Starting phenix.real_space_refine on Fri Jul 3 03:05:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dg8_27418/07_2026/8dg8_27418.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dg8_27418/07_2026/8dg8_27418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dg8_27418/07_2026/8dg8_27418.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dg8_27418/07_2026/8dg8_27418.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dg8_27418/07_2026/8dg8_27418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dg8_27418/07_2026/8dg8_27418.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8dg8_27418/07_2026/8dg8_27418.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dg8_27418/07_2026/8dg8_27418.cif" } resolution = 3.62 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= 0.001 sd= 0.167 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 7323 2.51 5 N 1943 2.21 5 O 2291 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11617 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3251 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 406} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 955 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 120} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 783 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain breaks: 1 Chain: "A" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3251 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 406} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3251 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 406} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.61, per 1000 atoms: 0.22 Number of scatterers: 11617 At special positions: 0 Unit cell: (124.491, 104.943, 117.289, 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 2291 8.00 N 1943 7.00 C 7323 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 168 " distance=2.04 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 340 " distance=2.03 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 392 " distance=2.03 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS A 213 " - pdb=" SG CYS A 230 " distance=2.04 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.04 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 162 " - pdb=" SG CYS C 168 " distance=2.03 Simple disulfide: pdb=" SG CYS C 213 " - pdb=" SG CYS C 230 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 340 " distance=2.03 Simple disulfide: pdb=" SG CYS C 355 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 392 " distance=2.03 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 417 " 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 238 " " NAG A 602 " - " ASN A 359 " " NAG A 603 " - " ASN A 446 " " NAG B 601 " - " ASN B 238 " " NAG B 602 " - " ASN B 359 " " NAG B 603 " - " ASN B 446 " " NAG C 601 " - " ASN C 238 " " NAG C 602 " - " ASN C 359 " " NAG C 603 " - " ASN C 446 " Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 409.0 milliseconds 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2794 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 24 sheets defined 29.3% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 64 through 84 removed outlier: 3.500A pdb=" N LYS B 72 " --> pdb=" O ILE B 68 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU B 74 " --> pdb=" O GLN B 70 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU B 75 " --> pdb=" O TYR B 71 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG B 77 " --> pdb=" O ARG B 73 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) Proline residue: B 81 - end of helix Processing helix chain 'B' and resid 124 through 152 removed outlier: 4.090A pdb=" N ALA B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 134 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA B 137 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN B 139 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER B 142 " --> pdb=" O LYS B 138 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ASP B 143 " --> pdb=" O GLN B 139 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS B 146 " --> pdb=" O SER B 142 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA B 150 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG B 152 " --> pdb=" O LYS B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 190 removed outlier: 3.699A pdb=" N LYS B 181 " --> pdb=" O ASP B 177 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL B 184 " --> pdb=" O ASN B 180 " (cutoff:3.500A) Proline residue: B 185 - end of helix removed outlier: 4.559A pdb=" N ALA B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 210 removed outlier: 3.594A pdb=" N LEU B 199 " --> pdb=" O ALA B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 236 removed outlier: 3.927A pdb=" N TYR B 235 " --> pdb=" O ILE B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 243 removed outlier: 3.866A pdb=" N ILE B 242 " --> pdb=" O ASN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 249 Processing helix chain 'B' and resid 252 through 261 removed outlier: 3.637A pdb=" N LEU B 256 " --> pdb=" O ASP B 252 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 355 Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 452 through 471 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 100A through 100E removed outlier: 4.376A pdb=" N TRP H 100D" --> pdb=" O ASP H 100A" (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 28 Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 66 through 74 removed outlier: 3.760A pdb=" N GLN A 70 " --> pdb=" O GLN A 66 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR A 71 " --> pdb=" O GLN A 67 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG A 73 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 74 " --> pdb=" O GLN A 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 66 through 74' Processing helix chain 'A' and resid 75 through 83 removed outlier: 3.590A pdb=" N ILE A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Proline residue: A 81 - end of helix Processing helix chain 'A' and resid 124 through 152 removed outlier: 3.542A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN A 139 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N SER A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ASP A 143 " --> pdb=" O GLN A 139 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 150 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG A 152 " --> pdb=" O LYS A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 183 Processing helix chain 'A' and resid 184 through 189 Processing helix chain 'A' and resid 195 through 215 removed outlier: 4.613A pdb=" N CYS A 213 " --> pdb=" O GLU A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 234 Processing helix chain 'A' and resid 245 through 250 removed outlier: 4.450A pdb=" N LYS A 250 " --> pdb=" O SER A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 349 through 356 removed outlier: 4.034A pdb=" N LEU A 356 " --> pdb=" O MET A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 469 removed outlier: 3.612A pdb=" N LYS A 462 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU A 469 " --> pdb=" O SER A 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 71 removed outlier: 4.267A pdb=" N LYS C 69 " --> pdb=" O ASP C 65 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLN C 70 " --> pdb=" O GLN C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 78 removed outlier: 3.521A pdb=" N ASP C 76 " --> pdb=" O LYS C 72 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG C 77 " --> pdb=" O ARG C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 87 Processing helix chain 'C' and resid 124 through 136 removed outlier: 3.978A pdb=" N ALA C 133 " --> pdb=" O THR C 129 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU C 134 " --> pdb=" O ALA C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 151 removed outlier: 3.595A pdb=" N ALA C 140 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N SER C 142 " --> pdb=" O LYS C 138 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ASP C 143 " --> pdb=" O GLN C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 190 removed outlier: 4.134A pdb=" N VAL C 184 " --> pdb=" O ASN C 180 " (cutoff:3.500A) Proline residue: C 185 - end of helix removed outlier: 4.993A pdb=" N ALA C 188 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG C 189 " --> pdb=" O PRO C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 214 removed outlier: 3.517A pdb=" N ASN C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 234 Processing helix chain 'C' and resid 238 through 243 removed outlier: 3.625A pdb=" N ILE C 242 " --> pdb=" O ASN C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 260 removed outlier: 4.213A pdb=" N LEU C 257 " --> pdb=" O ILE C 253 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N PHE C 258 " --> pdb=" O TYR C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 358 removed outlier: 4.011A pdb=" N LEU C 356 " --> pdb=" O MET C 352 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY C 358 " --> pdb=" O SER C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 469 removed outlier: 3.869A pdb=" N LEU C 467 " --> pdb=" O VAL C 463 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU C 469 " --> pdb=" O SER C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 472 No H-bonds generated for 'chain 'C' and resid 470 through 472' Processing sheet with id=AA1, first strand: chain 'B' and resid 30 through 33 removed outlier: 4.080A pdb=" N HIS B 315 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 281 through 286 removed outlier: 4.528A pdb=" N ASN B 43 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N THR B 286 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N SER B 41 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 158 through 159 removed outlier: 3.721A pdb=" N ASP B 268 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLN B 279 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N VAL B 266 " --> pdb=" O GLN B 279 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B 226 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 301 through 303 Processing sheet with id=AA5, first strand: chain 'B' and resid 376 through 377 removed outlier: 3.534A pdb=" N ALA B 385 " --> pdb=" O LYS B 410 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AA7, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.146A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N HIS H 102 " --> pdb=" O LYS H 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.146A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.723A pdb=" N THR L 105 " --> pdb=" O VAL L 11 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 18 through 24 Processing sheet with id=AB2, first strand: chain 'L' and resid 45 through 50 removed outlier: 6.899A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 30 through 32 removed outlier: 3.501A pdb=" N ASP A 297 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 30 through 32 removed outlier: 3.501A pdb=" N ASP A 297 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASN A 43 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR A 286 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N SER A 41 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU A 288 " --> pdb=" O LYS A 39 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N LYS A 39 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 9.446A pdb=" N ASN A 290 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 9.668A pdb=" N GLY A 37 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 158 through 164 removed outlier: 3.621A pdb=" N SER A 163 " --> pdb=" O ASN A 167 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ASN A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR A 48 " --> pdb=" O CYS A 168 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 170 " --> pdb=" O TYR A 48 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 172 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP A 268 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLN A 279 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N VAL A 266 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE A 226 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 308 through 309 Processing sheet with id=AB7, first strand: chain 'A' and resid 376 through 377 removed outlier: 3.695A pdb=" N ALA A 385 " --> pdb=" O LYS A 410 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 419 through 420 Processing sheet with id=AB9, first strand: chain 'C' and resid 285 through 286 removed outlier: 4.973A pdb=" N LYS C 295 " --> pdb=" O ASN C 33 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE C 293 " --> pdb=" O PRO C 35 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N GLY C 37 " --> pdb=" O THR C 291 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N THR C 291 " --> pdb=" O GLY C 37 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 285 through 286 removed outlier: 8.047A pdb=" N TYR C 338 " --> pdb=" O PRO C 35 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLY C 37 " --> pdb=" O TYR C 338 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N CYS C 340 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LYS C 39 " --> pdb=" O CYS C 340 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 158 through 161 removed outlier: 3.629A pdb=" N VAL C 161 " --> pdb=" O ILE C 169 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE C 169 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 9.427A pdb=" N VAL C 170 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TYR C 48 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ILE C 172 " --> pdb=" O TYR C 48 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE C 50 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP C 268 " --> pdb=" O THR C 277 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 226 through 227 Processing sheet with id=AC4, first strand: chain 'C' and resid 301 through 303 removed outlier: 4.350A pdb=" N THR C 367 " --> pdb=" O VAL C 449 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 376 through 377 Processing sheet with id=AC6, first strand: chain 'C' and resid 392 through 394 387 hydrogen bonds defined for protein. 1038 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: 1.85 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3800 1.34 - 1.46: 2514 1.46 - 1.59: 5398 1.59 - 1.71: 0 1.71 - 1.84: 74 Bond restraints: 11786 Sorted by residual: bond pdb=" CA SER B 357 " pdb=" CB SER B 357 " ideal model delta sigma weight residual 1.528 1.469 0.059 1.34e-02 5.57e+03 1.96e+01 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.493 -0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" CA SER B 361 " pdb=" CB SER B 361 " ideal model delta sigma weight residual 1.530 1.476 0.055 1.69e-02 3.50e+03 1.05e+01 bond pdb=" C1 NAG C 602 " pdb=" O5 NAG C 602 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.10e+00 bond pdb=" N SER B 361 " pdb=" CA SER B 361 " ideal model delta sigma weight residual 1.457 1.486 -0.028 1.29e-02 6.01e+03 4.82e+00 ... (remaining 11781 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 15627 2.07 - 4.14: 298 4.14 - 6.22: 51 6.22 - 8.29: 10 8.29 - 10.36: 2 Bond angle restraints: 15988 Sorted by residual: angle pdb=" CA ASN B 359 " pdb=" CB ASN B 359 " pdb=" CG ASN B 359 " ideal model delta sigma weight residual 112.60 105.66 6.94 1.00e+00 1.00e+00 4.82e+01 angle pdb=" N SER B 357 " pdb=" CA SER B 357 " pdb=" C SER B 357 " ideal model delta sigma weight residual 111.87 103.19 8.68 1.41e+00 5.03e-01 3.79e+01 angle pdb=" N VAL B 328 " pdb=" CA VAL B 328 " pdb=" C VAL B 328 " ideal model delta sigma weight residual 111.91 107.52 4.39 8.90e-01 1.26e+00 2.44e+01 angle pdb=" C ASN A 380 " pdb=" CA ASN A 380 " pdb=" CB ASN A 380 " ideal model delta sigma weight residual 116.63 110.91 5.72 1.16e+00 7.43e-01 2.44e+01 angle pdb=" C LEU B 356 " pdb=" N SER B 357 " pdb=" CA SER B 357 " ideal model delta sigma weight residual 122.79 116.34 6.45 1.63e+00 3.76e-01 1.57e+01 ... (remaining 15983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 6488 17.67 - 35.34: 562 35.34 - 53.01: 86 53.01 - 70.68: 17 70.68 - 88.36: 13 Dihedral angle restraints: 7166 sinusoidal: 2835 harmonic: 4331 Sorted by residual: dihedral pdb=" CB CYS A 63 " pdb=" SG CYS A 63 " pdb=" SG CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sinusoidal sigma weight residual -86.00 -9.36 -76.64 1 1.00e+01 1.00e-02 7.38e+01 dihedral pdb=" CB CYS A 213 " pdb=" SG CYS A 213 " pdb=" SG CYS A 230 " pdb=" CB CYS A 230 " ideal model delta sinusoidal sigma weight residual -86.00 -162.25 76.25 1 1.00e+01 1.00e-02 7.32e+01 dihedral pdb=" CB CYS B 162 " pdb=" SG CYS B 162 " pdb=" SG CYS B 168 " pdb=" CB CYS B 168 " ideal model delta sinusoidal sigma weight residual 93.00 38.72 54.28 1 1.00e+01 1.00e-02 4.00e+01 ... (remaining 7163 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1733 0.077 - 0.153: 201 0.153 - 0.230: 6 0.230 - 0.306: 2 0.306 - 0.383: 3 Chirality restraints: 1945 Sorted by residual: chirality pdb=" C1 NAG C 602 " pdb=" ND2 ASN C 359 " pdb=" C2 NAG C 602 " pdb=" O5 NAG C 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.78 0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" CB ILE A 50 " pdb=" CA ILE A 50 " pdb=" CG1 ILE A 50 " pdb=" CG2 ILE A 50 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CB ILE B 50 " pdb=" CA ILE B 50 " pdb=" CG1 ILE B 50 " pdb=" CG2 ILE B 50 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.96e+00 ... (remaining 1942 not shown) Planarity restraints: 2035 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 602 " 0.279 2.00e-02 2.50e+03 2.37e-01 7.03e+02 pdb=" C7 NAG B 602 " -0.071 2.00e-02 2.50e+03 pdb=" C8 NAG B 602 " 0.175 2.00e-02 2.50e+03 pdb=" N2 NAG B 602 " -0.409 2.00e-02 2.50e+03 pdb=" O7 NAG B 602 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 356 " -0.022 2.00e-02 2.50e+03 4.47e-02 2.00e+01 pdb=" C LEU B 356 " 0.077 2.00e-02 2.50e+03 pdb=" O LEU B 356 " -0.029 2.00e-02 2.50e+03 pdb=" N SER B 357 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 238 " -0.001 2.00e-02 2.50e+03 3.62e-02 1.64e+01 pdb=" CG ASN A 238 " 0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN A 238 " -0.044 2.00e-02 2.50e+03 pdb=" ND2 ASN A 238 " 0.035 2.00e-02 2.50e+03 pdb=" C1 NAG A 601 " -0.036 2.00e-02 2.50e+03 ... (remaining 2032 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 358 2.68 - 3.24: 12316 3.24 - 3.79: 17549 3.79 - 4.35: 23828 4.35 - 4.90: 37648 Nonbonded interactions: 91699 Sorted by model distance: nonbonded pdb=" OH TYR C 251 " pdb=" O PRO C 283 " model vdw 2.129 3.040 nonbonded pdb=" OG1 THR C 393 " pdb=" O GLY C 396 " model vdw 2.145 3.040 nonbonded pdb=" ND2 ASN A 349 " pdb=" OD1 ASP C 455 " model vdw 2.154 3.120 nonbonded pdb=" NE2 GLN C 403 " pdb=" O GLY C 408 " model vdw 2.195 3.120 nonbonded pdb=" O ILE C 151 " pdb=" NZ LYS C 173 " model vdw 2.198 3.120 ... (remaining 91694 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.630 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5714 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 : 0.004 0.087 11818 Z= 0.181 Angle : 0.757 21.870 16061 Z= 0.399 Chirality : 0.049 0.383 1945 Planarity : 0.007 0.237 2026 Dihedral : 13.508 88.356 4303 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.37 % Favored : 91.56 % Rotamer: Outliers : 0.15 % Allowed : 0.31 % Favored : 99.54 % 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: -2.83 (0.20), residues: 1470 helix: -1.54 (0.26), residues: 379 sheet: -1.41 (0.31), residues: 273 loop : -2.25 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 71 TYR 0.014 0.001 TYR A 83 PHE 0.009 0.001 PHE L 62 TRP 0.014 0.002 TRP H 47 HIS 0.005 0.001 HIS C 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.18 (11786) covalent geometry : angle 0.71670 / 0.39 (15988) SS BOND : bond 0.00375 / 0.22 ( 23) SS BOND : angle 0.88145 / 0.60 ( 46) hydrogen bonds : bond 0.29256 / 19.47 ( 373) hydrogen bonds : angle 10.13912 / 7.05 ( 1038) link_NAG-ASN : bond 0.01139 / 0.58 ( 9) link_NAG-ASN : angle 5.95840 / 2.97 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 209 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 208 SER cc_start: 0.6852 (m) cc_final: 0.6531 (p) REVERT: B 281 ARG cc_start: 0.7336 (mtm-85) cc_final: 0.6930 (ptt180) REVERT: B 284 LEU cc_start: 0.6724 (tp) cc_final: 0.6133 (mt) REVERT: B 289 LEU cc_start: 0.7135 (mt) cc_final: 0.6892 (mp) REVERT: B 425 MET cc_start: 0.4509 (mtp) cc_final: 0.4244 (mtm) REVERT: H 3 GLN cc_start: 0.6844 (OUTLIER) cc_final: 0.6608 (pm20) REVERT: H 89 VAL cc_start: 0.8152 (m) cc_final: 0.7674 (p) REVERT: H 100 GLU cc_start: 0.6064 (tp30) cc_final: 0.5388 (tt0) REVERT: L 31 TYR cc_start: 0.6902 (m-80) cc_final: 0.6577 (m-80) REVERT: L 32 TYR cc_start: 0.6470 (m-10) cc_final: 0.5910 (m-10) REVERT: A 70 GLN cc_start: 0.8674 (tm-30) cc_final: 0.8214 (mm-40) REVERT: A 78 LEU cc_start: 0.6034 (pp) cc_final: 0.5593 (tt) REVERT: A 270 ASP cc_start: 0.5827 (t0) cc_final: 0.5350 (t0) REVERT: A 414 HIS cc_start: 0.4695 (p-80) cc_final: 0.4436 (p-80) REVERT: A 462 LYS cc_start: 0.7438 (ttpp) cc_final: 0.7016 (tmmt) REVERT: C 48 TYR cc_start: 0.7629 (m-80) cc_final: 0.6894 (m-80) REVERT: C 49 LEU cc_start: 0.5722 (mt) cc_final: 0.5363 (mp) REVERT: C 56 LYS cc_start: 0.7100 (tmtt) cc_final: 0.6883 (tppp) REVERT: C 236 ARG cc_start: 0.7090 (mtt90) cc_final: 0.5386 (mmt180) REVERT: C 278 LEU cc_start: 0.7413 (mp) cc_final: 0.7103 (mt) outliers start: 2 outliers final: 0 residues processed: 210 average time/residue: 0.0959 time to fit residues: 29.7274 Evaluate side-chains 152 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 151 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 380 ASN B 461 ASN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 89 GLN A 155 ASN ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN C 206 HIS C 290 ASN ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.240561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 120)---------------| | r_work = 0.4574 r_free = 0.4574 target = 0.231509 restraints weight = 10419.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.214881 restraints weight = 14879.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.214809 restraints weight = 14921.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.215048 restraints weight = 14650.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.215280 restraints weight = 12065.809| |-----------------------------------------------------------------------------| r_work (final): 0.4326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11818 Z= 0.177 Angle : 0.770 9.027 16061 Z= 0.394 Chirality : 0.052 0.327 1945 Planarity : 0.005 0.095 2026 Dihedral : 5.761 35.255 1591 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.10 % Favored : 91.84 % Rotamer: Outliers : 1.53 % Allowed : 8.43 % Favored : 90.04 % 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: -2.79 (0.20), residues: 1470 helix: -1.41 (0.25), residues: 376 sheet: -1.44 (0.31), residues: 276 loop : -2.25 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 71 TYR 0.026 0.002 TYR C 71 PHE 0.021 0.002 PHE A 437 TRP 0.013 0.002 TRP C 308 HIS 0.006 0.001 HIS C 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (11786) covalent geometry : angle 0.76316 / 0.39 (15988) SS BOND : bond 0.00515 / 0.29 ( 23) SS BOND : angle 0.97601 / 0.63 ( 46) hydrogen bonds : bond 0.05303 / 3.55 ( 373) hydrogen bonds : angle 6.78091 / 4.61 ( 1038) link_NAG-ASN : bond 0.00429 / 0.28 ( 9) link_NAG-ASN : angle 2.43153 / 1.30 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 284 LEU cc_start: 0.7479 (tp) cc_final: 0.7216 (mt) REVERT: B 289 LEU cc_start: 0.7643 (mt) cc_final: 0.7394 (mp) REVERT: C 48 TYR cc_start: 0.8132 (m-80) cc_final: 0.7524 (m-80) REVERT: C 158 VAL cc_start: 0.7366 (t) cc_final: 0.7020 (p) REVERT: C 236 ARG cc_start: 0.6754 (mtt90) cc_final: 0.5480 (mmt180) outliers start: 20 outliers final: 11 residues processed: 165 average time/residue: 0.1019 time to fit residues: 24.3535 Evaluate side-chains 134 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 388 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 58 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 84 optimal weight: 0.0870 chunk 123 optimal weight: 5.9990 chunk 82 optimal weight: 0.3980 chunk 45 optimal weight: 3.9990 chunk 7 optimal weight: 0.0870 chunk 69 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 42 GLN H 3 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 ASN ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 461 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.242513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 127)---------------| | r_work = 0.4603 r_free = 0.4603 target = 0.233398 restraints weight = 10751.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 76)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.214542 restraints weight = 16812.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.215693 restraints weight = 14648.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.215655 restraints weight = 13707.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.215732 restraints weight = 12456.057| |-----------------------------------------------------------------------------| r_work (final): 0.4314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11818 Z= 0.161 Angle : 0.717 10.241 16061 Z= 0.367 Chirality : 0.050 0.379 1945 Planarity : 0.005 0.072 2026 Dihedral : 5.548 21.676 1588 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.89 % Favored : 92.04 % Rotamer: Outliers : 2.91 % Allowed : 11.72 % Favored : 85.36 % 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: -2.71 (0.21), residues: 1470 helix: -1.28 (0.25), residues: 387 sheet: -1.30 (0.30), residues: 288 loop : -2.30 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 281 TYR 0.025 0.002 TYR L 32 PHE 0.022 0.002 PHE A 437 TRP 0.012 0.002 TRP C 308 HIS 0.012 0.002 HIS A 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (11786) covalent geometry : angle 0.71105 / 0.37 (15988) SS BOND : bond 0.00371 / 0.22 ( 23) SS BOND : angle 1.08297 / 0.84 ( 46) hydrogen bonds : bond 0.04271 / 2.91 ( 373) hydrogen bonds : angle 6.18966 / 4.15 ( 1038) link_NAG-ASN : bond 0.00342 / 0.21 ( 9) link_NAG-ASN : angle 2.12811 / 1.15 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 80 ILE cc_start: 0.5306 (OUTLIER) cc_final: 0.5072 (tp) REVERT: B 284 LEU cc_start: 0.7450 (tp) cc_final: 0.7235 (mt) REVERT: B 289 LEU cc_start: 0.7678 (mt) cc_final: 0.7397 (mp) REVERT: A 24 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8679 (ptmt) REVERT: A 70 GLN cc_start: 0.7939 (mp10) cc_final: 0.7580 (mp10) REVERT: A 417 CYS cc_start: 0.6224 (t) cc_final: 0.5562 (t) REVERT: C 38 MET cc_start: 0.6800 (tpt) cc_final: 0.6354 (tpt) REVERT: C 158 VAL cc_start: 0.7297 (t) cc_final: 0.6988 (p) REVERT: C 231 ILE cc_start: 0.6159 (mm) cc_final: 0.5766 (mt) REVERT: C 236 ARG cc_start: 0.6748 (mtt90) cc_final: 0.5420 (mmt180) outliers start: 38 outliers final: 19 residues processed: 169 average time/residue: 0.0995 time to fit residues: 24.6385 Evaluate side-chains 141 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 388 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 51 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 66 optimal weight: 0.5980 chunk 116 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 104 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 chunk 95 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 3 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN A 155 ASN A 315 HIS ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.217700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.209873 restraints weight = 11152.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.207976 restraints weight = 15928.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.207837 restraints weight = 19396.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.207681 restraints weight = 16377.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.207633 restraints weight = 14433.636| |-----------------------------------------------------------------------------| r_work (final): 0.4319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 11818 Z= 0.149 Angle : 0.687 10.570 16061 Z= 0.351 Chirality : 0.049 0.345 1945 Planarity : 0.004 0.060 2026 Dihedral : 5.472 20.953 1588 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.03 % Favored : 91.90 % Rotamer: Outliers : 3.60 % Allowed : 13.72 % Favored : 82.68 % 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: -2.60 (0.21), residues: 1470 helix: -1.16 (0.26), residues: 387 sheet: -1.28 (0.31), residues: 281 loop : -2.22 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 71 TYR 0.022 0.002 TYR L 32 PHE 0.019 0.002 PHE A 437 TRP 0.011 0.002 TRP C 308 HIS 0.013 0.002 HIS A 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (11786) covalent geometry : angle 0.68185 / 0.35 (15988) SS BOND : bond 0.00318 / 0.19 ( 23) SS BOND : angle 0.91212 / 0.65 ( 46) hydrogen bonds : bond 0.03746 / 2.54 ( 373) hydrogen bonds : angle 5.84791 / 3.92 ( 1038) link_NAG-ASN : bond 0.00310 / 0.18 ( 9) link_NAG-ASN : angle 2.00551 / 1.09 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 129 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 80 ILE cc_start: 0.5817 (OUTLIER) cc_final: 0.5468 (tp) REVERT: B 284 LEU cc_start: 0.7466 (tp) cc_final: 0.7257 (mt) REVERT: A 417 CYS cc_start: 0.6206 (t) cc_final: 0.5560 (t) REVERT: C 158 VAL cc_start: 0.7235 (t) cc_final: 0.6990 (p) REVERT: C 231 ILE cc_start: 0.5695 (mm) cc_final: 0.5391 (mt) REVERT: C 236 ARG cc_start: 0.6306 (mtt90) cc_final: 0.5248 (mmt180) outliers start: 47 outliers final: 24 residues processed: 164 average time/residue: 0.1011 time to fit residues: 24.0622 Evaluate side-chains 148 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 449 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 52 optimal weight: 0.0050 chunk 89 optimal weight: 0.9990 chunk 137 optimal weight: 0.2980 chunk 78 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 0 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 144 optimal weight: 0.6980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 89 GLN B 395 ASN H 3 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 ASN ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.218485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.211008 restraints weight = 11037.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.210176 restraints weight = 17676.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.197010 restraints weight = 18223.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.192860 restraints weight = 19372.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.193645 restraints weight = 20199.156| |-----------------------------------------------------------------------------| r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11818 Z= 0.143 Angle : 0.689 13.014 16061 Z= 0.350 Chirality : 0.049 0.341 1945 Planarity : 0.004 0.053 2026 Dihedral : 5.389 20.882 1588 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.89 % Favored : 92.04 % Rotamer: Outliers : 3.37 % Allowed : 15.56 % Favored : 81.07 % 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: -2.53 (0.21), residues: 1470 helix: -0.99 (0.27), residues: 377 sheet: -1.29 (0.30), residues: 294 loop : -2.22 (0.20), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 77 TYR 0.015 0.002 TYR L 49 PHE 0.019 0.002 PHE A 437 TRP 0.010 0.002 TRP C 308 HIS 0.012 0.002 HIS A 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (11786) covalent geometry : angle 0.68387 / 0.35 (15988) SS BOND : bond 0.00309 / 0.18 ( 23) SS BOND : angle 1.03649 / 0.66 ( 46) hydrogen bonds : bond 0.03508 / 2.40 ( 373) hydrogen bonds : angle 5.55691 / 3.70 ( 1038) link_NAG-ASN : bond 0.00295 / 0.17 ( 9) link_NAG-ASN : angle 1.92257 / 1.04 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 135 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: B 80 ILE cc_start: 0.5290 (OUTLIER) cc_final: 0.5017 (tp) REVERT: B 284 LEU cc_start: 0.7453 (tp) cc_final: 0.7236 (mt) REVERT: A 73 ARG cc_start: 0.7362 (mmm160) cc_final: 0.6687 (ttp-110) REVERT: A 371 ASP cc_start: 0.5998 (t70) cc_final: 0.5736 (m-30) REVERT: A 417 CYS cc_start: 0.6277 (t) cc_final: 0.5697 (t) REVERT: A 460 LEU cc_start: 0.6687 (OUTLIER) cc_final: 0.6338 (pp) REVERT: C 53 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7757 (mt) REVERT: C 90 LYS cc_start: 0.6587 (pttt) cc_final: 0.6386 (ptpt) REVERT: C 158 VAL cc_start: 0.7382 (t) cc_final: 0.7067 (p) REVERT: C 231 ILE cc_start: 0.5975 (mm) cc_final: 0.5701 (mt) REVERT: C 236 ARG cc_start: 0.6599 (mtt90) cc_final: 0.5374 (mmt180) outliers start: 44 outliers final: 28 residues processed: 167 average time/residue: 0.1052 time to fit residues: 25.8479 Evaluate side-chains 157 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 449 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 33 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 53 optimal weight: 0.1980 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 3 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 ASN ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.216168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.209103 restraints weight = 11187.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.197596 restraints weight = 16930.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.195303 restraints weight = 17186.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.194465 restraints weight = 14646.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.194114 restraints weight = 14995.112| |-----------------------------------------------------------------------------| r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11818 Z= 0.161 Angle : 0.704 11.077 16061 Z= 0.357 Chirality : 0.049 0.313 1945 Planarity : 0.004 0.052 2026 Dihedral : 5.432 22.113 1588 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.37 % Favored : 91.56 % Rotamer: Outliers : 4.06 % Allowed : 16.02 % Favored : 79.92 % 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: -2.51 (0.21), residues: 1470 helix: -0.92 (0.27), residues: 378 sheet: -1.29 (0.31), residues: 280 loop : -2.22 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 73 TYR 0.016 0.002 TYR A 309 PHE 0.018 0.002 PHE A 437 TRP 0.011 0.002 TRP C 308 HIS 0.013 0.002 HIS A 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (11786) covalent geometry : angle 0.69858 / 0.36 (15988) SS BOND : bond 0.00353 / 0.19 ( 23) SS BOND : angle 1.04065 / 0.66 ( 46) hydrogen bonds : bond 0.03495 / 2.38 ( 373) hydrogen bonds : angle 5.47559 / 3.65 ( 1038) link_NAG-ASN : bond 0.00277 / 0.16 ( 9) link_NAG-ASN : angle 1.96243 / 1.08 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 128 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: B 78 LEU cc_start: 0.7540 (tp) cc_final: 0.6992 (mt) REVERT: B 80 ILE cc_start: 0.5384 (OUTLIER) cc_final: 0.5007 (tp) REVERT: B 284 LEU cc_start: 0.7472 (tp) cc_final: 0.7199 (mt) REVERT: A 417 CYS cc_start: 0.6258 (t) cc_final: 0.5778 (t) REVERT: A 437 PHE cc_start: 0.7427 (t80) cc_final: 0.7100 (t80) REVERT: A 460 LEU cc_start: 0.6768 (OUTLIER) cc_final: 0.6414 (pp) REVERT: C 38 MET cc_start: 0.6907 (tpt) cc_final: 0.6450 (tpt) REVERT: C 53 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7792 (mt) REVERT: C 90 LYS cc_start: 0.6619 (pttt) cc_final: 0.6393 (ptpt) REVERT: C 153 ASP cc_start: 0.7059 (p0) cc_final: 0.6721 (p0) REVERT: C 231 ILE cc_start: 0.5988 (mm) cc_final: 0.5709 (mt) REVERT: C 236 ARG cc_start: 0.6521 (mtt90) cc_final: 0.5377 (mmt180) REVERT: C 422 ILE cc_start: 0.5926 (OUTLIER) cc_final: 0.5725 (pp) outliers start: 53 outliers final: 31 residues processed: 168 average time/residue: 0.0976 time to fit residues: 24.2703 Evaluate side-chains 154 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 449 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 109 optimal weight: 0.7980 chunk 137 optimal weight: 0.9990 chunk 120 optimal weight: 0.0770 chunk 119 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 123 optimal weight: 0.0870 chunk 8 optimal weight: 0.2980 chunk 124 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 380 ASN H 3 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 ASN ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.219361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.211426 restraints weight = 11070.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.194880 restraints weight = 15492.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.194341 restraints weight = 14758.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.194519 restraints weight = 13925.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.194787 restraints weight = 11982.328| |-----------------------------------------------------------------------------| r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11818 Z= 0.135 Angle : 0.682 11.110 16061 Z= 0.346 Chirality : 0.049 0.295 1945 Planarity : 0.004 0.065 2026 Dihedral : 5.308 20.291 1588 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.69 % Favored : 92.18 % Rotamer: Outliers : 3.14 % Allowed : 17.85 % Favored : 79.00 % 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: -2.45 (0.21), residues: 1470 helix: -0.83 (0.27), residues: 377 sheet: -1.32 (0.30), residues: 294 loop : -2.18 (0.21), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 61 TYR 0.012 0.001 TYR L 49 PHE 0.016 0.002 PHE A 437 TRP 0.010 0.002 TRP C 308 HIS 0.012 0.001 HIS A 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (11786) covalent geometry : angle 0.67712 / 0.35 (15988) SS BOND : bond 0.00532 / 0.39 ( 23) SS BOND : angle 0.90524 / 0.57 ( 46) hydrogen bonds : bond 0.03384 / 2.26 ( 373) hydrogen bonds : angle 5.36633 / 3.60 ( 1038) link_NAG-ASN : bond 0.00300 / 0.17 ( 9) link_NAG-ASN : angle 1.84485 / 1.02 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 129 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: B 80 ILE cc_start: 0.5099 (OUTLIER) cc_final: 0.4894 (tp) REVERT: B 360 ILE cc_start: 0.5520 (OUTLIER) cc_final: 0.5257 (pt) REVERT: L 91 ARG cc_start: 0.7610 (ttp-170) cc_final: 0.7377 (ttp-170) REVERT: A 417 CYS cc_start: 0.6212 (t) cc_final: 0.5781 (t) REVERT: A 434 THR cc_start: 0.7661 (t) cc_final: 0.7338 (m) REVERT: A 437 PHE cc_start: 0.7375 (t80) cc_final: 0.7123 (t80) REVERT: A 460 LEU cc_start: 0.6710 (OUTLIER) cc_final: 0.6364 (pp) REVERT: C 31 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7231 (tp) REVERT: C 53 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7700 (mt) REVERT: C 90 LYS cc_start: 0.6490 (pttt) cc_final: 0.6274 (ptpt) REVERT: C 158 VAL cc_start: 0.7371 (t) cc_final: 0.7118 (p) REVERT: C 231 ILE cc_start: 0.6054 (mm) cc_final: 0.5597 (mt) REVERT: C 236 ARG cc_start: 0.6548 (mtt90) cc_final: 0.5318 (mmt180) outliers start: 41 outliers final: 27 residues processed: 160 average time/residue: 0.0915 time to fit residues: 22.1150 Evaluate side-chains 154 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 449 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 144 optimal weight: 5.9990 chunk 104 optimal weight: 0.6980 chunk 15 optimal weight: 0.3980 chunk 84 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 chunk 119 optimal weight: 0.4980 chunk 38 optimal weight: 0.0570 chunk 35 optimal weight: 0.2980 chunk 86 optimal weight: 0.6980 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 3 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.220586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.213458 restraints weight = 11020.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.201239 restraints weight = 17022.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.199350 restraints weight = 16311.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.197171 restraints weight = 20627.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.197670 restraints weight = 18308.327| |-----------------------------------------------------------------------------| r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11818 Z= 0.129 Angle : 0.675 11.395 16061 Z= 0.340 Chirality : 0.048 0.305 1945 Planarity : 0.004 0.059 2026 Dihedral : 5.165 20.047 1588 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.89 % Favored : 91.97 % Rotamer: Outliers : 3.45 % Allowed : 18.47 % Favored : 78.08 % 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: -2.34 (0.21), residues: 1470 helix: -0.77 (0.27), residues: 383 sheet: -1.15 (0.31), residues: 287 loop : -2.15 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 61 TYR 0.014 0.001 TYR L 49 PHE 0.014 0.001 PHE A 437 TRP 0.009 0.002 TRP C 308 HIS 0.012 0.001 HIS A 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (11786) covalent geometry : angle 0.67057 / 0.34 (15988) SS BOND : bond 0.00312 / 0.18 ( 23) SS BOND : angle 0.95059 / 0.59 ( 46) hydrogen bonds : bond 0.03154 / 2.14 ( 373) hydrogen bonds : angle 5.18904 / 3.47 ( 1038) link_NAG-ASN : bond 0.00305 / 0.17 ( 9) link_NAG-ASN : angle 1.77726 / 0.97 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 128 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: B 78 LEU cc_start: 0.7595 (tp) cc_final: 0.6878 (mt) REVERT: B 80 ILE cc_start: 0.5365 (OUTLIER) cc_final: 0.5105 (tp) REVERT: B 172 ILE cc_start: 0.8007 (OUTLIER) cc_final: 0.7550 (pt) REVERT: A 73 ARG cc_start: 0.6744 (mmm160) cc_final: 0.6381 (ttp-110) REVERT: A 417 CYS cc_start: 0.6260 (t) cc_final: 0.5848 (t) REVERT: A 434 THR cc_start: 0.7576 (t) cc_final: 0.7291 (m) REVERT: A 460 LEU cc_start: 0.6641 (OUTLIER) cc_final: 0.6228 (pp) REVERT: C 31 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7224 (tp) REVERT: C 38 MET cc_start: 0.6847 (tpt) cc_final: 0.6502 (tpt) REVERT: C 53 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7665 (mt) REVERT: C 90 LYS cc_start: 0.6472 (pttt) cc_final: 0.6261 (ptpt) REVERT: C 153 ASP cc_start: 0.7164 (p0) cc_final: 0.6830 (p0) REVERT: C 231 ILE cc_start: 0.5982 (mm) cc_final: 0.5497 (mt) REVERT: C 236 ARG cc_start: 0.6446 (mtt90) cc_final: 0.5305 (mmt180) outliers start: 45 outliers final: 30 residues processed: 159 average time/residue: 0.0937 time to fit residues: 22.1727 Evaluate side-chains 151 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 449 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 0.0670 chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 0.0970 chunk 87 optimal weight: 0.9990 chunk 75 optimal weight: 0.0970 chunk 84 optimal weight: 0.5980 chunk 114 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 overall best weight: 0.3514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 3 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 95BHIS C 67 GLN ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.213361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.202969 restraints weight = 11146.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.201200 restraints weight = 15963.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.199345 restraints weight = 18397.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.198450 restraints weight = 17934.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.198288 restraints weight = 16040.081| |-----------------------------------------------------------------------------| r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6475 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11818 Z= 0.128 Angle : 0.678 11.477 16061 Z= 0.342 Chirality : 0.048 0.291 1945 Planarity : 0.004 0.055 2026 Dihedral : 5.159 19.902 1588 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.69 % Favored : 92.18 % Rotamer: Outliers : 3.45 % Allowed : 18.85 % Favored : 77.70 % 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: -2.31 (0.21), residues: 1470 helix: -0.74 (0.27), residues: 382 sheet: -1.15 (0.31), residues: 287 loop : -2.12 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 281 TYR 0.011 0.001 TYR L 49 PHE 0.021 0.001 PHE A 44 TRP 0.009 0.002 TRP C 308 HIS 0.012 0.001 HIS A 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (11786) covalent geometry : angle 0.67415 / 0.34 (15988) SS BOND : bond 0.00291 / 0.19 ( 23) SS BOND : angle 1.01360 / 0.68 ( 46) hydrogen bonds : bond 0.03154 / 2.15 ( 373) hydrogen bonds : angle 5.19435 / 3.47 ( 1038) link_NAG-ASN : bond 0.00281 / 0.16 ( 9) link_NAG-ASN : angle 1.71834 / 0.94 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 114 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: B 78 LEU cc_start: 0.7614 (tp) cc_final: 0.7050 (mt) REVERT: B 80 ILE cc_start: 0.5465 (OUTLIER) cc_final: 0.5215 (tp) REVERT: B 172 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7497 (pt) REVERT: B 360 ILE cc_start: 0.5413 (OUTLIER) cc_final: 0.5167 (pt) REVERT: A 417 CYS cc_start: 0.6240 (t) cc_final: 0.5834 (t) REVERT: A 434 THR cc_start: 0.7541 (t) cc_final: 0.7293 (m) REVERT: A 460 LEU cc_start: 0.6694 (OUTLIER) cc_final: 0.6343 (pp) REVERT: C 31 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7349 (tp) REVERT: C 38 MET cc_start: 0.6785 (tpt) cc_final: 0.6115 (tpt) REVERT: C 53 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7625 (mt) REVERT: C 90 LYS cc_start: 0.6425 (pttt) cc_final: 0.6218 (ptpt) REVERT: C 153 ASP cc_start: 0.6749 (p0) cc_final: 0.6442 (p0) REVERT: C 231 ILE cc_start: 0.5809 (mm) cc_final: 0.5310 (mt) REVERT: C 236 ARG cc_start: 0.6297 (mtt90) cc_final: 0.5328 (mmt180) outliers start: 45 outliers final: 28 residues processed: 149 average time/residue: 0.0920 time to fit residues: 20.4934 Evaluate side-chains 145 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 449 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 27 optimal weight: 0.2980 chunk 41 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 8 optimal weight: 0.0870 chunk 36 optimal weight: 0.0050 chunk 76 optimal weight: 0.4980 chunk 136 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.2772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 461 ASN C 67 GLN ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.222964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.215228 restraints weight = 11050.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.196754 restraints weight = 15164.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.196541 restraints weight = 14452.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.196614 restraints weight = 14289.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.196795 restraints weight = 12563.583| |-----------------------------------------------------------------------------| r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11818 Z= 0.122 Angle : 0.672 13.573 16061 Z= 0.338 Chirality : 0.048 0.288 1945 Planarity : 0.004 0.058 2026 Dihedral : 5.022 19.682 1588 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.94 % Favored : 92.93 % Rotamer: Outliers : 2.84 % Allowed : 19.46 % Favored : 77.70 % 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: -2.21 (0.21), residues: 1470 helix: -0.71 (0.27), residues: 384 sheet: -0.96 (0.32), residues: 287 loop : -2.09 (0.21), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 61 TYR 0.014 0.001 TYR L 32 PHE 0.012 0.001 PHE A 243 TRP 0.009 0.002 TRP A 308 HIS 0.012 0.001 HIS A 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (11786) covalent geometry : angle 0.66842 / 0.34 (15988) SS BOND : bond 0.00242 / 0.15 ( 23) SS BOND : angle 0.88845 / 0.59 ( 46) hydrogen bonds : bond 0.03043 / 2.06 ( 373) hydrogen bonds : angle 5.09042 / 3.39 ( 1038) link_NAG-ASN : bond 0.00305 / 0.17 ( 9) link_NAG-ASN : angle 1.66947 / 0.90 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 122 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: B 78 LEU cc_start: 0.7774 (tp) cc_final: 0.7004 (mt) REVERT: B 360 ILE cc_start: 0.5383 (OUTLIER) cc_final: 0.5135 (pt) REVERT: A 417 CYS cc_start: 0.6245 (t) cc_final: 0.5844 (t) REVERT: A 434 THR cc_start: 0.7361 (t) cc_final: 0.7148 (m) REVERT: A 460 LEU cc_start: 0.6646 (OUTLIER) cc_final: 0.6241 (pp) REVERT: C 31 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7316 (tp) REVERT: C 38 MET cc_start: 0.6446 (tpt) cc_final: 0.6120 (tpt) REVERT: C 53 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7671 (mt) REVERT: C 87 LYS cc_start: 0.4668 (tptp) cc_final: 0.4406 (ptmt) REVERT: C 153 ASP cc_start: 0.7572 (p0) cc_final: 0.7256 (p0) REVERT: C 231 ILE cc_start: 0.5907 (mm) cc_final: 0.5480 (mt) REVERT: C 236 ARG cc_start: 0.6690 (mtt90) cc_final: 0.5329 (mmt180) outliers start: 37 outliers final: 28 residues processed: 148 average time/residue: 0.0963 time to fit residues: 21.2923 Evaluate side-chains 145 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 449 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 14 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.217038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.209630 restraints weight = 11144.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.207820 restraints weight = 15104.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.207181 restraints weight = 18615.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.206529 restraints weight = 17328.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.206337 restraints weight = 17330.159| |-----------------------------------------------------------------------------| r_work (final): 0.4312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11818 Z= 0.166 Angle : 0.716 11.951 16061 Z= 0.360 Chirality : 0.049 0.284 1945 Planarity : 0.004 0.057 2026 Dihedral : 5.250 20.599 1588 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.44 % Favored : 91.43 % Rotamer: Outliers : 2.99 % Allowed : 19.54 % Favored : 77.47 % 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: -2.34 (0.21), residues: 1470 helix: -0.84 (0.27), residues: 384 sheet: -1.00 (0.32), residues: 289 loop : -2.18 (0.21), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 281 TYR 0.019 0.002 TYR A 309 PHE 0.023 0.002 PHE A 44 TRP 0.013 0.002 TRP H 103 HIS 0.012 0.002 HIS A 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (11786) covalent geometry : angle 0.71202 / 0.36 (15988) SS BOND : bond 0.00269 / 0.17 ( 23) SS BOND : angle 0.99536 / 0.64 ( 46) hydrogen bonds : bond 0.03251 / 2.22 ( 373) hydrogen bonds : angle 5.24867 / 3.52 ( 1038) link_NAG-ASN : bond 0.00250 / 0.15 ( 9) link_NAG-ASN : angle 1.82900 / 0.98 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1944.75 seconds wall clock time: 34 minutes 33.72 seconds (2073.72 seconds total)