Starting phenix.real_space_refine on Sat Jul 4 05:22:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8agc_15420/07_2026/8agc_15420.cif Found real_map, /net/cci-nas-00/data/ceres_data/8agc_15420/07_2026/8agc_15420.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8agc_15420/07_2026/8agc_15420.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8agc_15420/07_2026/8agc_15420.map" model { file = "/net/cci-nas-00/data/ceres_data/8agc_15420/07_2026/8agc_15420.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8agc_15420/07_2026/8agc_15420.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8agc_15420/07_2026/8agc_15420.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8agc_15420/07_2026/8agc_15420.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.062 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 1 5.21 5 S 57 5.16 5 C 11681 2.51 5 N 2758 2.21 5 O 3259 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17764 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 5594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 5594 Classifications: {'peptide': 697} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 25, 'TRANS': 671} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 251 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain: "C" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 666 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "D" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 883 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 105} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 3537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3537 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 24, 'TRANS': 413} Chain breaks: 1 Chain: "F" Number of atoms: 1892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1892 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 15, 'TRANS': 242} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'HIS:plan': 2, 'PHE:plan': 1, 'ARG:plan': 2, 'GLU:plan': 5, 'ASP:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 67 Chain: "G" Number of atoms: 3201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3201 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 16, 'TRANS': 377} Chain: "H" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1050 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "P" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 43 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'DAB:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'GLC': 3, 'MAN': 5, 'NAG': 1, 'NDG': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "A" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 124 Unusual residues: {' MG': 1, 'CPL': 1, 'ELU': 1, 'PTY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "P" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'323': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.44, per 1000 atoms: 0.19 Number of scatterers: 17764 At special positions: 0 Unit cell: (124.1, 117.3, 154.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 57 16.00 P 8 15.00 Mg 1 11.99 O 3259 8.00 N 2758 7.00 C 11681 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=2, symmetry=0 Links applied ALPHA1-2 " MAN I 4 " - " MAN I 5 " " MAN I 5 " - " MAN I 6 " " MAN L 4 " - " MAN L 5 " " MAN L 5 " - " MAN L 6 " " GLC L 8 " - " GLC L 9 " ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA L 3 " - " MAN L 4 " " MAN L 6 " - " GLC L 7 " " GLC L 7 " - " GLC L 8 " " MAN L 10 " - " MAN L 11 " ALPHA1-6 " BMA I 3 " - " MAN I 7 " " BMA L 3 " - " MAN L 10 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NDG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG G 501 " - " ASN G 332 " " NAG G 502 " - " ASN G 60 " " NAG I 1 " - " ASN A 539 " " NAG J 1 " - " ASN E 336 " " NAG K 1 " - " ASN E 400 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 731.1 milliseconds 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4078 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 20 sheets defined 46.1% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 Processing helix chain 'A' and resid 33 through 39 Processing helix chain 'A' and resid 46 through 61 removed outlier: 3.973A pdb=" N PHE A 50 " --> pdb=" O PHE A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 88 through 104 Processing helix chain 'A' and resid 110 through 117 Processing helix chain 'A' and resid 117 through 136 removed outlier: 3.613A pdb=" N LEU A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY A 124 " --> pdb=" O PRO A 120 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 153 removed outlier: 3.882A pdb=" N ILE A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 159 removed outlier: 4.389A pdb=" N ARG A 159 " --> pdb=" O GLY A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 189 removed outlier: 4.441A pdb=" N THR A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET A 176 " --> pdb=" O ILE A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 208 Processing helix chain 'A' and resid 211 through 228 Proline residue: A 219 - end of helix Processing helix chain 'A' and resid 232 through 251 removed outlier: 3.895A pdb=" N TYR A 236 " --> pdb=" O SER A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 263 removed outlier: 3.538A pdb=" N ARG A 262 " --> pdb=" O PHE A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 288 removed outlier: 4.027A pdb=" N LEU A 270 " --> pdb=" O HIS A 266 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN A 277 " --> pdb=" O PHE A 273 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 278 " --> pdb=" O GLY A 274 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A 280 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN A 288 " --> pdb=" O PHE A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 320 removed outlier: 3.537A pdb=" N ILE A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER A 301 " --> pdb=" O ILE A 297 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 341 removed outlier: 3.718A pdb=" N ILE A 340 " --> pdb=" O ASN A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 352 removed outlier: 3.539A pdb=" N GLN A 352 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 362 Processing helix chain 'A' and resid 365 through 380 Proline residue: A 371 - end of helix removed outlier: 3.886A pdb=" N ASP A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 402 Processing helix chain 'A' and resid 403 through 407 removed outlier: 4.031A pdb=" N LEU A 407 " --> pdb=" O ARG A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 429 removed outlier: 4.804A pdb=" N VAL A 412 " --> pdb=" O THR A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 473 Processing helix chain 'A' and resid 494 through 506 Processing helix chain 'A' and resid 516 through 518 No H-bonds generated for 'chain 'A' and resid 516 through 518' Processing helix chain 'A' and resid 519 through 527 Processing helix chain 'A' and resid 539 through 551 removed outlier: 3.903A pdb=" N ILE A 543 " --> pdb=" O ASN A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 564 Processing helix chain 'A' and resid 582 through 585 Processing helix chain 'A' and resid 586 through 598 removed outlier: 3.684A pdb=" N MET A 590 " --> pdb=" O LYS A 586 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 597 " --> pdb=" O ILE A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 607 removed outlier: 3.542A pdb=" N PHE A 607 " --> pdb=" O GLU A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 627 through 634 Processing helix chain 'A' and resid 691 through 701 Processing helix chain 'B' and resid 3 through 33 Processing helix chain 'C' and resid 3 through 12 Processing helix chain 'C' and resid 21 through 23 No H-bonds generated for 'chain 'C' and resid 21 through 23' Processing helix chain 'C' and resid 24 through 45 removed outlier: 3.542A pdb=" N PHE C 28 " --> pdb=" O THR C 24 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 82 Processing helix chain 'D' and resid 23 through 41 removed outlier: 3.964A pdb=" N LYS D 28 " --> pdb=" O GLN D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 69 removed outlier: 3.634A pdb=" N LEU D 46 " --> pdb=" O PRO D 42 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP D 48 " --> pdb=" O LEU D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 100 removed outlier: 3.633A pdb=" N ILE D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N CYS D 84 " --> pdb=" O GLY D 80 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN D 100 " --> pdb=" O LEU D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 129 removed outlier: 3.889A pdb=" N PHE D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 77 removed outlier: 3.710A pdb=" N LYS E 77 " --> pdb=" O GLY E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 279 Processing helix chain 'E' and resid 442 through 447 removed outlier: 3.507A pdb=" N PHE E 447 " --> pdb=" O LYS E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 469 removed outlier: 3.533A pdb=" N LEU E 451 " --> pdb=" O PHE E 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 128 Processing helix chain 'F' and resid 191 through 215 removed outlier: 3.573A pdb=" N ALA F 195 " --> pdb=" O ALA F 191 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU F 214 " --> pdb=" O ILE F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 252 removed outlier: 3.746A pdb=" N TYR F 232 " --> pdb=" O VAL F 228 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU F 244 " --> pdb=" O ILE F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 281 removed outlier: 3.683A pdb=" N SER F 263 " --> pdb=" O THR F 259 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU F 264 " --> pdb=" O LEU F 260 " (cutoff:3.500A) Proline residue: F 269 - end of helix removed outlier: 3.703A pdb=" N THR F 275 " --> pdb=" O LEU F 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 39 No H-bonds generated for 'chain 'G' and resid 37 through 39' Processing helix chain 'G' and resid 40 through 50 removed outlier: 4.004A pdb=" N LEU G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 94 removed outlier: 3.737A pdb=" N GLN G 93 " --> pdb=" O ASN G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 105 Processing helix chain 'G' and resid 119 through 129 Processing helix chain 'G' and resid 156 through 158 No H-bonds generated for 'chain 'G' and resid 156 through 158' Processing helix chain 'G' and resid 239 through 243 Processing helix chain 'G' and resid 247 through 258 Processing helix chain 'G' and resid 379 through 383 removed outlier: 4.201A pdb=" N TYR G 383 " --> pdb=" O ASN G 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 385 through 388 Processing helix chain 'G' and resid 389 through 416 Processing helix chain 'H' and resid 216 through 233 Processing helix chain 'H' and resid 236 through 241 Processing helix chain 'H' and resid 266 through 290 removed outlier: 4.170A pdb=" N THR H 270 " --> pdb=" O PHE H 266 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN H 271 " --> pdb=" O ALA H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 290 through 299 Processing helix chain 'H' and resid 305 through 335 removed outlier: 3.609A pdb=" N LYS H 334 " --> pdb=" O VAL H 330 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 71 Processing sheet with id=AA2, first strand: chain 'A' and resid 530 through 531 removed outlier: 6.126A pdb=" N GLN A 681 " --> pdb=" O GLU A 668 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N GLU A 668 " --> pdb=" O GLN A 681 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 646 through 647 Processing sheet with id=AA4, first strand: chain 'C' and resid 14 through 15 removed outlier: 3.804A pdb=" N LYS C 14 " --> pdb=" O VAL E 351 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU E 436 " --> pdb=" O ILE E 392 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILE E 392 " --> pdb=" O LEU E 436 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LYS E 438 " --> pdb=" O PHE E 390 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 78 through 85 removed outlier: 3.591A pdb=" N ILE E 47 " --> pdb=" O TYR E 137 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP E 35 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LYS E 56 " --> pdb=" O ASN E 33 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ASN E 33 " --> pdb=" O LYS E 56 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N SER E 174 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N TYR E 36 " --> pdb=" O SER E 174 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N THR E 176 " --> pdb=" O TYR E 36 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ARG E 38 " --> pdb=" O THR E 176 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ILE E 178 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE E 40 " --> pdb=" O ILE E 178 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU E 177 " --> pdb=" O PHE E 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 63 through 70 removed outlier: 6.747A pdb=" N THR E 64 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N TYR E 114 " --> pdb=" O LEU E 97 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN E 93 " --> pdb=" O GLN E 118 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 142 through 143 removed outlier: 4.591A pdb=" N ALA E 221 " --> pdb=" O TYR E 186 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 147 through 148 Processing sheet with id=AA9, first strand: chain 'E' and resid 309 through 310 removed outlier: 5.307A pdb=" N ASP E 301 " --> pdb=" O THR E 342 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N THR E 342 " --> pdb=" O ASP E 301 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N THR E 248 " --> pdb=" O LEU E 242 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N LEU E 242 " --> pdb=" O THR E 248 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLN E 250 " --> pdb=" O ILE E 240 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE E 240 " --> pdb=" O GLN E 250 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLU E 252 " --> pdb=" O ARG E 238 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ARG E 238 " --> pdb=" O GLU E 252 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TYR E 254 " --> pdb=" O LEU E 236 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU E 236 " --> pdb=" O TYR E 254 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N GLU E 256 " --> pdb=" O VAL E 234 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N GLU E 378 " --> pdb=" O VAL E 234 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU E 236 " --> pdb=" O GLU E 378 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N SER E 380 " --> pdb=" O LEU E 236 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ARG E 238 " --> pdb=" O SER E 380 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N PHE E 382 " --> pdb=" O ARG E 238 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE E 240 " --> pdb=" O PHE E 382 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 309 through 310 removed outlier: 5.307A pdb=" N ASP E 301 " --> pdb=" O THR E 342 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N THR E 342 " --> pdb=" O ASP E 301 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N THR E 248 " --> pdb=" O LEU E 242 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N LEU E 242 " --> pdb=" O THR E 248 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLN E 250 " --> pdb=" O ILE E 240 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE E 240 " --> pdb=" O GLN E 250 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLU E 252 " --> pdb=" O ARG E 238 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ARG E 238 " --> pdb=" O GLU E 252 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TYR E 254 " --> pdb=" O LEU E 236 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU E 236 " --> pdb=" O TYR E 254 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N GLU E 256 " --> pdb=" O VAL E 234 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 291 through 294 Processing sheet with id=AB3, first strand: chain 'F' and resid 68 through 69 removed outlier: 6.319A pdb=" N VAL F 26 " --> pdb=" O SER F 106 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N TYR F 108 " --> pdb=" O VAL F 26 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N PHE F 28 " --> pdb=" O TYR F 108 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N TYR F 110 " --> pdb=" O PHE F 28 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N SER F 30 " --> pdb=" O TYR F 110 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 94 through 95 removed outlier: 5.417A pdb=" N ILE F 132 " --> pdb=" O GLN F 155 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLN F 155 " --> pdb=" O ILE F 132 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ALA F 134 " --> pdb=" O ILE F 153 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 55 through 58 removed outlier: 6.830A pdb=" N THR G 26 " --> pdb=" O GLU G 55 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LEU G 57 " --> pdb=" O THR G 26 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL G 28 " --> pdb=" O LEU G 57 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU G 27 " --> pdb=" O ILE G 80 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N MET G 112 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE G 109 " --> pdb=" O VAL G 230 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N ILE G 232 " --> pdb=" O ILE G 109 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N CYS G 111 " --> pdb=" O ILE G 232 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 131 through 133 Processing sheet with id=AB7, first strand: chain 'G' and resid 138 through 141 removed outlier: 3.712A pdb=" N VAL G 139 " --> pdb=" O GLU G 201 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 152 through 154 Processing sheet with id=AB9, first strand: chain 'G' and resid 263 through 273 removed outlier: 6.536A pdb=" N ILE G 264 " --> pdb=" O TRP G 299 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N TRP G 299 " --> pdb=" O ILE G 264 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N SER G 266 " --> pdb=" O SER G 297 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N SER G 297 " --> pdb=" O SER G 266 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N HIS G 268 " --> pdb=" O GLY G 295 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLY G 295 " --> pdb=" O HIS G 268 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 263 through 273 removed outlier: 6.536A pdb=" N ILE G 264 " --> pdb=" O TRP G 299 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N TRP G 299 " --> pdb=" O ILE G 264 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N SER G 266 " --> pdb=" O SER G 297 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N SER G 297 " --> pdb=" O SER G 266 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N HIS G 268 " --> pdb=" O GLY G 295 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLY G 295 " --> pdb=" O HIS G 268 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL G 290 " --> pdb=" O GLU G 343 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU G 343 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR G 292 " --> pdb=" O THR G 341 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N TYR G 338 " --> pdb=" O SER G 330 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 321 through 326 removed outlier: 6.453A pdb=" N LEU G 316 " --> pdb=" O TYR G 322 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG G 324 " --> pdb=" O PHE G 314 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N PHE G 314 " --> pdb=" O ARG G 324 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N GLN G 313 " --> pdb=" O ASP G 358 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ASP G 358 " --> pdb=" O GLN G 313 " (cutoff:3.500A) 874 hydrogen bonds defined for protein. 2523 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: 3.38 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2711 1.30 - 1.43: 5223 1.43 - 1.56: 10141 1.56 - 1.68: 51 1.68 - 1.81: 96 Bond restraints: 18222 Sorted by residual: bond pdb=" C7 323 P 101 " pdb=" N2 323 P 101 " ideal model delta sigma weight residual 1.342 1.497 -0.155 2.00e-02 2.50e+03 6.04e+01 bond pdb=" C4 323 P 101 " pdb=" O1 323 P 101 " ideal model delta sigma weight residual 1.344 1.491 -0.147 2.00e-02 2.50e+03 5.42e+01 bond pdb=" C3 323 P 101 " pdb=" O1 323 P 101 " ideal model delta sigma weight residual 1.344 1.463 -0.119 2.00e-02 2.50e+03 3.56e+01 bond pdb=" O3A ELU A1001 " pdb=" PB ELU A1001 " ideal model delta sigma weight residual 1.747 1.644 0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" C11 CPL E 501 " pdb=" O3 CPL E 501 " ideal model delta sigma weight residual 1.327 1.423 -0.096 2.00e-02 2.50e+03 2.31e+01 ... (remaining 18217 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 24152 2.82 - 5.64: 493 5.64 - 8.46: 61 8.46 - 11.27: 9 11.27 - 14.09: 5 Bond angle restraints: 24720 Sorted by residual: angle pdb=" C3 MAN L 4 " pdb=" C2 MAN L 4 " pdb=" O2 MAN L 4 " ideal model delta sigma weight residual 111.77 97.68 14.09 3.00e+00 1.11e-01 2.21e+01 angle pdb=" O11 PTY A1003 " pdb=" P1 PTY A1003 " pdb=" O14 PTY A1003 " ideal model delta sigma weight residual 92.90 106.30 -13.40 3.00e+00 1.11e-01 2.00e+01 angle pdb=" O11 PTY H 901 " pdb=" P1 PTY H 901 " pdb=" O14 PTY H 901 " ideal model delta sigma weight residual 92.90 105.72 -12.82 3.00e+00 1.11e-01 1.83e+01 angle pdb=" N VAL A 296 " pdb=" CA VAL A 296 " pdb=" C VAL A 296 " ideal model delta sigma weight residual 113.07 107.29 5.78 1.37e+00 5.33e-01 1.78e+01 angle pdb=" N ILE A 297 " pdb=" CA ILE A 297 " pdb=" C ILE A 297 " ideal model delta sigma weight residual 111.09 105.99 5.10 1.25e+00 6.40e-01 1.66e+01 ... (remaining 24715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 10129 35.84 - 71.69: 337 71.69 - 107.53: 15 107.53 - 143.37: 0 143.37 - 179.21: 4 Dihedral angle restraints: 10485 sinusoidal: 4169 harmonic: 6316 Sorted by residual: dihedral pdb=" N CPL F 301 " pdb=" C4 CPL F 301 " pdb=" C5 CPL F 301 " pdb=" O4P CPL F 301 " ideal model delta sinusoidal sigma weight residual -71.08 108.13 -179.21 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1 ELU A1001 " pdb=" O3A ELU A1001 " pdb=" PA ELU A1001 " pdb=" PB ELU A1001 " ideal model delta sinusoidal sigma weight residual 94.92 -72.93 167.85 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" N CPL A1002 " pdb=" C4 CPL A1002 " pdb=" C5 CPL A1002 " pdb=" O4P CPL A1002 " ideal model delta sinusoidal sigma weight residual -71.08 80.85 -151.93 1 3.00e+01 1.11e-03 2.01e+01 ... (remaining 10482 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 2778 0.141 - 0.282: 37 0.282 - 0.423: 5 0.423 - 0.564: 1 0.564 - 0.705: 2 Chirality restraints: 2823 Sorted by residual: chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN E 400 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.24e+01 chirality pdb=" C1 NAG G 501 " pdb=" ND2 ASN G 332 " pdb=" C2 NAG G 501 " pdb=" O5 NAG G 501 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.68e+00 chirality pdb=" C1 NAG G 502 " pdb=" ND2 ASN G 60 " pdb=" C2 NAG G 502 " pdb=" O5 NAG G 502 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.64e+00 ... (remaining 2820 not shown) Planarity restraints: 3032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 323 P 101 " 0.160 2.00e-02 2.50e+03 3.03e-01 4.36e+03 pdb=" C10 323 P 101 " -0.012 2.00e-02 2.50e+03 pdb=" C11 323 P 101 " -0.077 2.00e-02 2.50e+03 pdb=" C12 323 P 101 " -0.039 2.00e-02 2.50e+03 pdb=" C13 323 P 101 " 0.062 2.00e-02 2.50e+03 pdb=" C16 323 P 101 " -0.939 2.00e-02 2.50e+03 pdb=" C17 323 P 101 " 0.710 2.00e-02 2.50e+03 pdb=" C18 323 P 101 " 0.315 2.00e-02 2.50e+03 pdb=" C2 323 P 101 " 0.090 2.00e-02 2.50e+03 pdb=" C3 323 P 101 " 0.126 2.00e-02 2.50e+03 pdb=" C4 323 P 101 " 0.089 2.00e-02 2.50e+03 pdb=" C5 323 P 101 " 0.054 2.00e-02 2.50e+03 pdb=" C6 323 P 101 " -0.011 2.00e-02 2.50e+03 pdb=" C7 323 P 101 " -0.145 2.00e-02 2.50e+03 pdb=" C8 323 P 101 " -0.182 2.00e-02 2.50e+03 pdb=" C9 323 P 101 " -0.084 2.00e-02 2.50e+03 pdb=" N1 323 P 101 " -0.098 2.00e-02 2.50e+03 pdb=" N2 323 P 101 " -0.252 2.00e-02 2.50e+03 pdb=" O1 323 P 101 " 0.233 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 CPL F 301 " 0.097 2.00e-02 2.50e+03 2.19e-01 4.81e+02 pdb=" C39 CPL F 301 " -0.291 2.00e-02 2.50e+03 pdb=" C40 CPL F 301 " 0.297 2.00e-02 2.50e+03 pdb=" C41 CPL F 301 " -0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 CPL A1002 " 0.096 2.00e-02 2.50e+03 2.16e-01 4.65e+02 pdb=" C42 CPL A1002 " -0.288 2.00e-02 2.50e+03 pdb=" C43 CPL A1002 " 0.290 2.00e-02 2.50e+03 pdb=" C44 CPL A1002 " -0.099 2.00e-02 2.50e+03 ... (remaining 3029 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 520 2.69 - 3.24: 17126 3.24 - 3.80: 27147 3.80 - 4.35: 36318 4.35 - 4.90: 62124 Nonbonded interactions: 143235 Sorted by model distance: nonbonded pdb=" OD2 ASP A 166 " pdb="MG MG A1004 " model vdw 2.139 2.170 nonbonded pdb=" OH TYR D 34 " pdb=" OD2 ASP D 48 " model vdw 2.205 3.040 nonbonded pdb=" OH TYR A 64 " pdb=" OD1 ASP G 381 " model vdw 2.234 3.040 nonbonded pdb=" OD1 ASP G 333 " pdb=" N SER G 334 " model vdw 2.238 3.120 nonbonded pdb=" O SER G 330 " pdb=" OG SER G 330 " model vdw 2.239 3.040 ... (remaining 143230 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 'J' selection = chain 'K' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 17.120 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 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 : 0.009 0.155 18247 Z= 0.407 Angle : 0.988 14.093 24789 Z= 0.503 Chirality : 0.058 0.705 2823 Planarity : 0.011 0.303 3027 Dihedral : 16.483 179.213 6407 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.80 % Favored : 95.06 % Rotamer: Outliers : 3.53 % Allowed : 12.77 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.18), residues: 2124 helix: 0.31 (0.17), residues: 898 sheet: -0.54 (0.26), residues: 391 loop : -1.99 (0.19), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 326 TYR 0.034 0.002 TYR A 52 PHE 0.039 0.002 PHE A 370 TRP 0.030 0.003 TRP G 299 HIS 0.013 0.002 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00897 / 0.41 (18222) covalent geometry : angle 0.96837 / 0.50 (24720) hydrogen bonds : bond 0.15043 / 10.03 ( 851) hydrogen bonds : angle 6.83231 / 4.93 ( 2523) Misc. bond : bond 0.00036 / 0.02 ( 2) link_ALPHA1-2 : bond 0.00548 / 0.34 ( 5) link_ALPHA1-2 : angle 3.63540 / 2.06 ( 15) link_ALPHA1-3 : bond 0.00634 / 0.32 ( 5) link_ALPHA1-3 : angle 1.91281 / 1.34 ( 15) link_ALPHA1-6 : bond 0.00434 / 0.21 ( 2) link_ALPHA1-6 : angle 1.66750 / 0.89 ( 6) link_BETA1-4 : bond 0.00683 / 0.35 ( 6) link_BETA1-4 : angle 3.98134 / 2.48 ( 18) link_NAG-ASN : bond 0.01083 / 0.56 ( 5) link_NAG-ASN : angle 5.60009 / 4.18 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 278 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: A 333 TRP cc_start: 0.7499 (t60) cc_final: 0.7269 (t60) REVERT: B 29 ASP cc_start: 0.8554 (t70) cc_final: 0.8273 (t0) REVERT: C 27 LYS cc_start: 0.8065 (mttp) cc_final: 0.7712 (ptmm) REVERT: D 31 LYS cc_start: 0.8765 (tttt) cc_final: 0.8556 (tttm) REVERT: D 45 LYS cc_start: 0.8503 (ttpt) cc_final: 0.8165 (ttmt) REVERT: E 195 LEU cc_start: 0.8398 (tp) cc_final: 0.8192 (tt) REVERT: F 98 GLU cc_start: 0.7069 (mt-10) cc_final: 0.6809 (pt0) REVERT: G 392 SER cc_start: 0.8907 (m) cc_final: 0.8651 (p) REVERT: H 273 MET cc_start: 0.8761 (mmm) cc_final: 0.8432 (mmp) outliers start: 65 outliers final: 22 residues processed: 332 average time/residue: 0.1333 time to fit residues: 66.5765 Evaluate side-chains 188 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 352 GLN Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 424 ARG Chi-restraints excluded: chain E residue 432 ASN Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain H residue 330 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 ASN A 216 ASN A 221 HIS A 352 GLN A 364 HIS ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 ASN A 645 GLN A 652 GLN A 653 GLN A 674 ASN C 80 ASN D 108 ASN D 127 HIS E 93 ASN E 121 ASN E 201 ASN E 232 GLN E 235 ASN E 343 ASN E 367 ASN E 416 HIS F 66 GLN F 79 GLN F 80 ASN F 123 GLN F 181 HIS G 32 GLN G 105 ASN G 108 ASN G 156 ASN G 214 GLN G 222 GLN G 225 ASN G 226 ASN G 242 ASN G 246 ASN G 247 GLN G 271 HIS G 318 GLN G 337 GLN H 238 ASN H 271 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.105913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.080989 restraints weight = 29249.888| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.91 r_work: 0.2849 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9080 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18247 Z= 0.154 Angle : 0.607 10.479 24789 Z= 0.317 Chirality : 0.045 0.486 2823 Planarity : 0.004 0.048 3027 Dihedral : 12.303 176.162 2583 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.40 % Favored : 97.55 % Rotamer: Outliers : 2.55 % Allowed : 14.95 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.18), residues: 2124 helix: 1.32 (0.17), residues: 916 sheet: -0.15 (0.27), residues: 396 loop : -1.60 (0.19), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 151 TYR 0.017 0.001 TYR E 409 PHE 0.025 0.001 PHE A 370 TRP 0.018 0.001 TRP G 299 HIS 0.007 0.001 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (18222) covalent geometry : angle 0.59532 / 0.32 (24720) hydrogen bonds : bond 0.06038 / 4.05 ( 851) hydrogen bonds : angle 4.81700 / 3.49 ( 2523) Misc. bond : bond 0.00079 / 0.04 ( 2) link_ALPHA1-2 : bond 0.00357 / 0.27 ( 5) link_ALPHA1-2 : angle 1.87212 / 1.13 ( 15) link_ALPHA1-3 : bond 0.00566 / 0.29 ( 5) link_ALPHA1-3 : angle 1.39603 / 1.00 ( 15) link_ALPHA1-6 : bond 0.00255 / 0.13 ( 2) link_ALPHA1-6 : angle 1.52402 / 0.88 ( 6) link_BETA1-4 : bond 0.00574 / 0.30 ( 6) link_BETA1-4 : angle 2.09830 / 1.39 ( 18) link_NAG-ASN : bond 0.01085 / 0.55 ( 5) link_NAG-ASN : angle 3.59038 / 3.07 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 190 time to evaluate : 0.503 Fit side-chains REVERT: A 582 ASP cc_start: 0.9077 (p0) cc_final: 0.8821 (p0) REVERT: B 29 ASP cc_start: 0.8940 (t70) cc_final: 0.8640 (t0) REVERT: C 27 LYS cc_start: 0.8396 (mttp) cc_final: 0.7722 (ptmm) REVERT: D 28 LYS cc_start: 0.8490 (tptt) cc_final: 0.8242 (tppt) REVERT: D 31 LYS cc_start: 0.8391 (tttt) cc_final: 0.7997 (tttm) REVERT: D 45 LYS cc_start: 0.8683 (ttpt) cc_final: 0.8236 (ttmt) REVERT: D 130 ASN cc_start: 0.8981 (t0) cc_final: 0.8652 (t0) REVERT: F 80 ASN cc_start: 0.8957 (OUTLIER) cc_final: 0.8386 (p0) REVERT: F 98 GLU cc_start: 0.7555 (mt-10) cc_final: 0.6896 (pt0) REVERT: G 392 SER cc_start: 0.8971 (m) cc_final: 0.8721 (p) outliers start: 47 outliers final: 30 residues processed: 224 average time/residue: 0.1295 time to fit residues: 43.8419 Evaluate side-chains 189 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 315 HIS Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain F residue 80 ASN Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain H residue 248 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 4 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 104 optimal weight: 0.4980 chunk 61 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 190 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 ASN D 97 GLN F 222 ASN G 223 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.108390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.083303 restraints weight = 29706.367| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.91 r_work: 0.2884 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9055 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18247 Z= 0.118 Angle : 0.532 10.441 24789 Z= 0.277 Chirality : 0.043 0.498 2823 Planarity : 0.004 0.046 3027 Dihedral : 11.232 164.298 2555 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.07 % Allowed : 16.36 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.18), residues: 2124 helix: 1.86 (0.17), residues: 910 sheet: -0.00 (0.27), residues: 404 loop : -1.32 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 249 TYR 0.016 0.001 TYR D 41 PHE 0.023 0.001 PHE H 293 TRP 0.015 0.001 TRP A 368 HIS 0.006 0.001 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (18222) covalent geometry : angle 0.52109 / 0.27 (24720) hydrogen bonds : bond 0.05003 / 3.35 ( 851) hydrogen bonds : angle 4.34713 / 3.15 ( 2523) Misc. bond : bond 0.00007 / 0.00 ( 2) link_ALPHA1-2 : bond 0.00329 / 0.24 ( 5) link_ALPHA1-2 : angle 1.66444 / 1.01 ( 15) link_ALPHA1-3 : bond 0.00642 / 0.34 ( 5) link_ALPHA1-3 : angle 1.28663 / 0.91 ( 15) link_ALPHA1-6 : bond 0.00417 / 0.21 ( 2) link_ALPHA1-6 : angle 1.41219 / 0.81 ( 6) link_BETA1-4 : bond 0.00454 / 0.25 ( 6) link_BETA1-4 : angle 1.84904 / 1.24 ( 18) link_NAG-ASN : bond 0.01036 / 0.53 ( 5) link_NAG-ASN : angle 3.33580 / 2.95 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 171 time to evaluate : 0.705 Fit side-chains REVERT: A 582 ASP cc_start: 0.9075 (p0) cc_final: 0.8814 (p0) REVERT: A 693 ARG cc_start: 0.8551 (ttm-80) cc_final: 0.8307 (tpp-160) REVERT: B 29 ASP cc_start: 0.8916 (t70) cc_final: 0.8632 (t0) REVERT: D 31 LYS cc_start: 0.8471 (tttt) cc_final: 0.8071 (tttm) REVERT: D 45 LYS cc_start: 0.8564 (ttpt) cc_final: 0.8054 (ttmt) REVERT: G 73 GLN cc_start: 0.8527 (tt0) cc_final: 0.8280 (tt0) REVERT: H 271 GLN cc_start: 0.9056 (mp10) cc_final: 0.8777 (mp10) outliers start: 38 outliers final: 24 residues processed: 198 average time/residue: 0.1357 time to fit residues: 41.1045 Evaluate side-chains 176 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain H residue 248 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 186 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 160 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 142 optimal weight: 0.3980 chunk 98 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 351 HIS ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 HIS B 26 HIS D 97 GLN G 223 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.104163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.078902 restraints weight = 29613.623| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.93 r_work: 0.2809 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9110 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 18247 Z= 0.201 Angle : 0.581 10.516 24789 Z= 0.300 Chirality : 0.045 0.510 2823 Planarity : 0.004 0.044 3027 Dihedral : 10.965 164.009 2550 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.32 % Allowed : 15.43 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.18), residues: 2124 helix: 2.02 (0.17), residues: 914 sheet: -0.26 (0.26), residues: 411 loop : -1.24 (0.20), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 249 TYR 0.022 0.002 TYR E 409 PHE 0.031 0.002 PHE A 370 TRP 0.014 0.001 TRP G 299 HIS 0.006 0.001 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.20 (18222) covalent geometry : angle 0.56931 / 0.30 (24720) hydrogen bonds : bond 0.05536 / 3.73 ( 851) hydrogen bonds : angle 4.35478 / 3.14 ( 2523) Misc. bond : bond 0.00036 / 0.02 ( 2) link_ALPHA1-2 : bond 0.00380 / 0.25 ( 5) link_ALPHA1-2 : angle 1.75771 / 1.08 ( 15) link_ALPHA1-3 : bond 0.00548 / 0.29 ( 5) link_ALPHA1-3 : angle 1.46338 / 1.07 ( 15) link_ALPHA1-6 : bond 0.00428 / 0.21 ( 2) link_ALPHA1-6 : angle 1.40456 / 0.81 ( 6) link_BETA1-4 : bond 0.00370 / 0.19 ( 6) link_BETA1-4 : angle 2.21175 / 1.47 ( 18) link_NAG-ASN : bond 0.00981 / 0.50 ( 5) link_NAG-ASN : angle 3.46942 / 3.04 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 158 time to evaluate : 0.657 Fit side-chains REVERT: A 582 ASP cc_start: 0.9160 (p0) cc_final: 0.8941 (p0) REVERT: A 693 ARG cc_start: 0.8596 (ttm-80) cc_final: 0.8295 (tpp-160) REVERT: B 29 ASP cc_start: 0.8993 (t70) cc_final: 0.8706 (t0) REVERT: C 27 LYS cc_start: 0.8444 (mttp) cc_final: 0.7718 (ptmm) REVERT: D 31 LYS cc_start: 0.8260 (tttt) cc_final: 0.7980 (tttm) REVERT: F 88 ASN cc_start: 0.8220 (OUTLIER) cc_final: 0.7955 (p0) REVERT: G 51 ASN cc_start: 0.8865 (p0) cc_final: 0.8588 (p0) REVERT: G 392 SER cc_start: 0.8822 (OUTLIER) cc_final: 0.8461 (p) REVERT: H 255 MET cc_start: 0.7212 (ptt) cc_final: 0.6926 (ptt) outliers start: 61 outliers final: 45 residues processed: 208 average time/residue: 0.1304 time to fit residues: 41.1799 Evaluate side-chains 191 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 144 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 226 HIS Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain F residue 88 ASN Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain G residue 390 SER Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain G residue 414 VAL Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 248 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 166 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 74 optimal weight: 0.4980 chunk 78 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 46 optimal weight: 0.0870 chunk 69 optimal weight: 0.7980 chunk 31 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 overall best weight: 0.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 HIS D 97 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.106310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.081423 restraints weight = 29424.239| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.88 r_work: 0.2867 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9075 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18247 Z= 0.120 Angle : 0.518 10.337 24789 Z= 0.267 Chirality : 0.043 0.508 2823 Planarity : 0.004 0.040 3027 Dihedral : 10.585 159.121 2550 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.45 % Allowed : 17.01 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.18), residues: 2124 helix: 2.28 (0.17), residues: 914 sheet: -0.18 (0.27), residues: 405 loop : -1.19 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 249 TYR 0.017 0.001 TYR D 41 PHE 0.025 0.001 PHE H 293 TRP 0.015 0.001 TRP A 368 HIS 0.024 0.001 HIS A 542 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (18222) covalent geometry : angle 0.50673 / 0.27 (24720) hydrogen bonds : bond 0.04743 / 3.19 ( 851) hydrogen bonds : angle 4.14438 / 2.99 ( 2523) Misc. bond : bond 0.00007 / 0.00 ( 2) link_ALPHA1-2 : bond 0.00313 / 0.22 ( 5) link_ALPHA1-2 : angle 1.65256 / 1.01 ( 15) link_ALPHA1-3 : bond 0.00618 / 0.33 ( 5) link_ALPHA1-3 : angle 1.28913 / 0.93 ( 15) link_ALPHA1-6 : bond 0.00401 / 0.20 ( 2) link_ALPHA1-6 : angle 1.42365 / 0.82 ( 6) link_BETA1-4 : bond 0.00424 / 0.23 ( 6) link_BETA1-4 : angle 1.85264 / 1.24 ( 18) link_NAG-ASN : bond 0.01021 / 0.52 ( 5) link_NAG-ASN : angle 3.22028 / 2.89 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 155 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: A 582 ASP cc_start: 0.9125 (p0) cc_final: 0.8916 (p0) REVERT: A 693 ARG cc_start: 0.8565 (ttm-80) cc_final: 0.8246 (tpp-160) REVERT: B 29 ASP cc_start: 0.8980 (t70) cc_final: 0.8699 (t0) REVERT: C 27 LYS cc_start: 0.8458 (mttp) cc_final: 0.7763 (ptmm) REVERT: D 31 LYS cc_start: 0.8296 (tttt) cc_final: 0.8026 (tttm) REVERT: F 88 ASN cc_start: 0.8167 (OUTLIER) cc_final: 0.7892 (p0) REVERT: G 51 ASN cc_start: 0.8834 (p0) cc_final: 0.8550 (p0) REVERT: G 392 SER cc_start: 0.8597 (OUTLIER) cc_final: 0.8352 (p) outliers start: 45 outliers final: 36 residues processed: 190 average time/residue: 0.1269 time to fit residues: 36.8388 Evaluate side-chains 184 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 226 HIS Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain F residue 88 ASN Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain G residue 390 SER Chi-restraints excluded: chain G residue 391 ASN Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain H residue 248 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 131 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 180 optimal weight: 0.0270 chunk 139 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.3244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 HIS D 97 GLN G 223 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.106568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.081441 restraints weight = 29561.334| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.90 r_work: 0.2850 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9087 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18247 Z= 0.147 Angle : 0.527 10.354 24789 Z= 0.271 Chirality : 0.044 0.512 2823 Planarity : 0.004 0.040 3027 Dihedral : 10.404 155.527 2550 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.66 % Allowed : 16.68 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.18), residues: 2124 helix: 2.35 (0.17), residues: 915 sheet: -0.16 (0.27), residues: 396 loop : -1.12 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 249 TYR 0.016 0.001 TYR E 409 PHE 0.026 0.001 PHE H 293 TRP 0.014 0.001 TRP A 368 HIS 0.012 0.001 HIS A 542 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (18222) covalent geometry : angle 0.51619 / 0.27 (24720) hydrogen bonds : bond 0.04826 / 3.25 ( 851) hydrogen bonds : angle 4.11540 / 2.97 ( 2523) Misc. bond : bond 0.00018 / 0.01 ( 2) link_ALPHA1-2 : bond 0.00322 / 0.22 ( 5) link_ALPHA1-2 : angle 1.67149 / 1.03 ( 15) link_ALPHA1-3 : bond 0.00577 / 0.30 ( 5) link_ALPHA1-3 : angle 1.34887 / 0.98 ( 15) link_ALPHA1-6 : bond 0.00398 / 0.20 ( 2) link_ALPHA1-6 : angle 1.42096 / 0.82 ( 6) link_BETA1-4 : bond 0.00384 / 0.20 ( 6) link_BETA1-4 : angle 1.96807 / 1.31 ( 18) link_NAG-ASN : bond 0.00987 / 0.50 ( 5) link_NAG-ASN : angle 3.25381 / 2.91 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 151 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: A 582 ASP cc_start: 0.9143 (p0) cc_final: 0.8940 (p0) REVERT: B 29 ASP cc_start: 0.9000 (t70) cc_final: 0.8735 (t0) REVERT: C 27 LYS cc_start: 0.8481 (mttp) cc_final: 0.7746 (ptmm) REVERT: D 31 LYS cc_start: 0.8340 (tttt) cc_final: 0.8007 (tttm) REVERT: E 473 ASN cc_start: 0.6073 (t0) cc_final: 0.5650 (m-40) REVERT: F 88 ASN cc_start: 0.8181 (OUTLIER) cc_final: 0.7908 (p0) REVERT: G 51 ASN cc_start: 0.8869 (p0) cc_final: 0.8580 (p0) REVERT: G 73 GLN cc_start: 0.8603 (tt0) cc_final: 0.8367 (tt0) REVERT: H 255 MET cc_start: 0.7268 (ptt) cc_final: 0.7002 (ptt) outliers start: 49 outliers final: 41 residues processed: 191 average time/residue: 0.1284 time to fit residues: 37.6161 Evaluate side-chains 187 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 145 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 226 HIS Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain F residue 88 ASN Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 390 SER Chi-restraints excluded: chain G residue 391 ASN Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 248 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 120 optimal weight: 0.9980 chunk 175 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 182 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 196 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 chunk 168 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 542 HIS D 97 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.106574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.081508 restraints weight = 29509.387| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.91 r_work: 0.2870 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9071 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18247 Z= 0.115 Angle : 0.504 10.272 24789 Z= 0.258 Chirality : 0.043 0.515 2823 Planarity : 0.003 0.040 3027 Dihedral : 10.146 149.677 2550 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.34 % Allowed : 17.01 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.19), residues: 2124 helix: 2.43 (0.17), residues: 920 sheet: -0.00 (0.27), residues: 389 loop : -1.08 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 249 TYR 0.016 0.001 TYR D 41 PHE 0.024 0.001 PHE H 293 TRP 0.014 0.001 TRP A 368 HIS 0.012 0.001 HIS A 542 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (18222) covalent geometry : angle 0.49267 / 0.26 (24720) hydrogen bonds : bond 0.04506 / 3.03 ( 851) hydrogen bonds : angle 4.02879 / 2.91 ( 2523) Misc. bond : bond 0.00008 / 0.00 ( 2) link_ALPHA1-2 : bond 0.00310 / 0.22 ( 5) link_ALPHA1-2 : angle 1.64618 / 1.01 ( 15) link_ALPHA1-3 : bond 0.00600 / 0.31 ( 5) link_ALPHA1-3 : angle 1.29711 / 0.94 ( 15) link_ALPHA1-6 : bond 0.00424 / 0.21 ( 2) link_ALPHA1-6 : angle 1.42189 / 0.82 ( 6) link_BETA1-4 : bond 0.00408 / 0.22 ( 6) link_BETA1-4 : angle 1.83976 / 1.23 ( 18) link_NAG-ASN : bond 0.01018 / 0.52 ( 5) link_NAG-ASN : angle 3.18282 / 2.86 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 157 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: A 582 ASP cc_start: 0.9119 (p0) cc_final: 0.8903 (p0) REVERT: A 693 ARG cc_start: 0.8687 (tpp-160) cc_final: 0.8486 (tpp-160) REVERT: B 29 ASP cc_start: 0.9000 (t70) cc_final: 0.8728 (t0) REVERT: C 27 LYS cc_start: 0.8460 (mttp) cc_final: 0.7706 (ptmm) REVERT: D 31 LYS cc_start: 0.8331 (tttt) cc_final: 0.7986 (tttm) REVERT: E 473 ASN cc_start: 0.6190 (t0) cc_final: 0.5783 (m-40) REVERT: F 88 ASN cc_start: 0.8200 (OUTLIER) cc_final: 0.7914 (p0) REVERT: G 51 ASN cc_start: 0.8869 (p0) cc_final: 0.8584 (p0) REVERT: G 73 GLN cc_start: 0.8618 (tt0) cc_final: 0.8360 (tt0) REVERT: G 392 SER cc_start: 0.8523 (OUTLIER) cc_final: 0.8271 (p) outliers start: 43 outliers final: 38 residues processed: 193 average time/residue: 0.1318 time to fit residues: 38.6015 Evaluate side-chains 189 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 149 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 226 HIS Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain F residue 88 ASN Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 390 SER Chi-restraints excluded: chain G residue 391 ASN Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 248 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 135 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 167 optimal weight: 0.0020 chunk 35 optimal weight: 0.4980 chunk 119 optimal weight: 0.3980 chunk 5 optimal weight: 0.9980 chunk 108 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 139 optimal weight: 0.0370 overall best weight: 0.3866 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 97 GLN G 223 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.108963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.084149 restraints weight = 29505.462| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.88 r_work: 0.2901 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9040 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18247 Z= 0.096 Angle : 0.489 10.143 24789 Z= 0.250 Chirality : 0.042 0.516 2823 Planarity : 0.003 0.039 3027 Dihedral : 9.838 143.902 2550 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.90 % Allowed : 17.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.19), residues: 2124 helix: 2.52 (0.17), residues: 919 sheet: 0.13 (0.28), residues: 388 loop : -1.02 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 249 TYR 0.018 0.001 TYR D 41 PHE 0.027 0.001 PHE H 293 TRP 0.016 0.001 TRP A 368 HIS 0.021 0.001 HIS A 542 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.10 (18222) covalent geometry : angle 0.47882 / 0.25 (24720) hydrogen bonds : bond 0.04112 / 2.76 ( 851) hydrogen bonds : angle 3.92387 / 2.83 ( 2523) Misc. bond : bond 0.00007 / 0.00 ( 2) link_ALPHA1-2 : bond 0.00282 / 0.20 ( 5) link_ALPHA1-2 : angle 1.60599 / 0.99 ( 15) link_ALPHA1-3 : bond 0.00603 / 0.32 ( 5) link_ALPHA1-3 : angle 1.24894 / 0.90 ( 15) link_ALPHA1-6 : bond 0.00455 / 0.23 ( 2) link_ALPHA1-6 : angle 1.42156 / 0.82 ( 6) link_BETA1-4 : bond 0.00437 / 0.24 ( 6) link_BETA1-4 : angle 1.70530 / 1.15 ( 18) link_NAG-ASN : bond 0.01044 / 0.53 ( 5) link_NAG-ASN : angle 3.10431 / 2.80 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 158 time to evaluate : 0.647 Fit side-chains REVERT: A 542 HIS cc_start: 0.8980 (OUTLIER) cc_final: 0.8490 (t-90) REVERT: A 582 ASP cc_start: 0.9048 (p0) cc_final: 0.8843 (p0) REVERT: B 29 ASP cc_start: 0.9013 (t70) cc_final: 0.8746 (t0) REVERT: C 27 LYS cc_start: 0.8366 (mttp) cc_final: 0.7582 (ptmm) REVERT: D 31 LYS cc_start: 0.8322 (tttt) cc_final: 0.8026 (tttm) REVERT: D 40 LYS cc_start: 0.8542 (ttpp) cc_final: 0.8334 (tttp) REVERT: E 473 ASN cc_start: 0.6123 (t0) cc_final: 0.5721 (m-40) REVERT: G 51 ASN cc_start: 0.8866 (p0) cc_final: 0.8577 (p0) REVERT: G 73 GLN cc_start: 0.8597 (tt0) cc_final: 0.8319 (tt0) REVERT: G 392 SER cc_start: 0.8481 (OUTLIER) cc_final: 0.8216 (p) REVERT: H 311 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8532 (mt) outliers start: 35 outliers final: 28 residues processed: 186 average time/residue: 0.1313 time to fit residues: 37.2588 Evaluate side-chains 177 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 226 HIS Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain G residue 390 SER Chi-restraints excluded: chain G residue 391 ASN Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 311 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 19 optimal weight: 0.8980 chunk 194 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 188 optimal weight: 0.8980 chunk 176 optimal weight: 5.9990 chunk 149 optimal weight: 0.0000 chunk 156 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 chunk 166 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 97 GLN E 161 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.108826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.083858 restraints weight = 29428.463| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.89 r_work: 0.2883 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9046 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 18247 Z= 0.106 Angle : 0.487 10.081 24789 Z= 0.248 Chirality : 0.042 0.520 2823 Planarity : 0.003 0.040 3027 Dihedral : 9.607 142.247 2550 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.12 % Allowed : 17.61 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.19), residues: 2124 helix: 2.54 (0.17), residues: 920 sheet: 0.13 (0.28), residues: 392 loop : -0.94 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 249 TYR 0.016 0.001 TYR D 41 PHE 0.026 0.001 PHE H 293 TRP 0.014 0.001 TRP A 368 HIS 0.003 0.001 HIS G 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (18222) covalent geometry : angle 0.47633 / 0.25 (24720) hydrogen bonds : bond 0.04125 / 2.77 ( 851) hydrogen bonds : angle 3.88977 / 2.80 ( 2523) Misc. bond : bond 0.00007 / 0.00 ( 2) link_ALPHA1-2 : bond 0.00266 / 0.19 ( 5) link_ALPHA1-2 : angle 1.61558 / 1.00 ( 15) link_ALPHA1-3 : bond 0.00581 / 0.31 ( 5) link_ALPHA1-3 : angle 1.28844 / 0.93 ( 15) link_ALPHA1-6 : bond 0.00439 / 0.22 ( 2) link_ALPHA1-6 : angle 1.42207 / 0.82 ( 6) link_BETA1-4 : bond 0.00403 / 0.21 ( 6) link_BETA1-4 : angle 1.77431 / 1.19 ( 18) link_NAG-ASN : bond 0.01006 / 0.52 ( 5) link_NAG-ASN : angle 3.11544 / 2.80 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 146 time to evaluate : 0.676 Fit side-chains REVERT: A 582 ASP cc_start: 0.9054 (p0) cc_final: 0.8844 (p0) REVERT: B 29 ASP cc_start: 0.9011 (t70) cc_final: 0.8761 (t0) REVERT: C 27 LYS cc_start: 0.8469 (mttp) cc_final: 0.7695 (ptmm) REVERT: D 31 LYS cc_start: 0.8295 (tttt) cc_final: 0.8046 (tttm) REVERT: E 473 ASN cc_start: 0.6167 (t0) cc_final: 0.5751 (m-40) REVERT: G 51 ASN cc_start: 0.8877 (p0) cc_final: 0.8596 (p0) REVERT: G 73 GLN cc_start: 0.8574 (tt0) cc_final: 0.8314 (tt0) REVERT: G 392 SER cc_start: 0.8476 (OUTLIER) cc_final: 0.8222 (p) REVERT: H 311 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8586 (mt) outliers start: 39 outliers final: 33 residues processed: 177 average time/residue: 0.1312 time to fit residues: 35.4226 Evaluate side-chains 177 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 226 HIS Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain G residue 390 SER Chi-restraints excluded: chain G residue 391 ASN Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 311 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 100 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 117 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 143 optimal weight: 0.5980 chunk 188 optimal weight: 0.6980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 97 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.105970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.080890 restraints weight = 29531.874| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.91 r_work: 0.2858 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9080 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18247 Z= 0.149 Angle : 0.519 10.167 24789 Z= 0.265 Chirality : 0.043 0.523 2823 Planarity : 0.004 0.041 3027 Dihedral : 9.648 143.069 2550 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.17 % Allowed : 17.72 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.19), residues: 2124 helix: 2.50 (0.17), residues: 920 sheet: 0.06 (0.27), residues: 391 loop : -0.92 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 249 TYR 0.016 0.001 TYR A 330 PHE 0.026 0.001 PHE A 370 TRP 0.009 0.001 TRP A 368 HIS 0.004 0.001 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (18222) covalent geometry : angle 0.50824 / 0.26 (24720) hydrogen bonds : bond 0.04635 / 3.12 ( 851) hydrogen bonds : angle 3.99043 / 2.88 ( 2523) Misc. bond : bond 0.00020 / 0.01 ( 2) link_ALPHA1-2 : bond 0.00309 / 0.21 ( 5) link_ALPHA1-2 : angle 1.65927 / 1.03 ( 15) link_ALPHA1-3 : bond 0.00541 / 0.28 ( 5) link_ALPHA1-3 : angle 1.35243 / 0.98 ( 15) link_ALPHA1-6 : bond 0.00384 / 0.19 ( 2) link_ALPHA1-6 : angle 1.42101 / 0.82 ( 6) link_BETA1-4 : bond 0.00359 / 0.19 ( 6) link_BETA1-4 : angle 1.97197 / 1.31 ( 18) link_NAG-ASN : bond 0.00966 / 0.50 ( 5) link_NAG-ASN : angle 3.19480 / 2.85 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 146 time to evaluate : 0.610 Fit side-chains REVERT: A 582 ASP cc_start: 0.9120 (p0) cc_final: 0.8905 (p0) REVERT: B 29 ASP cc_start: 0.9016 (t70) cc_final: 0.8763 (t0) REVERT: C 27 LYS cc_start: 0.8502 (mttp) cc_final: 0.7698 (ptmm) REVERT: D 31 LYS cc_start: 0.8318 (tttt) cc_final: 0.7998 (tttm) REVERT: E 473 ASN cc_start: 0.6129 (t0) cc_final: 0.5740 (m-40) REVERT: F 88 ASN cc_start: 0.8192 (OUTLIER) cc_final: 0.7913 (p0) REVERT: G 51 ASN cc_start: 0.8897 (p0) cc_final: 0.8646 (p0) REVERT: G 73 GLN cc_start: 0.8571 (tt0) cc_final: 0.8322 (tt0) REVERT: G 392 SER cc_start: 0.8590 (OUTLIER) cc_final: 0.8339 (p) REVERT: H 311 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8595 (mt) outliers start: 40 outliers final: 35 residues processed: 179 average time/residue: 0.1319 time to fit residues: 36.4560 Evaluate side-chains 181 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 143 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 226 HIS Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain F residue 88 ASN Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain G residue 390 SER Chi-restraints excluded: chain G residue 391 ASN Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 311 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 83 optimal weight: 0.6980 chunk 127 optimal weight: 4.9990 chunk 186 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 184 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 118 optimal weight: 0.4980 chunk 112 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 97 GLN G 223 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.107327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.082269 restraints weight = 29379.781| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.92 r_work: 0.2868 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9058 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18247 Z= 0.110 Angle : 0.499 10.356 24789 Z= 0.255 Chirality : 0.043 0.521 2823 Planarity : 0.003 0.041 3027 Dihedral : 9.449 139.629 2550 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.34 % Allowed : 17.72 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.19), residues: 2124 helix: 2.55 (0.17), residues: 921 sheet: 0.10 (0.27), residues: 393 loop : -0.89 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 249 TYR 0.012 0.001 TYR A 239 PHE 0.026 0.001 PHE H 293 TRP 0.014 0.001 TRP A 368 HIS 0.003 0.001 HIS G 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (18222) covalent geometry : angle 0.48855 / 0.25 (24720) hydrogen bonds : bond 0.04252 / 2.86 ( 851) hydrogen bonds : angle 3.90304 / 2.80 ( 2523) Misc. bond : bond 0.00008 / 0.00 ( 2) link_ALPHA1-2 : bond 0.00277 / 0.20 ( 5) link_ALPHA1-2 : angle 1.61160 / 0.99 ( 15) link_ALPHA1-3 : bond 0.00576 / 0.30 ( 5) link_ALPHA1-3 : angle 1.26870 / 0.91 ( 15) link_ALPHA1-6 : bond 0.00434 / 0.21 ( 2) link_ALPHA1-6 : angle 1.42688 / 0.82 ( 6) link_BETA1-4 : bond 0.00399 / 0.21 ( 6) link_BETA1-4 : angle 1.76735 / 1.19 ( 18) link_NAG-ASN : bond 0.01003 / 0.51 ( 5) link_NAG-ASN : angle 3.09603 / 2.79 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4179.90 seconds wall clock time: 72 minutes 29.09 seconds (4349.09 seconds total)