Starting phenix.real_space_refine on Sun Jul 5 20:41:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dar_27273/07_2026/8dar_27273.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dar_27273/07_2026/8dar_27273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dar_27273/07_2026/8dar_27273.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dar_27273/07_2026/8dar_27273.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dar_27273/07_2026/8dar_27273.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dar_27273/07_2026/8dar_27273.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8dar_27273/07_2026/8dar_27273.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dar_27273/07_2026/8dar_27273.cif" } resolution = 3.0 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= -0.029 sd= 1.015 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 Zn 2 6.06 5 P 30 5.49 5 S 144 5.16 5 C 18857 2.51 5 N 5254 2.21 5 O 5870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s 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: 30157 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4294 Classifications: {'peptide': 553} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 523} Chain breaks: 4 Chain: "B" Number of atoms: 4298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4298 Classifications: {'peptide': 555} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 525} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 4248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4248 Classifications: {'peptide': 548} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 518} Chain breaks: 3 Chain: "D" Number of atoms: 4300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4300 Classifications: {'peptide': 554} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 524} Chain breaks: 4 Chain: "E" Number of atoms: 4166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4166 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 508} Chain breaks: 2 Chain: "F" Number of atoms: 4251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4251 Classifications: {'peptide': 548} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 518} Chain breaks: 4 Chain: "G" Number of atoms: 3815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3815 Classifications: {'peptide': 474} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 452} Chain: "H" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 435 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 5, 'TRANS': 51} Chain breaks: 1 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 25810 SG CYS G 137 42.448 45.406 95.749 1.00 47.25 S ATOM 25870 SG CYS G 145 46.040 46.333 95.040 1.00 40.29 S ATOM 25897 SG CYS G 148 44.681 46.030 98.508 1.00 38.91 S ATOM 26367 SG CYS G 204 72.459 88.210 114.209 1.00 51.99 S ATOM 26465 SG CYS G 216 72.400 89.333 110.696 1.00 38.69 S ATOM 26486 SG CYS G 219 69.772 90.456 112.988 1.00 37.73 S Time building chain proxies: 6.79, per 1000 atoms: 0.23 Number of scatterers: 30157 At special positions: 0 Unit cell: (145.768, 146.832, 172.368, 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) Zn 2 29.99 S 144 16.00 P 30 15.00 O 5870 8.00 N 5254 7.00 C 18857 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G 601 " pdb="ZN ZN G 601 " - pdb=" NE2 HIS G 139 " pdb="ZN ZN G 601 " - pdb=" SG CYS G 148 " pdb="ZN ZN G 601 " - pdb=" SG CYS G 137 " pdb="ZN ZN G 601 " - pdb=" SG CYS G 145 " pdb=" ZN G 602 " pdb="ZN ZN G 602 " - pdb=" NE2 HIS G 208 " pdb="ZN ZN G 602 " - pdb=" SG CYS G 216 " pdb="ZN ZN G 602 " - pdb=" SG CYS G 219 " pdb="ZN ZN G 602 " - pdb=" SG CYS G 204 " Number of angles added : 6 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7148 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 17 sheets defined 57.8% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 97 through 103 Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.638A pdb=" N ILE A 216 " --> pdb=" O TYR A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 236 removed outlier: 3.545A pdb=" N MET A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 238 through 244 Processing helix chain 'A' and resid 260 through 273 Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 291 through 305 Processing helix chain 'A' and resid 315 through 320 removed outlier: 4.170A pdb=" N ILE A 319 " --> pdb=" O GLU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 Processing helix chain 'A' and resid 329 through 344 removed outlier: 4.200A pdb=" N VAL A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 363 removed outlier: 4.108A pdb=" N ILE A 363 " --> pdb=" O PRO A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 383 through 395 Processing helix chain 'A' and resid 405 through 413 removed outlier: 3.539A pdb=" N LEU A 409 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 437 Processing helix chain 'A' and resid 438 through 440 No H-bonds generated for 'chain 'A' and resid 438 through 440' Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 458 through 468 Processing helix chain 'A' and resid 472 through 476 Processing helix chain 'A' and resid 492 through 509 removed outlier: 4.355A pdb=" N TYR A 505 " --> pdb=" O GLU A 501 " (cutoff:3.500A) Proline residue: A 506 - end of helix Processing helix chain 'A' and resid 509 through 516 removed outlier: 3.880A pdb=" N TYR A 513 " --> pdb=" O HIS A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 545 removed outlier: 3.545A pdb=" N VAL A 545 " --> pdb=" O VAL A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 563 Processing helix chain 'A' and resid 568 through 579 Processing helix chain 'A' and resid 588 through 592 Processing helix chain 'A' and resid 609 through 620 Processing helix chain 'A' and resid 635 through 639 Processing helix chain 'A' and resid 640 through 645 removed outlier: 3.521A pdb=" N ARG A 645 " --> pdb=" O ALA A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 671 Processing helix chain 'A' and resid 682 through 689 Processing helix chain 'A' and resid 693 through 719 removed outlier: 3.714A pdb=" N HIS A 719 " --> pdb=" O ALA A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 764 removed outlier: 3.723A pdb=" N PHE A 758 " --> pdb=" O THR A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 789 Processing helix chain 'B' and resid 212 through 216 Processing helix chain 'B' and resid 219 through 236 removed outlier: 4.211A pdb=" N LEU B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Proline residue: B 233 - end of helix Processing helix chain 'B' and resid 237 through 244 removed outlier: 3.776A pdb=" N LYS B 241 " --> pdb=" O PRO B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 273 Processing helix chain 'B' and resid 281 through 286 Processing helix chain 'B' and resid 290 through 306 removed outlier: 3.860A pdb=" N SER B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU B 296 " --> pdb=" O SER B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 320 removed outlier: 4.250A pdb=" N ILE B 319 " --> pdb=" O GLU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 326 Processing helix chain 'B' and resid 329 through 344 removed outlier: 3.635A pdb=" N VAL B 335 " --> pdb=" O GLU B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 363 removed outlier: 3.792A pdb=" N ILE B 363 " --> pdb=" O PRO B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 383 through 395 Processing helix chain 'B' and resid 405 through 413 Processing helix chain 'B' and resid 417 through 437 Processing helix chain 'B' and resid 438 through 440 No H-bonds generated for 'chain 'B' and resid 438 through 440' Processing helix chain 'B' and resid 448 through 454 Processing helix chain 'B' and resid 458 through 469 Processing helix chain 'B' and resid 472 through 476 Processing helix chain 'B' and resid 492 through 509 removed outlier: 4.505A pdb=" N TYR B 505 " --> pdb=" O GLU B 501 " (cutoff:3.500A) Proline residue: B 506 - end of helix Processing helix chain 'B' and resid 509 through 517 removed outlier: 3.897A pdb=" N TYR B 513 " --> pdb=" O HIS B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 545 removed outlier: 3.546A pdb=" N VAL B 545 " --> pdb=" O VAL B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 562 Processing helix chain 'B' and resid 568 through 579 Processing helix chain 'B' and resid 588 through 592 removed outlier: 3.604A pdb=" N ILE B 592 " --> pdb=" O LEU B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 620 Processing helix chain 'B' and resid 635 through 639 Processing helix chain 'B' and resid 640 through 645 Processing helix chain 'B' and resid 659 through 672 Processing helix chain 'B' and resid 682 through 689 Processing helix chain 'B' and resid 693 through 719 Processing helix chain 'B' and resid 754 through 764 removed outlier: 3.511A pdb=" N PHE B 758 " --> pdb=" O THR B 754 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR B 764 " --> pdb=" O GLU B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 788 Processing helix chain 'C' and resid 71 through 75 removed outlier: 3.566A pdb=" N LYS C 75 " --> pdb=" O LYS C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 211 removed outlier: 3.647A pdb=" N VAL C 211 " --> pdb=" O MET C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 216 Processing helix chain 'C' and resid 219 through 236 removed outlier: 4.278A pdb=" N LEU C 232 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Proline residue: C 233 - end of helix Processing helix chain 'C' and resid 237 through 244 Processing helix chain 'C' and resid 260 through 273 Processing helix chain 'C' and resid 281 through 286 Processing helix chain 'C' and resid 291 through 306 Processing helix chain 'C' and resid 315 through 319 Processing helix chain 'C' and resid 322 through 327 removed outlier: 3.572A pdb=" N THR C 326 " --> pdb=" O LYS C 322 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASN C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 322 through 327' Processing helix chain 'C' and resid 328 through 345 removed outlier: 3.805A pdb=" N VAL C 335 " --> pdb=" O GLU C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 363 removed outlier: 3.716A pdb=" N ILE C 363 " --> pdb=" O PRO C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 368 Processing helix chain 'C' and resid 383 through 395 Processing helix chain 'C' and resid 405 through 413 Processing helix chain 'C' and resid 417 through 437 Processing helix chain 'C' and resid 438 through 440 No H-bonds generated for 'chain 'C' and resid 438 through 440' Processing helix chain 'C' and resid 448 through 454 Processing helix chain 'C' and resid 458 through 468 Processing helix chain 'C' and resid 472 through 476 removed outlier: 3.721A pdb=" N GLU C 476 " --> pdb=" O ALA C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 509 removed outlier: 4.840A pdb=" N TYR C 505 " --> pdb=" O GLU C 501 " (cutoff:3.500A) Proline residue: C 506 - end of helix Processing helix chain 'C' and resid 509 through 517 removed outlier: 3.683A pdb=" N TYR C 513 " --> pdb=" O HIS C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 545 removed outlier: 3.500A pdb=" N VAL C 545 " --> pdb=" O VAL C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 563 Processing helix chain 'C' and resid 568 through 579 Processing helix chain 'C' and resid 609 through 621 Processing helix chain 'C' and resid 640 through 645 removed outlier: 3.610A pdb=" N ARG C 645 " --> pdb=" O ALA C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 659 through 671 Processing helix chain 'C' and resid 682 through 689 Processing helix chain 'C' and resid 693 through 719 Processing helix chain 'C' and resid 754 through 764 removed outlier: 3.904A pdb=" N THR C 764 " --> pdb=" O GLU C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 788 Processing helix chain 'D' and resid 212 through 216 removed outlier: 3.660A pdb=" N ILE D 216 " --> pdb=" O TYR D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 236 removed outlier: 4.143A pdb=" N LEU D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Proline residue: D 233 - end of helix Processing helix chain 'D' and resid 237 through 244 Processing helix chain 'D' and resid 260 through 273 removed outlier: 3.790A pdb=" N GLY D 273 " --> pdb=" O ALA D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 286 Processing helix chain 'D' and resid 291 through 306 Processing helix chain 'D' and resid 315 through 319 Processing helix chain 'D' and resid 322 through 326 Processing helix chain 'D' and resid 328 through 344 removed outlier: 3.937A pdb=" N ARG D 332 " --> pdb=" O GLY D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 363 removed outlier: 3.876A pdb=" N ILE D 363 " --> pdb=" O PRO D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 368 Processing helix chain 'D' and resid 383 through 395 Processing helix chain 'D' and resid 405 through 413 Processing helix chain 'D' and resid 417 through 437 Processing helix chain 'D' and resid 438 through 440 No H-bonds generated for 'chain 'D' and resid 438 through 440' Processing helix chain 'D' and resid 448 through 454 Processing helix chain 'D' and resid 458 through 468 Processing helix chain 'D' and resid 472 through 476 Processing helix chain 'D' and resid 492 through 509 removed outlier: 4.337A pdb=" N TYR D 505 " --> pdb=" O GLU D 501 " (cutoff:3.500A) Proline residue: D 506 - end of helix Processing helix chain 'D' and resid 509 through 517 removed outlier: 3.636A pdb=" N TYR D 513 " --> pdb=" O HIS D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 545 removed outlier: 3.686A pdb=" N VAL D 545 " --> pdb=" O VAL D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 563 Processing helix chain 'D' and resid 568 through 579 Processing helix chain 'D' and resid 588 through 592 Processing helix chain 'D' and resid 609 through 620 Processing helix chain 'D' and resid 635 through 639 Processing helix chain 'D' and resid 640 through 645 Processing helix chain 'D' and resid 659 through 671 Processing helix chain 'D' and resid 682 through 689 Processing helix chain 'D' and resid 693 through 719 Processing helix chain 'D' and resid 754 through 764 removed outlier: 3.800A pdb=" N PHE D 758 " --> pdb=" O THR D 754 " (cutoff:3.500A) Processing helix chain 'D' and resid 770 through 789 Processing helix chain 'E' and resid 212 through 216 removed outlier: 3.663A pdb=" N ILE E 216 " --> pdb=" O TYR E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 236 removed outlier: 4.257A pdb=" N LEU E 232 " --> pdb=" O GLU E 228 " (cutoff:3.500A) Proline residue: E 233 - end of helix Processing helix chain 'E' and resid 236 through 244 removed outlier: 4.487A pdb=" N PHE E 240 " --> pdb=" O HIS E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 273 Processing helix chain 'E' and resid 280 through 286 Processing helix chain 'E' and resid 290 through 306 removed outlier: 3.812A pdb=" N SER E 294 " --> pdb=" O GLY E 290 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN E 306 " --> pdb=" O GLU E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 319 Processing helix chain 'E' and resid 329 through 344 removed outlier: 4.177A pdb=" N VAL E 335 " --> pdb=" O GLU E 331 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER E 336 " --> pdb=" O ARG E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 368 Processing helix chain 'E' and resid 383 through 395 Processing helix chain 'E' and resid 405 through 413 Processing helix chain 'E' and resid 417 through 437 Processing helix chain 'E' and resid 438 through 440 No H-bonds generated for 'chain 'E' and resid 438 through 440' Processing helix chain 'E' and resid 448 through 454 removed outlier: 3.521A pdb=" N SER E 454 " --> pdb=" O GLU E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 468 Processing helix chain 'E' and resid 472 through 476 removed outlier: 3.692A pdb=" N GLU E 476 " --> pdb=" O ALA E 473 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 509 removed outlier: 4.220A pdb=" N TYR E 505 " --> pdb=" O GLU E 501 " (cutoff:3.500A) Proline residue: E 506 - end of helix Processing helix chain 'E' and resid 509 through 517 removed outlier: 3.809A pdb=" N TYR E 513 " --> pdb=" O HIS E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 545 removed outlier: 3.634A pdb=" N VAL E 545 " --> pdb=" O VAL E 541 " (cutoff:3.500A) Processing helix chain 'E' and resid 553 through 562 Processing helix chain 'E' and resid 568 through 579 Processing helix chain 'E' and resid 588 through 592 removed outlier: 3.716A pdb=" N ILE E 592 " --> pdb=" O LEU E 589 " (cutoff:3.500A) Processing helix chain 'E' and resid 609 through 621 Processing helix chain 'E' and resid 635 through 639 Processing helix chain 'E' and resid 640 through 645 Processing helix chain 'E' and resid 659 through 671 Processing helix chain 'E' and resid 682 through 689 Processing helix chain 'E' and resid 693 through 719 Processing helix chain 'E' and resid 754 through 764 removed outlier: 3.545A pdb=" N PHE E 758 " --> pdb=" O THR E 754 " (cutoff:3.500A) Processing helix chain 'E' and resid 770 through 787 Processing helix chain 'F' and resid 212 through 216 removed outlier: 3.608A pdb=" N ILE F 216 " --> pdb=" O TYR F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 236 removed outlier: 4.405A pdb=" N LEU F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Proline residue: F 233 - end of helix Processing helix chain 'F' and resid 237 through 244 Processing helix chain 'F' and resid 260 through 273 Processing helix chain 'F' and resid 281 through 286 Processing helix chain 'F' and resid 291 through 306 Processing helix chain 'F' and resid 316 through 319 Processing helix chain 'F' and resid 328 through 344 Processing helix chain 'F' and resid 364 through 368 Processing helix chain 'F' and resid 383 through 395 Processing helix chain 'F' and resid 405 through 413 Processing helix chain 'F' and resid 417 through 437 Processing helix chain 'F' and resid 438 through 440 No H-bonds generated for 'chain 'F' and resid 438 through 440' Processing helix chain 'F' and resid 448 through 454 Processing helix chain 'F' and resid 458 through 468 Processing helix chain 'F' and resid 472 through 476 removed outlier: 3.549A pdb=" N GLU F 476 " --> pdb=" O ALA F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 509 removed outlier: 4.237A pdb=" N TYR F 505 " --> pdb=" O GLU F 501 " (cutoff:3.500A) Proline residue: F 506 - end of helix Processing helix chain 'F' and resid 509 through 517 removed outlier: 3.863A pdb=" N TYR F 513 " --> pdb=" O HIS F 509 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 545 Processing helix chain 'F' and resid 553 through 562 Processing helix chain 'F' and resid 568 through 579 Processing helix chain 'F' and resid 588 through 592 Processing helix chain 'F' and resid 609 through 620 Processing helix chain 'F' and resid 635 through 639 Processing helix chain 'F' and resid 640 through 645 removed outlier: 3.970A pdb=" N ARG F 645 " --> pdb=" O ALA F 642 " (cutoff:3.500A) Processing helix chain 'F' and resid 659 through 671 Processing helix chain 'F' and resid 682 through 688 Processing helix chain 'F' and resid 693 through 719 Processing helix chain 'F' and resid 754 through 763 Processing helix chain 'F' and resid 770 through 787 Processing helix chain 'G' and resid 116 through 125 removed outlier: 3.574A pdb=" N GLU G 125 " --> pdb=" O GLU G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 163 Processing helix chain 'G' and resid 168 through 180 removed outlier: 3.851A pdb=" N TYR G 172 " --> pdb=" O SER G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 214 Processing helix chain 'G' and resid 242 through 256 removed outlier: 3.629A pdb=" N PHE G 248 " --> pdb=" O ILE G 244 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TRP G 252 " --> pdb=" O PHE G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 299 through 318 removed outlier: 3.987A pdb=" N GLN G 309 " --> pdb=" O ASN G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 364 Processing helix chain 'G' and resid 402 through 410 removed outlier: 3.908A pdb=" N THR G 410 " --> pdb=" O GLU G 406 " (cutoff:3.500A) Processing helix chain 'G' and resid 500 through 508 Processing helix chain 'G' and resid 516 through 525 Processing helix chain 'G' and resid 526 through 537 Processing helix chain 'G' and resid 540 through 553 Processing helix chain 'G' and resid 556 through 566 Processing helix chain 'G' and resid 566 through 579 Processing helix chain 'H' and resid 243 through 253 Processing sheet with id=AA1, first strand: chain 'A' and resid 275 through 278 removed outlier: 6.444A pdb=" N PHE A 275 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N PHE A 312 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N PHE A 277 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ASP A 314 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL A 251 " --> pdb=" O ALA A 355 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N THR A 357 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N MET A 253 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU A 252 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 550 through 552 removed outlier: 4.303A pdb=" N GLN A 651 " --> pdb=" O GLY A 523 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 375 through 378 removed outlier: 6.228A pdb=" N LEU B 252 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA B 309 " --> pdb=" O VAL B 352 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ILE B 354 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE B 311 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ALA B 356 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE B 313 " --> pdb=" O ALA B 356 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N PHE B 275 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N PHE B 312 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N PHE B 277 " --> pdb=" O PHE B 312 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ASP B 314 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE B 279 " --> pdb=" O ASP B 314 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE B 276 " --> pdb=" O ILE G 215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 548 through 552 removed outlier: 6.645A pdb=" N ASN B 548 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N PHE B 585 " --> pdb=" O ASN B 548 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE B 550 " --> pdb=" O PHE B 585 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N GLY B 523 " --> pdb=" O GLN B 651 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N ILE B 653 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU B 525 " --> pdb=" O ILE B 653 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 275 through 276 removed outlier: 6.198A pdb=" N PHE C 275 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N PHE C 312 " --> pdb=" O PHE C 275 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 275 through 276 removed outlier: 6.198A pdb=" N PHE C 275 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N PHE C 312 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N VAL C 377 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU C 252 " --> pdb=" O VAL C 377 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 550 through 552 removed outlier: 6.627A pdb=" N THR C 582 " --> pdb=" O PHE C 628 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE C 630 " --> pdb=" O THR C 582 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL C 584 " --> pdb=" O ILE C 630 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ALA C 632 " --> pdb=" O VAL C 584 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU C 586 " --> pdb=" O ALA C 632 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N GLY C 523 " --> pdb=" O GLN C 651 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N ILE C 653 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU C 525 " --> pdb=" O ILE C 653 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 275 through 280 removed outlier: 6.908A pdb=" N PHE D 275 " --> pdb=" O ILE D 310 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N PHE D 312 " --> pdb=" O PHE D 275 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N PHE D 277 " --> pdb=" O PHE D 312 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASP D 314 " --> pdb=" O PHE D 277 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE D 279 " --> pdb=" O ASP D 314 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA D 309 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ILE D 354 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE D 311 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ALA D 356 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ILE D 313 " --> pdb=" O ALA D 356 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL D 251 " --> pdb=" O ALA D 355 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N THR D 357 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N MET D 253 " --> pdb=" O THR D 357 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG D 375 " --> pdb=" O GLY D 250 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 548 through 552 removed outlier: 6.788A pdb=" N ASN D 548 " --> pdb=" O VAL D 583 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N PHE D 585 " --> pdb=" O ASN D 548 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE D 550 " --> pdb=" O PHE D 585 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N GLY D 523 " --> pdb=" O GLN D 651 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N ILE D 653 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU D 525 " --> pdb=" O ILE D 653 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 312 through 313 removed outlier: 3.506A pdb=" N ALA E 356 " --> pdb=" O ILE E 313 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N VAL E 377 " --> pdb=" O GLY E 250 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU E 252 " --> pdb=" O VAL E 377 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 548 through 552 removed outlier: 6.529A pdb=" N ASN E 548 " --> pdb=" O VAL E 583 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N PHE E 585 " --> pdb=" O ASN E 548 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE E 550 " --> pdb=" O PHE E 585 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N ILE E 653 " --> pdb=" O GLY E 523 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU E 525 " --> pdb=" O ILE E 653 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 275 through 280 removed outlier: 6.650A pdb=" N ALA F 309 " --> pdb=" O VAL F 352 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N ILE F 354 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE F 311 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ALA F 356 " --> pdb=" O ILE F 311 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE F 313 " --> pdb=" O ALA F 356 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL F 251 " --> pdb=" O ALA F 355 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N THR F 357 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N MET F 253 " --> pdb=" O THR F 357 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLY F 250 " --> pdb=" O ARG F 375 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N VAL F 377 " --> pdb=" O GLY F 250 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU F 252 " --> pdb=" O VAL F 377 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 550 through 552 removed outlier: 6.658A pdb=" N THR F 582 " --> pdb=" O PHE F 628 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N ILE F 630 " --> pdb=" O THR F 582 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL F 584 " --> pdb=" O ILE F 630 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ALA F 632 " --> pdb=" O VAL F 584 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU F 586 " --> pdb=" O ALA F 632 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 224 through 226 removed outlier: 6.052A pdb=" N ILE G 224 " --> pdb=" O PHE G 438 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N MET G 440 " --> pdb=" O ILE G 224 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU G 226 " --> pdb=" O MET G 440 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N SER G 442 " --> pdb=" O LEU G 226 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU G 451 " --> pdb=" O TYR G 439 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 463 through 465 removed outlier: 9.993A pdb=" N VAL G 382 " --> pdb=" O SER G 320 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE G 322 " --> pdb=" O VAL G 382 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N CYS G 384 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU G 324 " --> pdb=" O CYS G 384 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N ILE G 386 " --> pdb=" O LEU G 324 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N PHE G 326 " --> pdb=" O ILE G 386 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N MET G 263 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU G 324 " --> pdb=" O GLY G 261 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY G 261 " --> pdb=" O LEU G 324 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N SER G 266 " --> pdb=" O VAL G 281 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N VAL G 281 " --> pdb=" O SER G 266 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N SER G 268 " --> pdb=" O ALA G 279 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ALA G 279 " --> pdb=" O SER G 268 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N TYR G 270 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ILE G 277 " --> pdb=" O TYR G 270 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N HIS G 236 " --> pdb=" O ALA G 279 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N VAL G 281 " --> pdb=" O HIS G 236 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU G 238 " --> pdb=" O VAL G 281 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N ALA G 283 " --> pdb=" O GLU G 238 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 290 through 291 Processing sheet with id=AB8, first strand: chain 'G' and resid 415 through 416 removed outlier: 3.588A pdb=" N SER G 415 " --> pdb=" O TYR G 424 " (cutoff:3.500A) 1458 hydrogen bonds defined for protein. 4101 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: 6.48 Time building geometry restraints manager: 3.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10188 1.34 - 1.46: 4786 1.46 - 1.58: 15387 1.58 - 1.69: 48 1.69 - 1.81: 268 Bond restraints: 30677 Sorted by residual: bond pdb=" C4 ADP A 902 " pdb=" C5 ADP A 902 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.11e+01 bond pdb=" C4 ADP B 902 " pdb=" C5 ADP B 902 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.09e+01 bond pdb=" C4 ADP F 902 " pdb=" C5 ADP F 902 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C4 ADP E 902 " pdb=" C5 ADP E 902 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" C4 ADP D 902 " pdb=" C5 ADP D 902 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.02e+01 ... (remaining 30672 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 41101 2.59 - 5.18: 301 5.18 - 7.77: 69 7.77 - 10.36: 19 10.36 - 12.95: 3 Bond angle restraints: 41493 Sorted by residual: angle pdb=" C1' ADP A 902 " pdb=" C2' ADP A 902 " pdb=" C3' ADP A 902 " ideal model delta sigma weight residual 111.00 98.05 12.95 3.00e+00 1.11e-01 1.86e+01 angle pdb=" C1' ADP E 902 " pdb=" C2' ADP E 902 " pdb=" C3' ADP E 902 " ideal model delta sigma weight residual 111.00 98.75 12.25 3.00e+00 1.11e-01 1.67e+01 angle pdb=" C1' ADP B 902 " pdb=" C2' ADP B 902 " pdb=" C3' ADP B 902 " ideal model delta sigma weight residual 111.00 99.60 11.40 3.00e+00 1.11e-01 1.44e+01 angle pdb=" C1' ADP D 902 " pdb=" C2' ADP D 902 " pdb=" C3' ADP D 902 " ideal model delta sigma weight residual 111.00 100.69 10.31 3.00e+00 1.11e-01 1.18e+01 angle pdb=" C2' ADP A 902 " pdb=" C3' ADP A 902 " pdb=" C4' ADP A 902 " ideal model delta sigma weight residual 111.00 101.09 9.91 3.00e+00 1.11e-01 1.09e+01 ... (remaining 41488 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.31: 18630 35.31 - 70.61: 169 70.61 - 105.92: 3 105.92 - 141.23: 16 141.23 - 176.53: 4 Dihedral angle restraints: 18822 sinusoidal: 7777 harmonic: 11045 Sorted by residual: dihedral pdb=" C5' ADP F 902 " pdb=" O5' ADP F 902 " pdb=" PA ADP F 902 " pdb=" O2A ADP F 902 " ideal model delta sinusoidal sigma weight residual -60.00 116.54 -176.53 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP F 902 " pdb=" O3A ADP F 902 " pdb=" PB ADP F 902 " pdb=" PA ADP F 902 " ideal model delta sinusoidal sigma weight residual 300.00 148.77 151.23 1 2.00e+01 2.50e-03 4.50e+01 dihedral pdb=" O2A ADP B 902 " pdb=" O3A ADP B 902 " pdb=" PA ADP B 902 " pdb=" PB ADP B 902 " ideal model delta sinusoidal sigma weight residual -60.00 88.57 -148.57 1 2.00e+01 2.50e-03 4.45e+01 ... (remaining 18819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 4195 0.070 - 0.140: 411 0.140 - 0.210: 5 0.210 - 0.280: 9 0.280 - 0.349: 12 Chirality restraints: 4632 Sorted by residual: chirality pdb=" CA ASN G 510 " pdb=" N ASN G 510 " pdb=" C ASN G 510 " pdb=" CB ASN G 510 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" C3' ATP D 901 " pdb=" C2' ATP D 901 " pdb=" C4' ATP D 901 " pdb=" O3' ATP D 901 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" C2' ATP F 901 " pdb=" C1' ATP F 901 " pdb=" C3' ATP F 901 " pdb=" O2' ATP F 901 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 4629 not shown) Planarity restraints: 5398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 505 " -0.028 5.00e-02 4.00e+02 4.21e-02 2.84e+00 pdb=" N PRO E 506 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO E 506 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 506 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 505 " -0.024 5.00e-02 4.00e+02 3.59e-02 2.07e+00 pdb=" N PRO B 506 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 506 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 506 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 505 " -0.023 5.00e-02 4.00e+02 3.43e-02 1.89e+00 pdb=" N PRO A 506 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 506 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 506 " -0.019 5.00e-02 4.00e+02 ... (remaining 5395 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 315 2.59 - 3.17: 26913 3.17 - 3.74: 45704 3.74 - 4.32: 62157 4.32 - 4.90: 107011 Nonbonded interactions: 242100 Sorted by model distance: nonbonded pdb=" O ILE G 167 " pdb=" OG SER G 171 " model vdw 2.011 3.040 nonbonded pdb=" OG SER G 417 " pdb=" O MET G 422 " model vdw 2.059 3.040 nonbonded pdb=" OG SER B 294 " pdb=" OE1 GLU G 436 " model vdw 2.078 3.040 nonbonded pdb=" OG1 THR F 458 " pdb=" OD1 ASP F 460 " model vdw 2.090 3.040 nonbonded pdb=" OG1 THR A 485 " pdb=" OD1 ASP A 487 " model vdw 2.117 3.040 ... (remaining 242095 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 208 through 787 or resid 901 through 902)) selection = (chain 'B' and (resid 208 through 787 or resid 901 through 902)) selection = (chain 'C' and (resid 208 through 787 or resid 901 through 902)) selection = (chain 'D' and (resid 208 through 787 or resid 901 through 902)) selection = chain 'E' selection = (chain 'F' and resid 208 through 902) } 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: 5.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 32.080 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.144 30685 Z= 0.186 Angle : 0.598 12.947 41499 Z= 0.276 Chirality : 0.045 0.349 4632 Planarity : 0.003 0.042 5398 Dihedral : 11.659 176.532 11674 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.93 % Allowed : 5.23 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % 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: 1.67 (0.14), residues: 3767 helix: 2.04 (0.12), residues: 1910 sheet: -0.31 (0.24), residues: 458 loop : 0.44 (0.18), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 788 TYR 0.012 0.001 TYR G 172 PHE 0.011 0.001 PHE G 527 TRP 0.009 0.001 TRP E 486 HIS 0.004 0.001 HIS G 528 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (30677) covalent geometry : angle 0.59752 / 0.28 (41493) hydrogen bonds : bond 0.14926 / 9.85 ( 1458) hydrogen bonds : angle 5.17408 / 3.77 ( 4101) metal coordination : bond 0.07600 / 5.06 ( 8) metal coordination : angle 2.66256 / 1.34 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 521 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 609 ARG cc_start: 0.7412 (mtp-110) cc_final: 0.6711 (mtm110) REVERT: B 209 ASN cc_start: 0.7312 (t0) cc_final: 0.6925 (t0) REVERT: C 571 ASP cc_start: 0.8101 (t0) cc_final: 0.7852 (t0) REVERT: D 785 LYS cc_start: 0.8354 (tmmt) cc_final: 0.8116 (tppt) REVERT: E 331 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7400 (mt-10) REVERT: E 709 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8681 (tp) REVERT: G 257 MET cc_start: 0.7102 (mmp) cc_final: 0.6844 (mmm) outliers start: 62 outliers final: 14 residues processed: 568 average time/residue: 0.8209 time to fit residues: 530.8497 Evaluate side-chains 283 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 268 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain C residue 568 ASN Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 488 ASP Chi-restraints excluded: chain E residue 350 ASN Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain E residue 709 ILE Chi-restraints excluded: chain F residue 488 ASP Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 331 ASP Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 543 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.0010 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.0970 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 0.9980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 509 HIS A 716 HIS B 432 GLN B 568 ASN B 651 GLN C 512 GLN C 638 GLN C 651 GLN C 716 HIS D 306 ASN D 783 GLN E 361 ASN ** E 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 ASN F 470 ASN F 668 ASN G 309 GLN G 361 HIS G 537 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.124788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.090558 restraints weight = 47057.140| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.87 r_work: 0.3098 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 30685 Z= 0.131 Angle : 0.621 14.116 41499 Z= 0.300 Chirality : 0.043 0.214 4632 Planarity : 0.004 0.054 5398 Dihedral : 9.659 170.370 4248 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.83 % Allowed : 12.21 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % 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: 1.69 (0.14), residues: 3767 helix: 1.95 (0.12), residues: 1935 sheet: 0.07 (0.24), residues: 438 loop : 0.42 (0.18), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 775 TYR 0.019 0.001 TYR F 416 PHE 0.021 0.001 PHE B 464 TRP 0.016 0.002 TRP F 561 HIS 0.010 0.001 HIS A 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (30677) covalent geometry : angle 0.62028 / 0.30 (41493) hydrogen bonds : bond 0.03919 / 2.58 ( 1458) hydrogen bonds : angle 4.18315 / 3.04 ( 4101) metal coordination : bond 0.00593 / 0.43 ( 8) metal coordination : angle 2.64417 / 1.36 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 306 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7498 (mtp) REVERT: A 480 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7738 (pm20) REVERT: A 609 ARG cc_start: 0.6881 (mtp-110) cc_final: 0.6099 (mtm110) REVERT: B 214 ASP cc_start: 0.8526 (m-30) cc_final: 0.8308 (p0) REVERT: B 332 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.6841 (mpp-170) REVERT: B 345 MET cc_start: 0.7504 (ttp) cc_final: 0.7293 (ttm) REVERT: B 359 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7962 (ttm110) REVERT: B 553 LYS cc_start: 0.8443 (mmmt) cc_final: 0.8151 (mmtm) REVERT: B 556 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.7120 (mt-10) REVERT: B 571 ASP cc_start: 0.8397 (t0) cc_final: 0.8173 (t0) REVERT: B 635 ARG cc_start: 0.7394 (mmm160) cc_final: 0.6832 (mmm-85) REVERT: B 763 LYS cc_start: 0.8672 (mttt) cc_final: 0.8118 (mmpt) REVERT: C 437 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.7259 (ttp) REVERT: C 571 ASP cc_start: 0.8547 (t0) cc_final: 0.8185 (t0) REVERT: D 304 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7513 (mt-10) REVERT: D 398 MET cc_start: 0.8798 (mtp) cc_final: 0.8364 (ttm) REVERT: D 758 PHE cc_start: 0.8586 (m-80) cc_final: 0.8305 (m-80) REVERT: D 762 MET cc_start: 0.7916 (mmm) cc_final: 0.7668 (mmm) REVERT: D 785 LYS cc_start: 0.8269 (tmmt) cc_final: 0.7858 (tppt) REVERT: E 229 MET cc_start: 0.7716 (tpt) cc_final: 0.7260 (tpt) REVERT: E 331 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7789 (mp0) REVERT: E 375 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.6845 (mtm110) REVERT: E 438 ASP cc_start: 0.7612 (m-30) cc_final: 0.7238 (OUTLIER) REVERT: E 439 LEU cc_start: 0.8440 (tm) cc_final: 0.7854 (pp) REVERT: E 451 VAL cc_start: 0.6474 (t) cc_final: 0.5799 (p) REVERT: E 468 ASN cc_start: 0.7465 (m-40) cc_final: 0.7251 (t0) REVERT: F 278 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8595 (tm) REVERT: F 784 MET cc_start: 0.8209 (tpp) cc_final: 0.7712 (tpp) REVERT: G 206 ASN cc_start: 0.6307 (t0) cc_final: 0.5936 (t0) REVERT: G 257 MET cc_start: 0.8306 (mmp) cc_final: 0.7895 (mmm) REVERT: G 406 GLU cc_start: 0.8043 (tt0) cc_final: 0.7784 (tt0) REVERT: G 537 GLN cc_start: 0.7924 (tm-30) cc_final: 0.7706 (tm-30) outliers start: 91 outliers final: 27 residues processed: 364 average time/residue: 0.7049 time to fit residues: 298.0567 Evaluate side-chains 294 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 259 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 332 ARG Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 437 MET Chi-restraints excluded: chain C residue 568 ASN Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 784 MET Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 342 MET Chi-restraints excluded: chain E residue 375 ARG Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 309 GLN Chi-restraints excluded: chain G residue 331 ASP Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 309 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 99 optimal weight: 2.9990 chunk 246 optimal weight: 0.0000 chunk 93 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 339 optimal weight: 0.0470 chunk 271 optimal weight: 5.9990 chunk 38 optimal weight: 0.0670 chunk 153 optimal weight: 0.0050 chunk 62 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 overall best weight: 0.1434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 716 HIS B 568 ASN C 512 GLN C 568 ASN C 716 HIS D 568 ASN ** E 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 309 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.125795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.094223 restraints weight = 47628.822| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.80 r_work: 0.3115 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 30685 Z= 0.102 Angle : 0.553 12.571 41499 Z= 0.265 Chirality : 0.041 0.158 4632 Planarity : 0.004 0.045 5398 Dihedral : 8.790 151.935 4238 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.55 % Allowed : 13.17 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % 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: 1.73 (0.14), residues: 3767 helix: 1.98 (0.12), residues: 1936 sheet: 0.19 (0.24), residues: 446 loop : 0.40 (0.18), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 775 TYR 0.018 0.001 TYR G 189 PHE 0.017 0.001 PHE B 464 TRP 0.016 0.001 TRP B 561 HIS 0.009 0.001 HIS A 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (30677) covalent geometry : angle 0.55302 / 0.27 (41493) hydrogen bonds : bond 0.03122 / 2.05 ( 1458) hydrogen bonds : angle 3.86070 / 2.78 ( 4101) metal coordination : bond 0.00369 / 0.22 ( 8) metal coordination : angle 1.88492 / 1.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 285 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7543 (mtp) REVERT: A 332 ARG cc_start: 0.6894 (tpt170) cc_final: 0.6647 (tpp-160) REVERT: A 497 GLU cc_start: 0.8015 (mp0) cc_final: 0.7770 (mp0) REVERT: A 561 TRP cc_start: 0.6754 (t-100) cc_final: 0.6421 (t60) REVERT: A 609 ARG cc_start: 0.7033 (mtp-110) cc_final: 0.6259 (mtm110) REVERT: B 345 MET cc_start: 0.7773 (ttp) cc_final: 0.7527 (ttm) REVERT: B 375 ARG cc_start: 0.7581 (mmm-85) cc_final: 0.7295 (mmt90) REVERT: B 476 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6937 (pm20) REVERT: B 553 LYS cc_start: 0.8557 (mmmt) cc_final: 0.8294 (mmtm) REVERT: B 556 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7283 (mt-10) REVERT: B 571 ASP cc_start: 0.8548 (t0) cc_final: 0.8329 (t0) REVERT: B 635 ARG cc_start: 0.7503 (mmm160) cc_final: 0.6874 (mmm-85) REVERT: B 763 LYS cc_start: 0.8699 (mttt) cc_final: 0.8133 (mmpt) REVERT: C 302 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7357 (mp0) REVERT: C 437 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.7302 (ttp) REVERT: C 568 ASN cc_start: 0.7607 (OUTLIER) cc_final: 0.7097 (p0) REVERT: C 571 ASP cc_start: 0.8635 (t0) cc_final: 0.8379 (t0) REVERT: C 665 SER cc_start: 0.9002 (t) cc_final: 0.8710 (p) REVERT: C 755 LYS cc_start: 0.6873 (tttt) cc_final: 0.6554 (tptp) REVERT: D 264 MET cc_start: 0.8662 (mtp) cc_final: 0.8438 (mtp) REVERT: D 304 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7762 (mt-10) REVERT: D 398 MET cc_start: 0.8783 (mtp) cc_final: 0.8306 (ttm) REVERT: D 758 PHE cc_start: 0.8739 (m-80) cc_final: 0.8473 (m-80) REVERT: D 762 MET cc_start: 0.8004 (mmm) cc_final: 0.7765 (mmm) REVERT: E 229 MET cc_start: 0.7810 (tpt) cc_final: 0.7452 (tpt) REVERT: E 278 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8467 (tp) REVERT: E 331 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7763 (mp0) REVERT: E 635 ARG cc_start: 0.7282 (mtp85) cc_final: 0.6894 (mtp85) REVERT: F 298 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8136 (mmmt) REVERT: G 206 ASN cc_start: 0.6645 (t0) cc_final: 0.5931 (t0) REVERT: G 406 GLU cc_start: 0.8003 (tt0) cc_final: 0.7725 (tt0) REVERT: G 495 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.7023 (mtp) REVERT: G 537 GLN cc_start: 0.8018 (tm-30) cc_final: 0.7774 (tm-30) outliers start: 82 outliers final: 18 residues processed: 346 average time/residue: 0.7274 time to fit residues: 292.9039 Evaluate side-chains 284 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 256 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 437 MET Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 568 ASN Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 568 ASN Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 342 MET Chi-restraints excluded: chain F residue 298 LYS Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 331 ASP Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain G residue 543 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 281 optimal weight: 0.9980 chunk 324 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 336 optimal weight: 0.7980 chunk 359 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 295 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 118 optimal weight: 0.0030 chunk 17 optimal weight: 1.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 716 HIS B 568 ASN C 512 GLN D 361 ASN D 568 ASN E 670 GLN G 491 ASN G 493 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.123263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.091126 restraints weight = 47182.271| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.83 r_work: 0.3076 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 30685 Z= 0.143 Angle : 0.565 11.718 41499 Z= 0.272 Chirality : 0.042 0.170 4632 Planarity : 0.004 0.048 5398 Dihedral : 8.546 145.111 4232 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.87 % Allowed : 13.89 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % 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: 1.65 (0.14), residues: 3767 helix: 1.92 (0.12), residues: 1937 sheet: 0.24 (0.24), residues: 451 loop : 0.34 (0.18), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 249 TYR 0.015 0.001 TYR A 416 PHE 0.014 0.001 PHE C 277 TRP 0.016 0.002 TRP B 561 HIS 0.006 0.001 HIS A 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.14 (30677) covalent geometry : angle 0.56431 / 0.27 (41493) hydrogen bonds : bond 0.03535 / 2.31 ( 1458) hydrogen bonds : angle 3.82390 / 2.76 ( 4101) metal coordination : bond 0.00683 / 0.49 ( 8) metal coordination : angle 1.84556 / 0.95 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 264 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7639 (mtp) REVERT: A 480 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7809 (pm20) REVERT: A 497 GLU cc_start: 0.8037 (mp0) cc_final: 0.7776 (mp0) REVERT: A 556 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7517 (mt-10) REVERT: A 609 ARG cc_start: 0.7106 (mtp-110) cc_final: 0.6306 (mtm110) REVERT: A 621 MET cc_start: 0.7979 (ttm) cc_final: 0.7566 (ttp) REVERT: A 773 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7479 (mp0) REVERT: B 345 MET cc_start: 0.7756 (ttp) cc_final: 0.7207 (ttp) REVERT: B 375 ARG cc_start: 0.7633 (mmm-85) cc_final: 0.7355 (mmt90) REVERT: B 476 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.7043 (pm20) REVERT: B 553 LYS cc_start: 0.8549 (mmmt) cc_final: 0.8218 (mmtm) REVERT: B 556 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7206 (mt-10) REVERT: B 560 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.7240 (mtt) REVERT: B 635 ARG cc_start: 0.7505 (mmm160) cc_final: 0.6890 (mmm-85) REVERT: B 672 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.7389 (ptp-170) REVERT: B 763 LYS cc_start: 0.8701 (mttt) cc_final: 0.8128 (mmpt) REVERT: C 376 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8157 (mt-10) REVERT: C 437 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.7320 (ttp) REVERT: C 568 ASN cc_start: 0.7726 (OUTLIER) cc_final: 0.7153 (p0) REVERT: C 571 ASP cc_start: 0.8697 (t0) cc_final: 0.8210 (t0) REVERT: C 614 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8328 (tt) REVERT: C 665 SER cc_start: 0.9046 (t) cc_final: 0.8756 (p) REVERT: C 755 LYS cc_start: 0.6851 (tttt) cc_final: 0.6521 (tptp) REVERT: D 264 MET cc_start: 0.8727 (mtp) cc_final: 0.8442 (mtp) REVERT: D 304 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7902 (mt-10) REVERT: D 398 MET cc_start: 0.8931 (mtp) cc_final: 0.8426 (ttm) REVERT: D 758 PHE cc_start: 0.8803 (m-80) cc_final: 0.8586 (m-80) REVERT: D 762 MET cc_start: 0.8149 (mmm) cc_final: 0.7949 (mmm) REVERT: D 785 LYS cc_start: 0.8379 (tmmt) cc_final: 0.7899 (tppt) REVERT: E 229 MET cc_start: 0.7841 (tpt) cc_final: 0.7503 (tpt) REVERT: E 331 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7785 (mp0) REVERT: E 448 ASP cc_start: 0.7159 (OUTLIER) cc_final: 0.6821 (p0) REVERT: E 635 ARG cc_start: 0.7364 (mtp85) cc_final: 0.7043 (mtp85) REVERT: F 253 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8630 (mtp) REVERT: F 298 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8173 (mmmt) REVERT: F 427 GLU cc_start: 0.7767 (tt0) cc_final: 0.7319 (tt0) REVERT: F 784 MET cc_start: 0.8248 (tpp) cc_final: 0.7792 (tpp) REVERT: G 122 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7677 (mm) REVERT: G 206 ASN cc_start: 0.6825 (t0) cc_final: 0.6310 (t0) REVERT: G 406 GLU cc_start: 0.8080 (tt0) cc_final: 0.7819 (tt0) REVERT: G 422 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8314 (mtt) REVERT: G 495 MET cc_start: 0.7476 (OUTLIER) cc_final: 0.7052 (mtp) REVERT: G 537 GLN cc_start: 0.8049 (tm-30) cc_final: 0.7770 (tm-30) REVERT: H 237 SER cc_start: 0.8464 (m) cc_final: 0.8260 (t) outliers start: 92 outliers final: 32 residues processed: 330 average time/residue: 0.7139 time to fit residues: 274.3497 Evaluate side-chains 301 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 250 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain B residue 322 LYS Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 560 MET Chi-restraints excluded: chain B residue 672 ARG Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain C residue 437 MET Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 512 GLN Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 568 ASN Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 568 ASN Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 342 MET Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain F residue 253 MET Chi-restraints excluded: chain F residue 298 LYS Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 331 ASP Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 385 VAL Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 422 MET Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain H residue 228 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 10 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 chunk 215 optimal weight: 0.0570 chunk 375 optimal weight: 4.9990 chunk 29 optimal weight: 0.3980 chunk 330 optimal weight: 1.9990 chunk 273 optimal weight: 0.9990 chunk 115 optimal weight: 0.0030 chunk 79 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 overall best weight: 0.4910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 716 HIS B 716 HIS D 361 ASN D 470 ASN D 568 ASN G 365 HIS G 491 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.124439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.092748 restraints weight = 47270.965| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.77 r_work: 0.3094 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 30685 Z= 0.105 Angle : 0.542 10.870 41499 Z= 0.259 Chirality : 0.041 0.266 4632 Planarity : 0.004 0.047 5398 Dihedral : 8.245 144.996 4230 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.77 % Allowed : 14.01 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % 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: 1.69 (0.14), residues: 3767 helix: 1.96 (0.12), residues: 1936 sheet: 0.38 (0.24), residues: 444 loop : 0.29 (0.18), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 717 TYR 0.014 0.001 TYR G 189 PHE 0.012 0.001 PHE B 464 TRP 0.017 0.001 TRP B 561 HIS 0.011 0.001 HIS B 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (30677) covalent geometry : angle 0.54184 / 0.26 (41493) hydrogen bonds : bond 0.03120 / 2.04 ( 1458) hydrogen bonds : angle 3.73235 / 2.68 ( 4101) metal coordination : bond 0.00333 / 0.21 ( 8) metal coordination : angle 1.76550 / 0.96 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 268 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 480 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7771 (pm20) REVERT: A 556 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7548 (mt-10) REVERT: A 561 TRP cc_start: 0.6842 (t-100) cc_final: 0.6274 (t60) REVERT: A 621 MET cc_start: 0.8009 (ttm) cc_final: 0.7511 (ttp) REVERT: A 773 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7458 (mp0) REVERT: B 345 MET cc_start: 0.7696 (ttp) cc_final: 0.7268 (ttp) REVERT: B 375 ARG cc_start: 0.7642 (mmm-85) cc_final: 0.7390 (mmt90) REVERT: B 476 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.7005 (pm20) REVERT: B 553 LYS cc_start: 0.8467 (mmmt) cc_final: 0.8181 (mmtm) REVERT: B 556 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7241 (mt-10) REVERT: B 560 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7207 (mtt) REVERT: B 635 ARG cc_start: 0.7482 (mmm160) cc_final: 0.6873 (mmm-85) REVERT: B 672 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.7309 (ptp90) REVERT: B 763 LYS cc_start: 0.8669 (mttt) cc_final: 0.8113 (mmpt) REVERT: C 376 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8134 (mt-10) REVERT: C 437 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.7340 (ttp) REVERT: C 568 ASN cc_start: 0.7720 (OUTLIER) cc_final: 0.7235 (p0) REVERT: C 571 ASP cc_start: 0.8690 (t0) cc_final: 0.8383 (t0) REVERT: C 614 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8312 (tt) REVERT: C 618 MET cc_start: 0.8542 (mtp) cc_final: 0.8191 (mtm) REVERT: C 665 SER cc_start: 0.9032 (t) cc_final: 0.8747 (p) REVERT: C 752 TYR cc_start: 0.7735 (p90) cc_final: 0.7533 (p90) REVERT: C 755 LYS cc_start: 0.6950 (tttt) cc_final: 0.6624 (tptp) REVERT: D 264 MET cc_start: 0.8721 (mtp) cc_final: 0.8425 (mtp) REVERT: D 304 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7822 (mt-10) REVERT: D 398 MET cc_start: 0.8868 (mtp) cc_final: 0.8372 (ttm) REVERT: D 758 PHE cc_start: 0.8761 (m-80) cc_final: 0.8523 (m-80) REVERT: D 762 MET cc_start: 0.8163 (mmm) cc_final: 0.7939 (mmm) REVERT: D 785 LYS cc_start: 0.8434 (tmmt) cc_final: 0.7943 (tppt) REVERT: E 229 MET cc_start: 0.7926 (tpt) cc_final: 0.7615 (tpt) REVERT: E 331 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7787 (mp0) REVERT: E 396 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8495 (ttmm) REVERT: E 437 MET cc_start: 0.6785 (ttt) cc_final: 0.6567 (ttp) REVERT: E 635 ARG cc_start: 0.7293 (mtp85) cc_final: 0.6988 (mtp85) REVERT: E 762 MET cc_start: 0.7339 (mmm) cc_final: 0.7113 (tpt) REVERT: F 298 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8135 (mmmt) REVERT: G 122 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7617 (mm) REVERT: G 157 GLU cc_start: 0.8379 (tt0) cc_final: 0.8178 (tp30) REVERT: G 206 ASN cc_start: 0.6756 (t0) cc_final: 0.6263 (t0) REVERT: G 371 TYR cc_start: 0.8840 (m-80) cc_final: 0.8480 (m-80) REVERT: G 406 GLU cc_start: 0.8126 (tt0) cc_final: 0.7881 (tt0) REVERT: G 495 MET cc_start: 0.7508 (OUTLIER) cc_final: 0.7116 (mtp) REVERT: G 537 GLN cc_start: 0.8146 (tm-30) cc_final: 0.7861 (tm-30) REVERT: H 237 SER cc_start: 0.8585 (m) cc_final: 0.8326 (t) outliers start: 89 outliers final: 27 residues processed: 333 average time/residue: 0.7661 time to fit residues: 295.1153 Evaluate side-chains 290 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 247 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 560 MET Chi-restraints excluded: chain B residue 672 ARG Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain C residue 437 MET Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 568 ASN Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 568 ASN Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 396 LYS Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain F residue 298 LYS Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 331 ASP Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain H residue 228 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 111 optimal weight: 3.9990 chunk 255 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 174 optimal weight: 0.9980 chunk 267 optimal weight: 0.8980 chunk 189 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 253 optimal weight: 0.2980 chunk 14 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 716 HIS B 270 ASN C 512 GLN D 470 ASN D 568 ASN G 491 ASN G 493 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.123622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.091455 restraints weight = 47246.111| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.75 r_work: 0.3080 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 30685 Z= 0.127 Angle : 0.550 10.332 41499 Z= 0.263 Chirality : 0.041 0.220 4632 Planarity : 0.004 0.048 5398 Dihedral : 8.096 146.776 4230 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.43 % Allowed : 14.86 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % 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: 1.67 (0.14), residues: 3767 helix: 1.95 (0.12), residues: 1936 sheet: 0.34 (0.24), residues: 447 loop : 0.27 (0.18), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 359 TYR 0.012 0.001 TYR G 189 PHE 0.014 0.001 PHE D 276 TRP 0.017 0.001 TRP B 561 HIS 0.007 0.001 HIS A 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (30677) covalent geometry : angle 0.54939 / 0.26 (41493) hydrogen bonds : bond 0.03287 / 2.15 ( 1458) hydrogen bonds : angle 3.71239 / 2.67 ( 4101) metal coordination : bond 0.00475 / 0.33 ( 8) metal coordination : angle 1.81822 / 0.97 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 255 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 480 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7791 (pm20) REVERT: A 556 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7532 (mt-10) REVERT: A 561 TRP cc_start: 0.6791 (t-100) cc_final: 0.6341 (t60) REVERT: A 609 ARG cc_start: 0.6941 (mtm110) cc_final: 0.6112 (mtm110) REVERT: A 618 MET cc_start: 0.8320 (mtp) cc_final: 0.8099 (mtp) REVERT: A 621 MET cc_start: 0.8032 (ttm) cc_final: 0.7556 (ttp) REVERT: A 773 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7471 (mp0) REVERT: B 214 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7837 (p0) REVERT: B 345 MET cc_start: 0.7913 (ttp) cc_final: 0.7357 (ttp) REVERT: B 375 ARG cc_start: 0.7628 (mmm-85) cc_final: 0.7377 (mmt90) REVERT: B 553 LYS cc_start: 0.8489 (mmmt) cc_final: 0.8186 (mmtm) REVERT: B 556 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7200 (mt-10) REVERT: B 560 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.7371 (mtt) REVERT: B 635 ARG cc_start: 0.7438 (mmm160) cc_final: 0.6856 (mmm-85) REVERT: B 672 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7424 (ptp-170) REVERT: B 763 LYS cc_start: 0.8666 (mttt) cc_final: 0.8109 (mmpt) REVERT: C 376 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8156 (mt-10) REVERT: C 568 ASN cc_start: 0.7777 (OUTLIER) cc_final: 0.7322 (p0) REVERT: C 571 ASP cc_start: 0.8714 (t0) cc_final: 0.8223 (t0) REVERT: C 614 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8277 (tt) REVERT: C 618 MET cc_start: 0.8564 (mtp) cc_final: 0.8209 (mtm) REVERT: C 665 SER cc_start: 0.9036 (t) cc_final: 0.8746 (p) REVERT: C 755 LYS cc_start: 0.6926 (tttt) cc_final: 0.6592 (tptp) REVERT: D 304 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7894 (mt-10) REVERT: D 556 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7229 (mt-10) REVERT: D 709 ILE cc_start: 0.7941 (tt) cc_final: 0.7736 (tt) REVERT: D 758 PHE cc_start: 0.8772 (m-80) cc_final: 0.8542 (m-80) REVERT: D 762 MET cc_start: 0.8156 (mmm) cc_final: 0.7923 (mmm) REVERT: D 785 LYS cc_start: 0.8454 (tmmt) cc_final: 0.7962 (tppt) REVERT: E 229 MET cc_start: 0.7944 (tpt) cc_final: 0.7737 (tpt) REVERT: E 331 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7761 (mp0) REVERT: E 396 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8478 (ttmm) REVERT: E 437 MET cc_start: 0.6725 (ttt) cc_final: 0.6517 (ttp) REVERT: E 635 ARG cc_start: 0.7322 (mtp85) cc_final: 0.7032 (mtp85) REVERT: F 298 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8149 (mmmt) REVERT: F 571 ASP cc_start: 0.8710 (t0) cc_final: 0.8211 (m-30) REVERT: F 784 MET cc_start: 0.8277 (tpp) cc_final: 0.7819 (tpp) REVERT: G 206 ASN cc_start: 0.6770 (t0) cc_final: 0.6284 (t0) REVERT: G 406 GLU cc_start: 0.8144 (tt0) cc_final: 0.7901 (tt0) REVERT: G 495 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.7105 (mtp) REVERT: G 537 GLN cc_start: 0.8073 (tm-30) cc_final: 0.7796 (tm-30) REVERT: H 237 SER cc_start: 0.8587 (m) cc_final: 0.8340 (t) outliers start: 78 outliers final: 33 residues processed: 316 average time/residue: 0.7123 time to fit residues: 261.9976 Evaluate side-chains 297 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 250 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 322 LYS Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 560 MET Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain B residue 672 ARG Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 568 ASN Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 396 LYS Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain F residue 298 LYS Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 331 ASP Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 385 VAL Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain G residue 543 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 311 optimal weight: 6.9990 chunk 215 optimal weight: 0.0770 chunk 201 optimal weight: 0.8980 chunk 283 optimal weight: 2.9990 chunk 219 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 214 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 716 HIS C 512 GLN D 470 ASN D 719 HIS F 470 ASN G 491 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.123794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.091162 restraints weight = 47309.141| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.79 r_work: 0.3087 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 30685 Z= 0.121 Angle : 0.554 10.285 41499 Z= 0.263 Chirality : 0.041 0.210 4632 Planarity : 0.004 0.048 5398 Dihedral : 7.907 146.983 4230 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.37 % Allowed : 15.35 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % 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: 1.70 (0.14), residues: 3767 helix: 1.97 (0.12), residues: 1934 sheet: 0.38 (0.24), residues: 448 loop : 0.27 (0.18), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 348 TYR 0.011 0.001 TYR F 416 PHE 0.012 0.001 PHE D 276 TRP 0.017 0.001 TRP B 561 HIS 0.020 0.001 HIS A 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (30677) covalent geometry : angle 0.55324 / 0.26 (41493) hydrogen bonds : bond 0.03218 / 2.10 ( 1458) hydrogen bonds : angle 3.70256 / 2.67 ( 4101) metal coordination : bond 0.00415 / 0.29 ( 8) metal coordination : angle 1.66889 / 0.86 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 249 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 480 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.7804 (pm20) REVERT: A 556 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7572 (mt-10) REVERT: A 561 TRP cc_start: 0.6845 (t-100) cc_final: 0.6371 (t60) REVERT: A 609 ARG cc_start: 0.6999 (mtm110) cc_final: 0.6167 (mtm110) REVERT: A 618 MET cc_start: 0.8332 (mtp) cc_final: 0.8114 (mtp) REVERT: A 621 MET cc_start: 0.8087 (ttm) cc_final: 0.7622 (ttp) REVERT: A 773 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7473 (mp0) REVERT: B 214 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7807 (p0) REVERT: B 243 ILE cc_start: 0.8025 (tt) cc_final: 0.7815 (tt) REVERT: B 375 ARG cc_start: 0.7626 (mmm-85) cc_final: 0.7374 (mmt90) REVERT: B 553 LYS cc_start: 0.8505 (mmmt) cc_final: 0.8208 (mmtm) REVERT: B 556 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7247 (mt-10) REVERT: B 635 ARG cc_start: 0.7514 (mmm160) cc_final: 0.6931 (mmm-85) REVERT: B 763 LYS cc_start: 0.8668 (mttt) cc_final: 0.8103 (mmpt) REVERT: C 376 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8153 (mt-10) REVERT: C 568 ASN cc_start: 0.7826 (OUTLIER) cc_final: 0.7460 (p0) REVERT: C 571 ASP cc_start: 0.8725 (t0) cc_final: 0.8256 (t0) REVERT: C 614 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8319 (tt) REVERT: C 618 MET cc_start: 0.8596 (mtp) cc_final: 0.8240 (mtm) REVERT: C 665 SER cc_start: 0.9051 (t) cc_final: 0.8764 (p) REVERT: C 755 LYS cc_start: 0.6946 (tttt) cc_final: 0.6570 (tptp) REVERT: D 304 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7928 (mt-10) REVERT: D 398 MET cc_start: 0.8954 (mtp) cc_final: 0.8440 (ttm) REVERT: D 412 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8039 (mt-10) REVERT: D 556 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7269 (mt-10) REVERT: D 709 ILE cc_start: 0.7962 (tt) cc_final: 0.7754 (tt) REVERT: D 762 MET cc_start: 0.8176 (mmm) cc_final: 0.7944 (mmm) REVERT: D 785 LYS cc_start: 0.8416 (tmmt) cc_final: 0.7951 (tppt) REVERT: E 331 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7835 (mt-10) REVERT: E 396 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8473 (ttmm) REVERT: E 437 MET cc_start: 0.6721 (ttt) cc_final: 0.6515 (ttp) REVERT: E 635 ARG cc_start: 0.7359 (mtp85) cc_final: 0.7077 (mtp85) REVERT: F 298 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8168 (mmmt) REVERT: F 571 ASP cc_start: 0.8726 (t0) cc_final: 0.8229 (m-30) REVERT: F 784 MET cc_start: 0.8233 (tpp) cc_final: 0.7834 (tpp) REVERT: G 122 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.8009 (mt) REVERT: G 206 ASN cc_start: 0.6784 (t0) cc_final: 0.6273 (t0) REVERT: G 257 MET cc_start: 0.8201 (mmt) cc_final: 0.7992 (mmm) REVERT: G 406 GLU cc_start: 0.8126 (tt0) cc_final: 0.7882 (tt0) REVERT: G 495 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.7114 (mtp) REVERT: G 537 GLN cc_start: 0.8103 (tm-30) cc_final: 0.7833 (tm-30) REVERT: H 237 SER cc_start: 0.8607 (m) cc_final: 0.8388 (t) outliers start: 76 outliers final: 34 residues processed: 306 average time/residue: 0.7470 time to fit residues: 265.1983 Evaluate side-chains 295 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 247 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 322 LYS Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 512 GLN Chi-restraints excluded: chain C residue 568 ASN Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 412 GLU Chi-restraints excluded: chain D residue 784 MET Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 396 LYS Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain F residue 298 LYS Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 331 ASP Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 385 VAL Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 491 ASN Chi-restraints excluded: chain G residue 495 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 6 optimal weight: 0.0980 chunk 317 optimal weight: 6.9990 chunk 340 optimal weight: 0.8980 chunk 232 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 259 optimal weight: 0.0670 chunk 292 optimal weight: 4.9990 chunk 172 optimal weight: 0.8980 chunk 210 optimal weight: 0.2980 chunk 61 optimal weight: 0.0000 overall best weight: 0.2722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 716 HIS C 512 GLN D 470 ASN D 719 HIS G 491 ASN G 493 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.125150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.092459 restraints weight = 47065.588| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.66 r_work: 0.3110 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 30685 Z= 0.099 Angle : 0.548 12.467 41499 Z= 0.258 Chirality : 0.041 0.201 4632 Planarity : 0.003 0.047 5398 Dihedral : 7.608 142.952 4227 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.06 % Allowed : 15.82 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % 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: 1.79 (0.14), residues: 3767 helix: 2.04 (0.12), residues: 1934 sheet: 0.42 (0.24), residues: 449 loop : 0.33 (0.18), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 375 TYR 0.012 0.001 TYR G 189 PHE 0.011 0.001 PHE G 517 TRP 0.018 0.001 TRP B 561 HIS 0.012 0.001 HIS A 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (30677) covalent geometry : angle 0.54716 / 0.26 (41493) hydrogen bonds : bond 0.02876 / 1.88 ( 1458) hydrogen bonds : angle 3.63142 / 2.61 ( 4101) metal coordination : bond 0.00322 / 0.19 ( 8) metal coordination : angle 2.10424 / 1.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 265 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 332 ARG cc_start: 0.6789 (mtt90) cc_final: 0.6569 (mtt90) REVERT: A 480 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7751 (pm20) REVERT: A 556 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7547 (mt-10) REVERT: A 561 TRP cc_start: 0.6759 (t-100) cc_final: 0.6271 (t60) REVERT: A 609 ARG cc_start: 0.6904 (mtm110) cc_final: 0.6107 (mtm110) REVERT: A 618 MET cc_start: 0.8245 (mtp) cc_final: 0.8005 (mtp) REVERT: A 621 MET cc_start: 0.7976 (ttm) cc_final: 0.7488 (ttp) REVERT: B 214 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7701 (p0) REVERT: B 229 MET cc_start: 0.8041 (mtt) cc_final: 0.7587 (mmp) REVERT: B 345 MET cc_start: 0.7726 (ttp) cc_final: 0.7285 (ttp) REVERT: B 375 ARG cc_start: 0.7621 (mmm-85) cc_final: 0.7265 (mmt90) REVERT: B 553 LYS cc_start: 0.8393 (mmmt) cc_final: 0.8124 (mmtm) REVERT: B 556 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7230 (mt-10) REVERT: B 635 ARG cc_start: 0.7409 (mmm160) cc_final: 0.6798 (mmm-85) REVERT: B 763 LYS cc_start: 0.8653 (mttt) cc_final: 0.8085 (mmpt) REVERT: C 376 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8075 (mt-10) REVERT: C 568 ASN cc_start: 0.7632 (OUTLIER) cc_final: 0.7340 (OUTLIER) REVERT: C 571 ASP cc_start: 0.8686 (t0) cc_final: 0.8246 (t0) REVERT: C 614 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8227 (tt) REVERT: C 618 MET cc_start: 0.8483 (mtp) cc_final: 0.8116 (mtm) REVERT: C 665 SER cc_start: 0.9020 (t) cc_final: 0.8734 (p) REVERT: C 755 LYS cc_start: 0.7032 (tttt) cc_final: 0.6651 (tptp) REVERT: D 304 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7817 (mt-10) REVERT: D 398 MET cc_start: 0.8887 (mtp) cc_final: 0.8402 (ttm) REVERT: D 556 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7202 (mt-10) REVERT: D 709 ILE cc_start: 0.7888 (tt) cc_final: 0.7684 (tt) REVERT: D 762 MET cc_start: 0.8163 (mmm) cc_final: 0.7940 (mmm) REVERT: D 785 LYS cc_start: 0.8487 (tmmt) cc_final: 0.8004 (tppt) REVERT: E 229 MET cc_start: 0.7399 (tpt) cc_final: 0.7014 (mmm) REVERT: E 331 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7818 (mt-10) REVERT: E 396 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8455 (ttmm) REVERT: E 437 MET cc_start: 0.6739 (ttt) cc_final: 0.6519 (ttp) REVERT: E 635 ARG cc_start: 0.7257 (mtp85) cc_final: 0.6944 (mtp85) REVERT: F 72 LYS cc_start: 0.8402 (mtpt) cc_final: 0.7658 (pttt) REVERT: F 427 GLU cc_start: 0.7596 (tt0) cc_final: 0.7148 (tt0) REVERT: F 556 GLU cc_start: 0.7650 (tp30) cc_final: 0.7321 (mt-10) REVERT: F 571 ASP cc_start: 0.8674 (t0) cc_final: 0.8177 (m-30) REVERT: F 784 MET cc_start: 0.8139 (tpp) cc_final: 0.7797 (tpp) REVERT: G 206 ASN cc_start: 0.6644 (t0) cc_final: 0.6286 (t0) REVERT: G 371 TYR cc_start: 0.8838 (m-80) cc_final: 0.8445 (m-80) REVERT: G 406 GLU cc_start: 0.8009 (tt0) cc_final: 0.7777 (tt0) REVERT: G 495 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.7126 (mtp) REVERT: G 537 GLN cc_start: 0.8115 (tm-30) cc_final: 0.7820 (tm-30) REVERT: H 237 SER cc_start: 0.8503 (m) cc_final: 0.8237 (t) outliers start: 66 outliers final: 34 residues processed: 314 average time/residue: 0.7181 time to fit residues: 261.2542 Evaluate side-chains 294 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 251 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 752 TYR Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 512 GLN Chi-restraints excluded: chain C residue 568 ASN Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 784 MET Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 396 LYS Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain F residue 264 MET Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 385 VAL Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 491 ASN Chi-restraints excluded: chain G residue 495 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 199 optimal weight: 0.5980 chunk 279 optimal weight: 0.3980 chunk 371 optimal weight: 0.9990 chunk 165 optimal weight: 0.0070 chunk 252 optimal weight: 1.9990 chunk 222 optimal weight: 3.9990 chunk 218 optimal weight: 4.9990 chunk 220 optimal weight: 2.9990 chunk 248 optimal weight: 0.8980 chunk 178 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 716 HIS B 209 ASN C 512 GLN D 470 ASN D 719 HIS G 491 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.124587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.092465 restraints weight = 47175.688| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.75 r_work: 0.3099 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 30685 Z= 0.111 Angle : 0.560 11.948 41499 Z= 0.265 Chirality : 0.041 0.194 4632 Planarity : 0.004 0.048 5398 Dihedral : 7.454 139.791 4225 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.84 % Allowed : 16.57 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % 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: 1.82 (0.14), residues: 3767 helix: 2.07 (0.12), residues: 1925 sheet: 0.52 (0.24), residues: 442 loop : 0.32 (0.18), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 375 TYR 0.012 0.001 TYR G 189 PHE 0.015 0.001 PHE F 373 TRP 0.016 0.001 TRP B 561 HIS 0.007 0.001 HIS D 719 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (30677) covalent geometry : angle 0.55964 / 0.26 (41493) hydrogen bonds : bond 0.03014 / 1.97 ( 1458) hydrogen bonds : angle 3.62861 / 2.61 ( 4101) metal coordination : bond 0.00312 / 0.20 ( 8) metal coordination : angle 1.57567 / 0.88 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 253 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ARG cc_start: 0.6804 (mtt90) cc_final: 0.6592 (mtt90) REVERT: A 480 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7761 (pm20) REVERT: A 556 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7587 (mt-10) REVERT: A 561 TRP cc_start: 0.6800 (t-100) cc_final: 0.6318 (t60) REVERT: A 609 ARG cc_start: 0.6969 (mtm110) cc_final: 0.6163 (mtm110) REVERT: A 621 MET cc_start: 0.8086 (ttm) cc_final: 0.7617 (ttp) REVERT: B 214 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7709 (p0) REVERT: B 229 MET cc_start: 0.8090 (mtt) cc_final: 0.7606 (mmp) REVERT: B 345 MET cc_start: 0.7809 (ttp) cc_final: 0.7408 (ttp) REVERT: B 375 ARG cc_start: 0.7647 (mmm-85) cc_final: 0.7110 (mmt90) REVERT: B 553 LYS cc_start: 0.8419 (mmmt) cc_final: 0.8139 (mmtm) REVERT: B 556 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7258 (mt-10) REVERT: B 635 ARG cc_start: 0.7440 (mmm160) cc_final: 0.6837 (mmm-85) REVERT: B 763 LYS cc_start: 0.8660 (mttt) cc_final: 0.8091 (mmpt) REVERT: C 376 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8120 (mt-10) REVERT: C 568 ASN cc_start: 0.7699 (OUTLIER) cc_final: 0.7421 (OUTLIER) REVERT: C 571 ASP cc_start: 0.8707 (t0) cc_final: 0.8265 (t0) REVERT: C 614 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8288 (tt) REVERT: C 618 MET cc_start: 0.8543 (mtp) cc_final: 0.8184 (mtm) REVERT: C 665 SER cc_start: 0.9045 (t) cc_final: 0.8760 (p) REVERT: C 755 LYS cc_start: 0.7031 (tttt) cc_final: 0.6629 (tptp) REVERT: D 304 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7878 (mt-10) REVERT: D 398 MET cc_start: 0.8918 (mtp) cc_final: 0.8436 (ttm) REVERT: D 412 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8031 (mt-10) REVERT: D 556 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7230 (mt-10) REVERT: D 709 ILE cc_start: 0.7912 (tt) cc_final: 0.7707 (tt) REVERT: D 762 MET cc_start: 0.8178 (mmm) cc_final: 0.7960 (mmm) REVERT: D 785 LYS cc_start: 0.8496 (tmmt) cc_final: 0.8013 (tppt) REVERT: E 229 MET cc_start: 0.7512 (tpt) cc_final: 0.7295 (mpp) REVERT: E 331 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7836 (mt-10) REVERT: E 396 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8470 (ttmm) REVERT: E 437 MET cc_start: 0.6772 (ttt) cc_final: 0.6551 (ttp) REVERT: E 635 ARG cc_start: 0.7321 (mtp85) cc_final: 0.7025 (mtp85) REVERT: F 298 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8082 (mmmt) REVERT: F 427 GLU cc_start: 0.7623 (tt0) cc_final: 0.7410 (tm-30) REVERT: F 556 GLU cc_start: 0.7664 (tp30) cc_final: 0.7336 (mt-10) REVERT: F 571 ASP cc_start: 0.8710 (t0) cc_final: 0.8217 (m-30) REVERT: F 784 MET cc_start: 0.8156 (tpp) cc_final: 0.7820 (tpp) REVERT: G 206 ASN cc_start: 0.6738 (t0) cc_final: 0.6392 (t0) REVERT: G 371 TYR cc_start: 0.8875 (m-80) cc_final: 0.8538 (m-80) REVERT: G 406 GLU cc_start: 0.7999 (tt0) cc_final: 0.7772 (tt0) REVERT: G 495 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.7249 (mtp) REVERT: G 537 GLN cc_start: 0.8065 (tm-30) cc_final: 0.7811 (tm-30) REVERT: H 237 SER cc_start: 0.8511 (m) cc_final: 0.8262 (t) outliers start: 59 outliers final: 36 residues processed: 301 average time/residue: 0.7095 time to fit residues: 248.4079 Evaluate side-chains 299 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 252 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 322 LYS Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 568 ASN Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 412 GLU Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 784 MET Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 396 LYS Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain F residue 264 MET Chi-restraints excluded: chain F residue 298 LYS Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 385 VAL Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 495 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 201 optimal weight: 2.9990 chunk 269 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 261 optimal weight: 0.5980 chunk 185 optimal weight: 1.9990 chunk 195 optimal weight: 0.0570 chunk 359 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 307 optimal weight: 3.9990 chunk 158 optimal weight: 0.0570 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 716 HIS C 512 GLN D 470 ASN D 719 HIS G 289 GLN G 362 GLN G 491 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.123389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.091097 restraints weight = 47070.507| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.76 r_work: 0.3084 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 30685 Z= 0.138 Angle : 0.577 11.937 41499 Z= 0.274 Chirality : 0.042 0.194 4632 Planarity : 0.004 0.054 5398 Dihedral : 7.431 137.293 4225 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.93 % Allowed : 16.79 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % 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: 1.74 (0.14), residues: 3767 helix: 2.01 (0.12), residues: 1930 sheet: 0.47 (0.24), residues: 448 loop : 0.28 (0.18), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG B 348 TYR 0.012 0.001 TYR F 416 PHE 0.014 0.001 PHE F 573 TRP 0.017 0.001 TRP B 561 HIS 0.025 0.001 HIS A 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (30677) covalent geometry : angle 0.57712 / 0.27 (41493) hydrogen bonds : bond 0.03278 / 2.14 ( 1458) hydrogen bonds : angle 3.67623 / 2.64 ( 4101) metal coordination : bond 0.00507 / 0.35 ( 8) metal coordination : angle 1.47597 / 0.74 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 248 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ARG cc_start: 0.6843 (mtt90) cc_final: 0.6625 (mtt90) REVERT: A 480 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7791 (pm20) REVERT: A 556 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7599 (mt-10) REVERT: A 561 TRP cc_start: 0.6871 (t-100) cc_final: 0.6389 (t60) REVERT: A 609 ARG cc_start: 0.7012 (mtm110) cc_final: 0.6186 (mtm110) REVERT: A 618 MET cc_start: 0.8328 (mtp) cc_final: 0.8121 (mtp) REVERT: A 621 MET cc_start: 0.8132 (ttm) cc_final: 0.7716 (ttp) REVERT: B 214 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7787 (p0) REVERT: B 345 MET cc_start: 0.7949 (ttp) cc_final: 0.7539 (ttp) REVERT: B 375 ARG cc_start: 0.7610 (mmm-85) cc_final: 0.7346 (mmt90) REVERT: B 553 LYS cc_start: 0.8495 (mmmt) cc_final: 0.8217 (mmtm) REVERT: B 556 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7284 (mt-10) REVERT: B 635 ARG cc_start: 0.7494 (mmm160) cc_final: 0.6890 (mmm-85) REVERT: B 763 LYS cc_start: 0.8671 (mttt) cc_final: 0.8099 (mmpt) REVERT: C 376 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8148 (mt-10) REVERT: C 568 ASN cc_start: 0.7756 (OUTLIER) cc_final: 0.7509 (OUTLIER) REVERT: C 571 ASP cc_start: 0.8734 (t0) cc_final: 0.8276 (t0) REVERT: C 614 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8338 (tt) REVERT: C 618 MET cc_start: 0.8604 (mtp) cc_final: 0.8242 (mtm) REVERT: C 665 SER cc_start: 0.9063 (t) cc_final: 0.8777 (p) REVERT: C 755 LYS cc_start: 0.7072 (tttt) cc_final: 0.6701 (tptp) REVERT: D 304 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7933 (mt-10) REVERT: D 398 MET cc_start: 0.8937 (mtp) cc_final: 0.8468 (ttm) REVERT: D 412 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8030 (mt-10) REVERT: D 556 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7641 (mm-30) REVERT: D 709 ILE cc_start: 0.8005 (tt) cc_final: 0.7795 (tt) REVERT: D 762 MET cc_start: 0.8208 (mmm) cc_final: 0.7989 (mmm) REVERT: D 785 LYS cc_start: 0.8465 (tmmt) cc_final: 0.7972 (tppt) REVERT: E 331 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7851 (mt-10) REVERT: E 396 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8479 (ttmm) REVERT: E 437 MET cc_start: 0.6734 (ttt) cc_final: 0.6524 (ttp) REVERT: E 635 ARG cc_start: 0.7397 (mtp85) cc_final: 0.7072 (mtp85) REVERT: F 298 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8125 (mmmt) REVERT: F 427 GLU cc_start: 0.7712 (tt0) cc_final: 0.7475 (tm-30) REVERT: F 556 GLU cc_start: 0.7689 (tp30) cc_final: 0.7352 (mt-10) REVERT: F 571 ASP cc_start: 0.8739 (t0) cc_final: 0.8242 (m-30) REVERT: F 784 MET cc_start: 0.8180 (tpp) cc_final: 0.7816 (tpp) REVERT: G 206 ASN cc_start: 0.6856 (t0) cc_final: 0.6509 (t0) REVERT: G 406 GLU cc_start: 0.8091 (tt0) cc_final: 0.7873 (tt0) REVERT: G 495 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7278 (mtp) REVERT: G 537 GLN cc_start: 0.8036 (tm-30) cc_final: 0.7793 (tm-30) REVERT: H 237 SER cc_start: 0.8545 (m) cc_final: 0.8317 (t) outliers start: 62 outliers final: 35 residues processed: 297 average time/residue: 0.7488 time to fit residues: 258.0054 Evaluate side-chains 295 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 249 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 512 GLN Chi-restraints excluded: chain C residue 568 ASN Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 412 GLU Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 396 LYS Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain F residue 298 LYS Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain F residue 667 LEU Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 385 VAL Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 422 MET Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 491 ASN Chi-restraints excluded: chain G residue 495 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 359 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 217 optimal weight: 0.9990 chunk 295 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 296 optimal weight: 4.9990 chunk 138 optimal weight: 0.4980 chunk 203 optimal weight: 0.5980 chunk 182 optimal weight: 0.1980 chunk 8 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 470 ASN D 719 HIS G 493 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.123475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.091606 restraints weight = 47655.744| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.79 r_work: 0.3072 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.390 30685 Z= 0.251 Angle : 0.787 59.200 41499 Z= 0.449 Chirality : 0.050 1.600 4632 Planarity : 0.005 0.188 5398 Dihedral : 7.425 137.281 4225 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.51 % Favored : 95.46 % Rotamer: Outliers : 1.74 % Allowed : 17.00 % Favored : 81.25 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 5.15 % 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: 1.74 (0.14), residues: 3767 helix: 2.00 (0.12), residues: 1930 sheet: 0.47 (0.24), residues: 448 loop : 0.28 (0.18), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG E 375 TYR 0.011 0.001 TYR F 416 PHE 0.014 0.001 PHE F 573 TRP 0.015 0.001 TRP B 561 HIS 0.245 0.003 HIS A 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.25 (30677) covalent geometry : angle 0.78677 / 0.45 (41493) hydrogen bonds : bond 0.03264 / 2.12 ( 1458) hydrogen bonds : angle 3.67559 / 2.64 ( 4101) metal coordination : bond 0.00482 / 0.33 ( 8) metal coordination : angle 1.48196 / 0.75 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8778.50 seconds wall clock time: 150 minutes 21.04 seconds (9021.04 seconds total)