Starting phenix.real_space_refine on Mon Jun 16 01:09:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cvy_27021/06_2025/8cvy_27021.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cvy_27021/06_2025/8cvy_27021.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cvy_27021/06_2025/8cvy_27021.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cvy_27021/06_2025/8cvy_27021.map" model { file = "/net/cci-nas-00/data/ceres_data/8cvy_27021/06_2025/8cvy_27021.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cvy_27021/06_2025/8cvy_27021.cif" } resolution = 3.6 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= -0.000 sd= 0.092 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 88 5.16 5 C 11490 2.51 5 N 3092 2.21 5 O 3260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 147 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17930 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4862 Classifications: {'peptide': 605} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 24, 'TRANS': 580} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 277 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain: "C" Number of atoms: 4867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4867 Classifications: {'peptide': 605} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 24, 'TRANS': 580} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 285 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "D" Number of atoms: 4851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4851 Classifications: {'peptide': 605} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 24, 'TRANS': 580} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 285 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "B" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2503 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 13, 'TRANS': 296} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 10.01, per 1000 atoms: 0.56 Number of scatterers: 17930 At special positions: 0 Unit cell: (119.76, 126.16, 136.216, 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 88 16.00 O 3260 8.00 N 3092 7.00 C 11490 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.93 Conformation dependent library (CDL) restraints added in 2.2 seconds 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4180 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 12 sheets defined 56.7% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'A' and resid 42 through 59 removed outlier: 4.846A pdb=" N LYS A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N VAL A 53 " --> pdb=" O THR A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 76 Processing helix chain 'A' and resid 84 through 97 removed outlier: 3.525A pdb=" N LYS A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 138 Processing helix chain 'A' and resid 146 through 169 Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 184 through 194 removed outlier: 3.885A pdb=" N LEU A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 217 removed outlier: 3.732A pdb=" N TYR A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ALA A 215 " --> pdb=" O ARG A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 236 Processing helix chain 'A' and resid 238 through 252 Processing helix chain 'A' and resid 259 through 270 Processing helix chain 'A' and resid 292 through 312 removed outlier: 3.617A pdb=" N LEU A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 356 Processing helix chain 'A' and resid 376 through 411 Processing helix chain 'A' and resid 415 through 420 removed outlier: 3.939A pdb=" N LEU A 420 " --> pdb=" O MET A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 435 Processing helix chain 'A' and resid 454 through 464 Processing helix chain 'A' and resid 492 through 500 Processing helix chain 'A' and resid 513 through 523 Processing helix chain 'A' and resid 532 through 542 Processing helix chain 'A' and resid 559 through 576 Processing helix chain 'A' and resid 578 through 590 Processing helix chain 'A' and resid 592 through 597 removed outlier: 3.887A pdb=" N LEU A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 616 removed outlier: 4.612A pdb=" N ARG A 603 " --> pdb=" O LYS A 599 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TYR A 604 " --> pdb=" O TYR A 600 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 616 " --> pdb=" O ALA A 612 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 328 removed outlier: 3.532A pdb=" N LYS E 322 " --> pdb=" O SER E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 347 Processing helix chain 'C' and resid 42 through 59 removed outlier: 4.535A pdb=" N LYS C 52 " --> pdb=" O GLN C 48 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VAL C 53 " --> pdb=" O THR C 49 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP C 56 " --> pdb=" O LYS C 52 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU C 57 " --> pdb=" O VAL C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 76 Processing helix chain 'C' and resid 84 through 97 removed outlier: 3.504A pdb=" N ARG C 89 " --> pdb=" O PRO C 85 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS C 97 " --> pdb=" O SER C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 136 Processing helix chain 'C' and resid 145 through 169 removed outlier: 3.992A pdb=" N LEU C 166 " --> pdb=" O LEU C 162 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA C 167 " --> pdb=" O GLY C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.631A pdb=" N VAL C 186 " --> pdb=" O TRP C 182 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N GLY C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 217 removed outlier: 3.725A pdb=" N TYR C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ALA C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 236 Processing helix chain 'C' and resid 238 through 252 Processing helix chain 'C' and resid 259 through 270 Processing helix chain 'C' and resid 283 through 288 Processing helix chain 'C' and resid 289 through 291 No H-bonds generated for 'chain 'C' and resid 289 through 291' Processing helix chain 'C' and resid 292 through 312 Processing helix chain 'C' and resid 338 through 356 Processing helix chain 'C' and resid 376 through 411 Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.617A pdb=" N LEU C 420 " --> pdb=" O MET C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 435 Processing helix chain 'C' and resid 454 through 464 Processing helix chain 'C' and resid 492 through 500 Processing helix chain 'C' and resid 513 through 523 Processing helix chain 'C' and resid 532 through 542 Processing helix chain 'C' and resid 559 through 577 Processing helix chain 'C' and resid 578 through 592 removed outlier: 3.531A pdb=" N LEU C 592 " --> pdb=" O ARG C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 597 removed outlier: 3.887A pdb=" N LEU C 596 " --> pdb=" O LEU C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 616 removed outlier: 4.404A pdb=" N ARG C 603 " --> pdb=" O LYS C 599 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N TYR C 604 " --> pdb=" O TYR C 600 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TYR C 605 " --> pdb=" O LEU C 601 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA C 616 " --> pdb=" O ALA C 612 " (cutoff:3.500A) Processing helix chain 'G' and resid 317 through 328 Processing helix chain 'G' and resid 337 through 348 removed outlier: 3.761A pdb=" N TYR G 348 " --> pdb=" O LYS G 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 59 removed outlier: 4.851A pdb=" N LYS D 52 " --> pdb=" O GLN D 48 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N VAL D 53 " --> pdb=" O THR D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 76 Processing helix chain 'D' and resid 84 through 97 removed outlier: 3.528A pdb=" N LYS D 97 " --> pdb=" O SER D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 removed outlier: 4.400A pdb=" N TRP D 124 " --> pdb=" O ALA D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 138 Processing helix chain 'D' and resid 146 through 169 Processing helix chain 'D' and resid 184 through 194 removed outlier: 3.963A pdb=" N LEU D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 217 removed outlier: 3.724A pdb=" N TYR D 212 " --> pdb=" O LEU D 208 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ALA D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 236 Processing helix chain 'D' and resid 238 through 252 Processing helix chain 'D' and resid 259 through 270 Processing helix chain 'D' and resid 283 through 287 Processing helix chain 'D' and resid 292 through 312 Processing helix chain 'D' and resid 338 through 356 Processing helix chain 'D' and resid 376 through 411 removed outlier: 3.548A pdb=" N GLN D 383 " --> pdb=" O THR D 379 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA D 384 " --> pdb=" O LEU D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 420 removed outlier: 4.474A pdb=" N LEU D 420 " --> pdb=" O MET D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 435 Processing helix chain 'D' and resid 454 through 464 Processing helix chain 'D' and resid 492 through 500 Processing helix chain 'D' and resid 513 through 523 Processing helix chain 'D' and resid 532 through 542 Processing helix chain 'D' and resid 559 through 576 Processing helix chain 'D' and resid 578 through 590 Processing helix chain 'D' and resid 592 through 597 removed outlier: 3.829A pdb=" N LEU D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 616 removed outlier: 4.425A pdb=" N ARG D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N TYR D 604 " --> pdb=" O TYR D 600 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR D 605 " --> pdb=" O LEU D 601 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA D 616 " --> pdb=" O ALA D 612 " (cutoff:3.500A) Processing helix chain 'H' and resid 317 through 328 removed outlier: 3.535A pdb=" N LYS H 322 " --> pdb=" O SER H 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 337 through 348 removed outlier: 3.719A pdb=" N TYR H 348 " --> pdb=" O LYS H 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 312 Processing helix chain 'B' and resid 338 through 356 Processing helix chain 'B' and resid 376 through 411 Processing helix chain 'B' and resid 415 through 420 removed outlier: 3.838A pdb=" N LEU B 420 " --> pdb=" O MET B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 435 Processing helix chain 'B' and resid 454 through 464 Processing helix chain 'B' and resid 492 through 500 Processing helix chain 'B' and resid 513 through 523 Processing helix chain 'B' and resid 532 through 542 Processing helix chain 'B' and resid 559 through 576 Processing helix chain 'B' and resid 578 through 590 Processing helix chain 'B' and resid 592 through 597 removed outlier: 3.886A pdb=" N LEU B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 79 removed outlier: 3.724A pdb=" N LEU A 116 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TYR A 62 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N VAL A 115 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU A 64 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU A 117 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N GLY A 66 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LEU A 29 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL A 65 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLU A 31 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR A 200 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N THR A 256 " --> pdb=" O THR A 200 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N PHE A 202 " --> pdb=" O THR A 256 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N PHE A 255 " --> pdb=" O ILE A 276 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 473 through 477 removed outlier: 6.511A pdb=" N VAL A 362 " --> pdb=" O LYS A 474 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE A 476 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA A 364 " --> pdb=" O ILE A 476 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU A 324 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N PHE A 365 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE A 326 " --> pdb=" O PHE A 365 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE A 367 " --> pdb=" O PHE A 326 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE A 328 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N TYR A 325 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL A 504 " --> pdb=" O TYR A 325 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N PHE A 327 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLY A 503 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N THR A 529 " --> pdb=" O GLY A 503 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N LEU A 553 " --> pdb=" O SER A 526 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N SER A 528 " --> pdb=" O LEU A 553 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 372 through 375 removed outlier: 4.623A pdb=" N ASN A 447 " --> pdb=" O ASN A 373 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 79 removed outlier: 6.381A pdb=" N TYR C 62 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL C 115 " --> pdb=" O TYR C 62 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU C 64 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU C 117 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N GLY C 66 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU C 29 " --> pdb=" O PHE C 63 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL C 65 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLU C 31 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR C 200 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N THR C 256 " --> pdb=" O THR C 200 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N PHE C 202 " --> pdb=" O THR C 256 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N PHE C 255 " --> pdb=" O ILE C 276 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 473 through 477 removed outlier: 6.507A pdb=" N VAL C 362 " --> pdb=" O LYS C 474 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ILE C 476 " --> pdb=" O VAL C 362 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA C 364 " --> pdb=" O ILE C 476 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU C 324 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N PHE C 365 " --> pdb=" O LEU C 324 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N PHE C 326 " --> pdb=" O PHE C 365 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE C 367 " --> pdb=" O PHE C 326 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE C 328 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TYR C 325 " --> pdb=" O LEU C 502 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N VAL C 504 " --> pdb=" O TYR C 325 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N PHE C 327 " --> pdb=" O VAL C 504 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLY C 503 " --> pdb=" O ILE C 527 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N THR C 529 " --> pdb=" O GLY C 503 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N LEU C 553 " --> pdb=" O SER C 526 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER C 528 " --> pdb=" O LEU C 553 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 372 through 375 removed outlier: 4.977A pdb=" N ASN C 447 " --> pdb=" O ASN C 373 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 62 through 63 removed outlier: 6.050A pdb=" N LEU D 29 " --> pdb=" O PHE D 63 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR D 200 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N THR D 256 " --> pdb=" O THR D 200 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE D 202 " --> pdb=" O THR D 256 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N PHE D 255 " --> pdb=" O ILE D 276 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 66 through 67 Processing sheet with id=AA9, first strand: chain 'D' and resid 473 through 478 removed outlier: 6.323A pdb=" N VAL D 362 " --> pdb=" O LYS D 474 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ILE D 476 " --> pdb=" O VAL D 362 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ALA D 364 " --> pdb=" O ILE D 476 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N HIS D 478 " --> pdb=" O ALA D 364 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N PHE D 366 " --> pdb=" O HIS D 478 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU D 324 " --> pdb=" O VAL D 363 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N PHE D 365 " --> pdb=" O LEU D 324 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE D 326 " --> pdb=" O PHE D 365 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ILE D 367 " --> pdb=" O PHE D 326 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE D 328 " --> pdb=" O ILE D 367 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TYR D 325 " --> pdb=" O LEU D 502 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N VAL D 504 " --> pdb=" O TYR D 325 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N PHE D 327 " --> pdb=" O VAL D 504 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLY D 503 " --> pdb=" O ILE D 527 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N THR D 529 " --> pdb=" O GLY D 503 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N LEU D 553 " --> pdb=" O SER D 526 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N SER D 528 " --> pdb=" O LEU D 553 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 372 through 375 removed outlier: 4.710A pdb=" N ASN D 447 " --> pdb=" O ASN D 373 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 473 through 477 removed outlier: 6.502A pdb=" N VAL B 362 " --> pdb=" O LYS B 474 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE B 476 " --> pdb=" O VAL B 362 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA B 364 " --> pdb=" O ILE B 476 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU B 324 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N PHE B 365 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N PHE B 326 " --> pdb=" O PHE B 365 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ILE B 367 " --> pdb=" O PHE B 326 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE B 328 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TYR B 325 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N VAL B 504 " --> pdb=" O TYR B 325 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N PHE B 327 " --> pdb=" O VAL B 504 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLY B 503 " --> pdb=" O ILE B 527 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N THR B 529 " --> pdb=" O GLY B 503 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU B 553 " --> pdb=" O SER B 526 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N SER B 528 " --> pdb=" O LEU B 553 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 372 through 375 removed outlier: 4.620A pdb=" N ASN B 447 " --> pdb=" O ASN B 373 " (cutoff:3.500A) 890 hydrogen bonds defined for protein. 2631 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: 5.87 Time building geometry restraints manager: 4.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3472 1.33 - 1.45: 5745 1.45 - 1.58: 9050 1.58 - 1.71: 0 1.71 - 1.84: 131 Bond restraints: 18398 Sorted by residual: bond pdb=" CE1 HIS B 311 " pdb=" NE2 HIS B 311 " ideal model delta sigma weight residual 1.321 1.368 -0.047 1.00e-02 1.00e+04 2.23e+01 bond pdb=" C PHE B 440 " pdb=" N PRO B 441 " ideal model delta sigma weight residual 1.331 1.366 -0.034 8.70e-03 1.32e+04 1.55e+01 bond pdb=" CE1 HIS C 501 " pdb=" NE2 HIS C 501 " ideal model delta sigma weight residual 1.321 1.360 -0.039 1.00e-02 1.00e+04 1.51e+01 bond pdb=" C PHE D 440 " pdb=" N PRO D 441 " ideal model delta sigma weight residual 1.331 1.364 -0.033 8.70e-03 1.32e+04 1.45e+01 bond pdb=" CE1 HIS B 446 " pdb=" NE2 HIS B 446 " ideal model delta sigma weight residual 1.321 1.359 -0.038 1.00e-02 1.00e+04 1.43e+01 ... (remaining 18393 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 23384 2.82 - 5.64: 1489 5.64 - 8.46: 53 8.46 - 11.28: 6 11.28 - 14.10: 3 Bond angle restraints: 24935 Sorted by residual: angle pdb=" C THR D 49 " pdb=" CA THR D 49 " pdb=" CB THR D 49 " ideal model delta sigma weight residual 109.24 123.32 -14.08 1.75e+00 3.27e-01 6.47e+01 angle pdb=" C THR A 49 " pdb=" CA THR A 49 " pdb=" CB THR A 49 " ideal model delta sigma weight residual 109.29 123.39 -14.10 1.82e+00 3.02e-01 6.00e+01 angle pdb=" CA PHE A 400 " pdb=" CB PHE A 400 " pdb=" CG PHE A 400 " ideal model delta sigma weight residual 113.80 107.20 6.60 1.00e+00 1.00e+00 4.35e+01 angle pdb=" C PHE A 617 " pdb=" CA PHE A 617 " pdb=" CB PHE A 617 " ideal model delta sigma weight residual 111.20 115.41 -4.21 7.10e-01 1.98e+00 3.52e+01 angle pdb=" C PHE D 617 " pdb=" CA PHE D 617 " pdb=" CB PHE D 617 " ideal model delta sigma weight residual 111.20 115.35 -4.15 7.10e-01 1.98e+00 3.41e+01 ... (remaining 24930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.70: 9312 14.70 - 29.41: 997 29.41 - 44.11: 363 44.11 - 58.81: 119 58.81 - 73.52: 23 Dihedral angle restraints: 10814 sinusoidal: 4321 harmonic: 6493 Sorted by residual: dihedral pdb=" C THR D 49 " pdb=" N THR D 49 " pdb=" CA THR D 49 " pdb=" CB THR D 49 " ideal model delta harmonic sigma weight residual -122.00 -141.54 19.54 0 2.50e+00 1.60e-01 6.11e+01 dihedral pdb=" C THR A 49 " pdb=" N THR A 49 " pdb=" CA THR A 49 " pdb=" CB THR A 49 " ideal model delta harmonic sigma weight residual -122.00 -141.26 19.26 0 2.50e+00 1.60e-01 5.94e+01 dihedral pdb=" C ASP A 424 " pdb=" N ASP A 424 " pdb=" CA ASP A 424 " pdb=" CB ASP A 424 " ideal model delta harmonic sigma weight residual -122.60 -135.78 13.18 0 2.50e+00 1.60e-01 2.78e+01 ... (remaining 10811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 2141 0.141 - 0.282: 474 0.282 - 0.423: 50 0.423 - 0.564: 2 0.564 - 0.705: 2 Chirality restraints: 2669 Sorted by residual: chirality pdb=" CA THR D 49 " pdb=" N THR D 49 " pdb=" C THR D 49 " pdb=" CB THR D 49 " both_signs ideal model delta sigma weight residual False 2.53 1.82 0.71 2.00e-01 2.50e+01 1.24e+01 chirality pdb=" CA THR A 49 " pdb=" N THR A 49 " pdb=" C THR A 49 " pdb=" CB THR A 49 " both_signs ideal model delta sigma weight residual False 2.53 1.84 0.69 2.00e-01 2.50e+01 1.19e+01 chirality pdb=" CA ASP B 424 " pdb=" N ASP B 424 " pdb=" C ASP B 424 " pdb=" CB ASP B 424 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.66e+00 ... (remaining 2666 not shown) Planarity restraints: 3222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 143 " 0.040 2.00e-02 2.50e+03 2.47e-02 1.52e+01 pdb=" CG TRP A 143 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP A 143 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP A 143 " -0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP A 143 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TRP A 143 " 0.024 2.00e-02 2.50e+03 pdb=" CE3 TRP A 143 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 143 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 143 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 143 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 44 " 0.042 2.00e-02 2.50e+03 2.36e-02 1.11e+01 pdb=" CG TYR C 44 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR C 44 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 44 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR C 44 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR C 44 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR C 44 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR C 44 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 400 " 0.029 2.00e-02 2.50e+03 2.37e-02 9.80e+00 pdb=" CG PHE A 400 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE A 400 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 400 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 400 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE A 400 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE A 400 " -0.003 2.00e-02 2.50e+03 ... (remaining 3219 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1149 2.75 - 3.29: 18768 3.29 - 3.83: 31457 3.83 - 4.36: 38684 4.36 - 4.90: 63087 Nonbonded interactions: 153145 Sorted by model distance: nonbonded pdb=" OH TYR A 242 " pdb=" O LEU A 269 " model vdw 2.214 3.040 nonbonded pdb=" OH TYR D 242 " pdb=" O LEU D 269 " model vdw 2.216 3.040 nonbonded pdb=" OH TYR C 242 " pdb=" O LEU C 269 " model vdw 2.216 3.040 nonbonded pdb=" O THR A 45 " pdb=" OG1 THR A 49 " model vdw 2.419 3.040 nonbonded pdb=" O THR D 45 " pdb=" OG1 THR D 49 " model vdw 2.428 3.040 ... (remaining 153140 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 108 or (resid 109 and (name N or name CA or nam \ e C or name O or name CB )) or resid 110 through 145 or (resid 146 and (name N o \ r name CA or name C or name O or name CB )) or resid 147 through 415 or (resid 4 \ 16 and (name N or name CA or name C or name O or name CB )) or resid 417 through \ 421 or (resid 422 and (name N or name CA or name C or name O or name CB )) or r \ esid 423 through 520 or (resid 521 and (name N or name CA or name C or name O or \ name CB )) or resid 522 through 626)) selection = (chain 'C' and (resid 22 through 70 or (resid 71 and (name N or name CA or name \ C or name O or name CB )) or resid 72 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 108 or (resid 109 and \ (name N or name CA or name C or name O or name CB )) or resid 110 through 145 o \ r (resid 146 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 47 through 421 or (resid 422 and (name N or name CA or name C or name O or name \ CB )) or resid 423 through 520 or (resid 521 and (name N or name CA or name C or \ name O or name CB )) or resid 522 through 626)) selection = (chain 'D' and (resid 22 through 70 or (resid 71 and (name N or name CA or name \ C or name O or name CB )) or resid 72 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 626)) } ncs_group { reference = chain 'E' selection = (chain 'G' and resid 316 through 348) selection = (chain 'H' and resid 316 through 348) } 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: 0.010 Normalize map: mean=0, sd=1: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.680 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 39.790 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 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 : 0.008 0.055 18398 Z= 0.552 Angle : 1.472 14.100 24935 Z= 1.028 Chirality : 0.115 0.705 2669 Planarity : 0.007 0.030 3222 Dihedral : 15.011 73.516 6634 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 6.05 % Allowed : 11.37 % Favored : 82.58 % Cbeta Deviations : 0.77 % 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: 0.51 (0.16), residues: 2212 helix: 1.38 (0.14), residues: 1132 sheet: -0.76 (0.32), residues: 281 loop : -0.67 (0.19), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.007 TRP A 143 HIS 0.032 0.005 HIS B 311 PHE 0.053 0.007 PHE A 400 TYR 0.042 0.006 TYR C 44 ARG 0.021 0.002 ARG C 582 Details of bonding type rmsd hydrogen bonds : bond 0.19433 ( 890) hydrogen bonds : angle 6.83983 ( 2631) covalent geometry : bond 0.00790 (18398) covalent geometry : angle 1.47175 (24935) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 652 time to evaluate : 1.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.8663 (m-30) cc_final: 0.8235 (t70) REVERT: A 227 PHE cc_start: 0.5242 (m-80) cc_final: 0.4742 (m-80) REVERT: A 321 ASP cc_start: 0.8103 (p0) cc_final: 0.7651 (m-30) REVERT: A 375 PHE cc_start: 0.7945 (m-80) cc_final: 0.7729 (m-80) REVERT: A 424 ASP cc_start: 0.8423 (p0) cc_final: 0.8087 (p0) REVERT: A 480 GLU cc_start: 0.8533 (tt0) cc_final: 0.8216 (mm-30) REVERT: A 606 MET cc_start: 0.6653 (mtm) cc_final: 0.6265 (mtp) REVERT: E 317 SER cc_start: 0.7753 (OUTLIER) cc_final: 0.7521 (p) REVERT: C 127 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6550 (tp30) REVERT: C 296 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8106 (mt) REVERT: C 316 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8111 (mp) REVERT: C 403 LYS cc_start: 0.7861 (mmmt) cc_final: 0.7400 (mttm) REVERT: C 409 LEU cc_start: 0.8588 (mt) cc_final: 0.8105 (mt) REVERT: C 425 PHE cc_start: 0.8399 (t80) cc_final: 0.8194 (t80) REVERT: C 509 TYR cc_start: 0.7858 (t80) cc_final: 0.7650 (t80) REVERT: C 552 ILE cc_start: 0.8661 (mm) cc_final: 0.8344 (mm) REVERT: C 554 ASP cc_start: 0.7732 (t0) cc_final: 0.7359 (t0) REVERT: C 579 ARG cc_start: 0.8122 (ttt180) cc_final: 0.7513 (tpp-160) REVERT: C 597 ASP cc_start: 0.8773 (t0) cc_final: 0.8221 (t0) REVERT: G 333 MET cc_start: 0.8728 (mmm) cc_final: 0.7876 (mtm) REVERT: G 346 ASP cc_start: 0.8352 (m-30) cc_final: 0.7743 (m-30) REVERT: D 162 LEU cc_start: 0.8693 (pp) cc_final: 0.7878 (mt) REVERT: D 273 LYS cc_start: 0.8253 (mttt) cc_final: 0.8033 (tptp) REVERT: D 483 SER cc_start: 0.8698 (m) cc_final: 0.8447 (p) REVERT: D 597 ASP cc_start: 0.8439 (t0) cc_final: 0.8023 (t0) REVERT: H 316 VAL cc_start: 0.6247 (OUTLIER) cc_final: 0.5831 (m) REVERT: H 317 SER cc_start: 0.6043 (OUTLIER) cc_final: 0.5185 (p) REVERT: B 299 GLN cc_start: 0.7782 (mt0) cc_final: 0.7334 (tm-30) REVERT: B 319 ASN cc_start: 0.7750 (OUTLIER) cc_final: 0.7494 (m-40) REVERT: B 360 GLN cc_start: 0.3343 (mt0) cc_final: 0.3138 (mm-40) REVERT: B 379 THR cc_start: 0.7962 (m) cc_final: 0.7619 (p) REVERT: B 391 ASP cc_start: 0.8382 (m-30) cc_final: 0.8019 (t0) REVERT: B 414 PRO cc_start: 0.8592 (Cg_endo) cc_final: 0.8032 (Cg_exo) REVERT: B 428 MET cc_start: 0.8283 (mtm) cc_final: 0.8032 (mtt) REVERT: B 443 VAL cc_start: 0.8054 (m) cc_final: 0.7781 (t) REVERT: B 471 ASP cc_start: 0.7130 (m-30) cc_final: 0.6497 (p0) REVERT: B 486 SER cc_start: 0.8580 (m) cc_final: 0.8320 (p) REVERT: B 524 ILE cc_start: 0.5224 (mm) cc_final: 0.4674 (tp) REVERT: B 568 THR cc_start: 0.3951 (p) cc_final: 0.3551 (p) REVERT: B 572 TYR cc_start: 0.6230 (t80) cc_final: 0.5554 (t80) REVERT: B 594 ASP cc_start: 0.6832 (m-30) cc_final: 0.6566 (m-30) outliers start: 115 outliers final: 23 residues processed: 723 average time/residue: 0.3483 time to fit residues: 357.8938 Evaluate side-chains 403 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 373 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 317 SER Chi-restraints excluded: chain B residue 297 HIS Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 492 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 0.7980 chunk 166 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 172 optimal weight: 0.3980 chunk 66 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 199 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 HIS A 253 HIS A 260 GLN A 283 ASN A 417 ASN A 530 ASN A 581 GLN ** A 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 ASN C 38 ASN C 71 GLN C 95 ASN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 HIS C 253 HIS C 260 GLN C 283 ASN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 373 ASN C 388 GLN C 530 ASN C 577 GLN C 585 GLN C 587 ASN D 95 ASN ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 GLN D 587 ASN B 297 HIS B 315 HIS B 374 ASN B 530 ASN B 576 GLN ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.206876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.171261 restraints weight = 23526.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.174329 restraints weight = 18040.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.176423 restraints weight = 13123.512| |-----------------------------------------------------------------------------| r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18398 Z= 0.170 Angle : 0.634 9.087 24935 Z= 0.342 Chirality : 0.046 0.226 2669 Planarity : 0.004 0.036 3222 Dihedral : 6.509 59.505 2508 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.84 % Allowed : 16.00 % Favored : 80.16 % 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: 1.03 (0.17), residues: 2212 helix: 2.05 (0.14), residues: 1139 sheet: -0.99 (0.32), residues: 278 loop : -0.68 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 34 HIS 0.013 0.001 HIS C 240 PHE 0.030 0.002 PHE B 334 TYR 0.026 0.002 TYR A 493 ARG 0.009 0.001 ARG C 461 Details of bonding type rmsd hydrogen bonds : bond 0.05390 ( 890) hydrogen bonds : angle 5.12351 ( 2631) covalent geometry : bond 0.00376 (18398) covalent geometry : angle 0.63371 (24935) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 389 time to evaluate : 1.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ARG cc_start: 0.7419 (mtm180) cc_final: 0.6871 (mtm-85) REVERT: A 378 GLU cc_start: 0.6861 (tm-30) cc_final: 0.6449 (tm-30) REVERT: C 127 GLU cc_start: 0.5584 (OUTLIER) cc_final: 0.5212 (tp30) REVERT: C 245 GLU cc_start: 0.8497 (tp30) cc_final: 0.7580 (tp30) REVERT: C 293 PHE cc_start: 0.6077 (OUTLIER) cc_final: 0.4899 (t80) REVERT: C 296 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8179 (mt) REVERT: C 303 ARG cc_start: 0.7344 (mtp180) cc_final: 0.7131 (mtp180) REVERT: C 316 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8175 (mp) REVERT: C 350 ASN cc_start: 0.7586 (t0) cc_final: 0.7067 (t0) REVERT: C 425 PHE cc_start: 0.8228 (t80) cc_final: 0.7935 (t80) REVERT: C 428 MET cc_start: 0.7826 (mtm) cc_final: 0.7564 (mtm) REVERT: C 597 ASP cc_start: 0.8069 (t0) cc_final: 0.7766 (t0) REVERT: D 285 LYS cc_start: 0.8211 (mptt) cc_final: 0.7885 (mmtp) REVERT: D 355 VAL cc_start: 0.8347 (p) cc_final: 0.8122 (m) REVERT: D 473 VAL cc_start: 0.8860 (t) cc_final: 0.8329 (p) REVERT: D 597 ASP cc_start: 0.8028 (t0) cc_final: 0.7674 (t0) REVERT: B 295 ASN cc_start: 0.5475 (t0) cc_final: 0.5147 (t0) REVERT: B 301 LYS cc_start: 0.8269 (ptmt) cc_final: 0.7694 (ptmt) REVERT: B 404 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.7996 (pp) REVERT: B 414 PRO cc_start: 0.7886 (Cg_endo) cc_final: 0.6899 (Cg_exo) REVERT: B 568 THR cc_start: 0.5688 (p) cc_final: 0.5170 (p) outliers start: 73 outliers final: 40 residues processed: 437 average time/residue: 0.3053 time to fit residues: 197.2011 Evaluate side-chains 345 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 300 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 584 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 176 optimal weight: 1.9990 chunk 200 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 chunk 189 optimal weight: 9.9990 chunk 187 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 191 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 HIS A 315 HIS ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN ** A 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 HIS ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 HIS C 283 ASN C 446 HIS ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 GLN D 360 GLN D 438 GLN D 446 HIS B 305 GLN ** B 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 HIS ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.183069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.149341 restraints weight = 22430.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.149126 restraints weight = 21793.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.150645 restraints weight = 21934.569| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 18398 Z= 0.271 Angle : 0.681 8.567 24935 Z= 0.362 Chirality : 0.046 0.190 2669 Planarity : 0.005 0.048 3222 Dihedral : 6.076 59.563 2479 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 5.21 % Allowed : 16.79 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.37 (0.17), residues: 2212 helix: 1.51 (0.14), residues: 1141 sheet: -1.80 (0.27), residues: 313 loop : -0.69 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 325 HIS 0.008 0.002 HIS B 311 PHE 0.031 0.003 PHE B 334 TYR 0.019 0.002 TYR D 572 ARG 0.012 0.001 ARG A 236 Details of bonding type rmsd hydrogen bonds : bond 0.04899 ( 890) hydrogen bonds : angle 5.03924 ( 2631) covalent geometry : bond 0.00635 (18398) covalent geometry : angle 0.68097 (24935) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 326 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ARG cc_start: 0.7383 (mtm180) cc_final: 0.7032 (mtm-85) REVERT: A 156 PHE cc_start: 0.6396 (m-80) cc_final: 0.6166 (m-10) REVERT: A 237 GLN cc_start: 0.6980 (mt0) cc_final: 0.6735 (tt0) REVERT: A 378 GLU cc_start: 0.7058 (tm-30) cc_final: 0.6560 (tm-30) REVERT: C 94 MET cc_start: 0.8122 (mmm) cc_final: 0.7867 (mmm) REVERT: C 127 GLU cc_start: 0.5898 (OUTLIER) cc_final: 0.5513 (tp30) REVERT: C 293 PHE cc_start: 0.6493 (OUTLIER) cc_final: 0.5032 (t80) REVERT: C 296 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8550 (mm) REVERT: C 425 PHE cc_start: 0.8293 (t80) cc_final: 0.8053 (t80) REVERT: C 553 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7922 (mt) REVERT: D 47 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8076 (mp) REVERT: D 355 VAL cc_start: 0.8359 (p) cc_final: 0.8095 (t) REVERT: D 597 ASP cc_start: 0.8091 (t0) cc_final: 0.7707 (t0) REVERT: B 419 MET cc_start: 0.7368 (OUTLIER) cc_final: 0.6854 (mpp) REVERT: B 495 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7586 (mp0) REVERT: B 568 THR cc_start: 0.5866 (p) cc_final: 0.5387 (p) outliers start: 99 outliers final: 75 residues processed: 395 average time/residue: 0.3190 time to fit residues: 187.4829 Evaluate side-chains 364 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 283 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 492 ASP Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 584 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 85 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 164 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 214 optimal weight: 0.0000 chunk 40 optimal weight: 1.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 HIS ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 GLN A 620 HIS ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 ASN C 620 HIS ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 HIS ** B 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.206419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.171254 restraints weight = 22767.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.174818 restraints weight = 17356.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.176526 restraints weight = 12656.692| |-----------------------------------------------------------------------------| r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18398 Z= 0.136 Angle : 0.559 8.680 24935 Z= 0.295 Chirality : 0.041 0.207 2669 Planarity : 0.004 0.047 3222 Dihedral : 5.928 59.870 2479 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.00 % Allowed : 19.58 % Favored : 76.42 % 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: 0.61 (0.18), residues: 2212 helix: 1.71 (0.15), residues: 1141 sheet: -1.67 (0.28), residues: 311 loop : -0.59 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 325 HIS 0.014 0.001 HIS A 620 PHE 0.023 0.002 PHE E 338 TYR 0.030 0.001 TYR B 493 ARG 0.006 0.000 ARG A 591 Details of bonding type rmsd hydrogen bonds : bond 0.04067 ( 890) hydrogen bonds : angle 4.71778 ( 2631) covalent geometry : bond 0.00308 (18398) covalent geometry : angle 0.55902 (24935) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 327 time to evaluate : 1.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 ASP cc_start: 0.7204 (t0) cc_final: 0.6970 (m-30) REVERT: A 333 GLU cc_start: 0.6934 (mm-30) cc_final: 0.6704 (mt-10) REVERT: A 449 LEU cc_start: 0.8678 (mm) cc_final: 0.8457 (mt) REVERT: A 480 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7640 (tp30) REVERT: C 94 MET cc_start: 0.8145 (mmm) cc_final: 0.7421 (mtp) REVERT: C 127 GLU cc_start: 0.5469 (OUTLIER) cc_final: 0.5173 (tp30) REVERT: C 153 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7745 (mm) REVERT: C 293 PHE cc_start: 0.6144 (OUTLIER) cc_final: 0.4798 (t80) REVERT: C 296 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8042 (mt) REVERT: D 232 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7424 (mm-30) REVERT: D 355 VAL cc_start: 0.8380 (p) cc_final: 0.8146 (t) REVERT: D 597 ASP cc_start: 0.7969 (t0) cc_final: 0.7645 (t0) REVERT: B 419 MET cc_start: 0.7149 (OUTLIER) cc_final: 0.6569 (mpp) REVERT: B 495 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7739 (mp0) REVERT: B 524 ILE cc_start: 0.6534 (OUTLIER) cc_final: 0.6328 (tt) REVERT: B 568 THR cc_start: 0.5821 (p) cc_final: 0.5333 (p) outliers start: 76 outliers final: 48 residues processed: 374 average time/residue: 0.3219 time to fit residues: 179.1547 Evaluate side-chains 348 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 294 time to evaluate : 2.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain G residue 347 THR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 524 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 68 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 143 optimal weight: 0.0370 chunk 211 optimal weight: 20.0000 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 HIS A 620 HIS ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 ASN C 438 GLN ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN B 383 GLN B 566 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.179903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.146448 restraints weight = 22572.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.145145 restraints weight = 23768.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.147246 restraints weight = 24890.172| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 18398 Z= 0.288 Angle : 0.669 10.468 24935 Z= 0.348 Chirality : 0.045 0.195 2669 Planarity : 0.004 0.051 3222 Dihedral : 5.928 58.123 2476 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 5.42 % Allowed : 18.89 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.17 (0.17), residues: 2212 helix: 1.40 (0.15), residues: 1141 sheet: -2.09 (0.27), residues: 323 loop : -0.76 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 325 HIS 0.021 0.002 HIS A 620 PHE 0.027 0.002 PHE E 338 TYR 0.023 0.002 TYR A 493 ARG 0.007 0.001 ARG A 591 Details of bonding type rmsd hydrogen bonds : bond 0.04395 ( 890) hydrogen bonds : angle 4.87784 ( 2631) covalent geometry : bond 0.00682 (18398) covalent geometry : angle 0.66890 (24935) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 312 time to evaluate : 2.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.5841 (mmt) cc_final: 0.5514 (mmt) REVERT: A 333 GLU cc_start: 0.7282 (mm-30) cc_final: 0.7018 (mt-10) REVERT: A 425 PHE cc_start: 0.7328 (OUTLIER) cc_final: 0.6901 (t80) REVERT: A 449 LEU cc_start: 0.8822 (mm) cc_final: 0.8566 (mt) REVERT: A 480 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7661 (tp30) REVERT: A 581 GLN cc_start: 0.7783 (tp40) cc_final: 0.7540 (tp-100) REVERT: C 94 MET cc_start: 0.8474 (mmm) cc_final: 0.8052 (mtp) REVERT: C 127 GLU cc_start: 0.5814 (OUTLIER) cc_final: 0.5412 (tp30) REVERT: C 245 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7495 (tp30) REVERT: C 293 PHE cc_start: 0.6472 (OUTLIER) cc_final: 0.5414 (t80) REVERT: C 597 ASP cc_start: 0.7843 (t0) cc_final: 0.7453 (m-30) REVERT: D 71 GLN cc_start: 0.8070 (tm-30) cc_final: 0.7824 (tm-30) REVERT: D 231 LYS cc_start: 0.8175 (ttpp) cc_final: 0.7939 (tttp) REVERT: D 355 VAL cc_start: 0.8400 (p) cc_final: 0.8068 (t) REVERT: D 524 ILE cc_start: 0.9083 (mm) cc_final: 0.8808 (mm) REVERT: D 597 ASP cc_start: 0.8190 (t0) cc_final: 0.7870 (t0) REVERT: B 415 ASP cc_start: 0.7060 (t0) cc_final: 0.6758 (t0) REVERT: B 419 MET cc_start: 0.7277 (OUTLIER) cc_final: 0.6479 (mpp) REVERT: B 568 THR cc_start: 0.5928 (p) cc_final: 0.5456 (p) outliers start: 103 outliers final: 77 residues processed: 382 average time/residue: 0.4315 time to fit residues: 251.5869 Evaluate side-chains 366 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 284 time to evaluate : 3.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 492 ASP Chi-restraints excluded: chain C residue 536 CYS Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 622 THR Chi-restraints excluded: chain G residue 347 THR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 536 CYS Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 491 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 46 optimal weight: 0.1980 chunk 31 optimal weight: 4.9990 chunk 172 optimal weight: 0.8980 chunk 147 optimal weight: 0.7980 chunk 213 optimal weight: 40.0000 chunk 3 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 210 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 446 HIS ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 438 GLN D 48 GLN ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 GLN B 576 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.202392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.167233 restraints weight = 22995.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.169401 restraints weight = 18189.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.171650 restraints weight = 14152.201| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.5407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 18398 Z= 0.143 Angle : 0.564 9.087 24935 Z= 0.296 Chirality : 0.041 0.186 2669 Planarity : 0.004 0.050 3222 Dihedral : 5.686 58.883 2475 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.79 % Allowed : 21.53 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.42 (0.18), residues: 2212 helix: 1.60 (0.15), residues: 1142 sheet: -1.96 (0.28), residues: 318 loop : -0.64 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 143 HIS 0.006 0.001 HIS C 620 PHE 0.027 0.002 PHE A 156 TYR 0.018 0.001 TYR C 68 ARG 0.015 0.001 ARG A 236 Details of bonding type rmsd hydrogen bonds : bond 0.03838 ( 890) hydrogen bonds : angle 4.66624 ( 2631) covalent geometry : bond 0.00337 (18398) covalent geometry : angle 0.56420 (24935) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 317 time to evaluate : 2.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.5700 (mmt) cc_final: 0.5144 (mmt) REVERT: A 425 PHE cc_start: 0.7288 (OUTLIER) cc_final: 0.6974 (t80) REVERT: A 449 LEU cc_start: 0.8664 (mm) cc_final: 0.8443 (mt) REVERT: A 480 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7600 (tp30) REVERT: A 494 GLU cc_start: 0.7377 (mm-30) cc_final: 0.6986 (mm-30) REVERT: A 581 GLN cc_start: 0.7605 (tp40) cc_final: 0.7373 (tp-100) REVERT: A 620 HIS cc_start: 0.7916 (OUTLIER) cc_final: 0.7494 (t-90) REVERT: C 94 MET cc_start: 0.8367 (mmm) cc_final: 0.8039 (mtp) REVERT: C 127 GLU cc_start: 0.5415 (OUTLIER) cc_final: 0.5056 (tp30) REVERT: C 153 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7766 (mm) REVERT: C 245 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.7514 (tp30) REVERT: C 293 PHE cc_start: 0.6085 (OUTLIER) cc_final: 0.5235 (t80) REVERT: C 296 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8067 (mt) REVERT: C 594 ASP cc_start: 0.7511 (t0) cc_final: 0.7298 (t0) REVERT: C 597 ASP cc_start: 0.7705 (t0) cc_final: 0.7442 (m-30) REVERT: D 355 VAL cc_start: 0.8284 (p) cc_final: 0.8052 (t) REVERT: D 474 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7956 (mmtm) REVERT: D 524 ILE cc_start: 0.9155 (mm) cc_final: 0.8879 (mm) REVERT: D 597 ASP cc_start: 0.8099 (t0) cc_final: 0.7792 (t0) REVERT: B 415 ASP cc_start: 0.7020 (t0) cc_final: 0.6778 (t0) REVERT: B 419 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.6438 (mpp) REVERT: B 527 ILE cc_start: 0.3485 (OUTLIER) cc_final: 0.3208 (mt) REVERT: B 568 THR cc_start: 0.5951 (p) cc_final: 0.5466 (p) outliers start: 72 outliers final: 48 residues processed: 365 average time/residue: 0.4351 time to fit residues: 241.1594 Evaluate side-chains 343 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 285 time to evaluate : 3.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 180 HIS Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 474 LYS Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 527 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 25 optimal weight: 0.6980 chunk 118 optimal weight: 0.5980 chunk 136 optimal weight: 0.6980 chunk 134 optimal weight: 0.9980 chunk 184 optimal weight: 0.6980 chunk 176 optimal weight: 2.9990 chunk 186 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 110 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.203401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.167663 restraints weight = 22918.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.170420 restraints weight = 17749.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.172386 restraints weight = 13141.542| |-----------------------------------------------------------------------------| r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.5571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 18398 Z= 0.136 Angle : 0.566 8.696 24935 Z= 0.295 Chirality : 0.041 0.237 2669 Planarity : 0.004 0.090 3222 Dihedral : 5.357 59.277 2471 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.79 % Allowed : 22.05 % Favored : 74.16 % 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: 0.50 (0.18), residues: 2212 helix: 1.68 (0.15), residues: 1145 sheet: -2.00 (0.28), residues: 328 loop : -0.58 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 106 HIS 0.006 0.001 HIS C 620 PHE 0.024 0.002 PHE A 156 TYR 0.020 0.001 TYR C 68 ARG 0.009 0.001 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.03701 ( 890) hydrogen bonds : angle 4.54526 ( 2631) covalent geometry : bond 0.00320 (18398) covalent geometry : angle 0.56620 (24935) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 296 time to evaluate : 2.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.5554 (mmt) cc_final: 0.4913 (mmt) REVERT: A 425 PHE cc_start: 0.7259 (OUTLIER) cc_final: 0.6961 (t80) REVERT: A 449 LEU cc_start: 0.8611 (mm) cc_final: 0.8410 (mt) REVERT: A 480 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7678 (tp30) REVERT: A 581 GLN cc_start: 0.7627 (tp40) cc_final: 0.7404 (tp-100) REVERT: A 620 HIS cc_start: 0.7926 (OUTLIER) cc_final: 0.7465 (t-90) REVERT: C 94 MET cc_start: 0.8321 (mmm) cc_final: 0.8033 (mtp) REVERT: C 127 GLU cc_start: 0.5295 (OUTLIER) cc_final: 0.4963 (tp30) REVERT: C 153 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7775 (mm) REVERT: C 245 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7518 (tp30) REVERT: C 293 PHE cc_start: 0.6159 (OUTLIER) cc_final: 0.5362 (t80) REVERT: C 296 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8018 (mt) REVERT: D 147 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8031 (mm-30) REVERT: D 337 LYS cc_start: 0.8691 (tppp) cc_final: 0.8461 (tppt) REVERT: D 355 VAL cc_start: 0.8283 (p) cc_final: 0.8018 (t) REVERT: D 474 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.8034 (mmtm) REVERT: D 597 ASP cc_start: 0.8061 (t0) cc_final: 0.7770 (t0) REVERT: B 415 ASP cc_start: 0.7100 (t0) cc_final: 0.6859 (t0) REVERT: B 419 MET cc_start: 0.7201 (OUTLIER) cc_final: 0.6383 (mpp) REVERT: B 568 THR cc_start: 0.5984 (p) cc_final: 0.5530 (p) outliers start: 72 outliers final: 53 residues processed: 343 average time/residue: 0.4537 time to fit residues: 233.7852 Evaluate side-chains 344 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 282 time to evaluate : 4.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 622 THR Chi-restraints excluded: chain G residue 347 THR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 180 HIS Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 474 LYS Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 491 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 99 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 150 optimal weight: 0.1980 chunk 81 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 165 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 218 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN B 566 GLN B 576 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.201153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.165426 restraints weight = 22845.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.166473 restraints weight = 18411.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.168565 restraints weight = 15922.872| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.5797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18398 Z= 0.169 Angle : 0.576 10.519 24935 Z= 0.299 Chirality : 0.042 0.203 2669 Planarity : 0.004 0.052 3222 Dihedral : 5.296 59.156 2470 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.89 % Allowed : 22.00 % Favored : 74.11 % 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: 0.43 (0.18), residues: 2212 helix: 1.64 (0.15), residues: 1145 sheet: -2.13 (0.28), residues: 309 loop : -0.65 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 106 HIS 0.009 0.001 HIS A 240 PHE 0.024 0.002 PHE C 156 TYR 0.023 0.002 TYR A 493 ARG 0.011 0.001 ARG C 211 Details of bonding type rmsd hydrogen bonds : bond 0.03694 ( 890) hydrogen bonds : angle 4.55552 ( 2631) covalent geometry : bond 0.00400 (18398) covalent geometry : angle 0.57557 (24935) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 302 time to evaluate : 2.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.5713 (mmt) cc_final: 0.5072 (mmt) REVERT: A 425 PHE cc_start: 0.7305 (OUTLIER) cc_final: 0.6991 (t80) REVERT: A 449 LEU cc_start: 0.8700 (mm) cc_final: 0.8495 (mt) REVERT: A 581 GLN cc_start: 0.7707 (tp40) cc_final: 0.7504 (tp-100) REVERT: A 620 HIS cc_start: 0.8013 (OUTLIER) cc_final: 0.7533 (t-90) REVERT: C 94 MET cc_start: 0.8382 (mmm) cc_final: 0.8145 (mtp) REVERT: C 127 GLU cc_start: 0.5262 (OUTLIER) cc_final: 0.4903 (tp30) REVERT: C 245 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7420 (tp30) REVERT: C 293 PHE cc_start: 0.6118 (OUTLIER) cc_final: 0.5525 (t80) REVERT: C 296 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7983 (mt) REVERT: D 337 LYS cc_start: 0.8860 (tppp) cc_final: 0.8578 (tppt) REVERT: D 355 VAL cc_start: 0.8289 (p) cc_final: 0.8042 (t) REVERT: D 474 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8054 (mmtp) REVERT: D 524 ILE cc_start: 0.9151 (mm) cc_final: 0.8864 (mm) REVERT: D 597 ASP cc_start: 0.8076 (t0) cc_final: 0.7820 (t0) REVERT: B 415 ASP cc_start: 0.7131 (t0) cc_final: 0.6887 (t0) REVERT: B 419 MET cc_start: 0.7152 (OUTLIER) cc_final: 0.6284 (mpp) REVERT: B 568 THR cc_start: 0.6039 (p) cc_final: 0.5598 (p) REVERT: B 577 GLN cc_start: 0.6789 (tt0) cc_final: 0.6581 (tt0) outliers start: 74 outliers final: 53 residues processed: 355 average time/residue: 0.3215 time to fit residues: 173.1885 Evaluate side-chains 351 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 290 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 492 ASP Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 622 THR Chi-restraints excluded: chain G residue 347 THR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 180 HIS Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 474 LYS Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 491 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 157 optimal weight: 2.9990 chunk 197 optimal weight: 5.9990 chunk 182 optimal weight: 0.8980 chunk 213 optimal weight: 30.0000 chunk 153 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 205 optimal weight: 20.0000 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.197250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.161132 restraints weight = 23122.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.163314 restraints weight = 19559.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.165029 restraints weight = 16145.725| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.5985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 18398 Z= 0.247 Angle : 0.635 8.682 24935 Z= 0.330 Chirality : 0.044 0.382 2669 Planarity : 0.004 0.054 3222 Dihedral : 5.369 58.720 2468 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.00 % Allowed : 21.74 % Favored : 74.26 % 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: 0.22 (0.18), residues: 2212 helix: 1.51 (0.15), residues: 1142 sheet: -2.42 (0.28), residues: 309 loop : -0.71 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 134 HIS 0.009 0.001 HIS A 240 PHE 0.026 0.002 PHE A 227 TYR 0.030 0.002 TYR A 493 ARG 0.007 0.001 ARG C 303 Details of bonding type rmsd hydrogen bonds : bond 0.03949 ( 890) hydrogen bonds : angle 4.69218 ( 2631) covalent geometry : bond 0.00588 (18398) covalent geometry : angle 0.63549 (24935) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 294 time to evaluate : 1.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 PHE cc_start: 0.7295 (OUTLIER) cc_final: 0.6944 (t80) REVERT: A 620 HIS cc_start: 0.8055 (OUTLIER) cc_final: 0.7628 (t-90) REVERT: C 94 MET cc_start: 0.8439 (mmm) cc_final: 0.8210 (mtp) REVERT: C 127 GLU cc_start: 0.5542 (OUTLIER) cc_final: 0.5163 (tp30) REVERT: C 136 THR cc_start: 0.8449 (t) cc_final: 0.8153 (p) REVERT: C 245 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.7366 (tp30) REVERT: C 293 PHE cc_start: 0.6141 (OUTLIER) cc_final: 0.5424 (t80) REVERT: C 296 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8138 (mm) REVERT: D 277 VAL cc_start: 0.9045 (OUTLIER) cc_final: 0.8790 (m) REVERT: D 290 MET cc_start: 0.3935 (pmm) cc_final: 0.2925 (ptp) REVERT: D 337 LYS cc_start: 0.8904 (tppp) cc_final: 0.8668 (tppt) REVERT: D 355 VAL cc_start: 0.8318 (p) cc_final: 0.8083 (t) REVERT: D 474 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8084 (mmtp) REVERT: D 524 ILE cc_start: 0.9150 (mm) cc_final: 0.8883 (mm) REVERT: D 597 ASP cc_start: 0.8151 (t0) cc_final: 0.7876 (t0) REVERT: B 415 ASP cc_start: 0.7118 (t0) cc_final: 0.6893 (t0) REVERT: B 419 MET cc_start: 0.7283 (OUTLIER) cc_final: 0.6376 (mpp) REVERT: B 568 THR cc_start: 0.6168 (p) cc_final: 0.5755 (p) outliers start: 76 outliers final: 61 residues processed: 351 average time/residue: 0.3289 time to fit residues: 176.9556 Evaluate side-chains 341 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 271 time to evaluate : 2.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 492 ASP Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 622 THR Chi-restraints excluded: chain G residue 347 THR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 180 HIS Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 474 LYS Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 536 CYS Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 491 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 182 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 164 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 208 optimal weight: 2.9990 chunk 209 optimal weight: 9.9990 chunk 133 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 190 optimal weight: 7.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 GLN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.198642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.163223 restraints weight = 22949.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.163865 restraints weight = 18463.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.165622 restraints weight = 16522.466| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.6135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18398 Z= 0.189 Angle : 0.604 11.492 24935 Z= 0.314 Chirality : 0.042 0.240 2669 Planarity : 0.004 0.080 3222 Dihedral : 5.370 58.880 2468 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.68 % Allowed : 22.26 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.23 (0.18), residues: 2212 helix: 1.55 (0.15), residues: 1139 sheet: -2.37 (0.28), residues: 306 loop : -0.77 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 134 HIS 0.009 0.001 HIS A 240 PHE 0.028 0.002 PHE A 227 TYR 0.028 0.002 TYR A 493 ARG 0.009 0.001 ARG C 211 Details of bonding type rmsd hydrogen bonds : bond 0.03839 ( 890) hydrogen bonds : angle 4.65939 ( 2631) covalent geometry : bond 0.00450 (18398) covalent geometry : angle 0.60368 (24935) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 278 time to evaluate : 3.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 ASN cc_start: 0.7049 (t0) cc_final: 0.6776 (t0) REVERT: A 425 PHE cc_start: 0.7383 (OUTLIER) cc_final: 0.6993 (t80) REVERT: A 620 HIS cc_start: 0.8119 (OUTLIER) cc_final: 0.7726 (t-90) REVERT: C 127 GLU cc_start: 0.5436 (OUTLIER) cc_final: 0.5074 (tp30) REVERT: C 136 THR cc_start: 0.8449 (t) cc_final: 0.8148 (p) REVERT: C 245 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7361 (tp30) REVERT: C 296 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8063 (mm) REVERT: D 277 VAL cc_start: 0.9026 (OUTLIER) cc_final: 0.8777 (m) REVERT: D 290 MET cc_start: 0.3942 (pmm) cc_final: 0.2962 (ptp) REVERT: D 355 VAL cc_start: 0.8261 (p) cc_final: 0.8037 (t) REVERT: D 406 GLU cc_start: 0.7241 (mt-10) cc_final: 0.7028 (mt-10) REVERT: D 474 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8138 (mmtp) REVERT: D 524 ILE cc_start: 0.9166 (mm) cc_final: 0.8903 (mm) REVERT: D 597 ASP cc_start: 0.8108 (t0) cc_final: 0.7841 (t0) REVERT: B 415 ASP cc_start: 0.7131 (t0) cc_final: 0.6877 (t0) REVERT: B 419 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.6492 (mpp) REVERT: B 568 THR cc_start: 0.6171 (p) cc_final: 0.5784 (p) outliers start: 70 outliers final: 56 residues processed: 330 average time/residue: 0.4972 time to fit residues: 247.3775 Evaluate side-chains 337 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 273 time to evaluate : 5.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 561 ASP Chi-restraints excluded: chain C residue 622 THR Chi-restraints excluded: chain G residue 347 THR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 180 HIS Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 474 LYS Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 536 CYS Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 491 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 55 optimal weight: 0.7980 chunk 145 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 102 optimal weight: 10.0000 chunk 180 optimal weight: 0.6980 chunk 175 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 chunk 192 optimal weight: 7.9990 chunk 201 optimal weight: 0.3980 chunk 117 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 ASN ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.202088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.168262 restraints weight = 22965.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.169093 restraints weight = 17379.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.171322 restraints weight = 15942.042| |-----------------------------------------------------------------------------| r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.6238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18398 Z= 0.129 Angle : 0.571 10.331 24935 Z= 0.296 Chirality : 0.040 0.217 2669 Planarity : 0.004 0.077 3222 Dihedral : 5.179 59.949 2468 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.11 % Allowed : 22.89 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.45 (0.18), residues: 2212 helix: 1.73 (0.15), residues: 1139 sheet: -2.28 (0.28), residues: 309 loop : -0.67 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 134 HIS 0.015 0.001 HIS C 174 PHE 0.029 0.002 PHE A 227 TYR 0.033 0.001 TYR D 405 ARG 0.010 0.001 ARG C 211 Details of bonding type rmsd hydrogen bonds : bond 0.03579 ( 890) hydrogen bonds : angle 4.52358 ( 2631) covalent geometry : bond 0.00305 (18398) covalent geometry : angle 0.57058 (24935) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6498.78 seconds wall clock time: 118 minutes 17.52 seconds (7097.52 seconds total)