Starting phenix.real_space_refine on Wed Mar 4 07:18:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dg8_27418/03_2026/8dg8_27418.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dg8_27418/03_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_27418/03_2026/8dg8_27418.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dg8_27418/03_2026/8dg8_27418.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dg8_27418/03_2026/8dg8_27418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dg8_27418/03_2026/8dg8_27418.map" } 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-5986/lib/python3.9/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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.35, per 1000 atoms: 0.20 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: 0.80 Conformation dependent library (CDL) restraints added in 502.5 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: 0.39 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: 1.91 Time building geometry restraints manager: 1.09 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 - 25.02: 6994 25.02 - 50.04: 312 50.04 - 75.06: 34 75.06 - 100.08: 14 100.08 - 125.10: 1 Dihedral angle restraints: 7355 sinusoidal: 3024 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 7352 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: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.830 Find NCS groups from input model: 0.180 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: 0.010 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: 14.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5442 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 : 14.018 125.103 4492 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 covalent geometry : bond 0.00363 (11786) covalent geometry : angle 0.71670 (15988) SS BOND : bond 0.00375 ( 23) SS BOND : angle 0.88145 ( 46) hydrogen bonds : bond 0.29256 ( 373) hydrogen bonds : angle 10.13912 ( 1038) link_NAG-ASN : bond 0.01139 ( 9) link_NAG-ASN : angle 5.95840 ( 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 : 0.479 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: 0.0995 time to fit residues: 30.5842 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 : 0.421 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.240459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 107)---------------| | r_work = 0.4571 r_free = 0.4571 target = 0.231131 restraints weight = 10397.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.214453 restraints weight = 15580.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.214860 restraints weight = 16149.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.214886 restraints weight = 13996.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.215375 restraints weight = 11948.433| |-----------------------------------------------------------------------------| r_work (final): 0.4326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11818 Z= 0.177 Angle : 0.774 9.059 16061 Z= 0.395 Chirality : 0.052 0.309 1945 Planarity : 0.005 0.096 2026 Dihedral : 8.672 114.198 1780 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.10 % Favored : 91.84 % Rotamer: Outliers : 1.61 % Allowed : 8.35 % 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: -2.76 (0.20), residues: 1470 helix: -1.38 (0.25), residues: 373 sheet: -1.44 (0.31), residues: 276 loop : -2.24 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 281 TYR 0.026 0.002 TYR C 71 PHE 0.019 0.002 PHE A 437 TRP 0.013 0.002 TRP C 308 HIS 0.007 0.001 HIS C 414 Details of bonding type rmsd covalent geometry : bond 0.00411 (11786) covalent geometry : angle 0.76623 (15988) SS BOND : bond 0.00436 ( 23) SS BOND : angle 1.00295 ( 46) hydrogen bonds : bond 0.04885 ( 373) hydrogen bonds : angle 6.68169 ( 1038) link_NAG-ASN : bond 0.00408 ( 9) link_NAG-ASN : angle 2.72902 ( 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 173 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 284 LEU cc_start: 0.7475 (tp) cc_final: 0.7214 (mt) REVERT: B 289 LEU cc_start: 0.7614 (mt) cc_final: 0.7376 (mp) REVERT: C 48 TYR cc_start: 0.8129 (m-80) cc_final: 0.7519 (m-80) REVERT: C 158 VAL cc_start: 0.7390 (t) cc_final: 0.7038 (p) REVERT: C 236 ARG cc_start: 0.6702 (mtt90) cc_final: 0.5468 (mmt180) outliers start: 21 outliers final: 13 residues processed: 165 average time/residue: 0.1047 time to fit residues: 24.8265 Evaluate side-chains 137 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL 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 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 A residue 419 THR 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: 0.0050 chunk 50 optimal weight: 8.9990 chunk 84 optimal weight: 0.6980 chunk 123 optimal weight: 5.9990 chunk 82 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 69 optimal weight: 4.9990 chunk 37 optimal weight: 0.2980 chunk 57 optimal weight: 1.9990 chunk 131 optimal weight: 0.0670 overall best weight: 0.3132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN B 395 ASN 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 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 461 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.244692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.236526 restraints weight = 10777.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.221659 restraints weight = 15079.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.219588 restraints weight = 16819.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.220015 restraints weight = 16164.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.220665 restraints weight = 12638.357| |-----------------------------------------------------------------------------| r_work (final): 0.4459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6468 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11818 Z= 0.134 Angle : 0.686 10.251 16061 Z= 0.350 Chirality : 0.048 0.372 1945 Planarity : 0.004 0.068 2026 Dihedral : 7.886 105.794 1777 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.80 % Favored : 93.13 % Rotamer: Outliers : 2.84 % Allowed : 11.11 % Favored : 86.05 % 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: -2.49 (0.21), residues: 1470 helix: -1.07 (0.26), residues: 375 sheet: -1.26 (0.30), residues: 291 loop : -2.13 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 281 TYR 0.022 0.002 TYR L 32 PHE 0.020 0.002 PHE A 437 TRP 0.010 0.002 TRP B 308 HIS 0.012 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00290 (11786) covalent geometry : angle 0.67886 (15988) SS BOND : bond 0.00421 ( 23) SS BOND : angle 1.02555 ( 46) hydrogen bonds : bond 0.04097 ( 373) hydrogen bonds : angle 6.05648 ( 1038) link_NAG-ASN : bond 0.00311 ( 9) link_NAG-ASN : angle 2.23195 ( 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 180 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 80 ILE cc_start: 0.5413 (OUTLIER) cc_final: 0.5150 (tp) REVERT: B 284 LEU cc_start: 0.7363 (tp) cc_final: 0.7155 (mt) REVERT: B 289 LEU cc_start: 0.7601 (mt) cc_final: 0.7372 (mp) REVERT: A 371 ASP cc_start: 0.5921 (t70) cc_final: 0.5670 (m-30) REVERT: A 417 CYS cc_start: 0.6162 (t) cc_final: 0.5430 (t) REVERT: C 158 VAL cc_start: 0.7321 (t) cc_final: 0.7046 (p) REVERT: C 231 ILE cc_start: 0.6015 (mm) cc_final: 0.5591 (mt) REVERT: C 236 ARG cc_start: 0.6729 (mtt90) cc_final: 0.5543 (mmt180) outliers start: 37 outliers final: 14 residues processed: 168 average time/residue: 0.0969 time to fit residues: 23.9881 Evaluate side-chains 133 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 302 ASN 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 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: 0.9980 chunk 116 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 104 optimal weight: 0.0060 chunk 105 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 395 ASN H 3 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN A 155 ASN ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 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 = 0.4680 r_free = 0.4680 target = 0.242946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.234347 restraints weight = 10544.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.218146 restraints weight = 14245.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.218723 restraints weight = 14582.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.218688 restraints weight = 12592.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.218960 restraints weight = 10824.488| |-----------------------------------------------------------------------------| r_work (final): 0.4370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6554 moved from start: 0.2528 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= 0.158 Angle : 0.693 10.770 16061 Z= 0.354 Chirality : 0.049 0.349 1945 Planarity : 0.004 0.057 2026 Dihedral : 7.624 99.759 1777 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.82 % Favored : 92.11 % Rotamer: Outliers : 3.37 % Allowed : 13.10 % Favored : 83.52 % 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: -2.42 (0.21), residues: 1470 helix: -0.94 (0.27), residues: 369 sheet: -1.17 (0.31), residues: 288 loop : -2.13 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 73 TYR 0.019 0.002 TYR L 32 PHE 0.028 0.002 PHE A 378 TRP 0.010 0.002 TRP C 308 HIS 0.012 0.002 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00372 (11786) covalent geometry : angle 0.68654 (15988) SS BOND : bond 0.00337 ( 23) SS BOND : angle 0.93154 ( 46) hydrogen bonds : bond 0.03772 ( 373) hydrogen bonds : angle 5.79105 ( 1038) link_NAG-ASN : bond 0.00266 ( 9) link_NAG-ASN : angle 2.20245 ( 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 173 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 129 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 80 ILE cc_start: 0.5449 (OUTLIER) cc_final: 0.5171 (tp) REVERT: B 284 LEU cc_start: 0.7348 (tp) cc_final: 0.7139 (mt) REVERT: A 371 ASP cc_start: 0.5831 (t70) cc_final: 0.5597 (m-30) REVERT: A 417 CYS cc_start: 0.6250 (t) cc_final: 0.5631 (t) REVERT: A 437 PHE cc_start: 0.7382 (t80) cc_final: 0.6897 (t80) REVERT: C 158 VAL cc_start: 0.7343 (t) cc_final: 0.7029 (p) REVERT: C 231 ILE cc_start: 0.5908 (mm) cc_final: 0.5574 (mt) REVERT: C 236 ARG cc_start: 0.6672 (mtt90) cc_final: 0.5451 (mmt180) outliers start: 44 outliers final: 26 residues processed: 159 average time/residue: 0.1047 time to fit residues: 24.2800 Evaluate side-chains 148 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 82 LEU 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 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 302 ASN Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 397 ILE 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 52 optimal weight: 0.3980 chunk 89 optimal weight: 0.7980 chunk 137 optimal weight: 0.5980 chunk 78 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 98 optimal weight: 0.0170 chunk 47 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 144 optimal weight: 0.0570 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.221899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.214005 restraints weight = 10928.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.197705 restraints weight = 15974.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.197505 restraints weight = 16025.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.197348 restraints weight = 16405.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.197736 restraints weight = 12619.175| |-----------------------------------------------------------------------------| r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11818 Z= 0.128 Angle : 0.661 10.853 16061 Z= 0.335 Chirality : 0.048 0.342 1945 Planarity : 0.004 0.052 2026 Dihedral : 7.112 91.844 1777 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.35 % Favored : 92.59 % Rotamer: Outliers : 3.52 % Allowed : 14.79 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.21), residues: 1470 helix: -0.83 (0.27), residues: 371 sheet: -1.19 (0.31), residues: 268 loop : -2.10 (0.20), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 77 TYR 0.012 0.001 TYR A 338 PHE 0.019 0.002 PHE A 378 TRP 0.010 0.002 TRP C 308 HIS 0.013 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00288 (11786) covalent geometry : angle 0.65559 (15988) SS BOND : bond 0.00327 ( 23) SS BOND : angle 0.75401 ( 46) hydrogen bonds : bond 0.03404 ( 373) hydrogen bonds : angle 5.47297 ( 1038) link_NAG-ASN : bond 0.00262 ( 9) link_NAG-ASN : angle 2.06481 ( 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 184 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 138 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 80 ILE cc_start: 0.5314 (OUTLIER) cc_final: 0.5042 (tp) REVERT: A 371 ASP cc_start: 0.5839 (t70) cc_final: 0.5621 (m-30) REVERT: A 417 CYS cc_start: 0.6190 (t) cc_final: 0.5620 (t) REVERT: A 434 THR cc_start: 0.7777 (t) cc_final: 0.7394 (m) REVERT: A 437 PHE cc_start: 0.7374 (t80) cc_final: 0.7057 (t80) REVERT: C 49 LEU cc_start: 0.7357 (mp) cc_final: 0.7110 (tp) REVERT: C 53 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7617 (mt) REVERT: C 158 VAL cc_start: 0.7245 (t) cc_final: 0.6910 (p) REVERT: C 231 ILE cc_start: 0.5961 (mm) cc_final: 0.5662 (mt) REVERT: C 236 ARG cc_start: 0.6530 (mtt90) cc_final: 0.5398 (mmt180) REVERT: C 302 ASN cc_start: 0.7086 (t0) cc_final: 0.6594 (p0) outliers start: 46 outliers final: 24 residues processed: 172 average time/residue: 0.1042 time to fit residues: 26.0614 Evaluate side-chains 151 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 82 LEU 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 82 MET 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 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 C residue 53 LEU Chi-restraints excluded: chain C residue 169 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 33 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 chunk 112 optimal weight: 0.0870 chunk 93 optimal weight: 2.9990 chunk 136 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 83 optimal weight: 0.3980 chunk 43 optimal weight: 0.6980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.220434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.213153 restraints weight = 11083.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.208018 restraints weight = 14235.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.206517 restraints weight = 24772.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.206616 restraints weight = 23124.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.206590 restraints weight = 17881.007| |-----------------------------------------------------------------------------| r_work (final): 0.4302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6282 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11818 Z= 0.135 Angle : 0.684 12.003 16061 Z= 0.343 Chirality : 0.048 0.303 1945 Planarity : 0.004 0.053 2026 Dihedral : 6.930 87.302 1777 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.89 % Favored : 92.04 % Rotamer: Outliers : 3.75 % Allowed : 16.17 % Favored : 80.08 % 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: -2.24 (0.21), residues: 1470 helix: -0.69 (0.28), residues: 369 sheet: -1.06 (0.32), residues: 276 loop : -2.06 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 77 TYR 0.014 0.002 TYR L 49 PHE 0.016 0.002 PHE A 437 TRP 0.009 0.002 TRP C 308 HIS 0.013 0.002 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00312 (11786) covalent geometry : angle 0.67746 (15988) SS BOND : bond 0.00304 ( 23) SS BOND : angle 1.14716 ( 46) hydrogen bonds : bond 0.03373 ( 373) hydrogen bonds : angle 5.35448 ( 1038) link_NAG-ASN : bond 0.00233 ( 9) link_NAG-ASN : angle 2.08470 ( 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 174 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 125 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: B 80 ILE cc_start: 0.5701 (OUTLIER) cc_final: 0.5357 (tp) REVERT: A 417 CYS cc_start: 0.6137 (t) cc_final: 0.5595 (t) REVERT: A 434 THR cc_start: 0.7763 (t) cc_final: 0.7469 (m) REVERT: A 437 PHE cc_start: 0.7297 (t80) cc_final: 0.7009 (t80) REVERT: A 460 LEU cc_start: 0.6647 (OUTLIER) cc_final: 0.6280 (pp) REVERT: C 53 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7600 (mt) REVERT: C 153 ASP cc_start: 0.6555 (p0) cc_final: 0.6265 (p0) REVERT: C 158 VAL cc_start: 0.7211 (t) cc_final: 0.6938 (p) REVERT: C 231 ILE cc_start: 0.5707 (mm) cc_final: 0.5407 (mt) REVERT: C 236 ARG cc_start: 0.6242 (mtt90) cc_final: 0.5242 (mmt180) outliers start: 49 outliers final: 31 residues processed: 160 average time/residue: 0.1000 time to fit residues: 23.2829 Evaluate side-chains 154 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 82 LEU 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 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 63 VAL Chi-restraints excluded: chain H residue 82 MET 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 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 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 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 370 SER Chi-restraints excluded: chain C residue 413 THR 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: 0.5980 chunk 137 optimal weight: 1.9990 chunk 120 optimal weight: 8.9990 chunk 119 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 8 optimal weight: 0.0970 chunk 124 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN H 3 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 HIS C 198 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.218004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.210789 restraints weight = 11106.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.209658 restraints weight = 17213.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.208141 restraints weight = 18207.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.202970 restraints weight = 23049.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.202349 restraints weight = 27413.083| |-----------------------------------------------------------------------------| r_work (final): 0.4253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6360 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11818 Z= 0.158 Angle : 0.702 11.131 16061 Z= 0.354 Chirality : 0.049 0.288 1945 Planarity : 0.004 0.053 2026 Dihedral : 6.879 82.492 1777 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.30 % Favored : 91.63 % Rotamer: Outliers : 3.45 % Allowed : 17.09 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.21), residues: 1470 helix: -0.74 (0.27), residues: 370 sheet: -1.14 (0.31), residues: 290 loop : -2.13 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 73 TYR 0.016 0.002 TYR A 309 PHE 0.019 0.002 PHE A 44 TRP 0.010 0.002 TRP C 308 HIS 0.011 0.002 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00377 (11786) covalent geometry : angle 0.69548 (15988) SS BOND : bond 0.00269 ( 23) SS BOND : angle 1.12456 ( 46) hydrogen bonds : bond 0.03465 ( 373) hydrogen bonds : angle 5.37237 ( 1038) link_NAG-ASN : bond 0.00215 ( 9) link_NAG-ASN : angle 2.17026 ( 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 169 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 124 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 80 ILE cc_start: 0.5582 (OUTLIER) cc_final: 0.5254 (tp) REVERT: A 417 CYS cc_start: 0.6212 (t) cc_final: 0.5718 (t) REVERT: A 460 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.6513 (pp) REVERT: C 31 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7251 (tp) REVERT: C 53 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7652 (mt) REVERT: C 153 ASP cc_start: 0.6700 (p0) cc_final: 0.6391 (p0) REVERT: C 231 ILE cc_start: 0.5779 (mm) cc_final: 0.5322 (mt) REVERT: C 236 ARG cc_start: 0.6196 (mtt90) cc_final: 0.5228 (mmt180) outliers start: 45 outliers final: 32 residues processed: 157 average time/residue: 0.1049 time to fit residues: 24.0005 Evaluate side-chains 155 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 119 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 82 LEU 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 82 MET 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 360 ILE 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 31 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 144 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 111 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 95BHIS C 407 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.216705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.209103 restraints weight = 11076.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.208413 restraints weight = 16169.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.207871 restraints weight = 17094.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.207188 restraints weight = 16871.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.206667 restraints weight = 17237.418| |-----------------------------------------------------------------------------| r_work (final): 0.4307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6294 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11818 Z= 0.165 Angle : 0.715 11.583 16061 Z= 0.360 Chirality : 0.049 0.273 1945 Planarity : 0.004 0.054 2026 Dihedral : 6.834 77.897 1777 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.64 % Favored : 91.22 % Rotamer: Outliers : 3.83 % Allowed : 17.24 % Favored : 78.93 % 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: -2.41 (0.21), residues: 1470 helix: -0.83 (0.27), residues: 375 sheet: -1.12 (0.31), residues: 292 loop : -2.22 (0.20), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 61 TYR 0.017 0.002 TYR A 309 PHE 0.012 0.002 PHE A 243 TRP 0.011 0.002 TRP C 308 HIS 0.011 0.002 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00398 (11786) covalent geometry : angle 0.70872 (15988) SS BOND : bond 0.00357 ( 23) SS BOND : angle 1.11497 ( 46) hydrogen bonds : bond 0.03442 ( 373) hydrogen bonds : angle 5.34280 ( 1038) link_NAG-ASN : bond 0.00212 ( 9) link_NAG-ASN : angle 2.22497 ( 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 169 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 119 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 80 ILE cc_start: 0.5728 (OUTLIER) cc_final: 0.5426 (tp) REVERT: A 417 CYS cc_start: 0.6273 (t) cc_final: 0.5873 (t) REVERT: A 460 LEU cc_start: 0.6931 (OUTLIER) cc_final: 0.6665 (pp) REVERT: C 31 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7212 (tp) REVERT: C 38 MET cc_start: 0.6663 (tpt) cc_final: 0.6236 (tpt) REVERT: C 53 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7627 (mt) REVERT: C 153 ASP cc_start: 0.6484 (p0) cc_final: 0.6197 (p0) REVERT: C 231 ILE cc_start: 0.5647 (mm) cc_final: 0.5174 (mt) REVERT: C 236 ARG cc_start: 0.6147 (mtt90) cc_final: 0.5248 (mmt180) outliers start: 50 outliers final: 38 residues processed: 153 average time/residue: 0.0988 time to fit residues: 22.1404 Evaluate side-chains 154 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 112 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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 82 LEU 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 3 GLN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 82 MET 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 86 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 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 419 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 49 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 9 optimal weight: 4.9990 chunk 6 optimal weight: 0.0370 chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 114 optimal weight: 0.5980 chunk 130 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.218073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.210755 restraints weight = 11009.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.194046 restraints weight = 15149.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.192957 restraints weight = 15450.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.192691 restraints weight = 14358.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.192797 restraints weight = 14246.336| |-----------------------------------------------------------------------------| r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11818 Z= 0.151 Angle : 0.715 11.858 16061 Z= 0.359 Chirality : 0.049 0.279 1945 Planarity : 0.004 0.054 2026 Dihedral : 6.737 74.759 1777 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.16 % Favored : 91.70 % Rotamer: Outliers : 3.37 % Allowed : 17.85 % Favored : 78.77 % 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: -2.37 (0.21), residues: 1470 helix: -0.78 (0.27), residues: 381 sheet: -1.09 (0.32), residues: 282 loop : -2.21 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 61 TYR 0.014 0.002 TYR A 309 PHE 0.019 0.002 PHE A 44 TRP 0.011 0.002 TRP C 308 HIS 0.012 0.002 HIS H 102 Details of bonding type rmsd covalent geometry : bond 0.00355 (11786) covalent geometry : angle 0.70878 (15988) SS BOND : bond 0.00303 ( 23) SS BOND : angle 0.87011 ( 46) hydrogen bonds : bond 0.03314 ( 373) hydrogen bonds : angle 5.33707 ( 1038) link_NAG-ASN : bond 0.00205 ( 9) link_NAG-ASN : angle 2.22208 ( 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 157 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 113 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 80 ILE cc_start: 0.5268 (OUTLIER) cc_final: 0.5016 (tp) REVERT: A 417 CYS cc_start: 0.6365 (t) cc_final: 0.5961 (t) REVERT: A 460 LEU cc_start: 0.6868 (OUTLIER) cc_final: 0.6617 (pp) REVERT: C 31 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7123 (tp) REVERT: C 38 MET cc_start: 0.6724 (tpt) cc_final: 0.6270 (tpt) REVERT: C 53 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7715 (mt) REVERT: C 153 ASP cc_start: 0.7423 (p0) cc_final: 0.7127 (p0) REVERT: C 231 ILE cc_start: 0.5978 (mm) cc_final: 0.5538 (mt) REVERT: C 236 ARG cc_start: 0.6600 (mtt90) cc_final: 0.5376 (mmt180) outliers start: 44 outliers final: 35 residues processed: 143 average time/residue: 0.0942 time to fit residues: 19.9258 Evaluate side-chains 149 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 110 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 82 LEU 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 82 MET 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 86 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 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 419 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 49 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 27 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 136 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 6 optimal weight: 0.0770 chunk 81 optimal weight: 3.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 380 ASN H 3 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.217623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.210609 restraints weight = 11090.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.198509 restraints weight = 16431.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.195415 restraints weight = 16820.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.195331 restraints weight = 20183.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.195423 restraints weight = 16558.153| |-----------------------------------------------------------------------------| r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11818 Z= 0.150 Angle : 0.704 12.297 16061 Z= 0.354 Chirality : 0.048 0.266 1945 Planarity : 0.004 0.057 2026 Dihedral : 6.633 70.387 1777 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.98 % Favored : 90.88 % Rotamer: Outliers : 3.30 % Allowed : 18.54 % Favored : 78.16 % 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: -2.33 (0.21), residues: 1470 helix: -0.80 (0.27), residues: 380 sheet: -0.95 (0.32), residues: 279 loop : -2.19 (0.20), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 61 TYR 0.016 0.002 TYR A 309 PHE 0.018 0.002 PHE A 243 TRP 0.011 0.002 TRP C 308 HIS 0.012 0.002 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00355 (11786) covalent geometry : angle 0.69775 (15988) SS BOND : bond 0.00270 ( 23) SS BOND : angle 0.86106 ( 46) hydrogen bonds : bond 0.03287 ( 373) hydrogen bonds : angle 5.27915 ( 1038) link_NAG-ASN : bond 0.00206 ( 9) link_NAG-ASN : angle 2.24791 ( 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 160 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 117 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 80 ILE cc_start: 0.5475 (OUTLIER) cc_final: 0.5206 (tp) REVERT: A 460 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6597 (pp) REVERT: C 31 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7333 (tp) REVERT: C 38 MET cc_start: 0.6750 (tpt) cc_final: 0.6288 (tpt) REVERT: C 53 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7683 (mt) REVERT: C 153 ASP cc_start: 0.7275 (p0) cc_final: 0.6934 (p0) REVERT: C 231 ILE cc_start: 0.5831 (mm) cc_final: 0.5429 (mt) REVERT: C 236 ARG cc_start: 0.6377 (mtt90) cc_final: 0.5297 (mmt180) outliers start: 43 outliers final: 35 residues processed: 146 average time/residue: 0.0914 time to fit residues: 20.1830 Evaluate side-chains 150 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 111 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 82 LEU 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 3 GLN Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain A residue 86 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 347 VAL Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 373 VAL 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 49 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: 0.0770 chunk 38 optimal weight: 0.0670 chunk 40 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 8 optimal weight: 0.3980 chunk 79 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 32 optimal weight: 0.0050 chunk 67 optimal weight: 0.9990 chunk 78 optimal weight: 0.3980 overall best weight: 0.1890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.223269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.216509 restraints weight = 10965.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 77)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.200469 restraints weight = 12527.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.199431 restraints weight = 14278.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.199301 restraints weight = 13959.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.199381 restraints weight = 13276.639| |-----------------------------------------------------------------------------| r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6446 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11818 Z= 0.125 Angle : 0.692 12.442 16061 Z= 0.347 Chirality : 0.047 0.269 1945 Planarity : 0.004 0.058 2026 Dihedral : 6.382 65.668 1777 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.28 % Favored : 92.59 % Rotamer: Outliers : 2.45 % Allowed : 19.62 % Favored : 77.93 % 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: -2.19 (0.22), residues: 1470 helix: -0.70 (0.27), residues: 386 sheet: -0.88 (0.32), residues: 280 loop : -2.09 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 61 TYR 0.011 0.001 TYR C 294 PHE 0.016 0.001 PHE A 243 TRP 0.012 0.002 TRP A 308 HIS 0.016 0.002 HIS H 102 Details of bonding type rmsd covalent geometry : bond 0.00272 (11786) covalent geometry : angle 0.68741 (15988) SS BOND : bond 0.00254 ( 23) SS BOND : angle 0.66667 ( 46) hydrogen bonds : bond 0.03106 ( 373) hydrogen bonds : angle 5.14777 ( 1038) link_NAG-ASN : bond 0.00243 ( 9) link_NAG-ASN : angle 2.16298 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1892.09 seconds wall clock time: 33 minutes 42.70 seconds (2022.70 seconds total)