Starting phenix.real_space_refine on Mon Dec 30 00:48:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dg8_27418/12_2024/8dg8_27418.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dg8_27418/12_2024/8dg8_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dg8_27418/12_2024/8dg8_27418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dg8_27418/12_2024/8dg8_27418.map" model { file = "/net/cci-nas-00/data/ceres_data/8dg8_27418/12_2024/8dg8_27418.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dg8_27418/12_2024/8dg8_27418.cif" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 7.46, per 1000 atoms: 0.64 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: 2.78 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.70 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: 4.04 Time building geometry restraints manager: 3.29 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: 2.170 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: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 29.400 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.490 ------------------------------------------------------------------------------- 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 11786 Z= 0.236 Angle : 0.717 10.362 15988 Z= 0.391 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.014 0.002 TRP H 47 HIS 0.005 0.001 HIS C 414 PHE 0.009 0.001 PHE L 62 TYR 0.014 0.001 TYR A 83 ARG 0.004 0.000 ARG H 71 *********************** 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 : 1.274 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: 0.6132 (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: 0.4245 (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: 0.2313 time to fit residues: 70.3873 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 : 1.287 ------------------------------------------------------------------------------- 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 124 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 38 optimal weight: 0.0470 chunk 75 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 70 optimal weight: 0.0020 chunk 86 optimal weight: 1.9990 chunk 134 optimal weight: 0.3980 overall best weight: 0.3686 ------------------------------------------------------------------------------- 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** C 461 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5463 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11786 Z= 0.214 Angle : 0.735 9.067 15988 Z= 0.378 Chirality : 0.051 0.322 1945 Planarity : 0.005 0.095 2026 Dihedral : 8.660 115.516 1780 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.35 % Favored : 92.59 % Rotamer: Outliers : 1.38 % Allowed : 8.20 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.21), residues: 1470 helix: -1.32 (0.25), residues: 377 sheet: -1.40 (0.31), residues: 276 loop : -2.19 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 308 HIS 0.007 0.001 HIS C 414 PHE 0.020 0.002 PHE A 437 TYR 0.024 0.002 TYR C 71 ARG 0.005 0.001 ARG A 281 *********************** 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 181 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 281 ARG cc_start: 0.7190 (mtm-85) cc_final: 0.6922 (ptt90) REVERT: B 284 LEU cc_start: 0.6637 (tp) cc_final: 0.6028 (mt) REVERT: B 289 LEU cc_start: 0.7252 (mt) cc_final: 0.7038 (mp) REVERT: B 425 MET cc_start: 0.4630 (mtp) cc_final: 0.4403 (mtm) REVERT: H 82 MET cc_start: 0.6328 (tpp) cc_final: 0.6115 (tpp) REVERT: H 100 GLU cc_start: 0.6135 (tp30) cc_final: 0.5487 (tt0) REVERT: L 31 TYR cc_start: 0.7137 (m-80) cc_final: 0.6712 (m-80) REVERT: L 32 TYR cc_start: 0.6486 (m-10) cc_final: 0.5989 (m-10) REVERT: A 56 LYS cc_start: 0.6846 (tptm) cc_final: 0.6228 (mmtt) REVERT: A 70 GLN cc_start: 0.8697 (tm-30) cc_final: 0.8262 (mm-40) REVERT: A 78 LEU cc_start: 0.6170 (pp) cc_final: 0.5800 (tt) REVERT: A 209 GLU cc_start: 0.7249 (tp30) cc_final: 0.5948 (mt-10) REVERT: A 270 ASP cc_start: 0.5543 (t0) cc_final: 0.5322 (t0) REVERT: A 371 ASP cc_start: 0.7057 (t70) cc_final: 0.6227 (m-30) REVERT: A 437 PHE cc_start: 0.6641 (t80) cc_final: 0.6334 (t80) REVERT: C 48 TYR cc_start: 0.7628 (m-80) cc_final: 0.6878 (m-80) REVERT: C 56 LYS cc_start: 0.7470 (tmtt) cc_final: 0.6894 (tppp) REVERT: C 158 VAL cc_start: 0.6394 (t) cc_final: 0.6102 (p) REVERT: C 236 ARG cc_start: 0.7025 (mtt90) cc_final: 0.5388 (mmt180) REVERT: C 278 LEU cc_start: 0.7523 (mp) cc_final: 0.7279 (mt) outliers start: 18 outliers final: 8 residues processed: 174 average time/residue: 0.2493 time to fit residues: 62.6744 Evaluate side-chains 130 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain C residue 370 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 111 optimal weight: 0.0980 chunk 91 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 145 optimal weight: 0.0370 chunk 119 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 108 optimal weight: 0.9990 overall best weight: 0.4058 ------------------------------------------------------------------------------- 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 155 ASN ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5463 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 11786 Z= 0.204 Angle : 0.683 10.145 15988 Z= 0.351 Chirality : 0.049 0.369 1945 Planarity : 0.004 0.071 2026 Dihedral : 8.015 108.139 1777 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.35 % Favored : 92.59 % Rotamer: Outliers : 2.22 % Allowed : 11.42 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.21), residues: 1470 helix: -1.13 (0.26), residues: 376 sheet: -1.26 (0.30), residues: 288 loop : -2.14 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 308 HIS 0.009 0.001 HIS C 414 PHE 0.018 0.002 PHE A 437 TYR 0.019 0.002 TYR L 49 ARG 0.004 0.000 ARG H 71 *********************** 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 170 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 281 ARG cc_start: 0.7102 (mtm-85) cc_final: 0.6795 (ptt90) REVERT: B 284 LEU cc_start: 0.6621 (tp) cc_final: 0.6057 (mt) REVERT: B 289 LEU cc_start: 0.7359 (mt) cc_final: 0.7156 (mp) REVERT: H 100 GLU cc_start: 0.6241 (tp30) cc_final: 0.5683 (tt0) REVERT: L 32 TYR cc_start: 0.6422 (m-10) cc_final: 0.5976 (m-10) REVERT: A 56 LYS cc_start: 0.6887 (tptm) cc_final: 0.6336 (mmmt) REVERT: A 67 GLN cc_start: 0.8006 (tm-30) cc_final: 0.7662 (tm-30) REVERT: A 70 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8133 (mm-40) REVERT: A 270 ASP cc_start: 0.5448 (t0) cc_final: 0.5201 (t0) REVERT: A 371 ASP cc_start: 0.7087 (t70) cc_final: 0.6201 (m-30) REVERT: A 378 PHE cc_start: 0.7582 (m-10) cc_final: 0.7367 (m-10) REVERT: A 465 SER cc_start: 0.9026 (t) cc_final: 0.8798 (m) REVERT: C 49 LEU cc_start: 0.6035 (mp) cc_final: 0.5493 (tp) REVERT: C 56 LYS cc_start: 0.7529 (tmtt) cc_final: 0.6967 (tppp) REVERT: C 158 VAL cc_start: 0.6469 (t) cc_final: 0.6195 (p) REVERT: C 236 ARG cc_start: 0.6918 (mtt90) cc_final: 0.5307 (mmt180) outliers start: 29 outliers final: 15 residues processed: 161 average time/residue: 0.2529 time to fit residues: 57.3284 Evaluate side-chains 137 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 LEU 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 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 133 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 14 optimal weight: 0.0370 chunk 64 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- 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 155 ASN ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5505 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11786 Z= 0.235 Angle : 0.676 10.538 15988 Z= 0.349 Chirality : 0.049 0.354 1945 Planarity : 0.004 0.058 2026 Dihedral : 7.611 99.213 1777 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.23 % Favored : 91.70 % Rotamer: Outliers : 3.45 % Allowed : 13.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.21), residues: 1470 helix: -0.96 (0.27), residues: 371 sheet: -1.20 (0.30), residues: 288 loop : -2.13 (0.21), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 308 HIS 0.013 0.002 HIS A 414 PHE 0.020 0.002 PHE A 437 TYR 0.019 0.002 TYR C 309 ARG 0.003 0.000 ARG C 73 *********************** 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 179 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 134 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 281 ARG cc_start: 0.6973 (mtm-85) cc_final: 0.6757 (ptt90) REVERT: B 284 LEU cc_start: 0.6699 (tp) cc_final: 0.6169 (mt) REVERT: H 100 GLU cc_start: 0.6256 (tp30) cc_final: 0.5539 (tt0) REVERT: L 32 TYR cc_start: 0.6588 (m-10) cc_final: 0.6071 (m-10) REVERT: A 56 LYS cc_start: 0.6879 (tptm) cc_final: 0.6294 (mmtt) REVERT: A 67 GLN cc_start: 0.8041 (tm-30) cc_final: 0.7692 (tm-30) REVERT: A 70 GLN cc_start: 0.8603 (tm-30) cc_final: 0.7958 (mp10) REVERT: A 270 ASP cc_start: 0.5499 (t0) cc_final: 0.5246 (t0) REVERT: A 371 ASP cc_start: 0.7015 (t70) cc_final: 0.6086 (m-30) REVERT: A 417 CYS cc_start: 0.6508 (t) cc_final: 0.5965 (t) REVERT: A 437 PHE cc_start: 0.6738 (t80) cc_final: 0.6405 (t80) REVERT: A 465 SER cc_start: 0.8976 (t) cc_final: 0.8634 (m) REVERT: C 38 MET cc_start: 0.6505 (tpt) cc_final: 0.5901 (tpt) REVERT: C 49 LEU cc_start: 0.6031 (mp) cc_final: 0.5591 (tp) REVERT: C 56 LYS cc_start: 0.7536 (tmtt) cc_final: 0.7099 (tmtt) REVERT: C 158 VAL cc_start: 0.6363 (t) cc_final: 0.6118 (p) REVERT: C 231 ILE cc_start: 0.5732 (mm) cc_final: 0.5479 (mt) REVERT: C 236 ARG cc_start: 0.6881 (mtt90) cc_final: 0.5256 (mmt180) outliers start: 45 outliers final: 27 residues processed: 165 average time/residue: 0.2541 time to fit residues: 60.8021 Evaluate side-chains 154 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 419 THR 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 L residue 51 LYS 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 379 VAL 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 172 ILE Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 370 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 0.0060 chunk 81 optimal weight: 0.2980 chunk 2 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.8198 ------------------------------------------------------------------------------- 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** ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5527 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11786 Z= 0.262 Angle : 0.695 12.327 15988 Z= 0.357 Chirality : 0.049 0.333 1945 Planarity : 0.004 0.055 2026 Dihedral : 7.313 93.119 1777 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.23 % Favored : 91.70 % Rotamer: Outliers : 3.91 % Allowed : 14.18 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.21), residues: 1470 helix: -1.03 (0.26), residues: 388 sheet: -1.27 (0.31), residues: 284 loop : -2.17 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 308 HIS 0.012 0.002 HIS A 414 PHE 0.019 0.002 PHE A 437 TYR 0.017 0.002 TYR C 309 ARG 0.003 0.000 ARG H 71 *********************** 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 187 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 136 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 281 ARG cc_start: 0.7125 (mtm-85) cc_final: 0.6877 (ptt90) REVERT: B 284 LEU cc_start: 0.6842 (tp) cc_final: 0.6315 (mt) REVERT: B 354 SER cc_start: 0.6747 (t) cc_final: 0.6457 (p) REVERT: H 100 GLU cc_start: 0.6326 (tp30) cc_final: 0.5620 (tt0) REVERT: L 32 TYR cc_start: 0.6682 (m-10) cc_final: 0.6121 (m-10) REVERT: A 56 LYS cc_start: 0.6888 (tptm) cc_final: 0.6294 (mmtt) REVERT: A 67 GLN cc_start: 0.8078 (tm-30) cc_final: 0.7836 (tm-30) REVERT: A 70 GLN cc_start: 0.8611 (tm-30) cc_final: 0.7961 (mp10) REVERT: A 270 ASP cc_start: 0.5516 (t0) cc_final: 0.5188 (t0) REVERT: A 417 CYS cc_start: 0.6491 (t) cc_final: 0.6052 (t) REVERT: A 437 PHE cc_start: 0.6749 (t80) cc_final: 0.6483 (t80) REVERT: A 465 SER cc_start: 0.8938 (t) cc_final: 0.8618 (m) REVERT: C 31 LEU cc_start: 0.5634 (OUTLIER) cc_final: 0.5051 (mt) REVERT: C 38 MET cc_start: 0.6581 (tpt) cc_final: 0.5927 (tpt) REVERT: C 56 LYS cc_start: 0.7531 (tmtt) cc_final: 0.7074 (tmtt) REVERT: C 158 VAL cc_start: 0.6369 (t) cc_final: 0.6158 (p) REVERT: C 236 ARG cc_start: 0.6799 (mtt90) cc_final: 0.5257 (mmt180) outliers start: 51 outliers final: 32 residues processed: 174 average time/residue: 0.2296 time to fit residues: 58.0516 Evaluate side-chains 161 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 395 ASN Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 449 VAL 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 110 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 51 LYS 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 312 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 449 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 143 optimal weight: 0.0030 chunk 118 optimal weight: 0.0270 chunk 66 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 overall best weight: 0.5248 ------------------------------------------------------------------------------- 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 ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5504 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11786 Z= 0.207 Angle : 0.673 10.792 15988 Z= 0.343 Chirality : 0.048 0.324 1945 Planarity : 0.004 0.052 2026 Dihedral : 7.041 87.988 1777 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.16 % Favored : 91.77 % Rotamer: Outliers : 3.45 % Allowed : 15.40 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.21), residues: 1470 helix: -0.80 (0.27), residues: 376 sheet: -1.20 (0.31), residues: 290 loop : -2.20 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 308 HIS 0.011 0.001 HIS A 414 PHE 0.016 0.002 PHE A 437 TYR 0.015 0.001 TYR L 49 ARG 0.013 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 136 time to evaluate : 1.337 Fit side-chains revert: symmetry clash REVERT: B 281 ARG cc_start: 0.7124 (mtm-85) cc_final: 0.6873 (ptt90) REVERT: B 284 LEU cc_start: 0.6661 (tp) cc_final: 0.6125 (mt) REVERT: B 354 SER cc_start: 0.6798 (t) cc_final: 0.6518 (p) REVERT: H 100 GLU cc_start: 0.6244 (tp30) cc_final: 0.5645 (tt0) REVERT: L 32 TYR cc_start: 0.6680 (m-10) cc_final: 0.6120 (m-10) REVERT: A 56 LYS cc_start: 0.6918 (tptm) cc_final: 0.6283 (mmtt) REVERT: A 67 GLN cc_start: 0.8164 (tm-30) cc_final: 0.7832 (tm-30) REVERT: A 70 GLN cc_start: 0.8526 (tm-30) cc_final: 0.7894 (mp10) REVERT: A 270 ASP cc_start: 0.5435 (t0) cc_final: 0.5177 (t0) REVERT: A 274 TYR cc_start: 0.6525 (m-80) cc_final: 0.6116 (m-80) REVERT: A 290 ASN cc_start: 0.6496 (t0) cc_final: 0.5897 (p0) REVERT: A 317 MET cc_start: 0.7606 (ttp) cc_final: 0.7266 (ttm) REVERT: A 371 ASP cc_start: 0.7043 (t70) cc_final: 0.6232 (m-30) REVERT: A 417 CYS cc_start: 0.6580 (t) cc_final: 0.6213 (t) REVERT: A 434 THR cc_start: 0.5929 (t) cc_final: 0.5723 (m) REVERT: A 460 LEU cc_start: 0.4780 (OUTLIER) cc_final: 0.4546 (pp) REVERT: A 465 SER cc_start: 0.9009 (t) cc_final: 0.8624 (m) REVERT: C 38 MET cc_start: 0.6560 (tpt) cc_final: 0.5907 (tpt) REVERT: C 56 LYS cc_start: 0.7515 (tmtt) cc_final: 0.7070 (tmtt) REVERT: C 158 VAL cc_start: 0.6446 (t) cc_final: 0.6229 (p) REVERT: C 236 ARG cc_start: 0.6738 (mtt90) cc_final: 0.5172 (mmt180) REVERT: C 378 PHE cc_start: 0.7667 (m-10) cc_final: 0.7451 (m-10) outliers start: 45 outliers final: 32 residues processed: 166 average time/residue: 0.2317 time to fit residues: 55.9295 Evaluate side-chains 157 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 110 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 51 LYS 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 312 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 413 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 chunk 120 optimal weight: 4.9990 chunk 79 optimal weight: 20.0000 chunk 142 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN B 395 ASN H 3 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 95BHIS C 67 GLN ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5526 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11786 Z= 0.243 Angle : 0.691 10.945 15988 Z= 0.350 Chirality : 0.049 0.304 1945 Planarity : 0.004 0.054 2026 Dihedral : 6.919 82.864 1777 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.64 % Favored : 91.22 % Rotamer: Outliers : 3.52 % Allowed : 16.78 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.21), residues: 1470 helix: -0.78 (0.27), residues: 375 sheet: -1.26 (0.31), residues: 294 loop : -2.18 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 308 HIS 0.013 0.002 HIS A 414 PHE 0.013 0.002 PHE C 378 TYR 0.016 0.002 TYR A 309 ARG 0.004 0.000 ARG L 61 *********************** 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 173 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 127 time to evaluate : 1.255 Fit side-chains revert: symmetry clash REVERT: B 281 ARG cc_start: 0.7138 (mtm-85) cc_final: 0.6882 (ptt90) REVERT: B 284 LEU cc_start: 0.6848 (tp) cc_final: 0.6329 (mt) REVERT: B 354 SER cc_start: 0.6904 (t) cc_final: 0.6599 (p) REVERT: H 3 GLN cc_start: 0.5812 (OUTLIER) cc_final: 0.5553 (pm20) REVERT: H 100 GLU cc_start: 0.6214 (tp30) cc_final: 0.5487 (tt0) REVERT: L 32 TYR cc_start: 0.6831 (m-10) cc_final: 0.6264 (m-10) REVERT: L 93 ARG cc_start: 0.7179 (pmt-80) cc_final: 0.6777 (pmt-80) REVERT: A 56 LYS cc_start: 0.6883 (tptm) cc_final: 0.6310 (mmtt) REVERT: A 67 GLN cc_start: 0.8197 (tm-30) cc_final: 0.7847 (tm-30) REVERT: A 70 GLN cc_start: 0.8535 (tm-30) cc_final: 0.7865 (mp10) REVERT: A 290 ASN cc_start: 0.6442 (t0) cc_final: 0.5819 (p0) REVERT: A 317 MET cc_start: 0.7599 (ttp) cc_final: 0.7287 (ttm) REVERT: A 371 ASP cc_start: 0.6957 (t70) cc_final: 0.6120 (m-30) REVERT: A 460 LEU cc_start: 0.4851 (OUTLIER) cc_final: 0.4622 (pp) REVERT: A 465 SER cc_start: 0.9061 (t) cc_final: 0.8706 (m) REVERT: C 38 MET cc_start: 0.6616 (tpt) cc_final: 0.5921 (tpt) REVERT: C 56 LYS cc_start: 0.7511 (tmtt) cc_final: 0.7050 (tppp) REVERT: C 236 ARG cc_start: 0.6802 (mtt90) cc_final: 0.5180 (mmt180) REVERT: C 378 PHE cc_start: 0.7718 (m-10) cc_final: 0.7517 (m-10) outliers start: 46 outliers final: 34 residues processed: 160 average time/residue: 0.2393 time to fit residues: 55.3621 Evaluate side-chains 161 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 388 ILE Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 51 LYS 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 312 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 49 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 317 MET 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 56 optimal weight: 0.0050 chunk 85 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 0.0670 chunk 13 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 129 optimal weight: 0.4980 overall best weight: 0.4132 ------------------------------------------------------------------------------- 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 ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5491 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11786 Z= 0.189 Angle : 0.669 11.275 15988 Z= 0.337 Chirality : 0.048 0.289 1945 Planarity : 0.004 0.054 2026 Dihedral : 6.693 77.968 1777 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.62 % Favored : 92.24 % Rotamer: Outliers : 3.07 % Allowed : 17.39 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.21), residues: 1470 helix: -0.75 (0.27), residues: 374 sheet: -1.12 (0.31), residues: 287 loop : -2.10 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 308 HIS 0.012 0.002 HIS A 414 PHE 0.011 0.001 PHE C 378 TYR 0.015 0.001 TYR L 49 ARG 0.004 0.000 ARG L 61 *********************** 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 170 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 130 time to evaluate : 1.200 Fit side-chains revert: symmetry clash REVERT: B 281 ARG cc_start: 0.7128 (mtm-85) cc_final: 0.6885 (ptt90) REVERT: B 284 LEU cc_start: 0.6663 (tp) cc_final: 0.6149 (mt) REVERT: B 354 SER cc_start: 0.6930 (t) cc_final: 0.6650 (p) REVERT: H 82 MET cc_start: 0.6462 (tpp) cc_final: 0.6220 (tpp) REVERT: H 100 GLU cc_start: 0.6308 (tp30) cc_final: 0.5665 (tt0) REVERT: L 32 TYR cc_start: 0.6761 (m-10) cc_final: 0.6255 (m-10) REVERT: L 93 ARG cc_start: 0.7193 (pmt-80) cc_final: 0.6788 (pmt-80) REVERT: A 56 LYS cc_start: 0.6856 (tptm) cc_final: 0.6296 (mmtt) REVERT: A 67 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7846 (tm-30) REVERT: A 70 GLN cc_start: 0.8366 (tm-30) cc_final: 0.7850 (mp10) REVERT: A 209 GLU cc_start: 0.7525 (tp30) cc_final: 0.7286 (tp30) REVERT: A 270 ASP cc_start: 0.5386 (t0) cc_final: 0.5160 (t0) REVERT: A 290 ASN cc_start: 0.6425 (t0) cc_final: 0.5841 (p0) REVERT: A 317 MET cc_start: 0.7581 (ttp) cc_final: 0.7272 (ttm) REVERT: A 371 ASP cc_start: 0.6949 (t70) cc_final: 0.6175 (m-30) REVERT: A 417 CYS cc_start: 0.6578 (t) cc_final: 0.6301 (t) REVERT: A 460 LEU cc_start: 0.4869 (OUTLIER) cc_final: 0.4615 (pp) REVERT: A 465 SER cc_start: 0.9093 (t) cc_final: 0.8705 (m) REVERT: C 38 MET cc_start: 0.6594 (tpt) cc_final: 0.5914 (tpt) REVERT: C 56 LYS cc_start: 0.7501 (tmtt) cc_final: 0.7048 (tppp) REVERT: C 158 VAL cc_start: 0.6459 (t) cc_final: 0.6185 (p) REVERT: C 236 ARG cc_start: 0.6765 (mtt90) cc_final: 0.5077 (mmt180) REVERT: C 378 PHE cc_start: 0.7718 (m-10) cc_final: 0.7391 (m-10) outliers start: 40 outliers final: 31 residues processed: 156 average time/residue: 0.2456 time to fit residues: 55.2264 Evaluate side-chains 158 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 110 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 51 LYS Chi-restraints excluded: chain L residue 82 ASP 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 312 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 449 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 0.9990 chunk 124 optimal weight: 0.0570 chunk 132 optimal weight: 0.5980 chunk 80 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 120 optimal weight: 6.9990 chunk 125 optimal weight: 0.0570 chunk 87 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 overall best weight: 0.4016 ------------------------------------------------------------------------------- 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 ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5481 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11786 Z= 0.189 Angle : 0.666 11.436 15988 Z= 0.336 Chirality : 0.048 0.281 1945 Planarity : 0.004 0.055 2026 Dihedral : 6.532 73.868 1777 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.96 % Favored : 91.90 % Rotamer: Outliers : 3.14 % Allowed : 17.70 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.22), residues: 1470 helix: -0.69 (0.27), residues: 374 sheet: -1.08 (0.32), residues: 283 loop : -2.07 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 308 HIS 0.012 0.002 HIS A 414 PHE 0.009 0.001 PHE C 378 TYR 0.014 0.001 TYR L 49 ARG 0.004 0.000 ARG L 61 *********************** 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 169 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 128 time to evaluate : 1.317 Fit side-chains revert: symmetry clash REVERT: B 281 ARG cc_start: 0.7125 (mtm-85) cc_final: 0.6894 (ptt90) REVERT: B 284 LEU cc_start: 0.6678 (tp) cc_final: 0.6132 (mt) REVERT: B 354 SER cc_start: 0.6957 (t) cc_final: 0.6716 (p) REVERT: H 100 GLU cc_start: 0.5976 (tp30) cc_final: 0.5314 (tt0) REVERT: L 32 TYR cc_start: 0.6654 (m-10) cc_final: 0.6182 (m-10) REVERT: L 93 ARG cc_start: 0.7195 (pmt-80) cc_final: 0.6798 (pmt-80) REVERT: A 56 LYS cc_start: 0.6811 (tptm) cc_final: 0.6280 (mmtt) REVERT: A 67 GLN cc_start: 0.8192 (tm-30) cc_final: 0.7816 (tm-30) REVERT: A 70 GLN cc_start: 0.8383 (tm-30) cc_final: 0.7840 (mp10) REVERT: A 73 ARG cc_start: 0.8174 (mmm160) cc_final: 0.6634 (ttp-110) REVERT: A 274 TYR cc_start: 0.6510 (m-80) cc_final: 0.6108 (m-80) REVERT: A 290 ASN cc_start: 0.6437 (t0) cc_final: 0.5853 (p0) REVERT: A 317 MET cc_start: 0.7588 (ttp) cc_final: 0.7286 (ttm) REVERT: A 371 ASP cc_start: 0.6879 (t70) cc_final: 0.6132 (m-30) REVERT: A 417 CYS cc_start: 0.6616 (t) cc_final: 0.6341 (t) REVERT: A 460 LEU cc_start: 0.4791 (OUTLIER) cc_final: 0.4522 (pp) REVERT: A 465 SER cc_start: 0.8959 (t) cc_final: 0.8640 (m) REVERT: C 38 MET cc_start: 0.6576 (tpt) cc_final: 0.5880 (tpt) REVERT: C 56 LYS cc_start: 0.7500 (tmtt) cc_final: 0.7075 (tppp) REVERT: C 236 ARG cc_start: 0.6760 (mtt90) cc_final: 0.5126 (mmt180) REVERT: C 378 PHE cc_start: 0.7651 (m-10) cc_final: 0.7279 (m-10) outliers start: 41 outliers final: 34 residues processed: 153 average time/residue: 0.2353 time to fit residues: 52.2583 Evaluate side-chains 157 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 122 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 37 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 51 LYS Chi-restraints excluded: chain L residue 82 ASP 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 312 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 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 85 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 117 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 90 optimal weight: 0.0000 chunk 71 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 125 optimal weight: 0.5980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN H 3 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5506 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11786 Z= 0.233 Angle : 0.691 11.749 15988 Z= 0.349 Chirality : 0.048 0.281 1945 Planarity : 0.004 0.055 2026 Dihedral : 6.559 71.325 1777 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.71 % Favored : 91.16 % Rotamer: Outliers : 2.99 % Allowed : 18.16 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.21), residues: 1470 helix: -0.73 (0.27), residues: 374 sheet: -1.09 (0.31), residues: 287 loop : -2.15 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 308 HIS 0.012 0.002 HIS A 414 PHE 0.019 0.002 PHE A 44 TYR 0.015 0.002 TYR A 309 ARG 0.004 0.000 ARG L 61 ********************** 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: 39 poor density : 121 time to evaluate : 1.296 Fit side-chains revert: symmetry clash REVERT: B 281 ARG cc_start: 0.7150 (mtm-85) cc_final: 0.6914 (ptt90) REVERT: B 284 LEU cc_start: 0.6619 (tp) cc_final: 0.6108 (mt) REVERT: B 354 SER cc_start: 0.6980 (t) cc_final: 0.6675 (p) REVERT: H 100 GLU cc_start: 0.6015 (tp30) cc_final: 0.5497 (tt0) REVERT: L 32 TYR cc_start: 0.6756 (m-10) cc_final: 0.6235 (m-10) REVERT: L 93 ARG cc_start: 0.7218 (pmt-80) cc_final: 0.6819 (pmt-80) REVERT: A 56 LYS cc_start: 0.6847 (tptm) cc_final: 0.6281 (mmtt) REVERT: A 67 GLN cc_start: 0.8179 (tm-30) cc_final: 0.7800 (tm-30) REVERT: A 70 GLN cc_start: 0.8391 (tm-30) cc_final: 0.7753 (mp10) REVERT: A 290 ASN cc_start: 0.6545 (t0) cc_final: 0.5849 (p0) REVERT: A 317 MET cc_start: 0.7654 (ttp) cc_final: 0.7365 (ttm) REVERT: A 371 ASP cc_start: 0.7051 (t70) cc_final: 0.6263 (m-30) REVERT: A 417 CYS cc_start: 0.6772 (t) cc_final: 0.6463 (t) REVERT: A 460 LEU cc_start: 0.4862 (OUTLIER) cc_final: 0.4604 (pp) REVERT: A 465 SER cc_start: 0.9092 (t) cc_final: 0.8711 (m) REVERT: C 56 LYS cc_start: 0.7504 (tmtt) cc_final: 0.7086 (tppp) REVERT: C 236 ARG cc_start: 0.6765 (mtt90) cc_final: 0.5202 (mmt180) REVERT: C 378 PHE cc_start: 0.7598 (m-10) cc_final: 0.7274 (m-10) outliers start: 39 outliers final: 36 residues processed: 148 average time/residue: 0.2271 time to fit residues: 49.1474 Evaluate side-chains 155 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 GLN 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 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 37 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 51 LYS Chi-restraints excluded: chain L residue 82 ASP 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 312 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 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 35 optimal weight: 0.0970 chunk 108 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 117 optimal weight: 0.0770 chunk 49 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 6 optimal weight: 0.0570 overall best weight: 0.3854 ------------------------------------------------------------------------------- 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 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.220120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.212272 restraints weight = 10970.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.194877 restraints weight = 15478.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.194550 restraints weight = 15386.330| |-----------------------------------------------------------------------------| r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11786 Z= 0.195 Angle : 0.681 11.790 15988 Z= 0.345 Chirality : 0.048 0.278 1945 Planarity : 0.004 0.055 2026 Dihedral : 6.473 68.773 1777 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.69 % Favored : 92.18 % Rotamer: Outliers : 2.84 % Allowed : 18.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.21), residues: 1470 helix: -0.66 (0.28), residues: 374 sheet: -1.04 (0.31), residues: 281 loop : -2.08 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 308 HIS 0.012 0.002 HIS A 414 PHE 0.021 0.001 PHE A 44 TYR 0.014 0.001 TYR L 49 ARG 0.004 0.000 ARG L 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2455.56 seconds wall clock time: 46 minutes 10.37 seconds (2770.37 seconds total)