Starting phenix.real_space_refine on Thu May 29 06:38:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rsb_19475/05_2025/8rsb_19475.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rsb_19475/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8rsb_19475/05_2025/8rsb_19475.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rsb_19475/05_2025/8rsb_19475.map" model { file = "/net/cci-nas-00/data/ceres_data/8rsb_19475/05_2025/8rsb_19475.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rsb_19475/05_2025/8rsb_19475.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 9, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 16, 'ARG:plan': 16} 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: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 9, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 16} 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: {'GLN:plan1': 3, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 9, 'ASP:plan': 16, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 16} 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: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 10, 'ASP:plan': 16, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 17} 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: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 9, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 16, 'ARG:plan': 16} 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: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 10, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 16, 'ARG:plan': 16} 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: 17.66, per 1000 atoms: 0.55 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: 7.68 Conformation dependent library (CDL) restraints added in 4.2 seconds 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: 4.04 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: 13.38 Time building geometry restraints manager: 8.89 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 762 or resid 901 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 762 or resid 901 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 762 or resid 901 th \ rough 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 762 or resid 901 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 762 or resid 901 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 762 or resid 901 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.220 Check model and map are aligned: 0.230 Set scattering table: 0.270 Process input model: 69.280 Find NCS groups from input model: 1.900 Set up NCS constraints: 0.240 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.810 ------------------------------------------------------------------------------- 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 : 6.08 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (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 TRP 0.006 0.001 TRP E 454 HIS 0.008 0.001 HIS D 499 PHE 0.014 0.001 PHE A 230 TYR 0.014 0.001 TYR A 203 ARG 0.008 0.000 ARG A 358 Details of bonding type rmsd hydrogen bonds : bond 0.17168 ( 1462) hydrogen bonds : angle 6.68227 ( 4104) covalent geometry : bond 0.00315 (32333) covalent geometry : angle 0.70962 (43956) *********************** 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 : 3.815 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: 0.4832 time to fit residues: 307.6106 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 : 3.469 ------------------------------------------------------------------------------- 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 374 optimal weight: 30.0000 chunk 336 optimal weight: 1.9990 chunk 186 optimal weight: 10.0000 chunk 114 optimal weight: 0.0270 chunk 227 optimal weight: 30.0000 chunk 179 optimal weight: 0.0670 chunk 348 optimal weight: 5.9990 chunk 134 optimal weight: 0.5980 chunk 211 optimal weight: 0.9980 chunk 259 optimal weight: 9.9990 chunk 403 optimal weight: 0.2980 overall best weight: 0.3976 ------------------------------------------------------------------------------- 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 ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN B 382 GLN B 692 GLN B 714 GLN C 401 ASN C 490 GLN C 714 GLN E 460 ASN F 382 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.198317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.170384 restraints weight = 43267.200| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 1.90 r_work: 0.3787 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32333 Z= 0.124 Angle : 0.612 8.586 43956 Z= 0.304 Chirality : 0.044 0.166 5111 Planarity : 0.004 0.064 5883 Dihedral : 5.529 95.597 4859 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.24 % Favored : 96.73 % Rotamer: Outliers : 1.79 % Allowed : 14.84 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.13), residues: 4440 helix: 1.25 (0.13), residues: 1842 sheet: -0.23 (0.20), residues: 702 loop : -1.22 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 476 HIS 0.006 0.001 HIS D 735 PHE 0.018 0.001 PHE C 674 TYR 0.016 0.002 TYR E 203 ARG 0.005 0.001 ARG B 377 Details of bonding type rmsd hydrogen bonds : bond 0.04251 ( 1462) hydrogen bonds : angle 4.74805 ( 4104) covalent geometry : bond 0.00261 (32333) covalent geometry : angle 0.61164 (43956) *********************** 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 469 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 419 time to evaluate : 3.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 GLN cc_start: 0.7502 (tp40) cc_final: 0.6764 (tp40) REVERT: A 389 LYS cc_start: 0.6280 (tptt) cc_final: 0.5854 (ttmt) REVERT: A 502 LYS cc_start: 0.5198 (mmmt) cc_final: 0.4632 (ttmt) REVERT: A 508 MET cc_start: 0.6876 (OUTLIER) cc_final: 0.6550 (tmt) REVERT: A 741 ARG cc_start: 0.4874 (mmp-170) cc_final: 0.3569 (ptp-170) REVERT: B 294 GLU cc_start: 0.7023 (tm-30) cc_final: 0.6626 (tt0) REVERT: B 658 LYS cc_start: 0.6381 (tptt) cc_final: 0.6018 (mmmt) REVERT: C 368 ASP cc_start: 0.7673 (t0) cc_final: 0.7372 (t0) REVERT: C 390 LEU cc_start: 0.7140 (tp) cc_final: 0.6780 (mp) REVERT: C 453 ARG cc_start: 0.6755 (mtp85) cc_final: 0.6491 (mmm-85) REVERT: C 486 LYS cc_start: 0.7191 (mmtp) cc_final: 0.6788 (mmtm) REVERT: C 706 GLU cc_start: 0.6470 (tm-30) cc_final: 0.5711 (mm-30) REVERT: C 737 GLU cc_start: 0.3582 (tt0) cc_final: 0.2901 (mm-30) REVERT: D 427 MET cc_start: 0.4216 (mmp) cc_final: 0.3381 (tpt) REVERT: E 757 MET cc_start: 0.6013 (OUTLIER) cc_final: 0.5738 (tmm) REVERT: F 402 GLU cc_start: 0.6282 (tt0) cc_final: 0.5988 (tt0) REVERT: F 641 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7281 (mt0) outliers start: 50 outliers final: 19 residues processed: 452 average time/residue: 0.4657 time to fit residues: 321.8336 Evaluate side-chains 389 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 367 time to evaluate : 3.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 387 ASN Chi-restraints excluded: chain F residue 464 LEU 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 705 SER 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 361 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 chunk 34 optimal weight: 2.9990 chunk 341 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 133 optimal weight: 0.0870 chunk 66 optimal weight: 5.9990 chunk 182 optimal weight: 5.9990 chunk 318 optimal weight: 2.9990 chunk 244 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- 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 616 ASN ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN B 317 HIS B 382 GLN B 384 HIS C 327 GLN D 616 ASN ** E 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 589 ASN E 602 ASN E 660 ASN F 602 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.184992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.153217 restraints weight = 43363.024| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.46 r_work: 0.3555 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 32333 Z= 0.185 Angle : 0.704 8.719 43956 Z= 0.351 Chirality : 0.049 0.217 5111 Planarity : 0.005 0.061 5883 Dihedral : 6.128 96.910 4853 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.03 % Favored : 95.95 % Rotamer: Outliers : 2.54 % Allowed : 15.59 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.12), residues: 4440 helix: 0.80 (0.12), residues: 1836 sheet: 0.26 (0.21), residues: 648 loop : -1.26 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 476 HIS 0.010 0.002 HIS C 384 PHE 0.028 0.002 PHE F 674 TYR 0.021 0.002 TYR D 244 ARG 0.009 0.001 ARG A 653 Details of bonding type rmsd hydrogen bonds : bond 0.05534 ( 1462) hydrogen bonds : angle 4.67835 ( 4104) covalent geometry : bond 0.00437 (32333) covalent geometry : angle 0.70415 (43956) *********************** 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 475 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 404 time to evaluate : 3.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 322 ARG cc_start: 0.6564 (mtm-85) cc_final: 0.6236 (mtm-85) REVERT: A 327 GLN cc_start: 0.7899 (tp40) cc_final: 0.7437 (tp40) REVERT: A 389 LYS cc_start: 0.6612 (tptt) cc_final: 0.6276 (ttpt) REVERT: A 427 MET cc_start: 0.6283 (ppp) cc_final: 0.6000 (ppp) REVERT: A 657 LEU cc_start: 0.6529 (OUTLIER) cc_final: 0.6167 (mt) REVERT: A 709 ARG cc_start: 0.4723 (tmm-80) cc_final: 0.4252 (tmm160) REVERT: B 229 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.6864 (tt) REVERT: B 265 PHE cc_start: 0.8464 (t80) cc_final: 0.7950 (t80) REVERT: B 294 GLU cc_start: 0.7139 (tm-30) cc_final: 0.6622 (tt0) REVERT: B 430 ILE cc_start: 0.6862 (tt) cc_final: 0.6612 (mm) REVERT: B 732 ARG cc_start: 0.6366 (ptt-90) cc_final: 0.6053 (ptt-90) REVERT: C 390 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6882 (mp) REVERT: C 486 LYS cc_start: 0.7371 (mmtp) cc_final: 0.6987 (mmtm) REVERT: C 706 GLU cc_start: 0.6622 (tm-30) cc_final: 0.5705 (mm-30) REVERT: C 737 GLU cc_start: 0.4336 (tt0) cc_final: 0.3269 (mm-30) REVERT: C 757 MET cc_start: 0.6098 (OUTLIER) cc_final: 0.5871 (mmm) REVERT: E 389 LYS cc_start: 0.6734 (ttmt) cc_final: 0.6180 (tttm) REVERT: E 392 ASP cc_start: 0.5653 (m-30) cc_final: 0.5450 (m-30) REVERT: E 724 GLU cc_start: 0.5060 (pt0) cc_final: 0.4194 (mm-30) REVERT: E 757 MET cc_start: 0.6365 (OUTLIER) cc_final: 0.5967 (tmm) REVERT: F 402 GLU cc_start: 0.6585 (OUTLIER) cc_final: 0.6330 (tm-30) REVERT: F 423 ILE cc_start: 0.8208 (tt) cc_final: 0.7896 (mt) REVERT: F 616 ASN cc_start: 0.8143 (OUTLIER) cc_final: 0.7940 (m110) REVERT: F 641 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7337 (mp10) REVERT: F 731 ILE cc_start: 0.6578 (OUTLIER) cc_final: 0.6286 (pt) outliers start: 71 outliers final: 39 residues processed: 449 average time/residue: 0.4569 time to fit residues: 316.9223 Evaluate side-chains 401 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 353 time to evaluate : 3.190 ------------------------------------------------------------------------------- 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 229 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 464 LEU 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 222 LEU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 656 ILE Chi-restraints excluded: chain C residue 666 VAL 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 C residue 757 MET Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 565 LYS Chi-restraints excluded: chain D residue 703 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 394 VAL Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain F residue 402 GLU 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 616 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 722 VAL Chi-restraints excluded: chain F residue 731 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 243 optimal weight: 0.6980 chunk 376 optimal weight: 10.0000 chunk 389 optimal weight: 0.7980 chunk 374 optimal weight: 30.0000 chunk 18 optimal weight: 2.9990 chunk 87 optimal weight: 30.0000 chunk 122 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 278 optimal weight: 5.9990 chunk 258 optimal weight: 2.9990 chunk 343 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN A 568 GLN ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 ASN C 616 ASN D 616 ASN D 624 ASN E 260 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.182273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.152285 restraints weight = 43273.088| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.24 r_work: 0.3553 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 32333 Z= 0.168 Angle : 0.655 10.535 43956 Z= 0.325 Chirality : 0.046 0.171 5111 Planarity : 0.005 0.060 5883 Dihedral : 6.132 100.491 4853 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.96 % Favored : 96.01 % Rotamer: Outliers : 2.90 % Allowed : 17.05 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.13), residues: 4440 helix: 0.85 (0.12), residues: 1818 sheet: -0.01 (0.20), residues: 702 loop : -1.23 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 454 HIS 0.009 0.001 HIS B 735 PHE 0.021 0.002 PHE F 674 TYR 0.023 0.002 TYR C 203 ARG 0.025 0.001 ARG F 358 Details of bonding type rmsd hydrogen bonds : bond 0.04603 ( 1462) hydrogen bonds : angle 4.43519 ( 4104) covalent geometry : bond 0.00392 (32333) covalent geometry : angle 0.65543 (43956) *********************** 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 469 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 388 time to evaluate : 3.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.8120 (tp) cc_final: 0.7810 (tp) REVERT: A 291 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7289 (mt-10) REVERT: A 322 ARG cc_start: 0.6583 (mtm-85) cc_final: 0.6223 (mtm180) REVERT: A 389 LYS cc_start: 0.6690 (tptt) cc_final: 0.6380 (ttpt) REVERT: A 614 LYS cc_start: 0.7005 (mmtt) cc_final: 0.6296 (mmtm) REVERT: A 709 ARG cc_start: 0.5041 (tmm-80) cc_final: 0.4464 (tmm160) REVERT: B 265 PHE cc_start: 0.8429 (t80) cc_final: 0.7892 (t80) REVERT: B 294 GLU cc_start: 0.7034 (tm-30) cc_final: 0.6495 (tt0) REVERT: B 556 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: B 658 LYS cc_start: 0.6149 (tptt) cc_final: 0.5831 (mmmt) REVERT: B 671 ASP cc_start: 0.7118 (t70) cc_final: 0.6752 (p0) REVERT: B 732 ARG cc_start: 0.6281 (ptt-90) cc_final: 0.5962 (ptt90) REVERT: C 229 LEU cc_start: 0.7735 (tt) cc_final: 0.7447 (tp) REVERT: C 230 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.6084 (m-80) REVERT: C 283 GLU cc_start: 0.5919 (mt-10) cc_final: 0.5346 (mm-30) REVERT: C 390 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.7030 (mp) REVERT: C 706 GLU cc_start: 0.6639 (tm-30) cc_final: 0.5712 (mm-30) REVERT: C 737 GLU cc_start: 0.4503 (tt0) cc_final: 0.3686 (mm-30) REVERT: D 599 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7458 (mtp85) REVERT: D 757 MET cc_start: 0.6156 (mmp) cc_final: 0.5916 (mmt) REVERT: E 389 LYS cc_start: 0.6686 (ttmt) cc_final: 0.6130 (tttm) REVERT: E 657 LEU cc_start: 0.7054 (OUTLIER) cc_final: 0.6694 (mt) REVERT: E 678 MET cc_start: 0.6529 (mmm) cc_final: 0.6306 (mmm) REVERT: E 703 ILE cc_start: 0.7387 (OUTLIER) cc_final: 0.7100 (mp) REVERT: E 757 MET cc_start: 0.6142 (OUTLIER) cc_final: 0.5883 (tmm) REVERT: F 423 ILE cc_start: 0.8319 (tt) cc_final: 0.8019 (mt) REVERT: F 508 MET cc_start: 0.6146 (OUTLIER) cc_final: 0.5704 (ttt) REVERT: F 599 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7374 (mtp85) REVERT: F 616 ASN cc_start: 0.8118 (OUTLIER) cc_final: 0.7915 (m110) REVERT: F 641 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7441 (mt0) REVERT: F 731 ILE cc_start: 0.6692 (OUTLIER) cc_final: 0.6353 (pt) outliers start: 81 outliers final: 41 residues processed: 445 average time/residue: 0.4650 time to fit residues: 318.7597 Evaluate side-chains 404 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 350 time to evaluate : 3.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 GLU 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 399 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 747 VAL 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 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 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 390 LEU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 416 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 728 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 417 GLU 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 747 VAL 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 616 ASN Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 641 GLN Chi-restraints excluded: chain F residue 731 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 9 optimal weight: 30.0000 chunk 282 optimal weight: 0.9990 chunk 169 optimal weight: 2.9990 chunk 82 optimal weight: 40.0000 chunk 71 optimal weight: 5.9990 chunk 190 optimal weight: 10.0000 chunk 240 optimal weight: 6.9990 chunk 260 optimal weight: 6.9990 chunk 366 optimal weight: 0.1980 chunk 196 optimal weight: 0.0870 chunk 279 optimal weight: 6.9990 overall best weight: 2.0564 ------------------------------------------------------------------------------- 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** ** B 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 GLN D 616 ASN E 270 ASN E 285 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.178688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.147766 restraints weight = 43416.981| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 2.22 r_work: 0.3519 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 32333 Z= 0.177 Angle : 0.673 9.819 43956 Z= 0.334 Chirality : 0.047 0.255 5111 Planarity : 0.005 0.063 5883 Dihedral : 6.295 101.193 4853 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.28 % Favored : 95.70 % Rotamer: Outliers : 3.97 % Allowed : 17.34 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.12), residues: 4440 helix: 0.65 (0.12), residues: 1818 sheet: -0.05 (0.20), residues: 702 loop : -1.26 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 476 HIS 0.009 0.001 HIS B 735 PHE 0.027 0.002 PHE F 674 TYR 0.026 0.002 TYR B 203 ARG 0.009 0.001 ARG D 239 Details of bonding type rmsd hydrogen bonds : bond 0.05025 ( 1462) hydrogen bonds : angle 4.47953 ( 4104) covalent geometry : bond 0.00413 (32333) covalent geometry : angle 0.67350 (43956) *********************** 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 487 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 376 time to evaluate : 3.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 ARG cc_start: 0.6658 (mtm-85) cc_final: 0.6311 (mtm180) REVERT: A 389 LYS cc_start: 0.6777 (tptt) cc_final: 0.6532 (ttpt) REVERT: A 512 LYS cc_start: 0.7806 (pptt) cc_final: 0.7118 (mmmt) REVERT: A 614 LYS cc_start: 0.6962 (mmtt) cc_final: 0.6192 (mmtm) REVERT: A 709 ARG cc_start: 0.5178 (tmm-80) cc_final: 0.4678 (tmm160) REVERT: B 265 PHE cc_start: 0.8360 (t80) cc_final: 0.7829 (t80) REVERT: B 294 GLU cc_start: 0.7027 (tm-30) cc_final: 0.6434 (tt0) REVERT: B 560 ARG cc_start: 0.7090 (ttm170) cc_final: 0.6757 (mtm180) REVERT: B 732 ARG cc_start: 0.6421 (ptt-90) cc_final: 0.6151 (ptt90) REVERT: B 745 ARG cc_start: 0.7127 (mtm180) cc_final: 0.6911 (ptp-110) REVERT: C 229 LEU cc_start: 0.7899 (tt) cc_final: 0.7644 (tp) REVERT: C 230 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.6198 (m-80) REVERT: C 244 TYR cc_start: 0.7880 (p90) cc_final: 0.7582 (p90) REVERT: C 283 GLU cc_start: 0.5969 (mt-10) cc_final: 0.5478 (mm-30) REVERT: C 360 PHE cc_start: 0.8008 (m-80) cc_final: 0.7788 (m-80) REVERT: C 366 GLU cc_start: 0.6913 (pt0) cc_final: 0.6698 (pt0) REVERT: C 696 LYS cc_start: 0.7350 (OUTLIER) cc_final: 0.6658 (tptt) REVERT: C 737 GLU cc_start: 0.5263 (tt0) cc_final: 0.4170 (mm-30) REVERT: C 757 MET cc_start: 0.6294 (OUTLIER) cc_final: 0.6034 (mmm) REVERT: D 229 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7297 (tt) REVERT: D 599 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7498 (mtp85) REVERT: E 657 LEU cc_start: 0.7044 (OUTLIER) cc_final: 0.6665 (mt) REVERT: E 677 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.7050 (ttpt) REVERT: E 740 MET cc_start: 0.7892 (mmm) cc_final: 0.7627 (mmt) REVERT: E 757 MET cc_start: 0.6174 (OUTLIER) cc_final: 0.5887 (tmm) REVERT: F 354 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7647 (m-30) REVERT: F 423 ILE cc_start: 0.8315 (tt) cc_final: 0.8058 (mt) REVERT: F 508 MET cc_start: 0.6306 (OUTLIER) cc_final: 0.5925 (ttt) REVERT: F 550 MET cc_start: 0.8347 (mtp) cc_final: 0.8091 (mtt) REVERT: F 641 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7256 (mp10) outliers start: 111 outliers final: 62 residues processed: 450 average time/residue: 0.4767 time to fit residues: 329.6914 Evaluate side-chains 417 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 344 time to evaluate : 3.352 ------------------------------------------------------------------------------- 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 491 GLU Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 747 VAL 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 364 ASP 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 599 ARG Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 364 ASP 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 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 C residue 757 MET Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 230 PHE 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 475 THR 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 222 LEU Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 417 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 677 LYS Chi-restraints excluded: chain E residue 724 GLU Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain F residue 340 HIS 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 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 672 LEU Chi-restraints excluded: chain F residue 705 SER Chi-restraints excluded: chain F residue 722 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 122 optimal weight: 0.9980 chunk 345 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 305 optimal weight: 40.0000 chunk 373 optimal weight: 50.0000 chunk 181 optimal weight: 1.9990 chunk 431 optimal weight: 1.9990 chunk 297 optimal weight: 20.0000 chunk 275 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 616 ASN D 624 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.176382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.147545 restraints weight = 43879.384| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.30 r_work: 0.3492 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 32333 Z= 0.192 Angle : 0.691 10.603 43956 Z= 0.342 Chirality : 0.047 0.330 5111 Planarity : 0.005 0.064 5883 Dihedral : 6.500 104.252 4853 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.44 % Favored : 95.54 % Rotamer: Outliers : 3.97 % Allowed : 18.09 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.12), residues: 4440 helix: 0.53 (0.12), residues: 1836 sheet: -0.21 (0.20), residues: 708 loop : -1.36 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 476 HIS 0.008 0.001 HIS B 735 PHE 0.020 0.002 PHE B 230 TYR 0.025 0.002 TYR D 244 ARG 0.015 0.001 ARG F 322 Details of bonding type rmsd hydrogen bonds : bond 0.05161 ( 1462) hydrogen bonds : angle 4.56508 ( 4104) covalent geometry : bond 0.00457 (32333) covalent geometry : angle 0.69080 (43956) *********************** 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 484 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 373 time to evaluate : 3.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 ARG cc_start: 0.6877 (mtm-85) cc_final: 0.6512 (mtm180) REVERT: A 389 LYS cc_start: 0.6976 (tptt) cc_final: 0.6649 (ttpt) REVERT: A 442 MET cc_start: 0.2849 (mtt) cc_final: 0.2500 (mtt) REVERT: A 614 LYS cc_start: 0.6948 (mmtt) cc_final: 0.6255 (mmtm) REVERT: A 709 ARG cc_start: 0.5189 (tmm-80) cc_final: 0.4770 (tmm160) REVERT: B 265 PHE cc_start: 0.8381 (t80) cc_final: 0.7861 (t80) REVERT: B 294 GLU cc_start: 0.7017 (tm-30) cc_final: 0.6438 (tt0) REVERT: B 366 GLU cc_start: 0.7129 (mp0) cc_final: 0.6631 (mt-10) REVERT: B 650 GLU cc_start: 0.5841 (tt0) cc_final: 0.5485 (mt-10) REVERT: B 671 ASP cc_start: 0.6653 (t70) cc_final: 0.6451 (p0) REVERT: B 682 PHE cc_start: 0.7023 (m-80) cc_final: 0.6818 (m-80) REVERT: B 732 ARG cc_start: 0.6645 (ptt-90) cc_final: 0.5169 (mtt90) REVERT: B 737 GLU cc_start: 0.3596 (mm-30) cc_final: 0.3243 (tm-30) REVERT: B 745 ARG cc_start: 0.7245 (mtm180) cc_final: 0.6950 (ptp-110) REVERT: C 229 LEU cc_start: 0.7931 (tt) cc_final: 0.7667 (tp) REVERT: C 230 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.6162 (m-80) REVERT: C 283 GLU cc_start: 0.6098 (mt-10) cc_final: 0.5500 (mm-30) REVERT: C 402 GLU cc_start: 0.6853 (tt0) cc_final: 0.6621 (tt0) REVERT: C 696 LYS cc_start: 0.7456 (OUTLIER) cc_final: 0.6719 (tptt) REVERT: C 709 ARG cc_start: 0.6401 (ttp80) cc_final: 0.6061 (ttp80) REVERT: C 757 MET cc_start: 0.6398 (OUTLIER) cc_final: 0.6114 (mmm) REVERT: D 390 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7488 (mp) REVERT: D 427 MET cc_start: 0.5077 (mmp) cc_final: 0.4626 (tpt) REVERT: D 599 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7356 (mtp85) REVERT: D 720 MET cc_start: 0.4031 (OUTLIER) cc_final: 0.3251 (tmm) REVERT: E 230 PHE cc_start: 0.7685 (OUTLIER) cc_final: 0.5819 (m-80) REVERT: E 305 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8133 (mt-10) REVERT: E 657 LEU cc_start: 0.6977 (OUTLIER) cc_final: 0.6661 (mt) REVERT: E 677 LYS cc_start: 0.7281 (OUTLIER) cc_final: 0.7004 (ttpt) REVERT: E 703 ILE cc_start: 0.7568 (OUTLIER) cc_final: 0.7274 (mp) REVERT: E 710 GLU cc_start: 0.7173 (tp30) cc_final: 0.6764 (tp30) REVERT: E 740 MET cc_start: 0.7874 (mmm) cc_final: 0.7603 (mmt) REVERT: F 354 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7779 (m-30) REVERT: F 423 ILE cc_start: 0.8418 (tt) cc_final: 0.8088 (mt) REVERT: F 508 MET cc_start: 0.6182 (OUTLIER) cc_final: 0.5942 (ttt) REVERT: F 599 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7608 (mtp85) REVERT: F 641 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7488 (mt0) outliers start: 111 outliers final: 69 residues processed: 453 average time/residue: 0.4809 time to fit residues: 335.6394 Evaluate side-chains 428 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 345 time to evaluate : 3.520 ------------------------------------------------------------------------------- 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 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 494 GLN 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 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 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 599 ARG Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 312 LYS 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 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 757 MET 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 390 LEU Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 728 VAL 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 340 HIS Chi-restraints excluded: chain E residue 417 GLU 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 677 LYS Chi-restraints excluded: chain E residue 703 ILE Chi-restraints excluded: chain E residue 724 GLU Chi-restraints excluded: chain E residue 747 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 459 SER 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 508 MET Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 531 ILE 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 705 SER Chi-restraints excluded: chain F residue 722 VAL Chi-restraints excluded: chain F residue 747 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 349 optimal weight: 2.9990 chunk 351 optimal weight: 2.9990 chunk 265 optimal weight: 2.9990 chunk 228 optimal weight: 20.0000 chunk 183 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 219 optimal weight: 0.0050 chunk 248 optimal weight: 7.9990 chunk 90 optimal weight: 40.0000 chunk 352 optimal weight: 5.9990 overall best weight: 2.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 458 GLN D 404 HIS E 750 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.174208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.145315 restraints weight = 44139.350| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.34 r_work: 0.3458 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 32333 Z= 0.204 Angle : 0.714 10.148 43956 Z= 0.354 Chirality : 0.048 0.164 5111 Planarity : 0.005 0.072 5883 Dihedral : 6.703 104.250 4853 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.98 % Favored : 95.00 % Rotamer: Outliers : 4.15 % Allowed : 18.23 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.12), residues: 4440 helix: 0.37 (0.12), residues: 1830 sheet: -0.39 (0.19), residues: 738 loop : -1.32 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 476 HIS 0.008 0.001 HIS B 735 PHE 0.022 0.002 PHE E 230 TYR 0.026 0.002 TYR D 244 ARG 0.009 0.001 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.05415 ( 1462) hydrogen bonds : angle 4.65608 ( 4104) covalent geometry : bond 0.00489 (32333) covalent geometry : angle 0.71389 (43956) *********************** 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 481 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 365 time to evaluate : 3.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 ARG cc_start: 0.6947 (mtm-85) cc_final: 0.6519 (ttm170) REVERT: A 389 LYS cc_start: 0.7070 (tptt) cc_final: 0.6775 (ttpt) REVERT: A 427 MET cc_start: 0.6589 (ppp) cc_final: 0.6290 (ppp) REVERT: A 614 LYS cc_start: 0.7012 (mmtt) cc_final: 0.6758 (mptt) REVERT: A 709 ARG cc_start: 0.5304 (tmm-80) cc_final: 0.4736 (tmm160) REVERT: B 265 PHE cc_start: 0.8326 (t80) cc_final: 0.7864 (t80) REVERT: B 366 GLU cc_start: 0.7143 (mp0) cc_final: 0.6643 (mt-10) REVERT: B 650 GLU cc_start: 0.6203 (tt0) cc_final: 0.5854 (mt-10) REVERT: B 682 PHE cc_start: 0.6979 (m-80) cc_final: 0.6738 (m-80) REVERT: B 732 ARG cc_start: 0.6894 (ptt-90) cc_final: 0.5490 (mtt90) REVERT: B 737 GLU cc_start: 0.4006 (mm-30) cc_final: 0.3668 (tm-30) REVERT: C 229 LEU cc_start: 0.7986 (tt) cc_final: 0.7729 (tp) REVERT: C 230 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.6209 (m-80) REVERT: C 360 PHE cc_start: 0.7837 (m-80) cc_final: 0.7467 (m-80) REVERT: C 389 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.6914 (tptt) REVERT: C 696 LYS cc_start: 0.7431 (OUTLIER) cc_final: 0.6772 (tptt) REVERT: C 757 MET cc_start: 0.6465 (OUTLIER) cc_final: 0.6176 (mmm) REVERT: D 427 MET cc_start: 0.5566 (mmp) cc_final: 0.5058 (tpt) REVERT: D 599 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7371 (mtp85) REVERT: D 720 MET cc_start: 0.3965 (OUTLIER) cc_final: 0.3649 (ppp) REVERT: E 221 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7397 (pm20) REVERT: E 222 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.7837 (mp) REVERT: E 230 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.5894 (m-80) REVERT: E 657 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6588 (mt) REVERT: E 677 LYS cc_start: 0.7472 (OUTLIER) cc_final: 0.7180 (ttpt) REVERT: E 740 MET cc_start: 0.7958 (mmm) cc_final: 0.7706 (mmt) REVERT: F 354 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7867 (m-30) REVERT: F 402 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.7002 (tm-30) REVERT: F 423 ILE cc_start: 0.8504 (tt) cc_final: 0.8107 (mt) REVERT: F 531 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8493 (mm) REVERT: F 641 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7293 (mp10) outliers start: 116 outliers final: 78 residues processed: 445 average time/residue: 0.4587 time to fit residues: 314.3425 Evaluate side-chains 438 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 345 time to evaluate : 3.263 ------------------------------------------------------------------------------- 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 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 494 GLN Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 741 ARG Chi-restraints excluded: chain A residue 747 VAL 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 416 SER Chi-restraints excluded: chain B residue 427 MET 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 599 ARG 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 312 LYS 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 458 GLN 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 508 MET 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 720 MET 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 C residue 757 MET Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 312 LYS Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 556 GLU Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 720 MET 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 222 LEU Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 417 GLU 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 677 LYS Chi-restraints excluded: chain E residue 724 GLU Chi-restraints excluded: chain E residue 747 VAL 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 354 ASP Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 402 GLU 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 531 ILE 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 Chi-restraints excluded: chain F residue 747 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 133 optimal weight: 0.6980 chunk 328 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 chunk 60 optimal weight: 0.1980 chunk 100 optimal weight: 5.9990 chunk 206 optimal weight: 0.5980 chunk 90 optimal weight: 30.0000 chunk 302 optimal weight: 30.0000 chunk 20 optimal weight: 0.8980 chunk 306 optimal weight: 20.0000 chunk 132 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 GLN ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 GLN D 624 ASN E 285 ASN ** E 406 HIS ** 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 = 0.4136 r_free = 0.4136 target = 0.177853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.148615 restraints weight = 43628.784| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.33 r_work: 0.3518 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 32333 Z= 0.113 Angle : 0.606 12.188 43956 Z= 0.295 Chirality : 0.044 0.310 5111 Planarity : 0.005 0.072 5883 Dihedral : 6.132 102.195 4853 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.42 % Favored : 96.55 % Rotamer: Outliers : 2.50 % Allowed : 20.06 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.13), residues: 4440 helix: 0.89 (0.12), residues: 1830 sheet: -0.21 (0.20), residues: 738 loop : -1.13 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 476 HIS 0.004 0.001 HIS B 735 PHE 0.010 0.001 PHE E 360 TYR 0.017 0.001 TYR D 244 ARG 0.009 0.000 ARG F 322 Details of bonding type rmsd hydrogen bonds : bond 0.03813 ( 1462) hydrogen bonds : angle 4.28511 ( 4104) covalent geometry : bond 0.00250 (32333) covalent geometry : angle 0.60602 (43956) *********************** 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 439 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 369 time to evaluate : 3.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 ARG cc_start: 0.6841 (mtm-85) cc_final: 0.6339 (ttm170) REVERT: A 389 LYS cc_start: 0.7052 (tptt) cc_final: 0.6760 (ttpt) REVERT: A 512 LYS cc_start: 0.7783 (pptt) cc_final: 0.7526 (ptmm) REVERT: A 614 LYS cc_start: 0.6995 (mmtt) cc_final: 0.6763 (mptt) REVERT: A 709 ARG cc_start: 0.5356 (tmm-80) cc_final: 0.4823 (tmm160) REVERT: B 265 PHE cc_start: 0.8295 (t80) cc_final: 0.7774 (t80) REVERT: B 366 GLU cc_start: 0.6931 (mp0) cc_final: 0.6431 (mt-10) REVERT: B 389 LYS cc_start: 0.8078 (tptp) cc_final: 0.7554 (ttpp) REVERT: B 445 LEU cc_start: 0.6899 (tp) cc_final: 0.6566 (tp) REVERT: B 682 PHE cc_start: 0.6960 (m-80) cc_final: 0.6682 (m-80) REVERT: B 732 ARG cc_start: 0.6775 (ptt-90) cc_final: 0.6518 (ptt90) REVERT: B 737 GLU cc_start: 0.3862 (mm-30) cc_final: 0.3601 (tm-30) REVERT: C 229 LEU cc_start: 0.7860 (tt) cc_final: 0.7597 (tp) REVERT: C 230 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.6114 (m-80) REVERT: C 283 GLU cc_start: 0.6106 (mt-10) cc_final: 0.5553 (mm-30) REVERT: C 295 LYS cc_start: 0.8286 (ttpp) cc_final: 0.7899 (ptpt) REVERT: C 402 GLU cc_start: 0.6857 (tt0) cc_final: 0.6652 (tt0) REVERT: C 696 LYS cc_start: 0.7322 (OUTLIER) cc_final: 0.6643 (tptt) REVERT: C 706 GLU cc_start: 0.6905 (tm-30) cc_final: 0.6034 (mm-30) REVERT: C 757 MET cc_start: 0.6378 (OUTLIER) cc_final: 0.6128 (mmm) REVERT: D 427 MET cc_start: 0.5461 (mmp) cc_final: 0.5018 (tpt) REVERT: D 720 MET cc_start: 0.3938 (OUTLIER) cc_final: 0.3665 (ppp) REVERT: E 239 ARG cc_start: 0.7063 (mmt-90) cc_final: 0.6769 (mmt90) REVERT: E 502 LYS cc_start: 0.6103 (mmtt) cc_final: 0.5824 (mmtp) REVERT: E 657 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6714 (mt) REVERT: E 740 MET cc_start: 0.7896 (mmm) cc_final: 0.7649 (mmt) REVERT: F 358 ARG cc_start: 0.7513 (mtt180) cc_final: 0.7309 (mtt-85) REVERT: F 402 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6815 (tm-30) REVERT: F 423 ILE cc_start: 0.8397 (tt) cc_final: 0.8067 (mt) REVERT: F 531 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8433 (mm) REVERT: F 641 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7474 (mt0) outliers start: 70 outliers final: 41 residues processed: 416 average time/residue: 0.4728 time to fit residues: 303.3425 Evaluate side-chains 402 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 353 time to evaluate : 3.345 ------------------------------------------------------------------------------- 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 342 ILE Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 678 MET 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 556 GLU Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 689 GLU Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 312 LYS 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 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 C residue 757 MET Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 312 LYS Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 258 VAL 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 670 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 531 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 216 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 420 optimal weight: 3.9990 chunk 374 optimal weight: 10.0000 chunk 323 optimal weight: 0.3980 chunk 372 optimal weight: 20.0000 chunk 203 optimal weight: 0.1980 chunk 231 optimal weight: 30.0000 chunk 416 optimal weight: 2.9990 chunk 319 optimal weight: 0.9980 chunk 439 optimal weight: 9.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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** C 458 GLN D 624 ASN E 260 ASN E 421 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.176544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.148364 restraints weight = 44106.214| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.26 r_work: 0.3504 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32333 Z= 0.125 Angle : 0.617 11.610 43956 Z= 0.299 Chirality : 0.044 0.242 5111 Planarity : 0.005 0.075 5883 Dihedral : 6.054 101.411 4853 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.85 % Favored : 96.13 % Rotamer: Outliers : 2.25 % Allowed : 20.77 % Favored : 76.98 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 6.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.13), residues: 4440 helix: 0.94 (0.12), residues: 1830 sheet: -0.13 (0.20), residues: 738 loop : -1.05 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 454 HIS 0.004 0.001 HIS B 735 PHE 0.012 0.001 PHE E 230 TYR 0.012 0.001 TYR C 203 ARG 0.010 0.000 ARG F 322 Details of bonding type rmsd hydrogen bonds : bond 0.04014 ( 1462) hydrogen bonds : angle 4.24319 ( 4104) covalent geometry : bond 0.00288 (32333) covalent geometry : angle 0.61736 (43956) *********************** 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 421 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 358 time to evaluate : 3.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 ARG cc_start: 0.6810 (mtm-85) cc_final: 0.6333 (ttm170) REVERT: A 366 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7074 (mt-10) REVERT: A 389 LYS cc_start: 0.6931 (tptt) cc_final: 0.6675 (ttpt) REVERT: A 512 LYS cc_start: 0.7747 (pptt) cc_final: 0.7504 (ptmm) REVERT: A 614 LYS cc_start: 0.6936 (mmtt) cc_final: 0.6700 (mptt) REVERT: A 709 ARG cc_start: 0.5332 (tmm-80) cc_final: 0.4787 (tmm160) REVERT: A 757 MET cc_start: 0.7171 (mmt) cc_final: 0.6908 (mpp) REVERT: B 265 PHE cc_start: 0.8278 (t80) cc_final: 0.7767 (t80) REVERT: B 366 GLU cc_start: 0.6970 (mp0) cc_final: 0.6487 (mt-10) REVERT: B 389 LYS cc_start: 0.8109 (tptp) cc_final: 0.7609 (ttpp) REVERT: B 445 LEU cc_start: 0.6894 (tp) cc_final: 0.6560 (tp) REVERT: B 682 PHE cc_start: 0.7027 (m-80) cc_final: 0.6812 (m-80) REVERT: B 737 GLU cc_start: 0.3977 (mm-30) cc_final: 0.3700 (tm-30) REVERT: C 229 LEU cc_start: 0.7908 (tt) cc_final: 0.7651 (tp) REVERT: C 230 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.6267 (m-80) REVERT: C 283 GLU cc_start: 0.6111 (mt-10) cc_final: 0.5566 (mm-30) REVERT: C 360 PHE cc_start: 0.7831 (m-80) cc_final: 0.7494 (m-80) REVERT: C 402 GLU cc_start: 0.6901 (tt0) cc_final: 0.6685 (tt0) REVERT: C 487 ARG cc_start: 0.7363 (ttt90) cc_final: 0.6973 (mtm180) REVERT: C 696 LYS cc_start: 0.7341 (OUTLIER) cc_final: 0.6676 (tptt) REVERT: C 706 GLU cc_start: 0.6790 (tm-30) cc_final: 0.5775 (mm-30) REVERT: C 757 MET cc_start: 0.6359 (OUTLIER) cc_final: 0.6123 (mmm) REVERT: D 427 MET cc_start: 0.5668 (mmp) cc_final: 0.5238 (tpt) REVERT: D 720 MET cc_start: 0.3949 (OUTLIER) cc_final: 0.3702 (ppp) REVERT: E 221 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7424 (pm20) REVERT: E 222 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7528 (mp) REVERT: E 230 PHE cc_start: 0.7727 (OUTLIER) cc_final: 0.5904 (m-80) REVERT: E 239 ARG cc_start: 0.7085 (mmt-90) cc_final: 0.6784 (mmt90) REVERT: E 502 LYS cc_start: 0.6100 (mmtt) cc_final: 0.5851 (mmtp) REVERT: E 508 MET cc_start: 0.6992 (tpt) cc_final: 0.6699 (mmt) REVERT: E 657 LEU cc_start: 0.6863 (OUTLIER) cc_final: 0.6622 (mt) REVERT: E 740 MET cc_start: 0.7890 (mmm) cc_final: 0.7660 (mmt) REVERT: F 423 ILE cc_start: 0.8448 (tt) cc_final: 0.8111 (mt) REVERT: F 531 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8420 (mm) REVERT: F 641 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7457 (mt0) outliers start: 63 outliers final: 42 residues processed: 398 average time/residue: 0.4997 time to fit residues: 305.9031 Evaluate side-chains 398 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 345 time to evaluate : 3.281 ------------------------------------------------------------------------------- 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 342 ILE 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 599 ARG Chi-restraints excluded: chain A residue 678 MET 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 556 GLU Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 689 GLU Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 508 MET 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 757 MET Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 312 LYS Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 221 GLU 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 464 LEU Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 657 LEU Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain F residue 531 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 296 optimal weight: 20.0000 chunk 367 optimal weight: 0.8980 chunk 280 optimal weight: 0.7980 chunk 169 optimal weight: 2.9990 chunk 311 optimal weight: 8.9990 chunk 276 optimal weight: 2.9990 chunk 227 optimal weight: 40.0000 chunk 191 optimal weight: 0.9990 chunk 144 optimal weight: 6.9990 chunk 404 optimal weight: 4.9990 chunk 309 optimal weight: 20.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 285 ASN E 421 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.174413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.146181 restraints weight = 44334.774| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.28 r_work: 0.3476 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.5570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32333 Z= 0.154 Angle : 0.653 13.546 43956 Z= 0.320 Chirality : 0.046 0.201 5111 Planarity : 0.005 0.074 5883 Dihedral : 6.263 103.662 4853 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.73 % Favored : 95.25 % Rotamer: Outliers : 2.22 % Allowed : 20.95 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.13), residues: 4440 helix: 0.80 (0.12), residues: 1812 sheet: -0.16 (0.19), residues: 756 loop : -1.14 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 476 HIS 0.005 0.001 HIS A 406 PHE 0.018 0.002 PHE A 230 TYR 0.024 0.002 TYR D 244 ARG 0.009 0.001 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.04625 ( 1462) hydrogen bonds : angle 4.41149 ( 4104) covalent geometry : bond 0.00364 (32333) covalent geometry : angle 0.65321 (43956) ********************** 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 416 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 354 time to evaluate : 3.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 322 ARG cc_start: 0.6973 (mtm-85) cc_final: 0.6473 (ttm170) REVERT: A 366 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7164 (mt-10) REVERT: A 389 LYS cc_start: 0.7026 (tptt) cc_final: 0.6776 (ttpt) REVERT: A 599 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7640 (mtp180) REVERT: A 614 LYS cc_start: 0.6901 (mmtt) cc_final: 0.6654 (tttt) REVERT: A 709 ARG cc_start: 0.5354 (tmm-80) cc_final: 0.4815 (tmm160) REVERT: B 315 LYS cc_start: 0.6549 (mttt) cc_final: 0.6268 (mtmt) REVERT: B 366 GLU cc_start: 0.6986 (mp0) cc_final: 0.6511 (mt-10) REVERT: B 389 LYS cc_start: 0.8146 (tptp) cc_final: 0.7650 (ttpp) REVERT: B 445 LEU cc_start: 0.6988 (tp) cc_final: 0.6658 (tp) REVERT: B 682 PHE cc_start: 0.7008 (m-80) cc_final: 0.6804 (m-80) REVERT: B 737 GLU cc_start: 0.4157 (mm-30) cc_final: 0.3857 (tm-30) REVERT: C 229 LEU cc_start: 0.7950 (tt) cc_final: 0.7688 (tp) REVERT: C 230 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.6323 (m-80) REVERT: C 283 GLU cc_start: 0.6129 (mt-10) cc_final: 0.5590 (mm-30) REVERT: C 295 LYS cc_start: 0.8262 (ttpp) cc_final: 0.7877 (ptpt) REVERT: C 360 PHE cc_start: 0.7762 (m-80) cc_final: 0.7424 (m-80) REVERT: C 402 GLU cc_start: 0.6947 (tt0) cc_final: 0.6732 (tt0) REVERT: C 696 LYS cc_start: 0.7410 (OUTLIER) cc_final: 0.6750 (tptt) REVERT: C 706 GLU cc_start: 0.6875 (tm-30) cc_final: 0.5931 (mm-30) REVERT: C 748 SER cc_start: 0.6004 (t) cc_final: 0.5773 (p) REVERT: C 757 MET cc_start: 0.6366 (OUTLIER) cc_final: 0.6116 (mmm) REVERT: D 388 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.6953 (mtp) REVERT: D 427 MET cc_start: 0.5728 (mmp) cc_final: 0.5348 (tpt) REVERT: D 442 MET cc_start: 0.3473 (tpt) cc_final: 0.2992 (tpp) REVERT: D 720 MET cc_start: 0.3952 (OUTLIER) cc_final: 0.3726 (ppp) REVERT: D 728 VAL cc_start: 0.6510 (OUTLIER) cc_final: 0.6258 (m) REVERT: E 221 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7393 (pm20) REVERT: E 222 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.7663 (mp) REVERT: E 230 PHE cc_start: 0.7822 (OUTLIER) cc_final: 0.5959 (m-80) REVERT: E 239 ARG cc_start: 0.7098 (mmt-90) cc_final: 0.6805 (mmt90) REVERT: E 657 LEU cc_start: 0.6886 (OUTLIER) cc_final: 0.6642 (mt) REVERT: E 740 MET cc_start: 0.7919 (mmm) cc_final: 0.7666 (mmt) REVERT: F 423 ILE cc_start: 0.8512 (tt) cc_final: 0.8133 (mt) REVERT: F 508 MET cc_start: 0.5950 (ttt) cc_final: 0.5425 (ttt) REVERT: F 531 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8454 (mm) REVERT: F 641 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.7461 (mt0) outliers start: 62 outliers final: 43 residues processed: 397 average time/residue: 0.4767 time to fit residues: 292.8922 Evaluate side-chains 404 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 347 time to evaluate : 3.216 ------------------------------------------------------------------------------- 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 342 ILE 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 599 ARG Chi-restraints excluded: chain A residue 678 MET 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 556 GLU Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 508 MET 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 757 MET Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 312 LYS Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 221 GLU 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 392 ASP 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 670 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 235 VAL 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 531 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 335 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 163 optimal weight: 40.0000 chunk 401 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 116 optimal weight: 8.9990 chunk 81 optimal weight: 20.0000 chunk 319 optimal weight: 0.7980 chunk 311 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 chunk 300 optimal weight: 10.0000 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 317 HIS D 317 HIS D 624 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.172608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.143660 restraints weight = 43837.202| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.33 r_work: 0.3453 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.5818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 32333 Z= 0.187 Angle : 0.689 13.265 43956 Z= 0.341 Chirality : 0.047 0.243 5111 Planarity : 0.005 0.073 5883 Dihedral : 6.482 104.471 4853 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.11 % Favored : 94.86 % Rotamer: Outliers : 2.32 % Allowed : 20.84 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.13), residues: 4440 helix: 0.63 (0.12), residues: 1794 sheet: -0.19 (0.20), residues: 720 loop : -1.23 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 476 HIS 0.010 0.001 HIS D 317 PHE 0.019 0.002 PHE E 230 TYR 0.021 0.002 TYR D 244 ARG 0.009 0.001 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.05049 ( 1462) hydrogen bonds : angle 4.53934 ( 4104) covalent geometry : bond 0.00447 (32333) covalent geometry : angle 0.68894 (43956) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14682.00 seconds wall clock time: 254 minutes 8.90 seconds (15248.90 seconds total)