaluate side-chains 200 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 139 SER 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 550 SER 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 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 B residue 183 MET Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain E residue 39 GLU Chi-restraints excluded: chain F residue 25 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 137 LEU Chi-restraints excluded: chain I residue 161 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 77 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 123 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 142 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 247 HIS G 87 HIS H 199 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.098682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.067450 restraints weight = 43245.470| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 3.66 r_work: 0.2895 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 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 = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17216 Z= 0.167 Angle : 0.675 12.503 23326 Z= 0.345 Chirality : 0.044 0.206 2625 Planarity : 0.005 0.087 2934 Dihedral : 7.300 94.950 2324 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 2.32 % Allowed : 18.87 % Favored : 78.80 % 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: -1.21 (0.19), residues: 2020 helix: 1.17 (0.20), residues: 711 sheet: -0.28 (0.25), residues: 455 loop : -2.96 (0.19), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 20 TYR 0.012 0.001 TYR G 136 PHE 0.019 0.001 PHE A 128 TRP 0.011 0.001 TRP G 61 HIS 0.003 0.001 HIS A 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (17211) covalent geometry : angle 0.67021 / 0.34 (23312) SS BOND : bond 0.00356 / 0.19 ( 1) SS BOND : angle 5.08796 / 2.90 ( 2) hydrogen bonds : bond 0.03514 / 2.31 ( 711) hydrogen bonds : angle 4.30708 / 2.97 ( 2010) link_NAG-ASN : bond 0.00277 / 0.14 ( 4) link_NAG-ASN : angle 2.75157 / 1.68 ( 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 216 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 174 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8652 (tptp) REVERT: A 177 MET cc_start: 0.7113 (ttm) cc_final: 0.6736 (mtp) REVERT: A 231 ASP cc_start: 0.8215 (t70) cc_final: 0.7879 (t0) REVERT: A 550 SER cc_start: 0.9153 (OUTLIER) cc_final: 0.8829 (p) REVERT: A 759 ILE cc_start: 0.9057 (mm) cc_final: 0.8694 (tt) REVERT: C 51 ASP cc_start: 0.8886 (m-30) cc_final: 0.8656 (m-30) REVERT: C 82 ASN cc_start: 0.7978 (t0) cc_final: 0.7651 (t0) REVERT: C 236 ASP cc_start: 0.9274 (t0) cc_final: 0.8911 (t0) REVERT: D 51 GLN cc_start: 0.9104 (mm-40) cc_final: 0.8623 (mm110) REVERT: D 154 MET cc_start: 0.6833 (mmp) cc_final: 0.6293 (ptt) REVERT: D 172 GLU cc_start: 0.8691 (pp20) cc_final: 0.8029 (pp20) REVERT: E 39 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6740 (pp20) REVERT: E 70 MET cc_start: 0.8900 (ptt) cc_final: 0.8531 (ptt) REVERT: H 5 LYS cc_start: 0.7497 (mptt) cc_final: 0.6078 (tttp) REVERT: H 96 ASN cc_start: 0.8554 (m-40) cc_final: 0.8040 (t0) REVERT: H 109 GLU cc_start: 0.9269 (mt-10) cc_final: 0.8788 (mm-30) REVERT: H 142 HIS cc_start: 0.6704 (t-90) cc_final: 0.6341 (t-90) REVERT: H 181 GLU cc_start: 0.8691 (mp0) cc_final: 0.8298 (mp0) REVERT: H 188 ASN cc_start: 0.9166 (m110) cc_final: 0.8793 (m110) REVERT: I 151 ASP cc_start: 0.8130 (p0) cc_final: 0.7847 (p0) outliers start: 42 outliers final: 35 residues processed: 204 average time/residue: 0.1359 time to fit residues: 41.7400 Evaluate side-chains 208 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 170 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 139 SER 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 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 550 SER 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 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 B residue 183 MET Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain E residue 39 GLU Chi-restraints excluded: chain E residue 81 PHE Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 33 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 I residue 82 THR Chi-restraints excluded: chain I residue 137 LEU 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: 3.9990 chunk 172 optimal weight: 10.0000 chunk 98 optimal weight: 0.9980 chunk 180 optimal weight: 0.4980 chunk 144 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 167 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 200 optimal weight: 0.0470 chunk 7 optimal weight: 0.9980 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 188 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.100438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.069458 restraints weight = 43012.747| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.66 r_work: 0.2942 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 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 = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17216 Z= 0.119 Angle : 0.655 12.290 23326 Z= 0.333 Chirality : 0.043 0.192 2625 Planarity : 0.005 0.084 2934 Dihedral : 7.058 90.607 2324 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 2.27 % Allowed : 19.37 % Favored : 78.36 % 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: -1.03 (0.19), residues: 2020 helix: 1.34 (0.20), residues: 708 sheet: -0.14 (0.25), residues: 460 loop : -2.90 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 20 TYR 0.015 0.001 TYR H 93 PHE 0.017 0.001 PHE A 128 TRP 0.012 0.001 TRP A 219 HIS 0.003 0.001 HIS A 783 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (17211) covalent geometry : angle 0.65155 / 0.33 (23312) SS BOND : bond 0.00077 / 0.04 ( 1) SS BOND : angle 4.56447 / 2.60 ( 2) hydrogen bonds : bond 0.03094 / 2.04 ( 711) hydrogen bonds : angle 4.15663 / 2.86 ( 2010) link_NAG-ASN : bond 0.00301 / 0.15 ( 4) link_NAG-ASN : angle 2.49264 / 1.54 ( 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 226 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 185 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8475 (tppt) REVERT: A 177 MET cc_start: 0.7103 (ttm) cc_final: 0.6717 (mtp) REVERT: A 550 SER cc_start: 0.8942 (OUTLIER) cc_final: 0.8627 (p) REVERT: A 759 ILE cc_start: 0.9022 (mm) cc_final: 0.8711 (tt) REVERT: B 24 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8319 (mt-10) REVERT: B 163 GLU cc_start: 0.7878 (tt0) cc_final: 0.7664 (tm-30) REVERT: B 288 MET cc_start: 0.8693 (tpt) cc_final: 0.8374 (tpt) REVERT: C 51 ASP cc_start: 0.8885 (m-30) cc_final: 0.8660 (m-30) REVERT: C 82 ASN cc_start: 0.7928 (t0) cc_final: 0.7591 (t0) REVERT: C 236 ASP cc_start: 0.9257 (t0) cc_final: 0.8867 (t0) REVERT: D 51 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8694 (mm-40) REVERT: D 154 MET cc_start: 0.6770 (mmp) cc_final: 0.6262 (ptt) REVERT: D 172 GLU cc_start: 0.8705 (pp20) cc_final: 0.8056 (pp20) REVERT: E 39 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7163 (pp20) REVERT: E 70 MET cc_start: 0.8861 (ptt) cc_final: 0.8464 (ptt) REVERT: H 5 LYS cc_start: 0.7513 (mptt) cc_final: 0.6088 (tttp) REVERT: H 96 ASN cc_start: 0.8518 (m-40) cc_final: 0.8000 (t0) REVERT: H 109 GLU cc_start: 0.9253 (mt-10) cc_final: 0.8780 (mm-30) REVERT: H 142 HIS cc_start: 0.6715 (t-90) cc_final: 0.6343 (t-90) REVERT: H 181 GLU cc_start: 0.8697 (mp0) cc_final: 0.8328 (mp0) REVERT: H 188 ASN cc_start: 0.9116 (m-40) cc_final: 0.8820 (m-40) REVERT: I 151 ASP cc_start: 0.8130 (p0) cc_final: 0.7860 (p0) outliers start: 41 outliers final: 34 residues processed: 212 average time/residue: 0.1225 time to fit residues: 39.4712 Evaluate side-chains 211 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 139 SER 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 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 550 SER Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 662 LEU 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 B residue 182 MET Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain E residue 39 GLU Chi-restraints excluded: chain E residue 81 PHE Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 33 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 161 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 9 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 202 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 187 optimal weight: 10.0000 chunk 161 optimal weight: 0.6980 chunk 182 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 14 optimal weight: 20.0000 chunk 199 optimal weight: 0.3980 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 HIS ** E 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.098341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.067166 restraints weight = 42965.281| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 3.63 r_work: 0.2889 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 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 = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 17216 Z= 0.193 Angle : 0.699 11.861 23326 Z= 0.353 Chirality : 0.045 0.187 2625 Planarity : 0.005 0.083 2934 Dihedral : 7.091 88.506 2324 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.55 % Favored : 89.45 % Rotamer: Outliers : 2.16 % Allowed : 19.48 % Favored : 78.36 % 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: -1.11 (0.19), residues: 2020 helix: 1.26 (0.20), residues: 712 sheet: -0.23 (0.25), residues: 455 loop : -2.90 (0.19), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 20 TYR 0.013 0.001 TYR H 93 PHE 0.018 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/Z covalent geometry : bond 0.00460 / 0.19 (17211) covalent geometry : angle 0.69523 / 0.35 (23312) SS BOND : bond 0.00083 / 0.04 ( 1) SS BOND : angle 4.84234 / 2.76 ( 2) hydrogen bonds : bond 0.03600 / 2.37 ( 711) hydrogen bonds : angle 4.29578 / 2.96 ( 2010) link_NAG-ASN : bond 0.00278 / 0.14 ( 4) link_NAG-ASN : angle 2.61075 / 1.59 ( 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 213 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 174 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8645 (tptp) REVERT: A 177 MET cc_start: 0.7121 (ttm) cc_final: 0.6759 (mtp) REVERT: A 231 ASP cc_start: 0.8232 (t70) cc_final: 0.7910 (t0) REVERT: A 550 SER cc_start: 0.9191 (OUTLIER) cc_final: 0.8896 (p) REVERT: A 759 ILE cc_start: 0.9064 (mm) cc_final: 0.8691 (tt) REVERT: B 163 GLU cc_start: 0.7943 (tt0) cc_final: 0.7730 (tm-30) REVERT: B 288 MET cc_start: 0.8702 (tpt) cc_final: 0.8391 (tpt) REVERT: C 51 ASP cc_start: 0.8887 (m-30) cc_final: 0.8638 (m-30) REVERT: C 236 ASP cc_start: 0.9300 (t0) cc_final: 0.8919 (t0) REVERT: D 154 MET cc_start: 0.6628 (mmp) cc_final: 0.6204 (ptt) REVERT: D 172 GLU cc_start: 0.8685 (pp20) cc_final: 0.8012 (pp20) REVERT: E 39 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7152 (pp20) REVERT: E 70 MET cc_start: 0.8910 (ptt) cc_final: 0.8566 (ptt) REVERT: G 140 MET cc_start: 0.5545 (mmp) cc_final: 0.3792 (tmm) REVERT: H 5 LYS cc_start: 0.7526 (mptt) cc_final: 0.6075 (tttp) REVERT: H 96 ASN cc_start: 0.8570 (m-40) cc_final: 0.8098 (t0) REVERT: H 109 GLU cc_start: 0.9270 (mt-10) cc_final: 0.8804 (mm-30) REVERT: H 142 HIS cc_start: 0.6785 (t-90) cc_final: 0.6408 (t-90) REVERT: H 181 GLU cc_start: 0.8723 (mp0) cc_final: 0.8380 (mp0) REVERT: H 188 ASN cc_start: 0.9127 (m-40) cc_final: 0.8852 (m-40) REVERT: I 151 ASP cc_start: 0.8129 (p0) cc_final: 0.7870 (p0) outliers start: 39 outliers final: 33 residues processed: 200 average time/residue: 0.1217 time to fit residues: 36.8686 Evaluate side-chains 208 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 139 SER 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 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 550 SER Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 662 LEU 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 B residue 183 MET Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain E residue 39 GLU 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 I residue 82 THR 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 89 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 92 optimal weight: 0.0270 chunk 55 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 160 optimal weight: 0.3980 chunk 49 optimal weight: 0.9980 chunk 183 optimal weight: 0.6980 chunk 192 optimal weight: 0.7980 chunk 20 optimal weight: 9.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.100776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.069770 restraints weight = 42925.334| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.66 r_work: 0.2951 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 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 = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17216 Z= 0.116 Angle : 0.664 11.916 23326 Z= 0.335 Chirality : 0.043 0.191 2625 Planarity : 0.005 0.081 2934 Dihedral : 6.806 83.711 2324 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 2.16 % Allowed : 19.92 % Favored : 77.92 % 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: -0.89 (0.19), residues: 2020 helix: 1.44 (0.21), residues: 706 sheet: -0.00 (0.25), residues: 449 loop : -2.80 (0.19), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 20 TYR 0.014 0.001 TYR H 180 PHE 0.017 0.001 PHE A 128 TRP 0.012 0.001 TRP A 219 HIS 0.004 0.001 HIS A 783 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (17211) covalent geometry : angle 0.66069 / 0.33 (23312) SS BOND : bond 0.00009 / 0.00 ( 1) SS BOND : angle 4.32461 / 2.45 ( 2) hydrogen bonds : bond 0.03019 / 1.99 ( 711) hydrogen bonds : angle 4.14282 / 2.85 ( 2010) link_NAG-ASN : bond 0.00324 / 0.16 ( 4) link_NAG-ASN : angle 2.30984 / 1.43 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4680.26 seconds wall clock time: 80 minutes 41.17 seconds (4841.17 seconds total)