Starting phenix.real_space_refine on Thu Feb 5 08:42:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qn8_53239/02_2026/9qn8_53239.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qn8_53239/02_2026/9qn8_53239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qn8_53239/02_2026/9qn8_53239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qn8_53239/02_2026/9qn8_53239.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qn8_53239/02_2026/9qn8_53239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qn8_53239/02_2026/9qn8_53239.map" } resolution = 3.14 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= 0.007 sd= 0.134 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: 7 Type Number sf(0) Gaussians Ca 7 9.91 5 K 7 8.98 5 P 42 5.49 5 S 78 5.16 5 C 9861 2.51 5 N 2802 2.21 5 O 3153 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15950 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 2437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2437 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 308} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 50 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2423 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 305} Chain breaks: 1 Chain: "D" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 128 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 2, 'TRANS': 13} Chain: "E" Number of atoms: 2443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2443 Classifications: {'peptide': 321} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 309} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "F" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 159 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 2, 'TRANS': 17} Chain: "G" Number of atoms: 2452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2452 Classifications: {'peptide': 322} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 310} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 134 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "I" Number of atoms: 2443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2443 Classifications: {'peptide': 321} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 309} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 136 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "K" Number of atoms: 2437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2437 Classifications: {'peptide': 319} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 307} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "L" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "Z" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 421 Classifications: {'DNA': 21} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 20} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' K': 2, ' CA': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' CA': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' CA': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' CA': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' CA': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 65 Unusual residues: {' K': 1, ' CA': 2, 'ATP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 3.54, per 1000 atoms: 0.22 Number of scatterers: 15950 At special positions: 0 Unit cell: (118.8, 122.04, 163.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 7 19.99 K 7 19.00 S 78 16.00 P 42 15.00 O 3153 8.00 N 2802 7.00 C 9861 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 559.9 milliseconds 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3660 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 18 sheets defined 49.8% alpha, 15.3% beta 0 base pairs and 12 stacking pairs defined. Time for finding SS restraints: 2.16 Creating SS restraints... Processing helix chain 'A' and resid 24 through 29 Processing helix chain 'A' and resid 34 through 45 Processing helix chain 'A' and resid 48 through 55 removed outlier: 3.510A pdb=" N ALA A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 63 removed outlier: 3.713A pdb=" N LEU A 60 " --> pdb=" O PRO A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 82 removed outlier: 4.445A pdb=" N LYS A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 97 Processing helix chain 'A' and resid 106 through 114 Processing helix chain 'A' and resid 132 through 144 Processing helix chain 'A' and resid 145 through 146 No H-bonds generated for 'chain 'A' and resid 145 through 146' Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 169 through 178 Processing helix chain 'A' and resid 181 through 188 removed outlier: 3.549A pdb=" N VAL A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 212 Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 237 through 260 Processing helix chain 'A' and resid 288 through 296 removed outlier: 4.094A pdb=" N ILE A 292 " --> pdb=" O GLY A 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 26 No H-bonds generated for 'chain 'C' and resid 24 through 26' Processing helix chain 'C' and resid 27 through 32 removed outlier: 4.169A pdb=" N CYS C 31 " --> pdb=" O ARG C 27 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 27 through 32' Processing helix chain 'C' and resid 36 through 45 removed outlier: 3.572A pdb=" N LYS C 40 " --> pdb=" O ASN C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 55 Processing helix chain 'C' and resid 56 through 63 removed outlier: 3.633A pdb=" N LEU C 60 " --> pdb=" O PRO C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 80 Processing helix chain 'C' and resid 89 through 98 removed outlier: 3.514A pdb=" N GLU C 98 " --> pdb=" O GLN C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 113 Processing helix chain 'C' and resid 132 through 144 Processing helix chain 'C' and resid 145 through 146 No H-bonds generated for 'chain 'C' and resid 145 through 146' Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 167 through 179 removed outlier: 3.914A pdb=" N LEU C 171 " --> pdb=" O ARG C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 188 Processing helix chain 'C' and resid 196 through 211 Processing helix chain 'C' and resid 225 through 232 removed outlier: 3.775A pdb=" N ARG C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N THR C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR C 232 " --> pdb=" O TYR C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 259 Processing helix chain 'C' and resid 288 through 296 removed outlier: 3.933A pdb=" N ILE C 292 " --> pdb=" O GLY C 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 32 removed outlier: 3.559A pdb=" N GLN E 30 " --> pdb=" O ARG E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 45 Processing helix chain 'E' and resid 48 through 54 Processing helix chain 'E' and resid 56 through 63 removed outlier: 3.739A pdb=" N LEU E 60 " --> pdb=" O PRO E 56 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE E 63 " --> pdb=" O GLU E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 80 Processing helix chain 'E' and resid 89 through 97 Processing helix chain 'E' and resid 106 through 114 Processing helix chain 'E' and resid 132 through 144 Processing helix chain 'E' and resid 145 through 146 No H-bonds generated for 'chain 'E' and resid 145 through 146' Processing helix chain 'E' and resid 147 through 151 removed outlier: 3.509A pdb=" N GLY E 151 " --> pdb=" O ILE E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 178 removed outlier: 3.964A pdb=" N LEU E 171 " --> pdb=" O ARG E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 188 Processing helix chain 'E' and resid 196 through 214 removed outlier: 3.841A pdb=" N LEU E 204 " --> pdb=" O GLN E 200 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR E 205 " --> pdb=" O THR E 201 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA E 209 " --> pdb=" O TYR E 205 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER E 214 " --> pdb=" O MET E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 232 removed outlier: 3.579A pdb=" N ARG E 229 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR E 230 " --> pdb=" O ALA E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 260 Processing helix chain 'E' and resid 289 through 296 Processing helix chain 'G' and resid 24 through 29 Processing helix chain 'G' and resid 34 through 45 Processing helix chain 'G' and resid 48 through 54 Processing helix chain 'G' and resid 56 through 63 removed outlier: 3.540A pdb=" N LEU G 60 " --> pdb=" O PRO G 56 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE G 63 " --> pdb=" O GLU G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 82 removed outlier: 3.582A pdb=" N LEU G 81 " --> pdb=" O GLU G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 98 removed outlier: 3.904A pdb=" N GLU G 98 " --> pdb=" O GLN G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 113 Processing helix chain 'G' and resid 132 through 144 Processing helix chain 'G' and resid 145 through 146 No H-bonds generated for 'chain 'G' and resid 145 through 146' Processing helix chain 'G' and resid 147 through 151 Processing helix chain 'G' and resid 167 through 179 removed outlier: 3.836A pdb=" N LEU G 171 " --> pdb=" O ARG G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 188 Processing helix chain 'G' and resid 196 through 214 removed outlier: 4.200A pdb=" N LEU G 204 " --> pdb=" O GLN G 200 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N TYR G 205 " --> pdb=" O THR G 201 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN G 206 " --> pdb=" O GLN G 202 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLU G 213 " --> pdb=" O ALA G 209 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER G 214 " --> pdb=" O MET G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 232 removed outlier: 3.757A pdb=" N ARG G 229 " --> pdb=" O THR G 225 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR G 230 " --> pdb=" O ALA G 226 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR G 232 " --> pdb=" O TYR G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 236 No H-bonds generated for 'chain 'G' and resid 234 through 236' Processing helix chain 'G' and resid 237 through 260 Processing helix chain 'G' and resid 289 through 296 Processing helix chain 'I' and resid 24 through 32 Processing helix chain 'I' and resid 34 through 44 Processing helix chain 'I' and resid 48 through 55 Processing helix chain 'I' and resid 56 through 62 Processing helix chain 'I' and resid 67 through 82 Processing helix chain 'I' and resid 89 through 98 removed outlier: 3.612A pdb=" N GLU I 98 " --> pdb=" O GLN I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 114 Processing helix chain 'I' and resid 132 through 144 Processing helix chain 'I' and resid 167 through 179 removed outlier: 3.967A pdb=" N LEU I 171 " --> pdb=" O ARG I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 188 Processing helix chain 'I' and resid 196 through 212 removed outlier: 4.246A pdb=" N VAL I 212 " --> pdb=" O SER I 208 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 232 removed outlier: 3.647A pdb=" N TYR I 232 " --> pdb=" O TYR I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 260 Processing helix chain 'I' and resid 274 through 279 removed outlier: 3.589A pdb=" N PHE I 279 " --> pdb=" O ALA I 276 " (cutoff:3.500A) Processing helix chain 'I' and resid 288 through 296 removed outlier: 3.946A pdb=" N ILE I 292 " --> pdb=" O GLY I 288 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 32 removed outlier: 3.589A pdb=" N ARG K 27 " --> pdb=" O PRO K 24 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY K 32 " --> pdb=" O GLU K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 45 Processing helix chain 'K' and resid 48 through 54 Processing helix chain 'K' and resid 56 through 63 removed outlier: 3.951A pdb=" N LEU K 60 " --> pdb=" O PRO K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 82 removed outlier: 3.866A pdb=" N LYS K 73 " --> pdb=" O ALA K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 98 removed outlier: 3.653A pdb=" N PHE K 92 " --> pdb=" O THR K 88 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU K 98 " --> pdb=" O GLN K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 114 Processing helix chain 'K' and resid 132 through 144 Processing helix chain 'K' and resid 145 through 146 No H-bonds generated for 'chain 'K' and resid 145 through 146' Processing helix chain 'K' and resid 147 through 151 removed outlier: 3.566A pdb=" N GLY K 151 " --> pdb=" O ILE K 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 167 through 179 removed outlier: 4.106A pdb=" N LEU K 171 " --> pdb=" O ARG K 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 187 Processing helix chain 'K' and resid 196 through 211 Processing helix chain 'K' and resid 226 through 232 removed outlier: 4.049A pdb=" N THR K 230 " --> pdb=" O ALA K 226 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR K 232 " --> pdb=" O TYR K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 234 through 236 No H-bonds generated for 'chain 'K' and resid 234 through 236' Processing helix chain 'K' and resid 237 through 259 removed outlier: 3.527A pdb=" N ARG K 241 " --> pdb=" O GLU K 237 " (cutoff:3.500A) Processing helix chain 'K' and resid 288 through 296 removed outlier: 4.047A pdb=" N ILE K 292 " --> pdb=" O GLY K 288 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 88 removed outlier: 5.594A pdb=" N LYS C 156 " --> pdb=" O TYR C 216 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU C 218 " --> pdb=" O LYS C 156 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA C 217 " --> pdb=" O ALA C 262 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N VAL C 264 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU C 219 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N THR C 266 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL C 221 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N THR C 123 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ASN C 267 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N MET C 125 " --> pdb=" O ASN C 267 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ARG C 299 " --> pdb=" O TYR C 315 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA3, first strand: chain 'A' and resid 189 through 193 removed outlier: 6.685A pdb=" N ALA A 157 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N ALA A 192 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N TYR A 159 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LYS A 156 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU A 218 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ALA A 217 " --> pdb=" O ALA A 262 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N VAL A 264 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU A 219 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N THR A 266 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR A 123 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ASN A 267 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N MET A 125 " --> pdb=" O ASN A 267 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE A 122 " --> pdb=" O THR A 298 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N LEU A 300 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLU A 124 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LEU A 302 " --> pdb=" O GLU A 124 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE A 126 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N LYS A 304 " --> pdb=" O PHE A 126 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ARG A 299 " --> pdb=" O TYR A 315 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 269 through 270 Processing sheet with id=AA5, first strand: chain 'C' and resid 87 through 88 removed outlier: 6.451A pdb=" N ALA E 157 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ALA E 192 " --> pdb=" O ALA E 157 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N TYR E 159 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LYS E 156 " --> pdb=" O TYR E 216 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU E 218 " --> pdb=" O LYS E 156 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA E 217 " --> pdb=" O ALA E 262 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N VAL E 264 " --> pdb=" O ALA E 217 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU E 219 " --> pdb=" O VAL E 264 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N THR E 266 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL E 221 " --> pdb=" O THR E 266 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N THR E 123 " --> pdb=" O ILE E 265 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ASN E 267 " --> pdb=" O THR E 123 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N MET E 125 " --> pdb=" O ASN E 267 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ARG E 299 " --> pdb=" O TYR E 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AA7, first strand: chain 'C' and resid 269 through 271 Processing sheet with id=AA8, first strand: chain 'E' and resid 87 through 88 removed outlier: 6.438A pdb=" N ALA G 157 " --> pdb=" O ALA G 190 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ALA G 192 " --> pdb=" O ALA G 157 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N TYR G 159 " --> pdb=" O ALA G 192 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LYS G 156 " --> pdb=" O TYR G 216 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU G 218 " --> pdb=" O LYS G 156 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ALA G 217 " --> pdb=" O ALA G 262 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL G 264 " --> pdb=" O ALA G 217 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU G 219 " --> pdb=" O VAL G 264 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N THR G 266 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL G 221 " --> pdb=" O THR G 266 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N THR G 123 " --> pdb=" O ILE G 265 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ASN G 267 " --> pdb=" O THR G 123 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N MET G 125 " --> pdb=" O ASN G 267 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE G 122 " --> pdb=" O THR G 298 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU G 300 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLU G 124 " --> pdb=" O LEU G 300 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU G 302 " --> pdb=" O GLU G 124 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N PHE G 126 " --> pdb=" O LEU G 302 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N LYS G 304 " --> pdb=" O PHE G 126 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG G 299 " --> pdb=" O TYR G 315 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 101 through 102 Processing sheet with id=AB1, first strand: chain 'E' and resid 269 through 271 Processing sheet with id=AB2, first strand: chain 'G' and resid 87 through 88 removed outlier: 6.612A pdb=" N ALA I 157 " --> pdb=" O ALA I 190 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N ALA I 192 " --> pdb=" O ALA I 157 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N TYR I 159 " --> pdb=" O ALA I 192 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LYS I 156 " --> pdb=" O LEU I 218 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N ILE I 220 " --> pdb=" O LYS I 156 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N MET I 158 " --> pdb=" O ILE I 220 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ASP I 222 " --> pdb=" O MET I 158 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ILE I 160 " --> pdb=" O ASP I 222 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA I 262 " --> pdb=" O ALA I 217 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ARG I 299 " --> pdb=" O TYR I 315 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 101 through 102 Processing sheet with id=AB4, first strand: chain 'G' and resid 269 through 271 Processing sheet with id=AB5, first strand: chain 'I' and resid 87 through 88 removed outlier: 6.432A pdb=" N ALA K 157 " --> pdb=" O ALA K 190 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N ALA K 192 " --> pdb=" O ALA K 157 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N TYR K 159 " --> pdb=" O ALA K 192 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU K 219 " --> pdb=" O VAL K 264 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N THR K 266 " --> pdb=" O LEU K 219 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL K 221 " --> pdb=" O THR K 266 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY K 127 " --> pdb=" O ASN K 267 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ARG K 299 " --> pdb=" O TYR K 315 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 101 through 102 Processing sheet with id=AB7, first strand: chain 'I' and resid 269 through 271 Processing sheet with id=AB8, first strand: chain 'K' and resid 101 through 102 Processing sheet with id=AB9, first strand: chain 'K' and resid 269 through 271 734 hydrogen bonds defined for protein. 2040 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 12 stacking parallelities Total time for adding SS restraints: 2.71 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4520 1.33 - 1.45: 2449 1.45 - 1.57: 9039 1.57 - 1.69: 76 1.69 - 1.81: 126 Bond restraints: 16210 Sorted by residual: bond pdb=" CB ASN K 36 " pdb=" CG ASN K 36 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.25e+00 bond pdb=" CB GLU E 176 " pdb=" CG GLU E 176 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.13e+00 bond pdb=" CB GLN A 202 " pdb=" CG GLN A 202 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.12e+00 bond pdb=" CB GLU I 308 " pdb=" CG GLU I 308 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.38e-01 bond pdb=" CB GLU E 59 " pdb=" CG GLU E 59 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.73e-01 ... (remaining 16205 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 21668 1.62 - 3.24: 295 3.24 - 4.86: 26 4.86 - 6.48: 10 6.48 - 8.11: 4 Bond angle restraints: 22003 Sorted by residual: angle pdb=" CA GLU E 176 " pdb=" CB GLU E 176 " pdb=" CG GLU E 176 " ideal model delta sigma weight residual 114.10 119.86 -5.76 2.00e+00 2.50e-01 8.30e+00 angle pdb=" CB LYS K 39 " pdb=" CG LYS K 39 " pdb=" CD LYS K 39 " ideal model delta sigma weight residual 111.30 117.73 -6.43 2.30e+00 1.89e-01 7.82e+00 angle pdb=" N VAL A 273 " pdb=" CA VAL A 273 " pdb=" C VAL A 273 " ideal model delta sigma weight residual 112.29 109.86 2.43 9.40e-01 1.13e+00 6.67e+00 angle pdb=" CB GLU E 176 " pdb=" CG GLU E 176 " pdb=" CD GLU E 176 " ideal model delta sigma weight residual 112.60 116.84 -4.24 1.70e+00 3.46e-01 6.21e+00 angle pdb=" CA GLU K 59 " pdb=" CB GLU K 59 " pdb=" CG GLU K 59 " ideal model delta sigma weight residual 114.10 119.01 -4.91 2.00e+00 2.50e-01 6.02e+00 ... (remaining 21998 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 8360 17.92 - 35.84: 1124 35.84 - 53.76: 322 53.76 - 71.68: 91 71.68 - 89.60: 22 Dihedral angle restraints: 9919 sinusoidal: 4209 harmonic: 5710 Sorted by residual: dihedral pdb=" CB GLU I 237 " pdb=" CG GLU I 237 " pdb=" CD GLU I 237 " pdb=" OE1 GLU I 237 " ideal model delta sinusoidal sigma weight residual 0.00 89.60 -89.60 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU A 42 " pdb=" CG GLU A 42 " pdb=" CD GLU A 42 " pdb=" OE1 GLU A 42 " ideal model delta sinusoidal sigma weight residual 0.00 88.87 -88.87 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU I 176 " pdb=" CG GLU I 176 " pdb=" CD GLU I 176 " pdb=" OE1 GLU I 176 " ideal model delta sinusoidal sigma weight residual 0.00 88.84 -88.84 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 9916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1631 0.028 - 0.057: 573 0.057 - 0.085: 159 0.085 - 0.113: 125 0.113 - 0.142: 18 Chirality restraints: 2506 Sorted by residual: chirality pdb=" CA ILE C 33 " pdb=" N ILE C 33 " pdb=" C ILE C 33 " pdb=" CB ILE C 33 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA ILE G 160 " pdb=" N ILE G 160 " pdb=" C ILE G 160 " pdb=" CB ILE G 160 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA ILE K 66 " pdb=" N ILE K 66 " pdb=" C ILE K 66 " pdb=" CB ILE K 66 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 2503 not shown) Planarity restraints: 2764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 282 " 0.038 5.00e-02 4.00e+02 5.79e-02 5.37e+00 pdb=" N PRO E 283 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO E 283 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 283 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 282 " -0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO A 283 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 283 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 283 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE K 248 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.30e+00 pdb=" C PHE K 248 " 0.026 2.00e-02 2.50e+03 pdb=" O PHE K 248 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU K 249 " -0.009 2.00e-02 2.50e+03 ... (remaining 2761 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.92: 6268 2.92 - 3.47: 17242 3.47 - 4.03: 28101 4.03 - 4.58: 41011 4.58 - 5.14: 59001 Nonbonded interactions: 151623 Sorted by model distance: nonbonded pdb=" O1G ATP K 401 " pdb="CA CA K 403 " model vdw 2.361 2.510 nonbonded pdb=" OG1 THR A 134 " pdb="CA CA A 402 " model vdw 2.362 2.510 nonbonded pdb=" O3G ATP A 401 " pdb="CA CA A 402 " model vdw 2.382 2.510 nonbonded pdb=" OG1 THR K 134 " pdb="CA CA K 403 " model vdw 2.386 2.510 nonbonded pdb=" O1G ATP A 401 " pdb="CA CA A 402 " model vdw 2.391 2.510 ... (remaining 151618 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 275 or resid 282 through 401)) selection = (chain 'C' and (resid 20 through 275 or resid 282 through 401)) selection = (chain 'E' and (resid 20 through 275 or resid 282 through 401)) selection = (chain 'G' and (resid 20 through 275 or resid 282 through 401)) selection = (chain 'I' and (resid 20 through 275 or resid 282 through 401)) selection = (chain 'K' and (resid 20 through 275 or resid 282 through 401)) } ncs_group { reference = (chain 'B' and resid 333 through 338) selection = (chain 'L' and ((resid 333 and (name N or name CA or name C or name O or name CB \ )) or resid 334 through 338)) } ncs_group { reference = (chain 'D' and resid 332 through 346) selection = (chain 'H' and resid 332 through 346) selection = (chain 'J' and resid 332 through 346) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.990 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 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 : 0.002 0.035 16210 Z= 0.100 Angle : 0.466 8.106 22003 Z= 0.250 Chirality : 0.037 0.142 2506 Planarity : 0.003 0.058 2764 Dihedral : 18.224 89.603 6259 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.38 % Allowed : 25.47 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % Twisted Proline : 0.00 % 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: 0.25 (0.19), residues: 1976 helix: 0.98 (0.18), residues: 868 sheet: 0.78 (0.32), residues: 294 loop : -0.92 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 306 TYR 0.016 0.001 TYR K 191 PHE 0.007 0.001 PHE C 126 HIS 0.001 0.000 HIS C 47 Details of bonding type rmsd covalent geometry : bond 0.00207 (16210) covalent geometry : angle 0.46560 (22003) hydrogen bonds : bond 0.12735 ( 734) hydrogen bonds : angle 5.89283 ( 2040) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 175 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: A 191 TYR cc_start: 0.8890 (t80) cc_final: 0.8596 (t80) REVERT: C 43 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7444 (mp0) REVERT: E 98 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8241 (mt-10) REVERT: E 216 TYR cc_start: 0.8675 (m-80) cc_final: 0.8255 (m-80) REVERT: E 235 ARG cc_start: 0.7964 (ptp90) cc_final: 0.7051 (ttp80) REVERT: G 29 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7621 (mm-30) REVERT: G 158 MET cc_start: 0.9114 (mtp) cc_final: 0.8823 (ttm) REVERT: G 251 MET cc_start: 0.8831 (tpp) cc_final: 0.8359 (tpp) REVERT: I 213 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7762 (tm-30) REVERT: K 158 MET cc_start: 0.8512 (ttm) cc_final: 0.8186 (mtp) REVERT: K 211 MET cc_start: 0.8363 (ttt) cc_final: 0.8157 (ttm) outliers start: 6 outliers final: 5 residues processed: 179 average time/residue: 0.1503 time to fit residues: 38.9417 Evaluate side-chains 177 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 172 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain F residue 333 ARG Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain I residue 230 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.126093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.097140 restraints weight = 25148.763| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.59 r_work: 0.3103 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.0751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16210 Z= 0.187 Angle : 0.495 7.021 22003 Z= 0.267 Chirality : 0.039 0.143 2506 Planarity : 0.003 0.044 2764 Dihedral : 12.592 88.429 2646 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.09 % Allowed : 23.77 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % Twisted Proline : 0.00 % 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: 0.37 (0.19), residues: 1976 helix: 1.15 (0.18), residues: 885 sheet: 0.74 (0.31), residues: 304 loop : -0.96 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 306 TYR 0.019 0.001 TYR C 315 PHE 0.010 0.001 PHE I 248 HIS 0.003 0.001 HIS G 138 Details of bonding type rmsd covalent geometry : bond 0.00440 (16210) covalent geometry : angle 0.49506 (22003) hydrogen bonds : bond 0.04123 ( 734) hydrogen bonds : angle 4.59700 ( 2040) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 167 time to evaluate : 0.609 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.7807 (mtp) REVERT: A 191 TYR cc_start: 0.8842 (t80) cc_final: 0.8595 (t80) REVERT: C 99 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7992 (tt) REVERT: E 98 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8313 (mt-10) REVERT: G 158 MET cc_start: 0.8991 (mtp) cc_final: 0.8558 (mtp) REVERT: G 251 MET cc_start: 0.8837 (tpp) cc_final: 0.8333 (tpp) REVERT: I 77 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7193 (mt-10) REVERT: K 80 LYS cc_start: 0.8532 (ptpt) cc_final: 0.8209 (ptpp) REVERT: K 158 MET cc_start: 0.8288 (ttm) cc_final: 0.7894 (mtp) REVERT: K 211 MET cc_start: 0.8432 (ttt) cc_final: 0.8228 (ttt) REVERT: L 336 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6495 (mp) outliers start: 49 outliers final: 30 residues processed: 201 average time/residue: 0.1494 time to fit residues: 43.6547 Evaluate side-chains 196 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 163 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 313 LYS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain F residue 333 ARG Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain G residue 31 CYS Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 243 MET Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain I residue 63 ILE Chi-restraints excluded: chain I residue 64 LYS Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 219 LEU Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 125 MET Chi-restraints excluded: chain K residue 336 ASP Chi-restraints excluded: chain L residue 336 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 122 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 chunk 181 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.127032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.098602 restraints weight = 25358.380| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.56 r_work: 0.3101 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.0819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16210 Z= 0.128 Angle : 0.447 6.870 22003 Z= 0.242 Chirality : 0.038 0.142 2506 Planarity : 0.003 0.037 2764 Dihedral : 12.522 89.638 2645 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.09 % Allowed : 23.96 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % Twisted Proline : 0.00 % 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: 0.50 (0.19), residues: 1976 helix: 1.31 (0.18), residues: 884 sheet: 0.74 (0.30), residues: 306 loop : -0.95 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 27 TYR 0.012 0.001 TYR C 315 PHE 0.007 0.001 PHE K 126 HIS 0.002 0.000 HIS E 294 Details of bonding type rmsd covalent geometry : bond 0.00294 (16210) covalent geometry : angle 0.44742 (22003) hydrogen bonds : bond 0.03378 ( 734) hydrogen bonds : angle 4.28728 ( 2040) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 173 time to evaluate : 0.608 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.7816 (mtp) REVERT: A 191 TYR cc_start: 0.8865 (t80) cc_final: 0.8639 (t80) REVERT: C 40 LYS cc_start: 0.7848 (tttt) cc_final: 0.7389 (tttt) REVERT: C 43 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7512 (mp0) REVERT: C 247 ARG cc_start: 0.8778 (ttm-80) cc_final: 0.8486 (mtp180) REVERT: E 98 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8209 (mt-10) REVERT: E 235 ARG cc_start: 0.7707 (ttp80) cc_final: 0.7325 (ttt-90) REVERT: G 158 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.8527 (mtp) REVERT: G 251 MET cc_start: 0.8821 (tpp) cc_final: 0.8308 (tpp) REVERT: I 60 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8411 (mm) REVERT: I 77 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7208 (mt-10) REVERT: K 80 LYS cc_start: 0.8486 (ptpt) cc_final: 0.8164 (ptpp) REVERT: K 158 MET cc_start: 0.8305 (ttm) cc_final: 0.7941 (mtp) REVERT: K 211 MET cc_start: 0.8377 (ttt) cc_final: 0.8172 (ttt) REVERT: K 229 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8559 (ttt180) REVERT: K 243 MET cc_start: 0.8803 (mtp) cc_final: 0.8600 (mtp) outliers start: 49 outliers final: 31 residues processed: 210 average time/residue: 0.1482 time to fit residues: 44.7742 Evaluate side-chains 202 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 167 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 313 LYS Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain F residue 329 ASN Chi-restraints excluded: chain F residue 333 ARG Chi-restraints excluded: chain G residue 31 CYS Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 243 MET Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain H residue 332 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 144 CYS Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain K residue 37 ASP Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 70 LYS Chi-restraints excluded: chain K residue 125 MET Chi-restraints excluded: chain K residue 229 ARG Chi-restraints excluded: chain K residue 284 LYS Chi-restraints excluded: chain K residue 336 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 75 optimal weight: 1.9990 chunk 96 optimal weight: 20.0000 chunk 149 optimal weight: 3.9990 chunk 191 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 137 optimal weight: 0.4980 chunk 139 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 147 optimal weight: 3.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.125946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.097233 restraints weight = 25172.614| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.57 r_work: 0.3083 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16210 Z= 0.154 Angle : 0.466 7.348 22003 Z= 0.251 Chirality : 0.038 0.141 2506 Planarity : 0.003 0.037 2764 Dihedral : 12.597 89.347 2643 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.97 % Allowed : 23.71 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % Twisted Proline : 0.00 % 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: 0.47 (0.19), residues: 1976 helix: 1.35 (0.18), residues: 872 sheet: 0.69 (0.30), residues: 306 loop : -0.99 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 27 TYR 0.015 0.001 TYR C 315 PHE 0.009 0.001 PHE I 248 HIS 0.003 0.000 HIS E 294 Details of bonding type rmsd covalent geometry : bond 0.00361 (16210) covalent geometry : angle 0.46577 (22003) hydrogen bonds : bond 0.03611 ( 734) hydrogen bonds : angle 4.28131 ( 2040) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 172 time to evaluate : 0.578 Fit side-chains REVERT: A 84 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.7851 (mtp) REVERT: C 40 LYS cc_start: 0.7843 (tttt) cc_final: 0.7458 (tttt) REVERT: C 43 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7549 (mp0) REVERT: C 99 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7975 (tt) REVERT: C 184 ASP cc_start: 0.8703 (t0) cc_final: 0.8257 (t0) REVERT: C 247 ARG cc_start: 0.8811 (ttm-80) cc_final: 0.8510 (mtp180) REVERT: E 98 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8256 (mt-10) REVERT: E 235 ARG cc_start: 0.7790 (ttp80) cc_final: 0.7358 (ttt-90) REVERT: G 158 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8536 (mtp) REVERT: G 251 MET cc_start: 0.8805 (tpp) cc_final: 0.8316 (tpp) REVERT: I 60 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8416 (mm) REVERT: I 77 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7295 (mt-10) REVERT: K 80 LYS cc_start: 0.8488 (ptpt) cc_final: 0.8258 (ptmm) REVERT: K 158 MET cc_start: 0.8316 (ttm) cc_final: 0.7928 (mtp) REVERT: K 229 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8536 (ttt180) REVERT: K 315 TYR cc_start: 0.9202 (OUTLIER) cc_final: 0.8993 (t80) REVERT: L 336 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6539 (mp) outliers start: 63 outliers final: 42 residues processed: 221 average time/residue: 0.1346 time to fit residues: 43.1101 Evaluate side-chains 217 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 168 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 313 LYS Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain F residue 329 ASN Chi-restraints excluded: chain F residue 333 ARG Chi-restraints excluded: chain G residue 31 CYS Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 243 MET Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain H residue 332 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 63 ILE Chi-restraints excluded: chain I residue 64 LYS Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 144 CYS Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 219 LEU Chi-restraints excluded: chain I residue 223 SER Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain K residue 37 ASP Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 70 LYS Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 125 MET Chi-restraints excluded: chain K residue 204 LEU Chi-restraints excluded: chain K residue 229 ARG Chi-restraints excluded: chain K residue 284 LYS Chi-restraints excluded: chain K residue 315 TYR Chi-restraints excluded: chain K residue 336 ASP Chi-restraints excluded: chain L residue 336 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 181 optimal weight: 9.9990 chunk 127 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 119 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 156 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.125526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.096988 restraints weight = 25100.904| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.56 r_work: 0.3076 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16210 Z= 0.163 Angle : 0.478 8.348 22003 Z= 0.258 Chirality : 0.039 0.141 2506 Planarity : 0.003 0.038 2764 Dihedral : 12.646 89.900 2643 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.35 % Allowed : 23.83 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % Twisted Proline : 0.00 % 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: 0.43 (0.19), residues: 1976 helix: 1.33 (0.18), residues: 873 sheet: 0.69 (0.30), residues: 305 loop : -1.05 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 27 TYR 0.014 0.001 TYR C 315 PHE 0.009 0.001 PHE I 248 HIS 0.003 0.001 HIS E 294 Details of bonding type rmsd covalent geometry : bond 0.00383 (16210) covalent geometry : angle 0.47809 (22003) hydrogen bonds : bond 0.03648 ( 734) hydrogen bonds : angle 4.27717 ( 2040) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 171 time to evaluate : 0.509 Fit side-chains REVERT: A 84 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.7859 (mtp) REVERT: C 40 LYS cc_start: 0.7923 (tttt) cc_final: 0.7555 (tttt) REVERT: C 43 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7513 (mp0) REVERT: C 99 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.7970 (tt) REVERT: C 184 ASP cc_start: 0.8694 (t0) cc_final: 0.8269 (t0) REVERT: C 247 ARG cc_start: 0.8816 (ttm-80) cc_final: 0.8519 (mtp180) REVERT: E 33 ILE cc_start: 0.8442 (mm) cc_final: 0.7906 (mm) REVERT: E 37 ASP cc_start: 0.7760 (m-30) cc_final: 0.7480 (p0) REVERT: E 98 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8212 (mt-10) REVERT: E 235 ARG cc_start: 0.7828 (ttp80) cc_final: 0.7381 (ttt-90) REVERT: G 98 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6843 (pm20) REVERT: G 158 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8544 (mtp) REVERT: G 251 MET cc_start: 0.8803 (tpp) cc_final: 0.8325 (tpp) REVERT: I 60 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8433 (mm) REVERT: I 77 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7299 (mt-10) REVERT: K 80 LYS cc_start: 0.8494 (ptpt) cc_final: 0.8258 (ptmm) REVERT: K 229 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8532 (ttt180) REVERT: L 336 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6556 (mp) outliers start: 69 outliers final: 47 residues processed: 225 average time/residue: 0.1416 time to fit residues: 45.7704 Evaluate side-chains 219 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 165 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 313 LYS Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain F residue 329 ASN Chi-restraints excluded: chain F residue 333 ARG Chi-restraints excluded: chain G residue 31 CYS Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 98 GLU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 243 MET Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain H residue 332 LEU Chi-restraints excluded: chain I residue 23 GLN Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 63 ILE Chi-restraints excluded: chain I residue 64 LYS Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 144 CYS Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 219 LEU Chi-restraints excluded: chain I residue 223 SER Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain K residue 37 ASP Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 70 LYS Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 125 MET Chi-restraints excluded: chain K residue 204 LEU Chi-restraints excluded: chain K residue 229 ARG Chi-restraints excluded: chain K residue 284 LYS Chi-restraints excluded: chain K residue 336 ASP Chi-restraints excluded: chain L residue 336 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 90 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 187 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.124228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.096155 restraints weight = 25166.431| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.52 r_work: 0.3069 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16210 Z= 0.185 Angle : 0.501 8.194 22003 Z= 0.269 Chirality : 0.039 0.141 2506 Planarity : 0.003 0.039 2764 Dihedral : 12.748 89.001 2643 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.48 % Allowed : 23.52 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % Twisted Proline : 0.00 % 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: 0.33 (0.19), residues: 1976 helix: 1.28 (0.18), residues: 871 sheet: 0.73 (0.31), residues: 288 loop : -1.13 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 27 TYR 0.015 0.001 TYR C 315 PHE 0.010 0.001 PHE I 248 HIS 0.003 0.001 HIS E 294 Details of bonding type rmsd covalent geometry : bond 0.00438 (16210) covalent geometry : angle 0.50135 (22003) hydrogen bonds : bond 0.03901 ( 734) hydrogen bonds : angle 4.34617 ( 2040) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 164 time to evaluate : 0.633 Fit side-chains REVERT: A 84 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.7868 (mtp) REVERT: C 99 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.8044 (tt) REVERT: C 184 ASP cc_start: 0.8702 (t0) cc_final: 0.8393 (t0) REVERT: C 247 ARG cc_start: 0.8766 (ttm-80) cc_final: 0.8474 (mtp180) REVERT: E 33 ILE cc_start: 0.8512 (mm) cc_final: 0.8139 (mm) REVERT: E 98 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8259 (mt-10) REVERT: E 235 ARG cc_start: 0.7894 (ttp80) cc_final: 0.7450 (ttt-90) REVERT: G 158 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8573 (mtp) REVERT: G 213 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8515 (pm20) REVERT: G 251 MET cc_start: 0.8827 (tpp) cc_final: 0.8366 (tpp) REVERT: I 60 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8448 (mm) REVERT: I 77 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7320 (mt-10) REVERT: K 80 LYS cc_start: 0.8480 (ptpt) cc_final: 0.8244 (ptmm) REVERT: K 229 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.7544 (ttp-170) REVERT: K 315 TYR cc_start: 0.9212 (OUTLIER) cc_final: 0.8790 (t80) REVERT: L 336 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6585 (mp) outliers start: 71 outliers final: 51 residues processed: 222 average time/residue: 0.1393 time to fit residues: 44.8091 Evaluate side-chains 220 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 161 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 313 LYS Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 346 HIS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain F residue 329 ASN Chi-restraints excluded: chain F residue 333 ARG Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain G residue 31 CYS Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 213 GLU Chi-restraints excluded: chain G residue 243 MET Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain H residue 332 LEU Chi-restraints excluded: chain I residue 23 GLN Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 63 ILE Chi-restraints excluded: chain I residue 64 LYS Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 144 CYS Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 223 SER Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain K residue 37 ASP Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 70 LYS Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 125 MET Chi-restraints excluded: chain K residue 229 ARG Chi-restraints excluded: chain K residue 284 LYS Chi-restraints excluded: chain K residue 315 TYR Chi-restraints excluded: chain K residue 336 ASP Chi-restraints excluded: chain L residue 336 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 64 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 180 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 196 optimal weight: 5.9990 chunk 193 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.127554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.099325 restraints weight = 24905.653| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.54 r_work: 0.3110 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16210 Z= 0.099 Angle : 0.444 9.930 22003 Z= 0.239 Chirality : 0.037 0.142 2506 Planarity : 0.003 0.036 2764 Dihedral : 12.530 88.674 2643 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.03 % Allowed : 25.16 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % Twisted Proline : 0.00 % 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: 0.52 (0.19), residues: 1976 helix: 1.44 (0.18), residues: 873 sheet: 0.84 (0.31), residues: 289 loop : -1.05 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 27 TYR 0.008 0.001 TYR A 191 PHE 0.007 0.001 PHE K 126 HIS 0.002 0.000 HIS C 47 Details of bonding type rmsd covalent geometry : bond 0.00219 (16210) covalent geometry : angle 0.44410 (22003) hydrogen bonds : bond 0.02853 ( 734) hydrogen bonds : angle 4.03149 ( 2040) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 170 time to evaluate : 0.637 Fit side-chains REVERT: A 84 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.7770 (mtp) REVERT: A 98 GLU cc_start: 0.7787 (pt0) cc_final: 0.7527 (mm-30) REVERT: C 40 LYS cc_start: 0.8027 (tttt) cc_final: 0.7679 (tttt) REVERT: C 43 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7572 (mp0) REVERT: C 158 MET cc_start: 0.8608 (mtp) cc_final: 0.8341 (ttm) REVERT: C 184 ASP cc_start: 0.8750 (t0) cc_final: 0.8302 (t0) REVERT: C 247 ARG cc_start: 0.8793 (ttm-80) cc_final: 0.8523 (mtp180) REVERT: E 98 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8254 (mt-10) REVERT: E 235 ARG cc_start: 0.7739 (ttp80) cc_final: 0.7279 (ttt-90) REVERT: F 329 ASN cc_start: 0.5720 (OUTLIER) cc_final: 0.5239 (m110) REVERT: G 158 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8694 (mtp) REVERT: G 251 MET cc_start: 0.8787 (tpp) cc_final: 0.8315 (tpp) REVERT: I 60 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8451 (mm) REVERT: I 77 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7333 (mt-10) REVERT: K 80 LYS cc_start: 0.8504 (ptpt) cc_final: 0.8260 (ptmm) REVERT: K 211 MET cc_start: 0.8380 (ttt) cc_final: 0.8165 (ttt) REVERT: K 229 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8538 (ttt180) outliers start: 48 outliers final: 34 residues processed: 209 average time/residue: 0.1347 time to fit residues: 40.3563 Evaluate side-chains 203 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 164 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 313 LYS Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain F residue 329 ASN Chi-restraints excluded: chain F residue 333 ARG Chi-restraints excluded: chain G residue 31 CYS Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 243 MET Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 306 ARG Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 144 CYS Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 219 LEU Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain K residue 37 ASP Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 125 MET Chi-restraints excluded: chain K residue 204 LEU Chi-restraints excluded: chain K residue 229 ARG Chi-restraints excluded: chain K residue 336 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 191 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 194 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.126086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.097699 restraints weight = 25145.266| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.55 r_work: 0.3107 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16210 Z= 0.142 Angle : 0.469 9.272 22003 Z= 0.252 Chirality : 0.038 0.140 2506 Planarity : 0.003 0.036 2764 Dihedral : 12.581 89.596 2643 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.09 % Allowed : 25.16 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % Twisted Proline : 0.00 % 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: 0.48 (0.19), residues: 1976 helix: 1.41 (0.18), residues: 872 sheet: 0.86 (0.31), residues: 287 loop : -1.09 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 27 TYR 0.016 0.001 TYR K 191 PHE 0.008 0.001 PHE I 248 HIS 0.002 0.000 HIS E 294 Details of bonding type rmsd covalent geometry : bond 0.00331 (16210) covalent geometry : angle 0.46858 (22003) hydrogen bonds : bond 0.03359 ( 734) hydrogen bonds : angle 4.11071 ( 2040) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 165 time to evaluate : 0.794 Fit side-chains REVERT: A 84 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.7801 (mtp) REVERT: C 40 LYS cc_start: 0.7930 (tttt) cc_final: 0.7499 (tttt) REVERT: C 43 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7515 (mp0) REVERT: C 158 MET cc_start: 0.8653 (mtp) cc_final: 0.8346 (ttm) REVERT: C 184 ASP cc_start: 0.8785 (t0) cc_final: 0.8330 (t0) REVERT: C 247 ARG cc_start: 0.8791 (ttm-80) cc_final: 0.8496 (mtp180) REVERT: E 98 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8236 (mt-10) REVERT: E 235 ARG cc_start: 0.7787 (ttp80) cc_final: 0.7285 (ttt-90) REVERT: G 158 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8758 (mtp) REVERT: G 251 MET cc_start: 0.8768 (tpp) cc_final: 0.8315 (tpp) REVERT: I 60 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8379 (mm) REVERT: I 77 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7327 (mt-10) REVERT: K 80 LYS cc_start: 0.8518 (ptpt) cc_final: 0.8273 (ptmm) REVERT: K 211 MET cc_start: 0.8386 (ttt) cc_final: 0.8155 (ttt) REVERT: K 229 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8532 (ttt180) REVERT: L 336 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6455 (mp) outliers start: 49 outliers final: 40 residues processed: 204 average time/residue: 0.1440 time to fit residues: 42.4856 Evaluate side-chains 207 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 162 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 313 LYS Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 346 HIS Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain F residue 329 ASN Chi-restraints excluded: chain F residue 333 ARG Chi-restraints excluded: chain G residue 31 CYS Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 243 MET Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 306 ARG Chi-restraints excluded: chain H residue 332 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 144 CYS Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain K residue 37 ASP Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 70 LYS Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 125 MET Chi-restraints excluded: chain K residue 204 LEU Chi-restraints excluded: chain K residue 229 ARG Chi-restraints excluded: chain K residue 336 ASP Chi-restraints excluded: chain L residue 336 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 70 optimal weight: 4.9990 chunk 184 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 172 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 154 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.124643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.096160 restraints weight = 25186.424| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.55 r_work: 0.3067 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16210 Z= 0.186 Angle : 0.506 8.922 22003 Z= 0.271 Chirality : 0.039 0.142 2506 Planarity : 0.003 0.037 2764 Dihedral : 12.744 87.999 2643 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.15 % Allowed : 25.03 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % Twisted Proline : 0.00 % 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: 0.35 (0.19), residues: 1976 helix: 1.29 (0.18), residues: 873 sheet: 0.81 (0.31), residues: 287 loop : -1.16 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 27 TYR 0.016 0.001 TYR K 191 PHE 0.011 0.001 PHE I 248 HIS 0.003 0.001 HIS E 294 Details of bonding type rmsd covalent geometry : bond 0.00442 (16210) covalent geometry : angle 0.50633 (22003) hydrogen bonds : bond 0.03848 ( 734) hydrogen bonds : angle 4.28507 ( 2040) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 165 time to evaluate : 0.557 Fit side-chains REVERT: A 84 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.7918 (mtp) REVERT: C 40 LYS cc_start: 0.7979 (tttt) cc_final: 0.7587 (tttt) REVERT: C 43 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7527 (mp0) REVERT: C 99 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.7987 (tt) REVERT: C 158 MET cc_start: 0.8616 (mtp) cc_final: 0.8315 (ttm) REVERT: C 184 ASP cc_start: 0.8788 (t0) cc_final: 0.8419 (t0) REVERT: C 247 ARG cc_start: 0.8794 (ttm-80) cc_final: 0.8493 (mtp180) REVERT: E 33 ILE cc_start: 0.8612 (mm) cc_final: 0.8062 (mm) REVERT: E 37 ASP cc_start: 0.7530 (m-30) cc_final: 0.7266 (p0) REVERT: E 98 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8234 (mt-10) REVERT: E 235 ARG cc_start: 0.7846 (ttp80) cc_final: 0.7342 (ttt-90) REVERT: G 251 MET cc_start: 0.8788 (tpp) cc_final: 0.8336 (tpp) REVERT: I 60 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8383 (mm) REVERT: I 77 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7358 (mt-10) REVERT: K 80 LYS cc_start: 0.8523 (ptpt) cc_final: 0.8282 (ptmm) REVERT: K 211 MET cc_start: 0.8457 (ttt) cc_final: 0.8241 (ttt) REVERT: K 229 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8519 (ttt180) REVERT: L 336 LEU cc_start: 0.7137 (OUTLIER) cc_final: 0.6477 (mp) outliers start: 50 outliers final: 43 residues processed: 206 average time/residue: 0.1301 time to fit residues: 38.6362 Evaluate side-chains 210 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 162 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 313 LYS Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 346 HIS Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain F residue 329 ASN Chi-restraints excluded: chain F residue 333 ARG Chi-restraints excluded: chain G residue 31 CYS Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 243 MET Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 306 ARG Chi-restraints excluded: chain H residue 332 LEU Chi-restraints excluded: chain I residue 23 GLN Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 64 LYS Chi-restraints excluded: chain I residue 144 CYS Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain K residue 37 ASP Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 70 LYS Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 125 MET Chi-restraints excluded: chain K residue 204 LEU Chi-restraints excluded: chain K residue 229 ARG Chi-restraints excluded: chain K residue 336 ASP Chi-restraints excluded: chain L residue 336 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 2 optimal weight: 4.9990 chunk 188 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 117 optimal weight: 0.7980 chunk 189 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 186 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.125122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.096727 restraints weight = 25170.061| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.54 r_work: 0.3075 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16210 Z= 0.162 Angle : 0.492 8.811 22003 Z= 0.264 Chirality : 0.039 0.141 2506 Planarity : 0.003 0.039 2764 Dihedral : 12.726 88.746 2643 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.09 % Allowed : 25.28 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % Twisted Proline : 0.00 % 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: 0.38 (0.19), residues: 1976 helix: 1.32 (0.18), residues: 871 sheet: 0.79 (0.31), residues: 287 loop : -1.14 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 27 TYR 0.016 0.001 TYR K 191 PHE 0.009 0.001 PHE I 248 HIS 0.002 0.000 HIS E 294 Details of bonding type rmsd covalent geometry : bond 0.00382 (16210) covalent geometry : angle 0.49228 (22003) hydrogen bonds : bond 0.03587 ( 734) hydrogen bonds : angle 4.24815 ( 2040) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 165 time to evaluate : 0.414 Fit side-chains REVERT: A 84 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.7915 (mtp) REVERT: C 40 LYS cc_start: 0.8053 (tttt) cc_final: 0.7653 (tttt) REVERT: C 43 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7540 (mp0) REVERT: C 158 MET cc_start: 0.8607 (mtp) cc_final: 0.8318 (ttm) REVERT: C 184 ASP cc_start: 0.8770 (t0) cc_final: 0.8435 (t0) REVERT: C 247 ARG cc_start: 0.8788 (ttm-80) cc_final: 0.8501 (mtp180) REVERT: E 33 ILE cc_start: 0.8618 (mm) cc_final: 0.8273 (mm) REVERT: E 98 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8259 (mt-10) REVERT: E 235 ARG cc_start: 0.7848 (ttp80) cc_final: 0.7346 (ttt-90) REVERT: G 251 MET cc_start: 0.8816 (tpp) cc_final: 0.8346 (tpp) REVERT: I 60 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8464 (mm) REVERT: K 80 LYS cc_start: 0.8518 (ptpt) cc_final: 0.8273 (ptmm) REVERT: K 211 MET cc_start: 0.8443 (ttt) cc_final: 0.8235 (ttt) REVERT: K 229 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.8546 (ttt180) REVERT: L 336 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6433 (mp) outliers start: 49 outliers final: 45 residues processed: 206 average time/residue: 0.1363 time to fit residues: 40.1037 Evaluate side-chains 215 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 166 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 313 LYS Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 346 HIS Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain F residue 329 ASN Chi-restraints excluded: chain F residue 333 ARG Chi-restraints excluded: chain G residue 31 CYS Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 243 MET Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 306 ARG Chi-restraints excluded: chain H residue 332 LEU Chi-restraints excluded: chain I residue 23 GLN Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 64 LYS Chi-restraints excluded: chain I residue 144 CYS Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 219 LEU Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain K residue 37 ASP Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 70 LYS Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 125 MET Chi-restraints excluded: chain K residue 204 LEU Chi-restraints excluded: chain K residue 229 ARG Chi-restraints excluded: chain K residue 336 ASP Chi-restraints excluded: chain L residue 336 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 118 optimal weight: 0.3980 chunk 95 optimal weight: 0.0870 chunk 65 optimal weight: 6.9990 chunk 2 optimal weight: 0.3980 chunk 151 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.126755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.098523 restraints weight = 24894.378| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.54 r_work: 0.3099 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16210 Z= 0.113 Angle : 0.462 8.752 22003 Z= 0.248 Chirality : 0.038 0.142 2506 Planarity : 0.003 0.041 2764 Dihedral : 12.595 89.260 2643 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.96 % Allowed : 25.35 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % Twisted Proline : 0.00 % 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: 0.48 (0.19), residues: 1976 helix: 1.40 (0.18), residues: 872 sheet: 0.74 (0.31), residues: 291 loop : -1.05 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 27 TYR 0.017 0.001 TYR K 191 PHE 0.008 0.001 PHE K 126 HIS 0.002 0.000 HIS C 47 Details of bonding type rmsd covalent geometry : bond 0.00257 (16210) covalent geometry : angle 0.46173 (22003) hydrogen bonds : bond 0.03044 ( 734) hydrogen bonds : angle 4.09133 ( 2040) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4501.35 seconds wall clock time: 77 minutes 32.29 seconds (4652.29 seconds total)