Starting phenix.real_space_refine on Wed Feb 4 08:19:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l80_62880/02_2026/9l80_62880_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l80_62880/02_2026/9l80_62880.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l80_62880/02_2026/9l80_62880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l80_62880/02_2026/9l80_62880.map" model { file = "/net/cci-nas-00/data/ceres_data/9l80_62880/02_2026/9l80_62880_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l80_62880/02_2026/9l80_62880_neut.cif" } resolution = 3.33 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= -0.002 sd= 0.150 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: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 6044 2.51 5 N 1638 2.21 5 O 1748 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s 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: 9490 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1825 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2529 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'ASP:plan': 7, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 47 Chain: "G" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 420 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 960 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "R" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1937 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 8, 'TRANS': 254} Chain breaks: 3 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 5, 'TYR:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "S" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1717 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 40 Chain: "R" Number of atoms: 102 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 51 Classifications: {'peptide': 1} Conformer: "B" Number of residues, atoms: 1, 51 Classifications: {'peptide': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ADR7 R 401 " occ=0.54 ... (100 atoms not shown) pdb=" OBJBDR7 R 401 " occ=0.46 Time building chain proxies: 2.11, per 1000 atoms: 0.22 Number of scatterers: 9490 At special positions: 0 Unit cell: (98.9, 126.42, 132.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 1748 8.00 N 1638 7.00 C 6044 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.04 Simple disulfide: pdb=" SG CYS R 78 " - pdb=" SG CYS R 155 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 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: 0.54 Conformation dependent library (CDL) restraints added in 225.5 milliseconds 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2296 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 14 sheets defined 33.2% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 4.174A pdb=" N ALA A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL A 20 " --> pdb=" O ASP A 16 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 removed outlier: 3.501A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 52 through 57' Processing helix chain 'A' and resid 233 through 237 removed outlier: 3.917A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 237' Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.935A pdb=" N ALA A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 294 removed outlier: 4.413A pdb=" N LEU A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ALA A 288 " --> pdb=" O GLN A 284 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU A 289 " --> pdb=" O ASP A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 308 removed outlier: 3.761A pdb=" N ALA A 306 " --> pdb=" O PRO A 303 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR A 308 " --> pdb=" O PHE A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 340 removed outlier: 3.660A pdb=" N THR A 325 " --> pdb=" O ASP A 321 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 380 removed outlier: 3.773A pdb=" N ILE A 365 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN A 380 " --> pdb=" O MET A 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 24 Processing helix chain 'B' and resid 29 through 33 Processing helix chain 'G' and resid 9 through 21 removed outlier: 3.875A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 25 removed outlier: 4.042A pdb=" N ILE G 25 " --> pdb=" O GLU G 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 22 through 25' Processing helix chain 'G' and resid 29 through 43 removed outlier: 3.628A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 48 removed outlier: 3.710A pdb=" N GLU G 47 " --> pdb=" O HIS G 44 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 44 through 48' Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.656A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.798A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'R' and resid 9 through 35 removed outlier: 3.588A pdb=" N ILE R 19 " --> pdb=" O ALA R 15 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN R 22 " --> pdb=" O ILE R 18 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU R 24 " --> pdb=" O ALA R 20 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL R 25 " --> pdb=" O THR R 21 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA R 28 " --> pdb=" O LEU R 24 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS R 34 " --> pdb=" O LEU R 30 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS R 35 " --> pdb=" O LEU R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 63 removed outlier: 3.510A pdb=" N LEU R 45 " --> pdb=" O LEU R 41 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE R 54 " --> pdb=" O ALA R 50 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY R 55 " --> pdb=" O ASP R 51 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU R 62 " --> pdb=" O ILE R 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 109 removed outlier: 4.263A pdb=" N LEU R 80 " --> pdb=" O THR R 76 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG R 81 " --> pdb=" O LEU R 77 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA R 83 " --> pdb=" O SER R 79 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL R 85 " --> pdb=" O ARG R 81 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR R 86 " --> pdb=" O MET R 82 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER R 87 " --> pdb=" O ALA R 83 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL R 93 " --> pdb=" O ALA R 89 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL R 96 " --> pdb=" O SER R 92 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU R 105 " --> pdb=" O PHE R 101 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA R 106 " --> pdb=" O ASP R 102 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE R 107 " --> pdb=" O ARG R 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 109 through 115 removed outlier: 4.123A pdb=" N LEU R 114 " --> pdb=" O PRO R 110 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LYS R 115 " --> pdb=" O PHE R 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 118 through 139 removed outlier: 3.561A pdb=" N TRP R 130 " --> pdb=" O ILE R 126 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU R 131 " --> pdb=" O ALA R 127 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL R 132 " --> pdb=" O GLY R 128 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER R 133 " --> pdb=" O LEU R 129 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU R 135 " --> pdb=" O LEU R 131 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE R 136 " --> pdb=" O VAL R 132 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY R 137 " --> pdb=" O SER R 133 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU R 139 " --> pdb=" O LEU R 135 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 143 Processing helix chain 'R' and resid 162 through 204 removed outlier: 3.826A pdb=" N VAL R 166 " --> pdb=" O HIS R 162 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER R 170 " --> pdb=" O VAL R 166 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE R 175 " --> pdb=" O CYS R 171 " (cutoff:3.500A) Proline residue: R 176 - end of helix removed outlier: 3.871A pdb=" N LEU R 180 " --> pdb=" O PRO R 176 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR R 185 " --> pdb=" O PHE R 181 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP R 187 " --> pdb=" O PHE R 183 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN R 197 " --> pdb=" O SER R 193 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN R 198 " --> pdb=" O MET R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 219 through 231 removed outlier: 3.944A pdb=" N VAL R 227 " --> pdb=" O ALA R 223 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER R 228 " --> pdb=" O LEU R 224 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL R 229 " --> pdb=" O ARG R 225 " (cutoff:3.500A) Processing helix chain 'R' and resid 234 through 249 removed outlier: 4.509A pdb=" N TRP R 238 " --> pdb=" O PHE R 234 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR R 239 " --> pdb=" O ALA R 235 " (cutoff:3.500A) Proline residue: R 240 - end of helix Processing helix chain 'R' and resid 262 through 282 removed outlier: 4.120A pdb=" N SER R 272 " --> pdb=" O GLY R 268 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU R 273 " --> pdb=" O VAL R 269 " (cutoff:3.500A) Proline residue: R 276 - end of helix removed outlier: 4.073A pdb=" N TRP R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 293 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.882A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 28 through 32' Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 213 removed outlier: 3.613A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ASN A 282 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL A 248 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.778A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.009A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.948A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.805A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.942A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.790A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277 removed outlier: 4.111A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 296 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 4 removed outlier: 3.648A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET N 83 " --> pdb=" O LEU N 18 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU N 81 " --> pdb=" O LEU N 20 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.030A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR N 94 " --> pdb=" O THR N 122 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.830A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL S 37 " --> pdb=" O TYR S 95 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 143 through 148 removed outlier: 3.643A pdb=" N VAL S 143 " --> pdb=" O ILE S 204 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE S 200 " --> pdb=" O CYS S 147 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER S 194 " --> pdb=" O THR S 201 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 182 through 183 removed outlier: 3.886A pdb=" N ASN S 182 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR S 178 " --> pdb=" O ASN S 182 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 332 hydrogen bonds defined for protein. 936 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.19 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2895 1.34 - 1.46: 2074 1.46 - 1.58: 4634 1.58 - 1.70: 0 1.70 - 1.83: 87 Bond restraints: 9690 Sorted by residual: bond pdb=" C LEU R 139 " pdb=" N PRO R 140 " ideal model delta sigma weight residual 1.334 1.365 -0.031 1.51e-02 4.39e+03 4.18e+00 bond pdb=" N LEU S 117 " pdb=" CA LEU S 117 " ideal model delta sigma weight residual 1.460 1.487 -0.028 1.45e-02 4.76e+03 3.64e+00 bond pdb=" C LEU S 117 " pdb=" O LEU S 117 " ideal model delta sigma weight residual 1.233 1.251 -0.018 1.19e-02 7.06e+03 2.31e+00 bond pdb=" CB LYS N 43 " pdb=" CG LYS N 43 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.34e+00 bond pdb=" CA ILE R 143 " pdb=" CB ILE R 143 " ideal model delta sigma weight residual 1.537 1.524 0.013 1.29e-02 6.01e+03 1.06e+00 ... (remaining 9685 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 13021 2.27 - 4.54: 117 4.54 - 6.81: 11 6.81 - 9.09: 1 9.09 - 11.36: 2 Bond angle restraints: 13152 Sorted by residual: angle pdb=" CB MET R 97 " pdb=" CG MET R 97 " pdb=" SD MET R 97 " ideal model delta sigma weight residual 112.70 124.06 -11.36 3.00e+00 1.11e-01 1.43e+01 angle pdb=" C ALA S 131 " pdb=" N THR S 132 " pdb=" CA THR S 132 " ideal model delta sigma weight residual 121.54 127.68 -6.14 1.91e+00 2.74e-01 1.03e+01 angle pdb=" CA LYS N 43 " pdb=" CB LYS N 43 " pdb=" CG LYS N 43 " ideal model delta sigma weight residual 114.10 120.40 -6.30 2.00e+00 2.50e-01 9.94e+00 angle pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta sigma weight residual 121.54 127.15 -5.61 1.91e+00 2.74e-01 8.63e+00 angle pdb=" CA LEU R 242 " pdb=" CB LEU R 242 " pdb=" CG LEU R 242 " ideal model delta sigma weight residual 116.30 126.03 -9.73 3.50e+00 8.16e-02 7.73e+00 ... (remaining 13147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.97: 4972 16.97 - 33.93: 566 33.93 - 50.90: 182 50.90 - 67.87: 14 67.87 - 84.84: 23 Dihedral angle restraints: 5757 sinusoidal: 2192 harmonic: 3565 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 11.53 81.47 1 1.00e+01 1.00e-02 8.18e+01 dihedral pdb=" CB CYS R 78 " pdb=" SG CYS R 78 " pdb=" SG CYS R 155 " pdb=" CB CYS R 155 " ideal model delta sinusoidal sigma weight residual -86.00 -138.04 52.04 1 1.00e+01 1.00e-02 3.69e+01 dihedral pdb=" CA ASP S 62 " pdb=" C ASP S 62 " pdb=" N THR S 63 " pdb=" CA THR S 63 " ideal model delta harmonic sigma weight residual 180.00 151.12 28.88 0 5.00e+00 4.00e-02 3.34e+01 ... (remaining 5754 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 948 0.031 - 0.061: 367 0.061 - 0.092: 88 0.092 - 0.122: 73 0.122 - 0.153: 16 Chirality restraints: 1492 Sorted by residual: chirality pdb=" CA LEU S 117 " pdb=" N LEU S 117 " pdb=" C LEU S 117 " pdb=" CB LEU S 117 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.82e-01 chirality pdb=" CB THR B 223 " pdb=" CA THR B 223 " pdb=" OG1 THR B 223 " pdb=" CG2 THR B 223 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.74e-01 chirality pdb=" CA ASN B 268 " pdb=" N ASN B 268 " pdb=" C ASN B 268 " pdb=" CB ASN B 268 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.41e-01 ... (remaining 1489 not shown) Planarity restraints: 1668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR S 223 " -0.033 5.00e-02 4.00e+02 4.96e-02 3.94e+00 pdb=" N PRO S 224 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO S 224 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO S 224 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 262 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.53e+00 pdb=" CG ASP A 262 " -0.033 2.00e-02 2.50e+03 pdb=" OD1 ASP A 262 " 0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP A 262 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL S 187 " -0.027 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO S 188 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO S 188 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO S 188 " -0.023 5.00e-02 4.00e+02 ... (remaining 1665 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2383 2.80 - 3.32: 7600 3.32 - 3.85: 13548 3.85 - 4.37: 14816 4.37 - 4.90: 28162 Nonbonded interactions: 66509 Sorted by model distance: nonbonded pdb=" OD2 ASP R 51 " pdb=" OG SER R 272 " model vdw 2.269 3.040 nonbonded pdb=" O TYR R 281 " pdb=" NH2 ARG R 287 " model vdw 2.270 3.120 nonbonded pdb=" O ILE R 18 " pdb=" ND2 ASN R 22 " model vdw 2.274 3.120 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.275 3.040 nonbonded pdb=" NH1 ARG S 190 " pdb=" O ARG S 206 " model vdw 2.285 3.120 ... (remaining 66504 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.46 max=1.00 mean=0.99 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: 1.330 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.770 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 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 9696 Z= 0.114 Angle : 0.549 11.358 13164 Z= 0.299 Chirality : 0.041 0.153 1492 Planarity : 0.003 0.050 1668 Dihedral : 16.492 84.836 3443 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.41 % Allowed : 18.36 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.85 (0.24), residues: 1214 helix: 0.31 (0.28), residues: 338 sheet: 0.05 (0.29), residues: 337 loop : -1.51 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 38 TYR 0.020 0.001 TYR S 223 PHE 0.009 0.001 PHE R 234 TRP 0.013 0.001 TRP A 234 HIS 0.003 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 9690) covalent geometry : angle 0.54810 (13152) SS BOND : bond 0.00538 ( 6) SS BOND : angle 1.00179 ( 12) hydrogen bonds : bond 0.29448 ( 332) hydrogen bonds : angle 7.57788 ( 936) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 130 time to evaluate : 0.313 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 130 average time/residue: 0.1023 time to fit residues: 17.9312 Evaluate side-chains 127 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain N residue 39 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN B 259 GLN B 266 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.166113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.136736 restraints weight = 28301.813| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 5.17 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3553 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3553 r_free = 0.3553 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3553 r_free = 0.3553 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3553 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9696 Z= 0.214 Angle : 0.670 11.537 13164 Z= 0.353 Chirality : 0.046 0.190 1492 Planarity : 0.004 0.050 1668 Dihedral : 10.207 72.338 1436 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.69 % Allowed : 16.62 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.85 (0.23), residues: 1214 helix: 0.77 (0.28), residues: 347 sheet: -0.12 (0.29), residues: 315 loop : -1.72 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 287 TYR 0.022 0.002 TYR S 223 PHE 0.018 0.002 PHE N 108 TRP 0.018 0.002 TRP N 47 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00510 ( 9690) covalent geometry : angle 0.66759 (13152) SS BOND : bond 0.01288 ( 6) SS BOND : angle 1.83530 ( 12) hydrogen bonds : bond 0.07867 ( 332) hydrogen bonds : angle 5.01310 ( 936) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 0.297 Fit side-chains REVERT: A 262 ASP cc_start: 0.7921 (m-30) cc_final: 0.7714 (m-30) REVERT: R 62 LEU cc_start: 0.6588 (OUTLIER) cc_final: 0.6328 (mm) REVERT: R 175 PHE cc_start: 0.6411 (t80) cc_final: 0.5835 (m-10) REVERT: S 223 TYR cc_start: 0.7248 (OUTLIER) cc_final: 0.6897 (t80) outliers start: 36 outliers final: 19 residues processed: 156 average time/residue: 0.0888 time to fit residues: 19.0703 Evaluate side-chains 143 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 9 VAL Chi-restraints excluded: chain R residue 14 LEU Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 146 PHE Chi-restraints excluded: chain R residue 164 HIS Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 64 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 86 optimal weight: 0.0170 chunk 60 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 174 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.166927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.137489 restraints weight = 25254.572| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 4.77 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9696 Z= 0.174 Angle : 0.611 7.362 13164 Z= 0.321 Chirality : 0.044 0.179 1492 Planarity : 0.004 0.052 1668 Dihedral : 9.281 66.198 1431 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.51 % Allowed : 17.03 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.77 (0.23), residues: 1214 helix: 1.02 (0.28), residues: 347 sheet: -0.15 (0.29), residues: 317 loop : -1.76 (0.24), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 287 TYR 0.022 0.002 TYR S 223 PHE 0.014 0.002 PHE B 241 TRP 0.017 0.002 TRP N 47 HIS 0.004 0.001 HIS S 220 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 9690) covalent geometry : angle 0.60927 (13152) SS BOND : bond 0.01035 ( 6) SS BOND : angle 1.58450 ( 12) hydrogen bonds : bond 0.07109 ( 332) hydrogen bonds : angle 4.65290 ( 936) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 124 time to evaluate : 0.247 Fit side-chains REVERT: B 32 GLN cc_start: 0.8000 (tt0) cc_final: 0.7756 (tt0) REVERT: B 234 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.8281 (t80) REVERT: R 175 PHE cc_start: 0.6221 (t80) cc_final: 0.5950 (m-10) REVERT: S 223 TYR cc_start: 0.7085 (OUTLIER) cc_final: 0.6775 (t80) outliers start: 44 outliers final: 22 residues processed: 161 average time/residue: 0.0832 time to fit residues: 18.6785 Evaluate side-chains 143 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 9 VAL Chi-restraints excluded: chain R residue 14 LEU Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 146 PHE Chi-restraints excluded: chain R residue 164 HIS Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 174 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.165964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.136552 restraints weight = 27014.614| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 5.17 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3551 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3551 r_free = 0.3551 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3551 r_free = 0.3551 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3551 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9696 Z= 0.186 Angle : 0.632 10.764 13164 Z= 0.330 Chirality : 0.045 0.182 1492 Planarity : 0.004 0.050 1668 Dihedral : 8.980 77.777 1431 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 4.51 % Allowed : 17.85 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.83 (0.23), residues: 1214 helix: 1.03 (0.28), residues: 348 sheet: -0.27 (0.29), residues: 320 loop : -1.79 (0.24), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 287 TYR 0.023 0.002 TYR S 223 PHE 0.015 0.002 PHE B 199 TRP 0.016 0.002 TRP N 47 HIS 0.004 0.001 HIS S 220 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 9690) covalent geometry : angle 0.63032 (13152) SS BOND : bond 0.01115 ( 6) SS BOND : angle 1.71487 ( 12) hydrogen bonds : bond 0.07116 ( 332) hydrogen bonds : angle 4.61049 ( 936) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 121 time to evaluate : 0.336 Fit side-chains REVERT: B 32 GLN cc_start: 0.7992 (tt0) cc_final: 0.7763 (tt0) REVERT: B 234 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.8264 (t80) REVERT: G 37 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7633 (mp) REVERT: R 175 PHE cc_start: 0.6207 (t80) cc_final: 0.5954 (m-10) REVERT: S 223 TYR cc_start: 0.7143 (OUTLIER) cc_final: 0.6840 (t80) outliers start: 44 outliers final: 32 residues processed: 156 average time/residue: 0.0905 time to fit residues: 19.5536 Evaluate side-chains 154 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 9 VAL Chi-restraints excluded: chain R residue 14 LEU Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 42 CYS Chi-restraints excluded: chain R residue 146 PHE Chi-restraints excluded: chain R residue 164 HIS Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 226 THR Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 163 TYR Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 48 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 116 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 174 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.170064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.141105 restraints weight = 22481.054| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 4.49 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3600 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9696 Z= 0.115 Angle : 0.542 8.601 13164 Z= 0.279 Chirality : 0.042 0.149 1492 Planarity : 0.003 0.052 1668 Dihedral : 8.163 83.166 1431 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.18 % Allowed : 19.38 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 (0.24), residues: 1214 helix: 1.49 (0.28), residues: 349 sheet: -0.09 (0.29), residues: 317 loop : -1.71 (0.24), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 38 TYR 0.019 0.001 TYR S 223 PHE 0.012 0.001 PHE A 366 TRP 0.013 0.001 TRP N 47 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9690) covalent geometry : angle 0.54088 (13152) SS BOND : bond 0.00751 ( 6) SS BOND : angle 1.19361 ( 12) hydrogen bonds : bond 0.05234 ( 332) hydrogen bonds : angle 4.17013 ( 936) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.327 Fit side-chains REVERT: A 262 ASP cc_start: 0.7842 (m-30) cc_final: 0.7595 (m-30) REVERT: B 32 GLN cc_start: 0.7944 (tt0) cc_final: 0.7709 (tt0) outliers start: 31 outliers final: 19 residues processed: 152 average time/residue: 0.0882 time to fit residues: 18.5896 Evaluate side-chains 136 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 14 LEU Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 42 CYS Chi-restraints excluded: chain R residue 164 HIS Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 190 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 92 optimal weight: 0.0770 chunk 73 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 chunk 118 optimal weight: 30.0000 chunk 61 optimal weight: 0.0970 chunk 56 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 85 optimal weight: 0.0010 chunk 102 optimal weight: 4.9990 overall best weight: 0.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN S 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.173846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.139090 restraints weight = 15575.397| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 4.67 r_work: 0.3262 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9696 Z= 0.090 Angle : 0.493 9.210 13164 Z= 0.255 Chirality : 0.040 0.148 1492 Planarity : 0.003 0.049 1668 Dihedral : 7.599 81.939 1431 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.36 % Allowed : 21.03 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.09 (0.24), residues: 1214 helix: 1.91 (0.29), residues: 350 sheet: 0.28 (0.29), residues: 303 loop : -1.61 (0.24), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 129 TYR 0.021 0.001 TYR S 223 PHE 0.010 0.001 PHE R 234 TRP 0.012 0.001 TRP A 234 HIS 0.003 0.000 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00180 ( 9690) covalent geometry : angle 0.49295 (13152) SS BOND : bond 0.00476 ( 6) SS BOND : angle 0.87697 ( 12) hydrogen bonds : bond 0.03716 ( 332) hydrogen bonds : angle 3.77016 ( 936) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.330 Fit side-chains REVERT: R 202 MET cc_start: 0.5844 (OUTLIER) cc_final: 0.5583 (tpp) REVERT: S 98 ARG cc_start: 0.8721 (ptt180) cc_final: 0.8282 (ptt180) REVERT: S 190 ARG cc_start: 0.5766 (OUTLIER) cc_final: 0.5550 (ptt90) REVERT: S 223 TYR cc_start: 0.6423 (OUTLIER) cc_final: 0.6052 (t80) outliers start: 23 outliers final: 11 residues processed: 144 average time/residue: 0.0966 time to fit residues: 18.5932 Evaluate side-chains 127 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 202 MET Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 190 ARG Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 100 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN S 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.170942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.124739 restraints weight = 15766.436| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 3.10 r_work: 0.3228 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9696 Z= 0.117 Angle : 0.529 9.944 13164 Z= 0.274 Chirality : 0.041 0.152 1492 Planarity : 0.003 0.055 1668 Dihedral : 7.911 84.449 1431 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.08 % Allowed : 20.51 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.11 (0.24), residues: 1214 helix: 1.93 (0.28), residues: 351 sheet: 0.04 (0.29), residues: 321 loop : -1.54 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 38 TYR 0.019 0.001 TYR S 223 PHE 0.012 0.001 PHE A 366 TRP 0.010 0.001 TRP N 47 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 9690) covalent geometry : angle 0.52820 (13152) SS BOND : bond 0.00746 ( 6) SS BOND : angle 1.25217 ( 12) hydrogen bonds : bond 0.04951 ( 332) hydrogen bonds : angle 3.89200 ( 936) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 0.313 Fit side-chains REVERT: R 178 MET cc_start: 0.5797 (tpt) cc_final: 0.4867 (tpt) REVERT: S 190 ARG cc_start: 0.5849 (OUTLIER) cc_final: 0.5617 (ptt90) REVERT: S 223 TYR cc_start: 0.6500 (OUTLIER) cc_final: 0.6211 (t80) outliers start: 30 outliers final: 20 residues processed: 140 average time/residue: 0.0867 time to fit residues: 16.7207 Evaluate side-chains 135 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 9 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 42 CYS Chi-restraints excluded: chain R residue 164 HIS Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 202 MET Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 190 ARG Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 97 optimal weight: 0.0670 chunk 58 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 chunk 85 optimal weight: 0.0470 overall best weight: 0.4816 ------------------------------------------------------------------------------- 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 = 0.3961 r_free = 0.3961 target = 0.174899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.137448 restraints weight = 14988.473| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 4.20 r_work: 0.3282 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9696 Z= 0.089 Angle : 0.490 10.988 13164 Z= 0.252 Chirality : 0.040 0.153 1492 Planarity : 0.003 0.053 1668 Dihedral : 7.578 84.703 1431 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.56 % Allowed : 21.23 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.15 (0.24), residues: 1214 helix: 2.20 (0.28), residues: 350 sheet: 0.44 (0.30), residues: 303 loop : -1.54 (0.24), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 129 TYR 0.017 0.001 TYR S 223 PHE 0.010 0.001 PHE A 366 TRP 0.010 0.001 TRP A 234 HIS 0.003 0.000 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00185 ( 9690) covalent geometry : angle 0.48998 (13152) SS BOND : bond 0.00470 ( 6) SS BOND : angle 0.85134 ( 12) hydrogen bonds : bond 0.03681 ( 332) hydrogen bonds : angle 3.63120 ( 936) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 0.349 Fit side-chains REVERT: N 6 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7522 (mm-30) REVERT: R 202 MET cc_start: 0.5788 (OUTLIER) cc_final: 0.5581 (tpp) REVERT: S 190 ARG cc_start: 0.5777 (OUTLIER) cc_final: 0.5540 (ptt90) REVERT: S 223 TYR cc_start: 0.6359 (OUTLIER) cc_final: 0.6074 (t80) outliers start: 25 outliers final: 16 residues processed: 140 average time/residue: 0.0886 time to fit residues: 16.9896 Evaluate side-chains 133 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 9 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 42 CYS Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 202 MET Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 190 ARG Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 55 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 50 optimal weight: 0.3980 chunk 12 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 67 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.173437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.137643 restraints weight = 13616.923| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 3.57 r_work: 0.3286 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3277 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3277 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9696 Z= 0.098 Angle : 0.508 11.306 13164 Z= 0.261 Chirality : 0.041 0.154 1492 Planarity : 0.003 0.055 1668 Dihedral : 7.646 84.597 1431 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.67 % Allowed : 21.03 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.19 (0.24), residues: 1214 helix: 2.21 (0.28), residues: 351 sheet: 0.37 (0.30), residues: 308 loop : -1.46 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 129 TYR 0.017 0.001 TYR S 223 PHE 0.011 0.001 PHE A 366 TRP 0.009 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 9690) covalent geometry : angle 0.50690 (13152) SS BOND : bond 0.00700 ( 6) SS BOND : angle 1.07435 ( 12) hydrogen bonds : bond 0.04147 ( 332) hydrogen bonds : angle 3.65623 ( 936) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.310 Fit side-chains REVERT: A 304 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8238 (mm-30) REVERT: B 301 LYS cc_start: 0.8345 (mmtp) cc_final: 0.8035 (mptt) REVERT: N 6 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7569 (mm-30) REVERT: R 202 MET cc_start: 0.5927 (OUTLIER) cc_final: 0.5684 (tpp) REVERT: S 190 ARG cc_start: 0.5871 (OUTLIER) cc_final: 0.5659 (ptt90) REVERT: S 223 TYR cc_start: 0.6461 (OUTLIER) cc_final: 0.6244 (t80) outliers start: 26 outliers final: 18 residues processed: 137 average time/residue: 0.0890 time to fit residues: 16.7593 Evaluate side-chains 135 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 9 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 42 CYS Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 202 MET Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 190 ARG Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 22 optimal weight: 20.0000 chunk 65 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.3900 r_free = 0.3900 target = 0.168844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.133345 restraints weight = 16793.324| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 4.95 r_work: 0.3123 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9696 Z= 0.148 Angle : 0.580 12.018 13164 Z= 0.300 Chirality : 0.043 0.168 1492 Planarity : 0.003 0.055 1668 Dihedral : 8.204 89.196 1431 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.77 % Allowed : 20.82 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.07 (0.24), residues: 1214 helix: 1.94 (0.28), residues: 350 sheet: 0.05 (0.29), residues: 328 loop : -1.50 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 19 TYR 0.022 0.001 TYR S 223 PHE 0.014 0.001 PHE B 199 TRP 0.013 0.001 TRP R 238 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9690) covalent geometry : angle 0.57826 (13152) SS BOND : bond 0.00898 ( 6) SS BOND : angle 1.57019 ( 12) hydrogen bonds : bond 0.05783 ( 332) hydrogen bonds : angle 4.04328 ( 936) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 0.349 Fit side-chains REVERT: N 6 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7716 (mm-30) REVERT: S 190 ARG cc_start: 0.6036 (OUTLIER) cc_final: 0.5796 (ptt90) REVERT: S 223 TYR cc_start: 0.6855 (OUTLIER) cc_final: 0.6578 (t80) outliers start: 27 outliers final: 21 residues processed: 142 average time/residue: 0.0868 time to fit residues: 17.3710 Evaluate side-chains 139 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 9 VAL Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 42 CYS Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 202 MET Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 190 ARG Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 110 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.168469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.136853 restraints weight = 20850.507| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 4.59 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3554 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3554 r_free = 0.3554 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3554 r_free = 0.3554 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3554 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9696 Z= 0.148 Angle : 0.588 11.986 13164 Z= 0.302 Chirality : 0.043 0.145 1492 Planarity : 0.003 0.055 1668 Dihedral : 8.192 89.413 1431 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.77 % Allowed : 21.13 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.19 (0.24), residues: 1214 helix: 1.83 (0.28), residues: 350 sheet: -0.01 (0.29), residues: 321 loop : -1.55 (0.24), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 19 TYR 0.023 0.001 TYR S 223 PHE 0.015 0.001 PHE B 199 TRP 0.013 0.001 TRP R 238 HIS 0.003 0.001 HIS S 220 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 9690) covalent geometry : angle 0.58637 (13152) SS BOND : bond 0.00923 ( 6) SS BOND : angle 1.47572 ( 12) hydrogen bonds : bond 0.05758 ( 332) hydrogen bonds : angle 4.07011 ( 936) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1980.96 seconds wall clock time: 34 minutes 34.43 seconds (2074.43 seconds total)