Starting phenix.real_space_refine on Mon Aug 25 23:56:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rsb_19475/08_2025/8rsb_19475.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rsb_19475/08_2025/8rsb_19475.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8rsb_19475/08_2025/8rsb_19475.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rsb_19475/08_2025/8rsb_19475.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rsb_19475/08_2025/8rsb_19475.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rsb_19475/08_2025/8rsb_19475.map" } resolution = 3.4 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= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 138 5.16 5 C 19754 2.51 5 N 5770 2.21 5 O 6198 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31884 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5267 Classifications: {'peptide': 742} Incomplete info: {'truncation_to_alanine': 164} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 700} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 569 Unresolved non-hydrogen angles: 723 Unresolved non-hydrogen dihedrals: 455 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'ASN:plan1': 9, 'ARG:plan': 16, 'ASP:plan': 15, 'GLU:plan': 16, 'GLN:plan1': 3, 'PHE:plan': 5, 'TYR:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 303 Chain: "B" Number of atoms: 5263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5263 Classifications: {'peptide': 742} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 700} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 573 Unresolved non-hydrogen angles: 728 Unresolved non-hydrogen dihedrals: 458 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'ASN:plan1': 9, 'ARG:plan': 16, 'ASP:plan': 15, 'GLU:plan': 17, 'GLN:plan1': 3, 'PHE:plan': 5, 'TYR:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 307 Chain: "C" Number of atoms: 5255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5255 Classifications: {'peptide': 742} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 700} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 582 Unresolved non-hydrogen angles: 740 Unresolved non-hydrogen dihedrals: 466 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'ASN:plan1': 9, 'ARG:plan': 16, 'ASP:plan': 16, 'GLU:plan': 17, 'GLN:plan1': 3, 'PHE:plan': 5, 'TYR:plan': 5, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 315 Chain: "D" Number of atoms: 5244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5244 Classifications: {'peptide': 742} Incomplete info: {'truncation_to_alanine': 170} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 700} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 592 Unresolved non-hydrogen angles: 751 Unresolved non-hydrogen dihedrals: 473 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'ASN:plan1': 10, 'ARG:plan': 17, 'ASP:plan': 16, 'GLU:plan': 17, 'GLN:plan1': 3, 'PHE:plan': 5, 'TYR:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 318 Chain: "E" Number of atoms: 5267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5267 Classifications: {'peptide': 742} Incomplete info: {'truncation_to_alanine': 164} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 700} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 569 Unresolved non-hydrogen angles: 723 Unresolved non-hydrogen dihedrals: 455 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'ASN:plan1': 9, 'ARG:plan': 16, 'ASP:plan': 15, 'GLU:plan': 16, 'GLN:plan1': 3, 'PHE:plan': 5, 'TYR:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 303 Chain: "F" Number of atoms: 5264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5264 Classifications: {'peptide': 742} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 700} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 572 Unresolved non-hydrogen angles: 727 Unresolved non-hydrogen dihedrals: 457 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'ASN:plan1': 10, 'ARG:plan': 16, 'ASP:plan': 15, 'GLU:plan': 16, 'GLN:plan1': 3, 'PHE:plan': 5, 'TYR:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 306 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.82, per 1000 atoms: 0.25 Number of scatterers: 31884 At special positions: 0 Unit cell: (174.58, 129.86, 177.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 138 16.00 P 24 15.00 O 6198 8.00 N 5770 7.00 C 19754 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: 3.36 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 953.7 nanoseconds 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8328 Finding SS restraints... Secondary structure from input PDB file: 206 helices and 31 sheets defined 50.8% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 85 through 91 removed outlier: 4.089A pdb=" N ASN A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 135 Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 202 through 206 removed outlier: 3.707A pdb=" N ILE A 206 " --> pdb=" O TYR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 220 Processing helix chain 'A' and resid 221 through 226 Processing helix chain 'A' and resid 226 through 233 removed outlier: 3.555A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 261 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 278 through 296 removed outlier: 3.923A pdb=" N ARG A 287 " --> pdb=" O GLU A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 318 through 336 removed outlier: 3.857A pdb=" N VAL A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A 326 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS A 336 " --> pdb=" O MET A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.930A pdb=" N ILE A 353 " --> pdb=" O PRO A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 395 through 403 removed outlier: 3.816A pdb=" N VAL A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 432 removed outlier: 3.691A pdb=" N ALA A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP A 428 " --> pdb=" O ARG A 424 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 432 " --> pdb=" O ASP A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 445 removed outlier: 4.016A pdb=" N LEU A 445 " --> pdb=" O VAL A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 458 Processing helix chain 'A' and resid 482 through 499 removed outlier: 4.106A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 499 through 506 removed outlier: 4.188A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 536 removed outlier: 3.657A pdb=" N LEU A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS A 529 " --> pdb=" O THR A 525 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 554 removed outlier: 3.512A pdb=" N LEU A 547 " --> pdb=" O LYS A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 569 removed outlier: 4.307A pdb=" N ARG A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 586 Processing helix chain 'A' and resid 598 through 610 Processing helix chain 'A' and resid 612 through 615 removed outlier: 3.545A pdb=" N LYS A 615 " --> pdb=" O SER A 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 612 through 615' Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.696A pdb=" N ARG A 635 " --> pdb=" O ALA A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 662 removed outlier: 3.642A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 679 Processing helix chain 'A' and resid 683 through 716 removed outlier: 3.635A pdb=" N ARG A 713 " --> pdb=" O ARG A 709 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN A 714 " --> pdb=" O GLU A 710 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR A 715 " --> pdb=" O ARG A 711 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN A 716 " --> pdb=" O GLU A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 743 removed outlier: 3.647A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 762 removed outlier: 3.788A pdb=" N LEU A 762 " --> pdb=" O PHE A 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 93 removed outlier: 3.808A pdb=" N ASN B 91 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 92 " --> pdb=" O VAL B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 135 Processing helix chain 'B' and resid 135 through 140 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 209 through 226 removed outlier: 5.211A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 226 through 233 removed outlier: 4.052A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS B 231 " --> pdb=" O PRO B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 263 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 278 through 296 Processing helix chain 'B' and resid 305 through 309 Processing helix chain 'B' and resid 318 through 338 removed outlier: 3.506A pdb=" N THR B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET B 332 " --> pdb=" O LEU B 328 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS B 336 " --> pdb=" O MET B 332 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLN B 337 " --> pdb=" O ASP B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.121A pdb=" N ILE B 353 " --> pdb=" O PRO B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 358 Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 395 through 403 removed outlier: 3.836A pdb=" N VAL B 399 " --> pdb=" O ASP B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 432 removed outlier: 4.489A pdb=" N LYS B 425 " --> pdb=" O GLN B 421 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LYS B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 445 removed outlier: 4.053A pdb=" N LEU B 445 " --> pdb=" O VAL B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 499 removed outlier: 4.112A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 499 through 506 removed outlier: 4.141A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 536 removed outlier: 3.541A pdb=" N LEU B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS B 529 " --> pdb=" O THR B 525 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 554 removed outlier: 3.518A pdb=" N LEU B 547 " --> pdb=" O LYS B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 569 removed outlier: 4.380A pdb=" N ARG B 560 " --> pdb=" O GLU B 556 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 586 Processing helix chain 'B' and resid 598 through 610 removed outlier: 3.629A pdb=" N ASN B 602 " --> pdb=" O ASP B 598 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN B 603 " --> pdb=" O ARG B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 615 removed outlier: 3.640A pdb=" N LYS B 615 " --> pdb=" O SER B 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 612 through 615' Processing helix chain 'B' and resid 625 through 629 removed outlier: 3.542A pdb=" N ILE B 628 " --> pdb=" O ARG B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 634 Processing helix chain 'B' and resid 649 through 662 Processing helix chain 'B' and resid 671 through 679 Processing helix chain 'B' and resid 683 through 716 removed outlier: 3.677A pdb=" N ARG B 713 " --> pdb=" O ARG B 709 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N THR B 715 " --> pdb=" O ARG B 711 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASN B 716 " --> pdb=" O GLU B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 740 removed outlier: 3.771A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 762 removed outlier: 3.676A pdb=" N LEU B 762 " --> pdb=" O PHE B 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 91 removed outlier: 3.837A pdb=" N ASN C 91 " --> pdb=" O VAL C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 123 removed outlier: 4.137A pdb=" N VAL C 123 " --> pdb=" O ASP C 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 120 through 123' Processing helix chain 'C' and resid 130 through 135 Processing helix chain 'C' and resid 135 through 140 Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 209 through 221 Processing helix chain 'C' and resid 221 through 226 Processing helix chain 'C' and resid 226 through 233 Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 278 through 296 removed outlier: 3.768A pdb=" N ARG C 287 " --> pdb=" O GLU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.809A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 316 Processing helix chain 'C' and resid 318 through 336 removed outlier: 3.812A pdb=" N ARG C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS C 336 " --> pdb=" O MET C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.520A pdb=" N SER C 352 " --> pdb=" O ARG C 349 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE C 353 " --> pdb=" O PRO C 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 349 through 353' Processing helix chain 'C' and resid 354 through 359 removed outlier: 3.750A pdb=" N LEU C 357 " --> pdb=" O ASP C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 395 through 402 removed outlier: 4.203A pdb=" N VAL C 399 " --> pdb=" O ASP C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 434 removed outlier: 5.899A pdb=" N LYS C 425 " --> pdb=" O GLN C 421 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LYS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP C 428 " --> pdb=" O ARG C 424 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU C 429 " --> pdb=" O LYS C 425 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU C 433 " --> pdb=" O LEU C 429 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP C 434 " --> pdb=" O ILE C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 445 removed outlier: 3.932A pdb=" N LEU C 445 " --> pdb=" O VAL C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 459 Processing helix chain 'C' and resid 482 through 499 removed outlier: 4.111A pdb=" N TYR C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 499 through 506 removed outlier: 4.377A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU C 504 " --> pdb=" O PRO C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 536 removed outlier: 3.522A pdb=" N LEU C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA C 528 " --> pdb=" O LYS C 524 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS C 529 " --> pdb=" O THR C 525 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA C 532 " --> pdb=" O ALA C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 554 Processing helix chain 'C' and resid 556 through 568 removed outlier: 4.407A pdb=" N ARG C 560 " --> pdb=" O GLU C 556 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU C 561 " --> pdb=" O ALA C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 586 Processing helix chain 'C' and resid 598 through 610 removed outlier: 3.664A pdb=" N ASN C 602 " --> pdb=" O ASP C 598 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN C 603 " --> pdb=" O ARG C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 615 removed outlier: 3.803A pdb=" N LYS C 615 " --> pdb=" O SER C 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 612 through 615' Processing helix chain 'C' and resid 625 through 629 Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.939A pdb=" N ARG C 635 " --> pdb=" O ALA C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 662 Processing helix chain 'C' and resid 671 through 679 Processing helix chain 'C' and resid 683 through 716 removed outlier: 3.640A pdb=" N ILE C 690 " --> pdb=" O ASP C 686 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG C 713 " --> pdb=" O ARG C 709 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN C 714 " --> pdb=" O GLU C 710 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N THR C 715 " --> pdb=" O ARG C 711 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASN C 716 " --> pdb=" O GLU C 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 743 removed outlier: 3.783A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 762 removed outlier: 3.948A pdb=" N LEU C 762 " --> pdb=" O PHE C 758 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 91 removed outlier: 3.623A pdb=" N ASN D 91 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 135 Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 209 through 220 Processing helix chain 'D' and resid 221 through 226 Processing helix chain 'D' and resid 226 through 233 Processing helix chain 'D' and resid 250 through 263 Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 278 through 296 removed outlier: 3.613A pdb=" N ARG D 287 " --> pdb=" O GLU D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 309 Processing helix chain 'D' and resid 312 through 316 Processing helix chain 'D' and resid 318 through 336 removed outlier: 3.729A pdb=" N ARG D 322 " --> pdb=" O GLY D 318 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS D 336 " --> pdb=" O MET D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.863A pdb=" N ILE D 353 " --> pdb=" O PRO D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 385 Processing helix chain 'D' and resid 395 through 403 removed outlier: 4.184A pdb=" N VAL D 399 " --> pdb=" O ASP D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 434 removed outlier: 5.782A pdb=" N LYS D 425 " --> pdb=" O GLN D 421 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP D 428 " --> pdb=" O ARG D 424 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU D 429 " --> pdb=" O LYS D 425 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU D 433 " --> pdb=" O LEU D 429 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP D 434 " --> pdb=" O ILE D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 445 removed outlier: 3.960A pdb=" N LEU D 445 " --> pdb=" O VAL D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 459 Processing helix chain 'D' and resid 482 through 499 removed outlier: 4.013A pdb=" N TYR D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 499 through 506 removed outlier: 4.282A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU D 504 " --> pdb=" O PRO D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 536 removed outlier: 3.518A pdb=" N LEU D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA D 528 " --> pdb=" O LYS D 524 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS D 529 " --> pdb=" O THR D 525 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 554 Processing helix chain 'D' and resid 557 through 569 removed outlier: 3.827A pdb=" N GLU D 561 " --> pdb=" O ALA D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 586 Processing helix chain 'D' and resid 598 through 610 removed outlier: 3.762A pdb=" N ASN D 602 " --> pdb=" O ASP D 598 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN D 603 " --> pdb=" O ARG D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 615 removed outlier: 3.592A pdb=" N LYS D 615 " --> pdb=" O SER D 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 612 through 615' Processing helix chain 'D' and resid 625 through 629 Processing helix chain 'D' and resid 630 through 634 Processing helix chain 'D' and resid 649 through 662 removed outlier: 3.607A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 679 Processing helix chain 'D' and resid 683 through 716 removed outlier: 3.705A pdb=" N ARG D 713 " --> pdb=" O ARG D 709 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR D 715 " --> pdb=" O ARG D 711 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASN D 716 " --> pdb=" O GLU D 712 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 743 removed outlier: 3.774A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 762 removed outlier: 3.742A pdb=" N LEU D 762 " --> pdb=" O PHE D 758 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 93 removed outlier: 3.894A pdb=" N ASN E 91 " --> pdb=" O VAL E 87 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU E 92 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 135 Processing helix chain 'E' and resid 135 through 140 Processing helix chain 'E' and resid 202 through 206 removed outlier: 3.585A pdb=" N ILE E 206 " --> pdb=" O TYR E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 220 Processing helix chain 'E' and resid 221 through 226 Processing helix chain 'E' and resid 226 through 233 Processing helix chain 'E' and resid 250 through 261 Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 278 through 296 removed outlier: 3.881A pdb=" N ARG E 287 " --> pdb=" O GLU E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 309 Processing helix chain 'E' and resid 312 through 316 Processing helix chain 'E' and resid 318 through 336 removed outlier: 3.793A pdb=" N VAL E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER E 326 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN E 327 " --> pdb=" O ARG E 323 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU E 328 " --> pdb=" O ILE E 324 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS E 336 " --> pdb=" O MET E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 removed outlier: 4.132A pdb=" N ILE E 353 " --> pdb=" O PRO E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 395 through 403 removed outlier: 3.632A pdb=" N VAL E 399 " --> pdb=" O ASP E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 432 removed outlier: 3.679A pdb=" N ALA E 422 " --> pdb=" O ALA E 418 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP E 428 " --> pdb=" O ARG E 424 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU E 429 " --> pdb=" O LYS E 425 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU E 432 " --> pdb=" O ASP E 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 445 removed outlier: 3.950A pdb=" N LEU E 445 " --> pdb=" O VAL E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 458 Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 499 removed outlier: 3.993A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 499 through 506 removed outlier: 4.125A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 536 removed outlier: 3.588A pdb=" N LEU E 527 " --> pdb=" O GLY E 523 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA E 528 " --> pdb=" O LYS E 524 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS E 529 " --> pdb=" O THR E 525 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA E 532 " --> pdb=" O ALA E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 554 removed outlier: 3.515A pdb=" N LEU E 547 " --> pdb=" O LYS E 543 " (cutoff:3.500A) Processing helix chain 'E' and resid 556 through 569 removed outlier: 4.372A pdb=" N ARG E 560 " --> pdb=" O GLU E 556 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU E 561 " --> pdb=" O ALA E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 586 Processing helix chain 'E' and resid 598 through 610 Processing helix chain 'E' and resid 612 through 615 Processing helix chain 'E' and resid 625 through 629 Processing helix chain 'E' and resid 630 through 635 removed outlier: 3.743A pdb=" N ARG E 635 " --> pdb=" O ALA E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 662 removed outlier: 3.606A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 671 through 679 Processing helix chain 'E' and resid 683 through 716 removed outlier: 3.720A pdb=" N ARG E 713 " --> pdb=" O ARG E 709 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN E 714 " --> pdb=" O GLU E 710 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR E 715 " --> pdb=" O ARG E 711 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASN E 716 " --> pdb=" O GLU E 712 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 743 removed outlier: 3.653A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 762 removed outlier: 3.664A pdb=" N LEU E 762 " --> pdb=" O PHE E 758 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 93 removed outlier: 3.564A pdb=" N ASN F 91 " --> pdb=" O VAL F 87 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU F 92 " --> pdb=" O VAL F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 140 Processing helix chain 'F' and resid 202 through 206 removed outlier: 3.600A pdb=" N ILE F 206 " --> pdb=" O TYR F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 220 Processing helix chain 'F' and resid 221 through 226 Processing helix chain 'F' and resid 226 through 233 Processing helix chain 'F' and resid 250 through 261 Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 278 through 296 removed outlier: 3.817A pdb=" N ARG F 287 " --> pdb=" O GLU F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 309 Processing helix chain 'F' and resid 312 through 316 Processing helix chain 'F' and resid 318 through 336 removed outlier: 3.649A pdb=" N VAL F 325 " --> pdb=" O GLU F 321 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER F 326 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN F 327 " --> pdb=" O ARG F 323 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU F 328 " --> pdb=" O ILE F 324 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS F 336 " --> pdb=" O MET F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 353 removed outlier: 4.073A pdb=" N ILE F 353 " --> pdb=" O PRO F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 385 Processing helix chain 'F' and resid 395 through 403 removed outlier: 3.817A pdb=" N VAL F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 432 removed outlier: 3.655A pdb=" N ALA F 422 " --> pdb=" O ALA F 418 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP F 428 " --> pdb=" O ARG F 424 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU F 429 " --> pdb=" O LYS F 425 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU F 432 " --> pdb=" O ASP F 428 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 445 removed outlier: 4.004A pdb=" N LEU F 445 " --> pdb=" O VAL F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 458 Processing helix chain 'F' and resid 482 through 499 removed outlier: 4.120A pdb=" N TYR F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 499 through 506 removed outlier: 4.078A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE F 506 " --> pdb=" O LYS F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 536 removed outlier: 3.583A pdb=" N LEU F 527 " --> pdb=" O GLY F 523 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA F 528 " --> pdb=" O LYS F 524 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS F 529 " --> pdb=" O THR F 525 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA F 532 " --> pdb=" O ALA F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 554 removed outlier: 3.556A pdb=" N LEU F 547 " --> pdb=" O LYS F 543 " (cutoff:3.500A) Processing helix chain 'F' and resid 556 through 569 removed outlier: 4.282A pdb=" N ARG F 560 " --> pdb=" O GLU F 556 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU F 561 " --> pdb=" O ALA F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 586 Processing helix chain 'F' and resid 598 through 610 Processing helix chain 'F' and resid 612 through 615 removed outlier: 3.512A pdb=" N LYS F 615 " --> pdb=" O SER F 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 612 through 615' Processing helix chain 'F' and resid 625 through 629 Processing helix chain 'F' and resid 630 through 635 removed outlier: 3.771A pdb=" N ARG F 635 " --> pdb=" O ALA F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 662 removed outlier: 3.564A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 671 through 679 Processing helix chain 'F' and resid 683 through 716 removed outlier: 3.667A pdb=" N ARG F 713 " --> pdb=" O ARG F 709 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN F 714 " --> pdb=" O GLU F 710 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THR F 715 " --> pdb=" O ARG F 711 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASN F 716 " --> pdb=" O GLU F 712 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 743 removed outlier: 3.628A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG F 741 " --> pdb=" O GLU F 737 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 762 removed outlier: 3.697A pdb=" N LEU F 762 " --> pdb=" O PHE F 758 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 29 removed outlier: 8.305A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N LYS A 81 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N SER A 42 " --> pdb=" O LYS A 81 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL A 39 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ASP A 74 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU A 41 " --> pdb=" O ASP A 74 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER A 101 " --> pdb=" O LYS A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 118 removed outlier: 6.735A pdb=" N LEU A 117 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N VAL A 165 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.375A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE A 241 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N THR A 347 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU A 243 " --> pdb=" O THR A 347 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 538 through 542 removed outlier: 6.697A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU A 515 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 25 through 29 removed outlier: 8.527A pdb=" N ILE B 82 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N LYS B 81 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N SER B 42 " --> pdb=" O LYS B 81 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL B 39 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ASP B 74 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU B 41 " --> pdb=" O ASP B 74 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N SER B 101 " --> pdb=" O LYS B 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 115 through 118 removed outlier: 3.670A pdb=" N GLU B 167 " --> pdb=" O HIS B 115 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU B 117 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N VAL B 165 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 145 through 147 Processing sheet with id=AA9, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.414A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE B 241 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N THR B 347 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU B 243 " --> pdb=" O THR B 347 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG B 365 " --> pdb=" O GLY B 240 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.733A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N GLY B 513 " --> pdb=" O GLN B 641 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N ILE B 643 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU B 515 " --> pdb=" O ILE B 643 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 25 through 29 removed outlier: 8.487A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N LYS C 81 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N SER C 42 " --> pdb=" O LYS C 81 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP C 74 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER C 101 " --> pdb=" O LYS C 60 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 115 through 118 removed outlier: 7.149A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 145 through 146 Processing sheet with id=AB5, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.398A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE C 241 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N THR C 347 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU C 243 " --> pdb=" O THR C 347 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 538 through 542 removed outlier: 6.759A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N GLY C 513 " --> pdb=" O GLN C 641 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N ILE C 643 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU C 515 " --> pdb=" O ILE C 643 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 81 through 83 removed outlier: 6.680A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 38 through 42 removed outlier: 3.817A pdb=" N ASP D 74 " --> pdb=" O LEU D 41 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 115 through 118 removed outlier: 3.501A pdb=" N GLU D 167 " --> pdb=" O HIS D 115 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU D 117 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N VAL D 165 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 146 through 147 Processing sheet with id=AC2, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.399A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE D 241 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N THR D 347 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU D 243 " --> pdb=" O THR D 347 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 538 through 542 removed outlier: 6.692A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLY D 513 " --> pdb=" O GLN D 641 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N ILE D 643 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU D 515 " --> pdb=" O ILE D 643 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 38 through 42 removed outlier: 6.491A pdb=" N VAL E 39 " --> pdb=" O LEU E 72 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ASP E 74 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU E 41 " --> pdb=" O ASP E 74 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER E 101 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 115 through 118 removed outlier: 3.650A pdb=" N GLU E 167 " --> pdb=" O HIS E 115 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU E 117 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N VAL E 165 " --> pdb=" O LEU E 117 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 145 through 147 Processing sheet with id=AC7, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.377A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE E 241 " --> pdb=" O ALA E 345 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N THR E 347 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU E 243 " --> pdb=" O THR E 347 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 538 through 542 removed outlier: 6.721A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 25 through 29 removed outlier: 8.098A pdb=" N ILE F 82 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N LYS F 81 " --> pdb=" O SER F 42 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N SER F 42 " --> pdb=" O LYS F 81 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL F 39 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ASP F 74 " --> pdb=" O VAL F 39 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N LEU F 41 " --> pdb=" O ASP F 74 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N SER F 101 " --> pdb=" O LYS F 60 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 115 through 118 removed outlier: 3.599A pdb=" N GLU F 167 " --> pdb=" O HIS F 115 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU F 117 " --> pdb=" O VAL F 165 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N VAL F 165 " --> pdb=" O LEU F 117 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 146 through 147 Processing sheet with id=AD3, first strand: chain 'F' and resid 265 through 270 removed outlier: 6.516A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE F 241 " --> pdb=" O ALA F 345 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N THR F 347 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU F 243 " --> pdb=" O THR F 347 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 538 through 542 removed outlier: 6.668A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) 1462 hydrogen bonds defined for protein. 4104 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: 7.13 Time building geometry restraints manager: 4.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6692 1.33 - 1.45: 6550 1.45 - 1.57: 18821 1.57 - 1.69: 36 1.69 - 1.81: 234 Bond restraints: 32333 Sorted by residual: bond pdb=" CB LEU B 661 " pdb=" CG LEU B 661 " ideal model delta sigma weight residual 1.530 1.414 0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" CB LEU C 661 " pdb=" CG LEU C 661 " ideal model delta sigma weight residual 1.530 1.429 0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" CB LYS C 663 " pdb=" CG LYS C 663 " ideal model delta sigma weight residual 1.520 1.405 0.115 3.00e-02 1.11e+03 1.47e+01 bond pdb=" CB ASN C 660 " pdb=" CG ASN C 660 " ideal model delta sigma weight residual 1.516 1.424 0.092 2.50e-02 1.60e+03 1.34e+01 bond pdb=" C GLY D 61 " pdb=" N LYS D 62 " ideal model delta sigma weight residual 1.332 1.381 -0.048 1.40e-02 5.10e+03 1.20e+01 ... (remaining 32328 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.57: 43687 3.57 - 7.14: 254 7.14 - 10.71: 11 10.71 - 14.29: 3 14.29 - 17.86: 1 Bond angle restraints: 43956 Sorted by residual: angle pdb=" N PRO B 461 " pdb=" CD PRO B 461 " pdb=" CG PRO B 461 " ideal model delta sigma weight residual 103.20 89.84 13.36 1.50e+00 4.44e-01 7.93e+01 angle pdb=" N VAL F 201 " pdb=" CA VAL F 201 " pdb=" C VAL F 201 " ideal model delta sigma weight residual 109.34 127.20 -17.86 2.08e+00 2.31e-01 7.37e+01 angle pdb=" CA PRO B 461 " pdb=" CB PRO B 461 " pdb=" CG PRO B 461 " ideal model delta sigma weight residual 104.50 90.90 13.60 1.90e+00 2.77e-01 5.12e+01 angle pdb=" N THR B 122 " pdb=" CA THR B 122 " pdb=" C THR B 122 " ideal model delta sigma weight residual 111.36 104.41 6.95 1.09e+00 8.42e-01 4.07e+01 angle pdb=" O ILE E 119 " pdb=" C ILE E 119 " pdb=" N ASP E 120 " ideal model delta sigma weight residual 123.02 116.30 6.72 1.13e+00 7.83e-01 3.54e+01 ... (remaining 43951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.83: 17814 19.83 - 39.65: 1631 39.65 - 59.48: 312 59.48 - 79.31: 52 79.31 - 99.14: 15 Dihedral angle restraints: 19824 sinusoidal: 7014 harmonic: 12810 Sorted by residual: dihedral pdb=" C2' ADP B 901 " pdb=" C1' ADP B 901 " pdb=" N9 ADP B 901 " pdb=" C4 ADP B 901 " ideal model delta sinusoidal sigma weight residual 91.55 -169.32 -99.14 1 2.00e+01 2.50e-03 2.78e+01 dihedral pdb=" CA PRO D 23 " pdb=" C PRO D 23 " pdb=" N ASN D 24 " pdb=" CA ASN D 24 " ideal model delta harmonic sigma weight residual 180.00 156.88 23.12 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA VAL B 116 " pdb=" C VAL B 116 " pdb=" N LEU B 117 " pdb=" CA LEU B 117 " ideal model delta harmonic sigma weight residual 180.00 -156.89 -23.11 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 19821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 4817 0.100 - 0.200: 287 0.200 - 0.299: 4 0.299 - 0.399: 2 0.399 - 0.499: 1 Chirality restraints: 5111 Sorted by residual: chirality pdb=" CA VAL F 201 " pdb=" N VAL F 201 " pdb=" C VAL F 201 " pdb=" CB VAL F 201 " both_signs ideal model delta sigma weight residual False 2.44 1.94 0.50 2.00e-01 2.50e+01 6.22e+00 chirality pdb=" CA ASP F 120 " pdb=" N ASP F 120 " pdb=" C ASP F 120 " pdb=" CB ASP F 120 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CA VAL B 123 " pdb=" N VAL B 123 " pdb=" C VAL B 123 " pdb=" CB VAL B 123 " both_signs ideal model delta sigma weight residual False 2.44 2.75 -0.31 2.00e-01 2.50e+01 2.46e+00 ... (remaining 5108 not shown) Planarity restraints: 5883 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE E 119 " 0.037 2.00e-02 2.50e+03 7.15e-02 5.11e+01 pdb=" C ILE E 119 " -0.124 2.00e-02 2.50e+03 pdb=" O ILE E 119 " 0.046 2.00e-02 2.50e+03 pdb=" N ASP E 120 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE F 119 " 0.035 2.00e-02 2.50e+03 6.73e-02 4.53e+01 pdb=" C ILE F 119 " -0.116 2.00e-02 2.50e+03 pdb=" O ILE F 119 " 0.043 2.00e-02 2.50e+03 pdb=" N ASP F 120 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 120 " -0.026 2.00e-02 2.50e+03 5.30e-02 2.81e+01 pdb=" C ASP B 120 " 0.092 2.00e-02 2.50e+03 pdb=" O ASP B 120 " -0.035 2.00e-02 2.50e+03 pdb=" N ASP B 121 " -0.030 2.00e-02 2.50e+03 ... (remaining 5880 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 167 2.54 - 3.13: 25154 3.13 - 3.72: 47002 3.72 - 4.31: 59498 4.31 - 4.90: 101944 Nonbonded interactions: 233765 Sorted by model distance: nonbonded pdb=" OE1 GLN A 458 " pdb=" OG SER A 459 " model vdw 1.947 3.040 nonbonded pdb=" OE1 GLN F 458 " pdb=" OG SER F 459 " model vdw 1.981 3.040 nonbonded pdb=" CA MET A 158 " pdb=" O ASN A 387 " model vdw 1.996 3.470 nonbonded pdb=" OD1 ASN B 589 " pdb=" NH1 ARG B 625 " model vdw 2.077 3.120 nonbonded pdb=" O LYS A 663 " pdb=" NZ LYS A 663 " model vdw 2.161 3.120 ... (remaining 233760 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 21 through 200 and (name N or name CA or name C or name O \ or name CB )) or resid 201 through 204 or (resid 205 and (name N or name CA or \ name C or name O or name CB )) or resid 206 through 316 or (resid 317 and (name \ N or name CA or name C or name O or name CB )) or resid 318 through 659 or (resi \ d 660 through 663 and (name N or name CA or name C or name O or name CB )) or re \ sid 664 through 902)) selection = (chain 'B' and (resid 21 through 204 or (resid 205 and (name N or name CA or nam \ e C or name O or name CB )) or resid 206 through 316 or (resid 317 and (name N o \ r name CA or name C or name O or name CB )) or resid 318 through 659 or (resid 6 \ 60 through 663 and (name N or name CA or name C or name O or name CB )) or resid \ 664 through 902)) selection = (chain 'C' and (resid 21 through 659 or (resid 660 through 663 and (name N or na \ me CA or name C or name O or name CB )) or resid 664 through 902)) selection = (chain 'D' and (resid 21 through 316 or (resid 317 and (name N or name CA or nam \ e C or name O or name CB )) or resid 318 through 902)) selection = (chain 'E' and ((resid 21 through 200 and (name N or name CA or name C or name O \ or name CB )) or resid 201 through 204 or (resid 205 and (name N or name CA or \ name C or name O or name CB )) or resid 206 through 316 or (resid 317 and (name \ N or name CA or name C or name O or name CB )) or resid 318 through 659 or (resi \ d 660 through 663 and (name N or name CA or name C or name O or name CB )) or re \ sid 664 through 902)) selection = (chain 'F' and ((resid 21 through 200 and (name N or name CA or name C or name O \ or name CB )) or resid 201 through 204 or (resid 205 and (name N or name CA or \ name C or name O or name CB )) or resid 206 through 316 or (resid 317 and (name \ N or name CA or name C or name O or name CB )) or resid 318 through 660 or (resi \ d 661 through 663 and (name N or name CA or name C or name O or name CB )) or re \ sid 664 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: 3.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 31.250 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 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 : 0.003 0.116 32333 Z= 0.170 Angle : 0.710 17.857 43956 Z= 0.398 Chirality : 0.046 0.499 5111 Planarity : 0.005 0.095 5883 Dihedral : 15.795 99.136 11496 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.41 % Favored : 95.56 % Rotamer: Outliers : 0.14 % Allowed : 15.45 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % 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 aren not related in a simple way. whole: -0.48 (0.13), residues: 4440 helix: 0.89 (0.13), residues: 1812 sheet: -0.13 (0.21), residues: 660 loop : -1.55 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 358 TYR 0.014 0.001 TYR A 203 PHE 0.014 0.001 PHE A 230 TRP 0.006 0.001 TRP E 454 HIS 0.008 0.001 HIS D 499 Details of bonding type rmsd covalent geometry : bond 0.00315 (32333) covalent geometry : angle 0.70962 (43956) hydrogen bonds : bond 0.17168 ( 1462) hydrogen bonds : angle 6.68227 ( 4104) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 412 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 ARG cc_start: 0.6022 (mtm-85) cc_final: 0.5604 (ptt90) REVERT: A 327 GLN cc_start: 0.6826 (tp40) cc_final: 0.6485 (tp40) REVERT: A 389 LYS cc_start: 0.5935 (tptt) cc_final: 0.5635 (ttmt) REVERT: A 512 LYS cc_start: 0.6967 (ptmm) cc_final: 0.6707 (ptmt) REVERT: A 741 ARG cc_start: 0.4696 (mmp-170) cc_final: 0.3539 (ptp-170) REVERT: B 294 GLU cc_start: 0.6711 (tm-30) cc_final: 0.6467 (tt0) REVERT: B 586 ARG cc_start: 0.7843 (ptt90) cc_final: 0.7389 (ptm-80) REVERT: B 744 ARG cc_start: 0.5895 (mtt180) cc_final: 0.5589 (ptp90) REVERT: C 390 LEU cc_start: 0.6969 (tp) cc_final: 0.6625 (mp) REVERT: C 706 GLU cc_start: 0.6678 (tm-30) cc_final: 0.5768 (mm-30) REVERT: C 737 GLU cc_start: 0.3279 (tt0) cc_final: 0.2594 (mm-30) REVERT: D 427 MET cc_start: 0.3327 (mmp) cc_final: 0.2946 (tpt) outliers start: 4 outliers final: 3 residues processed: 415 average time/residue: 0.2278 time to fit residues: 144.0542 Evaluate side-chains 359 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 356 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain B residue 387 ASN Chi-restraints excluded: chain B residue 598 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 4.9990 chunk 424 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 GLN A 616 ASN B 327 GLN B 384 HIS B 692 GLN B 714 GLN C 490 GLN C 714 GLN D 404 HIS ** E 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 589 ASN E 602 ASN F 382 GLN F 602 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.186463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.155172 restraints weight = 43297.581| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 2.33 r_work: 0.3591 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 32333 Z= 0.208 Angle : 0.749 9.403 43956 Z= 0.377 Chirality : 0.050 0.173 5111 Planarity : 0.006 0.066 5883 Dihedral : 6.195 98.914 4859 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.83 % Favored : 96.13 % Rotamer: Outliers : 2.65 % Allowed : 15.80 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -0.55 (0.12), residues: 4440 helix: 0.60 (0.12), residues: 1830 sheet: 0.03 (0.20), residues: 648 loop : -1.43 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 693 TYR 0.022 0.003 TYR D 244 PHE 0.028 0.003 PHE A 575 TRP 0.014 0.002 TRP D 476 HIS 0.010 0.002 HIS C 384 Details of bonding type rmsd covalent geometry : bond 0.00495 (32333) covalent geometry : angle 0.74923 (43956) hydrogen bonds : bond 0.05502 ( 1462) hydrogen bonds : angle 4.92710 ( 4104) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 422 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 ARG cc_start: 0.6484 (mtm-85) cc_final: 0.6200 (mtm-85) REVERT: A 389 LYS cc_start: 0.6534 (tptt) cc_final: 0.6133 (ttpt) REVERT: A 502 LYS cc_start: 0.5700 (mmmt) cc_final: 0.4709 (ttmt) REVERT: A 657 LEU cc_start: 0.6618 (OUTLIER) cc_final: 0.6213 (mt) REVERT: A 709 ARG cc_start: 0.4941 (tmm-80) cc_final: 0.4483 (tmm160) REVERT: B 294 GLU cc_start: 0.7103 (tm-30) cc_final: 0.6620 (tt0) REVERT: B 658 LYS cc_start: 0.6416 (tptt) cc_final: 0.6017 (mmmt) REVERT: B 744 ARG cc_start: 0.5814 (mtt180) cc_final: 0.4993 (mtm-85) REVERT: C 390 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6791 (mp) REVERT: C 453 ARG cc_start: 0.7030 (mtp85) cc_final: 0.6741 (mmm-85) REVERT: C 706 GLU cc_start: 0.6609 (tm-30) cc_final: 0.5758 (mm-30) REVERT: C 737 GLU cc_start: 0.4099 (tt0) cc_final: 0.3061 (mm-30) REVERT: D 427 MET cc_start: 0.4459 (mmp) cc_final: 0.3599 (tpt) REVERT: E 389 LYS cc_start: 0.6690 (ttmt) cc_final: 0.6377 (ttmt) REVERT: E 757 MET cc_start: 0.6335 (OUTLIER) cc_final: 0.5951 (tmm) REVERT: F 373 ASP cc_start: 0.4528 (m-30) cc_final: 0.4314 (m-30) REVERT: F 641 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7211 (mp10) REVERT: F 731 ILE cc_start: 0.6618 (OUTLIER) cc_final: 0.6207 (pt) outliers start: 74 outliers final: 36 residues processed: 473 average time/residue: 0.2188 time to fit residues: 158.6668 Evaluate side-chains 395 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 354 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 599 ARG Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 705 SER Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 565 LYS Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 641 GLN Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain F residue 731 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 88 optimal weight: 50.0000 chunk 71 optimal weight: 3.9990 chunk 438 optimal weight: 10.0000 chunk 276 optimal weight: 0.7980 chunk 186 optimal weight: 7.9990 chunk 45 optimal weight: 0.0570 chunk 81 optimal weight: 20.0000 chunk 187 optimal weight: 5.9990 chunk 264 optimal weight: 10.0000 chunk 114 optimal weight: 0.7980 chunk 366 optimal weight: 7.9990 overall best weight: 2.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 HIS A 384 HIS A 401 ASN ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 HIS C 327 GLN C 616 ASN D 616 ASN D 624 ASN ** E 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 660 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.181099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.150582 restraints weight = 43440.381| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.31 r_work: 0.3533 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 32333 Z= 0.194 Angle : 0.691 7.252 43956 Z= 0.346 Chirality : 0.048 0.189 5111 Planarity : 0.005 0.063 5883 Dihedral : 6.290 102.482 4853 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.21 % Favored : 95.77 % Rotamer: Outliers : 3.40 % Allowed : 16.77 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -0.56 (0.12), residues: 4440 helix: 0.60 (0.12), residues: 1830 sheet: -0.20 (0.20), residues: 702 loop : -1.36 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 693 TYR 0.019 0.002 TYR C 644 PHE 0.028 0.002 PHE C 674 TRP 0.011 0.002 TRP C 476 HIS 0.011 0.002 HIS B 735 Details of bonding type rmsd covalent geometry : bond 0.00459 (32333) covalent geometry : angle 0.69105 (43956) hydrogen bonds : bond 0.05548 ( 1462) hydrogen bonds : angle 4.73548 ( 4104) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 387 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7745 (p0) REVERT: A 322 ARG cc_start: 0.6585 (mtm-85) cc_final: 0.6124 (mtm180) REVERT: A 389 LYS cc_start: 0.6670 (tptt) cc_final: 0.6362 (ttpt) REVERT: A 614 LYS cc_start: 0.6951 (mmtt) cc_final: 0.6344 (mmtm) REVERT: A 709 ARG cc_start: 0.5118 (tmm-80) cc_final: 0.4545 (tmm160) REVERT: B 265 PHE cc_start: 0.8318 (t80) cc_final: 0.7750 (t80) REVERT: B 294 GLU cc_start: 0.7060 (tm-30) cc_final: 0.6513 (tt0) REVERT: B 556 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6736 (mp0) REVERT: B 561 GLU cc_start: 0.6768 (mm-30) cc_final: 0.6373 (mm-30) REVERT: B 656 ILE cc_start: 0.4948 (mt) cc_final: 0.4718 (mt) REVERT: B 732 ARG cc_start: 0.6297 (ptt-90) cc_final: 0.5986 (ptt90) REVERT: B 744 ARG cc_start: 0.5894 (mtt180) cc_final: 0.5065 (mtm-85) REVERT: C 230 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.6098 (m-80) REVERT: C 390 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.7023 (mp) REVERT: C 486 LYS cc_start: 0.7383 (mmtp) cc_final: 0.6856 (mmtm) REVERT: C 696 LYS cc_start: 0.7313 (OUTLIER) cc_final: 0.6602 (tptt) REVERT: C 706 GLU cc_start: 0.6772 (tm-30) cc_final: 0.5774 (mm-30) REVERT: C 737 GLU cc_start: 0.4637 (tt0) cc_final: 0.3660 (mm-30) REVERT: D 229 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7270 (tt) REVERT: D 599 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7406 (mtp85) REVERT: D 757 MET cc_start: 0.6125 (mmp) cc_final: 0.5868 (mmt) REVERT: E 389 LYS cc_start: 0.6680 (ttmt) cc_final: 0.6110 (tttm) REVERT: E 657 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6631 (mt) REVERT: E 677 LYS cc_start: 0.7316 (OUTLIER) cc_final: 0.6987 (ttpt) REVERT: E 757 MET cc_start: 0.6134 (OUTLIER) cc_final: 0.5851 (tmm) REVERT: F 373 ASP cc_start: 0.4564 (m-30) cc_final: 0.4349 (m-30) REVERT: F 423 ILE cc_start: 0.8316 (tt) cc_final: 0.7909 (mt) REVERT: F 508 MET cc_start: 0.6178 (OUTLIER) cc_final: 0.5738 (ttt) REVERT: F 599 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7376 (mtp85) REVERT: F 641 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7364 (mp10) REVERT: F 731 ILE cc_start: 0.6656 (OUTLIER) cc_final: 0.6332 (pt) outliers start: 95 outliers final: 43 residues processed: 456 average time/residue: 0.2405 time to fit residues: 166.9243 Evaluate side-chains 396 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 339 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 689 GLU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 696 LYS Chi-restraints excluded: chain C residue 705 SER Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 565 LYS Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 657 LEU Chi-restraints excluded: chain E residue 677 LYS Chi-restraints excluded: chain E residue 724 GLU Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain F residue 599 ARG Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 641 GLN Chi-restraints excluded: chain F residue 722 VAL Chi-restraints excluded: chain F residue 731 ILE Chi-restraints excluded: chain F residue 747 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 157 optimal weight: 40.0000 chunk 45 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 399 optimal weight: 3.9990 chunk 349 optimal weight: 3.9990 chunk 242 optimal weight: 3.9990 chunk 244 optimal weight: 0.6980 chunk 38 optimal weight: 10.0000 chunk 149 optimal weight: 20.0000 chunk 8 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 HIS D 616 ASN E 285 ASN ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.179539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.148856 restraints weight = 42952.422| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.17 r_work: 0.3532 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 32333 Z= 0.165 Angle : 0.655 8.154 43956 Z= 0.324 Chirality : 0.046 0.162 5111 Planarity : 0.005 0.065 5883 Dihedral : 6.241 102.187 4853 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.12 % Favored : 95.86 % Rotamer: Outliers : 3.32 % Allowed : 18.38 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -0.56 (0.13), residues: 4440 helix: 0.55 (0.12), residues: 1836 sheet: -0.19 (0.20), residues: 702 loop : -1.33 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 358 TYR 0.019 0.002 TYR D 244 PHE 0.021 0.002 PHE B 230 TRP 0.008 0.001 TRP C 476 HIS 0.025 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00388 (32333) covalent geometry : angle 0.65482 (43956) hydrogen bonds : bond 0.04739 ( 1462) hydrogen bonds : angle 4.49999 ( 4104) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 364 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.8162 (tp) cc_final: 0.7918 (tp) REVERT: A 307 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.7728 (p0) REVERT: A 322 ARG cc_start: 0.6579 (mtm-85) cc_final: 0.6046 (mtm180) REVERT: A 389 LYS cc_start: 0.6724 (tptt) cc_final: 0.6444 (ttpt) REVERT: A 614 LYS cc_start: 0.6975 (mmtt) cc_final: 0.6247 (mmtm) REVERT: A 709 ARG cc_start: 0.5145 (tmm-80) cc_final: 0.4638 (tmm160) REVERT: B 294 GLU cc_start: 0.7097 (tm-30) cc_final: 0.6537 (tt0) REVERT: B 366 GLU cc_start: 0.6998 (mp0) cc_final: 0.6617 (mt-10) REVERT: B 561 GLU cc_start: 0.6831 (mm-30) cc_final: 0.6451 (mm-30) REVERT: B 656 ILE cc_start: 0.5112 (mt) cc_final: 0.4869 (mt) REVERT: B 732 ARG cc_start: 0.6426 (ptt-90) cc_final: 0.6208 (ptt90) REVERT: B 744 ARG cc_start: 0.5663 (mtt180) cc_final: 0.5347 (mtm-85) REVERT: C 229 LEU cc_start: 0.7724 (tt) cc_final: 0.7400 (tp) REVERT: C 230 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.6112 (m-80) REVERT: C 486 LYS cc_start: 0.7372 (mmtp) cc_final: 0.6857 (mmtm) REVERT: C 696 LYS cc_start: 0.7321 (OUTLIER) cc_final: 0.6619 (tptt) REVERT: C 737 GLU cc_start: 0.5018 (tt0) cc_final: 0.3928 (mm-30) REVERT: D 599 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7461 (mtp85) REVERT: E 305 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8027 (mt-10) REVERT: E 470 GLU cc_start: 0.8328 (pm20) cc_final: 0.8019 (pm20) REVERT: E 657 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6730 (mt) REVERT: E 703 ILE cc_start: 0.7489 (OUTLIER) cc_final: 0.7240 (mp) REVERT: E 740 MET cc_start: 0.7919 (mmm) cc_final: 0.7610 (mmt) REVERT: E 757 MET cc_start: 0.6263 (OUTLIER) cc_final: 0.5972 (tmm) REVERT: F 354 ASP cc_start: 0.7869 (OUTLIER) cc_final: 0.7621 (m-30) REVERT: F 402 GLU cc_start: 0.7174 (tm-30) cc_final: 0.6966 (tm-30) REVERT: F 423 ILE cc_start: 0.8393 (tt) cc_final: 0.7996 (mt) REVERT: F 508 MET cc_start: 0.6253 (ppp) cc_final: 0.5974 (ttt) REVERT: F 641 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.7237 (mp10) outliers start: 93 outliers final: 58 residues processed: 436 average time/residue: 0.2208 time to fit residues: 149.8991 Evaluate side-chains 402 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 334 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 696 LYS Chi-restraints excluded: chain C residue 720 MET Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 565 LYS Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 657 LEU Chi-restraints excluded: chain E residue 703 ILE Chi-restraints excluded: chain E residue 724 GLU Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain F residue 494 GLN Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 624 ASN Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 641 GLN Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain F residue 705 SER Chi-restraints excluded: chain F residue 722 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 29 optimal weight: 0.0470 chunk 171 optimal weight: 0.9980 chunk 293 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 69 optimal weight: 0.0060 chunk 160 optimal weight: 20.0000 chunk 341 optimal weight: 0.0040 chunk 391 optimal weight: 0.0980 chunk 237 optimal weight: 30.0000 chunk 56 optimal weight: 4.9990 chunk 90 optimal weight: 0.4980 overall best weight: 0.1306 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 GLN C 490 GLN D 616 ASN E 285 ASN ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.183718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.152727 restraints weight = 42974.634| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.32 r_work: 0.3566 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 32333 Z= 0.102 Angle : 0.570 8.379 43956 Z= 0.275 Chirality : 0.043 0.178 5111 Planarity : 0.004 0.061 5883 Dihedral : 5.753 99.854 4853 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.97 % Favored : 97.00 % Rotamer: Outliers : 2.15 % Allowed : 19.23 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % 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 aren not related in a simple way. whole: 0.00 (0.13), residues: 4440 helix: 1.09 (0.13), residues: 1848 sheet: 0.02 (0.20), residues: 702 loop : -1.08 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 709 TYR 0.023 0.001 TYR A 203 PHE 0.024 0.001 PHE A 674 TRP 0.019 0.001 TRP E 454 HIS 0.006 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00214 (32333) covalent geometry : angle 0.56997 (43956) hydrogen bonds : bond 0.03445 ( 1462) hydrogen bonds : angle 4.14798 ( 4104) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 375 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7787 (p0) REVERT: A 322 ARG cc_start: 0.6438 (mtm-85) cc_final: 0.5895 (mtm180) REVERT: A 389 LYS cc_start: 0.6651 (tptt) cc_final: 0.6373 (ttpt) REVERT: A 614 LYS cc_start: 0.6956 (mmtt) cc_final: 0.6192 (mmtm) REVERT: A 709 ARG cc_start: 0.4990 (tmm-80) cc_final: 0.4507 (tmm160) REVERT: B 265 PHE cc_start: 0.8230 (t80) cc_final: 0.7740 (t80) REVERT: B 294 GLU cc_start: 0.6957 (tm-30) cc_final: 0.6388 (tt0) REVERT: B 332 MET cc_start: 0.7267 (mmt) cc_final: 0.6931 (mmt) REVERT: B 366 GLU cc_start: 0.6977 (mp0) cc_final: 0.6504 (mt-10) REVERT: B 561 GLU cc_start: 0.6718 (mm-30) cc_final: 0.6502 (tp30) REVERT: B 650 GLU cc_start: 0.5927 (tt0) cc_final: 0.5524 (mt-10) REVERT: B 662 ARG cc_start: 0.5377 (ptt-90) cc_final: 0.5070 (ptt90) REVERT: B 732 ARG cc_start: 0.6413 (ptt-90) cc_final: 0.6142 (ptt90) REVERT: B 744 ARG cc_start: 0.5684 (mtt180) cc_final: 0.5269 (mtm-85) REVERT: C 222 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7814 (tt) REVERT: C 229 LEU cc_start: 0.7763 (tt) cc_final: 0.7479 (tp) REVERT: C 706 GLU cc_start: 0.6614 (tm-30) cc_final: 0.5796 (mm-30) REVERT: C 709 ARG cc_start: 0.6203 (ttp80) cc_final: 0.5946 (ttp80) REVERT: C 737 GLU cc_start: 0.5015 (tt0) cc_final: 0.3957 (mm-30) REVERT: D 390 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7108 (mp) REVERT: D 565 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8459 (tttt) REVERT: E 657 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6748 (mt) REVERT: E 703 ILE cc_start: 0.7416 (OUTLIER) cc_final: 0.7154 (mp) REVERT: E 740 MET cc_start: 0.7916 (mmm) cc_final: 0.7662 (mmt) REVERT: F 378 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6618 (tt) REVERT: F 402 GLU cc_start: 0.7036 (tm-30) cc_final: 0.6672 (tm-30) REVERT: F 423 ILE cc_start: 0.8293 (tt) cc_final: 0.8033 (mt) REVERT: F 508 MET cc_start: 0.5965 (OUTLIER) cc_final: 0.5728 (ttt) REVERT: F 550 MET cc_start: 0.8318 (mtp) cc_final: 0.8081 (mtt) REVERT: F 641 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7519 (mt0) REVERT: F 731 ILE cc_start: 0.6692 (OUTLIER) cc_final: 0.6290 (pt) outliers start: 60 outliers final: 26 residues processed: 417 average time/residue: 0.2206 time to fit residues: 142.7885 Evaluate side-chains 376 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 340 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 556 GLU Chi-restraints excluded: chain D residue 565 LYS Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 657 LEU Chi-restraints excluded: chain E residue 703 ILE Chi-restraints excluded: chain E residue 724 GLU Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 599 ARG Chi-restraints excluded: chain F residue 624 ASN Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 641 GLN Chi-restraints excluded: chain F residue 722 VAL Chi-restraints excluded: chain F residue 731 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 180 optimal weight: 0.4980 chunk 4 optimal weight: 10.0000 chunk 198 optimal weight: 4.9990 chunk 288 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 442 optimal weight: 0.1980 chunk 297 optimal weight: 20.0000 chunk 347 optimal weight: 8.9990 chunk 345 optimal weight: 4.9990 chunk 415 optimal weight: 0.7980 chunk 285 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 387 ASN D 443 ASN ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.179778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.149339 restraints weight = 43166.380| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.20 r_work: 0.3533 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32333 Z= 0.141 Angle : 0.622 12.352 43956 Z= 0.301 Chirality : 0.045 0.154 5111 Planarity : 0.005 0.065 5883 Dihedral : 5.892 100.479 4853 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.05 % Favored : 95.92 % Rotamer: Outliers : 2.97 % Allowed : 19.27 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % 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 aren not related in a simple way. whole: -0.05 (0.13), residues: 4440 helix: 1.04 (0.12), residues: 1836 sheet: -0.04 (0.20), residues: 714 loop : -1.07 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 358 TYR 0.025 0.002 TYR B 203 PHE 0.016 0.002 PHE F 674 TRP 0.013 0.001 TRP C 476 HIS 0.006 0.001 HIS B 735 Details of bonding type rmsd covalent geometry : bond 0.00329 (32333) covalent geometry : angle 0.62152 (43956) hydrogen bonds : bond 0.04330 ( 1462) hydrogen bonds : angle 4.23364 ( 4104) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 351 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.7816 (p0) REVERT: A 389 LYS cc_start: 0.6780 (tptt) cc_final: 0.6514 (ttpt) REVERT: A 614 LYS cc_start: 0.6985 (mmtt) cc_final: 0.6236 (mmtm) REVERT: A 709 ARG cc_start: 0.5052 (tmm-80) cc_final: 0.4581 (tmm160) REVERT: B 265 PHE cc_start: 0.8231 (t80) cc_final: 0.7795 (t80) REVERT: B 294 GLU cc_start: 0.6996 (tm-30) cc_final: 0.6639 (tm-30) REVERT: B 366 GLU cc_start: 0.6977 (mp0) cc_final: 0.6520 (mt-10) REVERT: B 561 GLU cc_start: 0.6778 (mm-30) cc_final: 0.6535 (tp30) REVERT: B 662 ARG cc_start: 0.5536 (ptt-90) cc_final: 0.5206 (ptt90) REVERT: B 732 ARG cc_start: 0.6408 (ptt-90) cc_final: 0.6153 (ptt90) REVERT: B 744 ARG cc_start: 0.5744 (mtt180) cc_final: 0.5065 (mtm-85) REVERT: C 229 LEU cc_start: 0.7863 (tt) cc_final: 0.7613 (tp) REVERT: C 230 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.6162 (m-80) REVERT: C 283 GLU cc_start: 0.6052 (mt-10) cc_final: 0.5499 (mm-30) REVERT: C 389 LYS cc_start: 0.7432 (OUTLIER) cc_final: 0.6563 (tptt) REVERT: C 402 GLU cc_start: 0.6965 (tt0) cc_final: 0.6731 (tt0) REVERT: C 486 LYS cc_start: 0.7306 (mmtp) cc_final: 0.6811 (mmtm) REVERT: C 608 MET cc_start: 0.8680 (ttm) cc_final: 0.8378 (mtm) REVERT: C 706 GLU cc_start: 0.6609 (tm-30) cc_final: 0.5753 (mm-30) REVERT: C 737 GLU cc_start: 0.5318 (tt0) cc_final: 0.4252 (mm-30) REVERT: D 427 MET cc_start: 0.5060 (mmp) cc_final: 0.4621 (tpt) REVERT: D 757 MET cc_start: 0.6240 (mmp) cc_final: 0.6027 (mmt) REVERT: E 221 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7461 (pm20) REVERT: E 508 MET cc_start: 0.7092 (tpt) cc_final: 0.6804 (tpt) REVERT: E 657 LEU cc_start: 0.7039 (OUTLIER) cc_final: 0.6744 (mt) REVERT: E 740 MET cc_start: 0.7862 (mmm) cc_final: 0.7629 (mmt) REVERT: E 757 MET cc_start: 0.6163 (OUTLIER) cc_final: 0.5891 (tmm) REVERT: F 354 ASP cc_start: 0.7891 (OUTLIER) cc_final: 0.7679 (m-30) REVERT: F 378 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6711 (tt) REVERT: F 402 GLU cc_start: 0.7056 (tm-30) cc_final: 0.6748 (tm-30) REVERT: F 423 ILE cc_start: 0.8388 (tt) cc_final: 0.8066 (mt) REVERT: F 508 MET cc_start: 0.6055 (OUTLIER) cc_final: 0.5807 (ttt) REVERT: F 550 MET cc_start: 0.8306 (mtp) cc_final: 0.8102 (mtt) REVERT: F 641 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7272 (mp10) outliers start: 83 outliers final: 50 residues processed: 410 average time/residue: 0.2292 time to fit residues: 145.6821 Evaluate side-chains 395 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 335 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 389 LYS Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 556 GLU Chi-restraints excluded: chain D residue 565 LYS Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 657 LEU Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 724 GLU Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 641 GLN Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain F residue 705 SER Chi-restraints excluded: chain F residue 722 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 183 optimal weight: 4.9990 chunk 354 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 185 optimal weight: 0.8980 chunk 324 optimal weight: 2.9990 chunk 357 optimal weight: 1.9990 chunk 331 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 403 optimal weight: 0.1980 chunk 218 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 ASN E 327 GLN ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.180909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.150606 restraints weight = 43325.903| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.23 r_work: 0.3547 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32333 Z= 0.113 Angle : 0.587 10.802 43956 Z= 0.282 Chirality : 0.044 0.158 5111 Planarity : 0.004 0.068 5883 Dihedral : 5.734 100.461 4853 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.24 % Favored : 96.73 % Rotamer: Outliers : 2.72 % Allowed : 19.81 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % 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 aren not related in a simple way. whole: 0.10 (0.13), residues: 4440 helix: 1.21 (0.13), residues: 1818 sheet: 0.01 (0.20), residues: 708 loop : -1.00 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 465 TYR 0.019 0.001 TYR A 203 PHE 0.012 0.001 PHE F 230 TRP 0.009 0.001 TRP D 454 HIS 0.007 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00259 (32333) covalent geometry : angle 0.58672 (43956) hydrogen bonds : bond 0.03674 ( 1462) hydrogen bonds : angle 4.10431 ( 4104) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 358 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.7819 (p0) REVERT: A 389 LYS cc_start: 0.6762 (tptt) cc_final: 0.6501 (ttpt) REVERT: A 427 MET cc_start: 0.6293 (ppp) cc_final: 0.6086 (ppp) REVERT: A 614 LYS cc_start: 0.6985 (mmtt) cc_final: 0.6236 (mmtm) REVERT: A 709 ARG cc_start: 0.5031 (tmm-80) cc_final: 0.4529 (tmm160) REVERT: B 265 PHE cc_start: 0.8224 (t80) cc_final: 0.7834 (t80) REVERT: B 294 GLU cc_start: 0.6956 (tm-30) cc_final: 0.6602 (tm-30) REVERT: B 332 MET cc_start: 0.7386 (mmt) cc_final: 0.7060 (mmt) REVERT: B 366 GLU cc_start: 0.6970 (mp0) cc_final: 0.6501 (mt-10) REVERT: B 561 GLU cc_start: 0.6769 (mm-30) cc_final: 0.6511 (tp30) REVERT: B 662 ARG cc_start: 0.5559 (ptt-90) cc_final: 0.5348 (ptt90) REVERT: B 732 ARG cc_start: 0.6409 (ptt-90) cc_final: 0.6160 (ptt90) REVERT: B 744 ARG cc_start: 0.5810 (mtt180) cc_final: 0.5256 (mtm-85) REVERT: C 229 LEU cc_start: 0.7811 (tt) cc_final: 0.7524 (tp) REVERT: C 283 GLU cc_start: 0.6116 (mt-10) cc_final: 0.5606 (mm-30) REVERT: C 389 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.6607 (tptt) REVERT: C 402 GLU cc_start: 0.6885 (tt0) cc_final: 0.6670 (tt0) REVERT: C 486 LYS cc_start: 0.7382 (mmtp) cc_final: 0.6915 (mmtm) REVERT: C 608 MET cc_start: 0.8653 (ttm) cc_final: 0.8446 (mtp) REVERT: C 706 GLU cc_start: 0.6671 (tm-30) cc_final: 0.5786 (mm-30) REVERT: C 709 ARG cc_start: 0.6244 (ttp80) cc_final: 0.5903 (ttp80) REVERT: C 737 GLU cc_start: 0.5303 (tt0) cc_final: 0.4265 (mm-30) REVERT: D 427 MET cc_start: 0.5369 (mmp) cc_final: 0.4869 (tpt) REVERT: D 565 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8445 (tttt) REVERT: E 221 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7438 (pm20) REVERT: E 230 PHE cc_start: 0.7471 (OUTLIER) cc_final: 0.5871 (m-80) REVERT: E 508 MET cc_start: 0.7094 (tpt) cc_final: 0.6880 (tpt) REVERT: E 657 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6731 (mt) REVERT: E 703 ILE cc_start: 0.7497 (OUTLIER) cc_final: 0.7233 (mp) REVERT: E 740 MET cc_start: 0.7765 (mmm) cc_final: 0.7516 (mmt) REVERT: E 757 MET cc_start: 0.6158 (OUTLIER) cc_final: 0.5888 (tmm) REVERT: F 378 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6686 (tt) REVERT: F 402 GLU cc_start: 0.7155 (tm-30) cc_final: 0.6854 (tm-30) REVERT: F 423 ILE cc_start: 0.8407 (tt) cc_final: 0.8092 (mt) REVERT: F 586 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7638 (ptt-90) REVERT: F 641 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7496 (mt0) outliers start: 76 outliers final: 50 residues processed: 412 average time/residue: 0.2351 time to fit residues: 149.3425 Evaluate side-chains 401 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 340 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 389 LYS Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 565 LYS Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 657 LEU Chi-restraints excluded: chain E residue 703 ILE Chi-restraints excluded: chain E residue 724 GLU Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain F residue 494 GLN Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain F residue 586 ARG Chi-restraints excluded: chain F residue 599 ARG Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 641 GLN Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain F residue 722 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 206 optimal weight: 1.9990 chunk 386 optimal weight: 0.9990 chunk 155 optimal weight: 30.0000 chunk 44 optimal weight: 0.0770 chunk 314 optimal weight: 2.9990 chunk 281 optimal weight: 5.9990 chunk 170 optimal weight: 0.8980 chunk 379 optimal weight: 30.0000 chunk 24 optimal weight: 3.9990 chunk 242 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 overall best weight: 0.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.179621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.150203 restraints weight = 43794.854| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.32 r_work: 0.3544 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32333 Z= 0.114 Angle : 0.582 11.410 43956 Z= 0.279 Chirality : 0.044 0.154 5111 Planarity : 0.004 0.076 5883 Dihedral : 5.702 99.901 4853 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.67 % Favored : 96.31 % Rotamer: Outliers : 2.65 % Allowed : 19.95 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % 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 aren not related in a simple way. whole: 0.14 (0.13), residues: 4440 helix: 1.20 (0.13), residues: 1842 sheet: -0.06 (0.19), residues: 744 loop : -0.93 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 358 TYR 0.017 0.001 TYR A 203 PHE 0.011 0.001 PHE F 230 TRP 0.008 0.001 TRP D 454 HIS 0.005 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00262 (32333) covalent geometry : angle 0.58208 (43956) hydrogen bonds : bond 0.03675 ( 1462) hydrogen bonds : angle 4.07393 ( 4104) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 355 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.7831 (p0) REVERT: A 366 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7051 (mt-10) REVERT: A 389 LYS cc_start: 0.6719 (tptt) cc_final: 0.6469 (ttpt) REVERT: A 397 GLU cc_start: 0.7579 (mp0) cc_final: 0.7274 (mt-10) REVERT: A 427 MET cc_start: 0.6401 (ppp) cc_final: 0.6186 (ppp) REVERT: A 508 MET cc_start: 0.7189 (tpt) cc_final: 0.6715 (tpt) REVERT: A 614 LYS cc_start: 0.6971 (mmtt) cc_final: 0.6715 (mptt) REVERT: A 693 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.7275 (tpp80) REVERT: A 709 ARG cc_start: 0.4940 (tmm-80) cc_final: 0.4497 (tmm160) REVERT: B 265 PHE cc_start: 0.8201 (t80) cc_final: 0.7807 (t80) REVERT: B 366 GLU cc_start: 0.6992 (mp0) cc_final: 0.6497 (mt-10) REVERT: B 561 GLU cc_start: 0.6799 (mm-30) cc_final: 0.6545 (tp30) REVERT: B 668 LYS cc_start: 0.5936 (mmtm) cc_final: 0.5736 (mmtm) REVERT: B 682 PHE cc_start: 0.7043 (m-80) cc_final: 0.6829 (m-80) REVERT: B 732 ARG cc_start: 0.6478 (ptt-90) cc_final: 0.6232 (ptt90) REVERT: B 737 GLU cc_start: 0.3432 (mm-30) cc_final: 0.3175 (tm-30) REVERT: B 745 ARG cc_start: 0.7124 (mtm180) cc_final: 0.6848 (ptp-110) REVERT: C 229 LEU cc_start: 0.7864 (tt) cc_final: 0.7617 (tp) REVERT: C 230 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.6031 (m-80) REVERT: C 283 GLU cc_start: 0.6133 (mt-10) cc_final: 0.5660 (mm-30) REVERT: C 389 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.6626 (tptt) REVERT: C 402 GLU cc_start: 0.6763 (tt0) cc_final: 0.6540 (tt0) REVERT: C 486 LYS cc_start: 0.7362 (mmtp) cc_final: 0.6908 (mmtm) REVERT: C 608 MET cc_start: 0.8732 (ttm) cc_final: 0.8526 (mtp) REVERT: C 706 GLU cc_start: 0.6709 (tm-30) cc_final: 0.5776 (mm-30) REVERT: C 709 ARG cc_start: 0.6115 (ttp80) cc_final: 0.5753 (ttp80) REVERT: D 427 MET cc_start: 0.5471 (mmp) cc_final: 0.5005 (tpt) REVERT: D 565 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8437 (tttt) REVERT: D 728 VAL cc_start: 0.6155 (OUTLIER) cc_final: 0.5842 (m) REVERT: E 221 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7431 (pm20) REVERT: E 230 PHE cc_start: 0.7536 (OUTLIER) cc_final: 0.5830 (m-80) REVERT: E 508 MET cc_start: 0.7137 (tpt) cc_final: 0.6884 (tpt) REVERT: E 657 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6738 (mt) REVERT: E 703 ILE cc_start: 0.7451 (OUTLIER) cc_final: 0.7180 (mp) REVERT: E 740 MET cc_start: 0.7774 (mmm) cc_final: 0.7530 (mmt) REVERT: E 757 MET cc_start: 0.6150 (OUTLIER) cc_final: 0.5864 (tmm) REVERT: F 423 ILE cc_start: 0.8327 (tt) cc_final: 0.8027 (mt) REVERT: F 586 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7638 (ptt-90) REVERT: F 641 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7468 (mt0) outliers start: 74 outliers final: 47 residues processed: 406 average time/residue: 0.2336 time to fit residues: 146.3848 Evaluate side-chains 405 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 344 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 693 ARG Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 389 LYS Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 565 LYS Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 657 LEU Chi-restraints excluded: chain E residue 703 ILE Chi-restraints excluded: chain E residue 724 GLU Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain F residue 586 ARG Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 641 GLN Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain F residue 722 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 221 optimal weight: 0.7980 chunk 7 optimal weight: 20.0000 chunk 90 optimal weight: 30.0000 chunk 132 optimal weight: 0.0000 chunk 421 optimal weight: 10.0000 chunk 129 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 327 optimal weight: 4.9990 chunk 354 optimal weight: 0.9980 chunk 346 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 270 ASN E 285 ASN ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.175968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.147197 restraints weight = 43526.062| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 2.25 r_work: 0.3492 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 32333 Z= 0.167 Angle : 0.657 11.101 43956 Z= 0.321 Chirality : 0.046 0.162 5111 Planarity : 0.005 0.070 5883 Dihedral : 6.149 103.008 4853 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.57 % Favored : 95.41 % Rotamer: Outliers : 2.97 % Allowed : 20.06 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % 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 aren not related in a simple way. whole: -0.16 (0.13), residues: 4440 helix: 0.88 (0.12), residues: 1836 sheet: -0.06 (0.20), residues: 714 loop : -1.06 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 732 TYR 0.027 0.002 TYR D 244 PHE 0.018 0.002 PHE B 230 TRP 0.015 0.001 TRP D 476 HIS 0.006 0.001 HIS D 226 Details of bonding type rmsd covalent geometry : bond 0.00397 (32333) covalent geometry : angle 0.65663 (43956) hydrogen bonds : bond 0.04738 ( 1462) hydrogen bonds : angle 4.35606 ( 4104) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 353 time to evaluate : 1.199 Fit side-chains revert: symmetry clash REVERT: A 307 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.7827 (p0) REVERT: A 366 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7127 (mt-10) REVERT: A 389 LYS cc_start: 0.6997 (tptt) cc_final: 0.6696 (ttpt) REVERT: A 397 GLU cc_start: 0.7535 (mp0) cc_final: 0.7246 (mt-10) REVERT: A 614 LYS cc_start: 0.7028 (mmtt) cc_final: 0.6808 (mptt) REVERT: A 693 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7480 (tpp80) REVERT: A 709 ARG cc_start: 0.5180 (tmm-80) cc_final: 0.4687 (tmm160) REVERT: B 265 PHE cc_start: 0.8224 (t80) cc_final: 0.7855 (t80) REVERT: B 294 GLU cc_start: 0.7031 (tm-30) cc_final: 0.6685 (tm-30) REVERT: B 366 GLU cc_start: 0.7053 (mp0) cc_final: 0.6557 (mt-10) REVERT: B 389 LYS cc_start: 0.8071 (tptp) cc_final: 0.7542 (ttpp) REVERT: B 561 GLU cc_start: 0.6923 (mm-30) cc_final: 0.6657 (tp30) REVERT: B 650 GLU cc_start: 0.5948 (tt0) cc_final: 0.5624 (mt-10) REVERT: B 682 PHE cc_start: 0.7047 (m-80) cc_final: 0.6780 (m-80) REVERT: B 732 ARG cc_start: 0.6716 (ptt-90) cc_final: 0.5270 (mtt90) REVERT: B 737 GLU cc_start: 0.3829 (mm-30) cc_final: 0.3530 (tm-30) REVERT: B 745 ARG cc_start: 0.7260 (mtm180) cc_final: 0.6930 (ptp-110) REVERT: C 229 LEU cc_start: 0.7953 (tt) cc_final: 0.7720 (tp) REVERT: C 230 PHE cc_start: 0.8281 (OUTLIER) cc_final: 0.6293 (m-80) REVERT: C 283 GLU cc_start: 0.6144 (mt-10) cc_final: 0.5645 (mm-30) REVERT: C 389 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.6888 (tptt) REVERT: C 402 GLU cc_start: 0.6918 (tt0) cc_final: 0.6680 (tt0) REVERT: C 486 LYS cc_start: 0.7417 (mmtp) cc_final: 0.6950 (mmtm) REVERT: C 608 MET cc_start: 0.8713 (ttm) cc_final: 0.8507 (mtp) REVERT: C 696 LYS cc_start: 0.7309 (OUTLIER) cc_final: 0.6634 (tptt) REVERT: C 706 GLU cc_start: 0.6811 (tm-30) cc_final: 0.5814 (mm-30) REVERT: C 709 ARG cc_start: 0.6289 (ttp80) cc_final: 0.5955 (ttp80) REVERT: D 427 MET cc_start: 0.5451 (mmp) cc_final: 0.4916 (tpt) REVERT: D 757 MET cc_start: 0.6409 (mmp) cc_final: 0.6144 (mmt) REVERT: E 222 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8075 (mt) REVERT: E 230 PHE cc_start: 0.7676 (OUTLIER) cc_final: 0.5701 (m-80) REVERT: E 508 MET cc_start: 0.7076 (tpt) cc_final: 0.6834 (tpt) REVERT: E 657 LEU cc_start: 0.6857 (OUTLIER) cc_final: 0.6613 (mt) REVERT: E 677 LYS cc_start: 0.7352 (OUTLIER) cc_final: 0.7050 (ttpt) REVERT: E 703 ILE cc_start: 0.7446 (OUTLIER) cc_final: 0.7161 (mp) REVERT: E 740 MET cc_start: 0.7842 (mmm) cc_final: 0.7604 (mmt) REVERT: E 757 MET cc_start: 0.6257 (OUTLIER) cc_final: 0.5955 (tmm) REVERT: F 317 HIS cc_start: 0.5848 (t70) cc_final: 0.5531 (t-90) REVERT: F 423 ILE cc_start: 0.8547 (tt) cc_final: 0.8174 (mt) REVERT: F 586 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7795 (ptt180) REVERT: F 641 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7499 (mt0) outliers start: 83 outliers final: 53 residues processed: 414 average time/residue: 0.2372 time to fit residues: 150.7732 Evaluate side-chains 402 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 335 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 693 ARG Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 389 LYS Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 696 LYS Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 565 LYS Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 657 LEU Chi-restraints excluded: chain E residue 677 LYS Chi-restraints excluded: chain E residue 703 ILE Chi-restraints excluded: chain E residue 724 GLU Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain F residue 494 GLN Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 586 ARG Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 641 GLN Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain F residue 705 SER Chi-restraints excluded: chain F residue 722 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 111 optimal weight: 5.9990 chunk 151 optimal weight: 8.9990 chunk 308 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 326 optimal weight: 0.9980 chunk 221 optimal weight: 5.9990 chunk 352 optimal weight: 5.9990 chunk 418 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 158 optimal weight: 10.0000 chunk 428 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.175555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.146196 restraints weight = 43670.141| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.32 r_work: 0.3487 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 32333 Z= 0.161 Angle : 0.643 12.452 43956 Z= 0.314 Chirality : 0.046 0.185 5111 Planarity : 0.005 0.070 5883 Dihedral : 6.194 103.637 4853 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.26 % Favored : 95.72 % Rotamer: Outliers : 2.68 % Allowed : 20.81 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % 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 aren not related in a simple way. whole: -0.18 (0.13), residues: 4440 helix: 0.86 (0.12), residues: 1836 sheet: -0.09 (0.20), residues: 738 loop : -1.07 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 322 TYR 0.021 0.002 TYR D 244 PHE 0.016 0.002 PHE E 230 TRP 0.008 0.001 TRP D 476 HIS 0.006 0.001 HIS D 226 Details of bonding type rmsd covalent geometry : bond 0.00382 (32333) covalent geometry : angle 0.64271 (43956) hydrogen bonds : bond 0.04516 ( 1462) hydrogen bonds : angle 4.33007 ( 4104) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 350 time to evaluate : 1.245 Fit side-chains revert: symmetry clash REVERT: A 307 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.7905 (p0) REVERT: A 366 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7087 (mt-10) REVERT: A 389 LYS cc_start: 0.7011 (tptt) cc_final: 0.6714 (ttpt) REVERT: A 397 GLU cc_start: 0.7565 (mp0) cc_final: 0.7257 (mt-10) REVERT: A 693 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7444 (tpp80) REVERT: A 709 ARG cc_start: 0.5210 (tmm-80) cc_final: 0.4746 (tmm160) REVERT: B 265 PHE cc_start: 0.8240 (t80) cc_final: 0.7860 (t80) REVERT: B 294 GLU cc_start: 0.6981 (tm-30) cc_final: 0.6628 (tm-30) REVERT: B 366 GLU cc_start: 0.7070 (mp0) cc_final: 0.6597 (mt-10) REVERT: B 389 LYS cc_start: 0.8105 (tptp) cc_final: 0.7594 (ttpp) REVERT: B 561 GLU cc_start: 0.6916 (mm-30) cc_final: 0.6644 (tp30) REVERT: B 682 PHE cc_start: 0.6979 (m-80) cc_final: 0.6759 (m-80) REVERT: B 737 GLU cc_start: 0.3980 (mm-30) cc_final: 0.3722 (tm-30) REVERT: C 229 LEU cc_start: 0.7938 (tt) cc_final: 0.7683 (tp) REVERT: C 230 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.6245 (m-80) REVERT: C 283 GLU cc_start: 0.6229 (mt-10) cc_final: 0.5682 (mm-30) REVERT: C 295 LYS cc_start: 0.8263 (ttpp) cc_final: 0.7868 (ptpt) REVERT: C 360 PHE cc_start: 0.7821 (m-80) cc_final: 0.7484 (m-80) REVERT: C 389 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.6804 (tptt) REVERT: C 486 LYS cc_start: 0.7395 (mmtp) cc_final: 0.6898 (mmtm) REVERT: C 696 LYS cc_start: 0.7338 (OUTLIER) cc_final: 0.6645 (tptt) REVERT: C 706 GLU cc_start: 0.6831 (tm-30) cc_final: 0.5773 (mm-30) REVERT: D 427 MET cc_start: 0.5619 (mmp) cc_final: 0.5101 (tpt) REVERT: E 230 PHE cc_start: 0.7738 (OUTLIER) cc_final: 0.5863 (m-80) REVERT: E 508 MET cc_start: 0.7146 (tpt) cc_final: 0.6897 (tpt) REVERT: E 657 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6640 (mt) REVERT: E 677 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.7180 (ttpt) REVERT: E 703 ILE cc_start: 0.7552 (OUTLIER) cc_final: 0.7267 (mp) REVERT: E 710 GLU cc_start: 0.7290 (tp30) cc_final: 0.6578 (tp30) REVERT: E 740 MET cc_start: 0.7891 (mmm) cc_final: 0.7658 (mmt) REVERT: F 317 HIS cc_start: 0.5837 (t70) cc_final: 0.5549 (t-90) REVERT: F 423 ILE cc_start: 0.8474 (tt) cc_final: 0.8068 (mt) REVERT: F 508 MET cc_start: 0.5933 (ttt) cc_final: 0.5378 (ttt) REVERT: F 586 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7671 (ptt-90) REVERT: F 641 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7505 (mt0) outliers start: 75 outliers final: 55 residues processed: 403 average time/residue: 0.2307 time to fit residues: 143.6604 Evaluate side-chains 405 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 338 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 693 ARG Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 389 LYS Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 696 LYS Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 565 LYS Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 657 LEU Chi-restraints excluded: chain E residue 677 LYS Chi-restraints excluded: chain E residue 703 ILE Chi-restraints excluded: chain E residue 724 GLU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 586 ARG Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 641 GLN Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain F residue 705 SER Chi-restraints excluded: chain F residue 722 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 421 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 233 optimal weight: 9.9990 chunk 165 optimal weight: 10.0000 chunk 409 optimal weight: 0.9980 chunk 124 optimal weight: 0.0970 chunk 97 optimal weight: 1.9990 chunk 342 optimal weight: 1.9990 chunk 286 optimal weight: 5.9990 chunk 361 optimal weight: 1.9990 chunk 428 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.176170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.146363 restraints weight = 43647.576| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.26 r_work: 0.3505 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.5298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 32333 Z= 0.135 Angle : 0.622 12.171 43956 Z= 0.301 Chirality : 0.045 0.157 5111 Planarity : 0.005 0.073 5883 Dihedral : 6.069 102.779 4853 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.03 % Favored : 95.95 % Rotamer: Outliers : 2.47 % Allowed : 21.09 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % 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 aren not related in a simple way. whole: -0.08 (0.13), residues: 4440 helix: 1.01 (0.12), residues: 1806 sheet: -0.04 (0.20), residues: 738 loop : -1.06 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 358 TYR 0.023 0.002 TYR D 244 PHE 0.014 0.001 PHE B 230 TRP 0.007 0.001 TRP D 454 HIS 0.005 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00320 (32333) covalent geometry : angle 0.62232 (43956) hydrogen bonds : bond 0.04112 ( 1462) hydrogen bonds : angle 4.23080 ( 4104) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7321.42 seconds wall clock time: 126 minutes 6.94 seconds (7566.94 seconds total)