Starting phenix.real_space_refine on Fri Mar 6 22:31:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rlb_24524/03_2026/7rlb_24524.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rlb_24524/03_2026/7rlb_24524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rlb_24524/03_2026/7rlb_24524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rlb_24524/03_2026/7rlb_24524.map" model { file = "/net/cci-nas-00/data/ceres_data/7rlb_24524/03_2026/7rlb_24524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rlb_24524/03_2026/7rlb_24524.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= -0.001 sd= 0.022 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 180 5.16 5 C 21870 2.51 5 N 6150 2.21 5 O 6660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34884 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5760 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "B" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5760 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "C" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5760 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "D" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5760 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "E" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5760 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "F" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5760 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.61, per 1000 atoms: 0.22 Number of scatterers: 34884 At special positions: 0 Unit cell: (179.488, 175.338, 106.862, 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 180 16.00 P 24 15.00 O 6660 8.00 N 6150 7.00 C 21870 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.67 Conformation dependent library (CDL) restraints added in 1.4 seconds 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8220 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 24 sheets defined 45.7% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 42 through 50 removed outlier: 3.852A pdb=" N MET A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASP A 47 " --> pdb=" O GLN A 43 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 93 Processing helix chain 'A' and resid 130 through 135 Processing helix chain 'A' and resid 202 through 206 removed outlier: 4.059A pdb=" N ILE A 206 " --> pdb=" O TYR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 226 removed outlier: 3.672A pdb=" N GLN A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 216 " --> pdb=" O GLN A 212 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU A 221 " --> pdb=" O LYS A 217 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix removed outlier: 3.679A pdb=" N HIS A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 233 removed outlier: 4.024A pdb=" N LYS A 231 " --> pdb=" O PRO A 227 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU A 232 " --> pdb=" O ALA A 228 " (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 281 through 296 removed outlier: 3.645A pdb=" N ALA A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU A 294 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 334 removed outlier: 3.735A pdb=" N ARG A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE A 324 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.638A pdb=" N ILE A 353 " --> pdb=" O PRO A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.872A pdb=" N ARG A 359 " --> pdb=" O ALA A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 382 removed outlier: 3.807A pdb=" N GLU A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 400 removed outlier: 4.134A pdb=" N VAL A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 428 removed outlier: 3.655A pdb=" N ALA A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A 421 " --> pdb=" O GLU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 444 Processing helix chain 'A' and resid 448 through 459 removed outlier: 3.584A pdb=" N PHE A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 499 removed outlier: 3.885A pdb=" N ARG A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU A 488 " --> pdb=" O ASP A 484 " (cutoff:3.500A) removed outlier: 4.444A 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 507 Processing helix chain 'A' and resid 523 through 535 removed outlier: 3.623A pdb=" N CYS A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 4.306A pdb=" N MET A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TRP A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 569 removed outlier: 3.923A pdb=" N GLU A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE A 562 " --> pdb=" O ASN A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 587 Processing helix chain 'A' and resid 599 through 610 removed outlier: 3.505A pdb=" N GLY A 610 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 649 through 661 removed outlier: 3.808A pdb=" N VAL A 654 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 679 removed outlier: 4.154A pdb=" N LEU A 675 " --> pdb=" O ASP A 671 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A 679 " --> pdb=" O LEU A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 707 removed outlier: 4.309A pdb=" N ILE A 707 " --> pdb=" O ILE A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 740 removed outlier: 3.800A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 743 No H-bonds generated for 'chain 'A' and resid 741 through 743' Processing helix chain 'A' and resid 748 through 764 removed outlier: 3.648A pdb=" N ARG A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS A 754 " --> pdb=" O ASN A 750 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR A 755 " --> pdb=" O ASP A 751 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU A 756 " --> pdb=" O ILE A 752 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE A 758 " --> pdb=" O LYS A 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 50 removed outlier: 3.851A pdb=" N MET B 46 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASP B 47 " --> pdb=" O GLN B 43 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 49 " --> pdb=" O LYS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 93 Processing helix chain 'B' and resid 130 through 135 Processing helix chain 'B' and resid 202 through 206 removed outlier: 4.058A pdb=" N ILE B 206 " --> pdb=" O TYR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 226 removed outlier: 3.672A pdb=" N GLN B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE B 216 " --> pdb=" O GLN B 212 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU B 221 " --> pdb=" O LYS B 217 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix removed outlier: 3.680A pdb=" N HIS B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 233 removed outlier: 4.024A pdb=" N LYS B 231 " --> pdb=" O PRO B 227 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 261 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 281 through 296 removed outlier: 3.645A pdb=" N ALA B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU B 294 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 334 removed outlier: 3.735A pdb=" N ARG B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE B 324 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.638A pdb=" N ILE B 353 " --> pdb=" O PRO B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 removed outlier: 3.872A pdb=" N ARG B 359 " --> pdb=" O ALA B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 382 removed outlier: 3.807A pdb=" N GLU B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 400 removed outlier: 4.134A pdb=" N VAL B 399 " --> pdb=" O ASP B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 428 removed outlier: 3.654A pdb=" N ALA B 412 " --> pdb=" O GLY B 408 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 444 Processing helix chain 'B' and resid 448 through 459 removed outlier: 3.583A pdb=" N PHE B 452 " --> pdb=" O THR B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 499 removed outlier: 3.884A pdb=" N ARG B 487 " --> pdb=" O GLU B 483 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU B 488 " --> pdb=" O ASP B 484 " (cutoff:3.500A) removed outlier: 4.443A 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 507 Processing helix chain 'B' and resid 523 through 535 removed outlier: 3.624A pdb=" N CYS B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 553 removed outlier: 4.306A pdb=" N MET B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TRP B 551 " --> pdb=" O LEU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 569 removed outlier: 3.923A pdb=" N GLU B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE B 562 " --> pdb=" O ASN B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 587 Processing helix chain 'B' and resid 599 through 610 removed outlier: 3.505A pdb=" N GLY B 610 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 630 through 634 Processing helix chain 'B' and resid 649 through 661 removed outlier: 3.808A pdb=" N VAL B 654 " --> pdb=" O GLU B 650 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 679 removed outlier: 4.156A pdb=" N LEU B 675 " --> pdb=" O ASP B 671 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR B 679 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 707 removed outlier: 4.310A pdb=" N ILE B 707 " --> pdb=" O ILE B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 740 removed outlier: 3.800A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 743 No H-bonds generated for 'chain 'B' and resid 741 through 743' Processing helix chain 'B' and resid 748 through 764 removed outlier: 3.648A pdb=" N ARG B 753 " --> pdb=" O ASP B 749 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS B 754 " --> pdb=" O ASN B 750 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR B 755 " --> pdb=" O ASP B 751 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU B 756 " --> pdb=" O ILE B 752 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE B 758 " --> pdb=" O LYS B 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 50 removed outlier: 3.852A pdb=" N MET C 46 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASP C 47 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 93 Processing helix chain 'C' and resid 130 through 135 Processing helix chain 'C' and resid 202 through 206 removed outlier: 4.058A pdb=" N ILE C 206 " --> pdb=" O TYR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 226 removed outlier: 3.672A pdb=" N GLN C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE C 216 " --> pdb=" O GLN C 212 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLU C 221 " --> pdb=" O LYS C 217 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix removed outlier: 3.679A pdb=" N HIS C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 233 removed outlier: 4.025A pdb=" N LYS C 231 " --> pdb=" O PRO C 227 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 281 through 296 removed outlier: 3.645A pdb=" N ALA C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU C 294 " --> pdb=" O PHE C 290 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 334 removed outlier: 3.737A pdb=" N ARG C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE C 324 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.638A pdb=" N ILE C 353 " --> pdb=" O PRO C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 359 removed outlier: 3.872A pdb=" N ARG C 359 " --> pdb=" O ALA C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 382 removed outlier: 3.808A pdb=" N GLU C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 400 removed outlier: 4.134A pdb=" N VAL C 399 " --> pdb=" O ASP C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 428 removed outlier: 3.655A pdb=" N ALA C 412 " --> pdb=" O GLY C 408 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN C 421 " --> pdb=" O GLU C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 444 Processing helix chain 'C' and resid 448 through 459 removed outlier: 3.582A pdb=" N PHE C 452 " --> pdb=" O THR C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 499 removed outlier: 3.885A pdb=" N ARG C 487 " --> pdb=" O GLU C 483 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU C 488 " --> pdb=" O ASP C 484 " (cutoff:3.500A) removed outlier: 4.443A 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 507 Processing helix chain 'C' and resid 523 through 535 removed outlier: 3.624A pdb=" N CYS C 535 " --> pdb=" O ILE C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 553 removed outlier: 4.305A pdb=" N MET C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TRP C 551 " --> pdb=" O LEU C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 569 removed outlier: 3.923A pdb=" N GLU C 561 " --> pdb=" O ALA C 557 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE C 562 " --> pdb=" O ASN C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 587 Processing helix chain 'C' and resid 599 through 610 removed outlier: 3.505A pdb=" N GLY C 610 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 629 Processing helix chain 'C' and resid 630 through 634 Processing helix chain 'C' and resid 649 through 661 removed outlier: 3.807A pdb=" N VAL C 654 " --> pdb=" O GLU C 650 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 679 removed outlier: 4.155A pdb=" N LEU C 675 " --> pdb=" O ASP C 671 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR C 679 " --> pdb=" O LEU C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 707 removed outlier: 4.308A pdb=" N ILE C 707 " --> pdb=" O ILE C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 740 removed outlier: 3.799A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 743 No H-bonds generated for 'chain 'C' and resid 741 through 743' Processing helix chain 'C' and resid 748 through 764 removed outlier: 3.648A pdb=" N ARG C 753 " --> pdb=" O ASP C 749 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS C 754 " --> pdb=" O ASN C 750 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TYR C 755 " --> pdb=" O ASP C 751 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU C 756 " --> pdb=" O ILE C 752 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE C 758 " --> pdb=" O LYS C 754 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 50 removed outlier: 3.852A pdb=" N MET D 46 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASP D 47 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU D 49 " --> pdb=" O LYS D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 93 Processing helix chain 'D' and resid 130 through 135 Processing helix chain 'D' and resid 202 through 206 removed outlier: 4.058A pdb=" N ILE D 206 " --> pdb=" O TYR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 226 removed outlier: 3.672A pdb=" N GLN D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE D 216 " --> pdb=" O GLN D 212 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLU D 221 " --> pdb=" O LYS D 217 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix removed outlier: 3.680A pdb=" N HIS D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 233 removed outlier: 4.024A pdb=" N LYS D 231 " --> pdb=" O PRO D 227 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 281 through 296 removed outlier: 3.647A pdb=" N ALA D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU D 294 " --> pdb=" O PHE D 290 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 334 removed outlier: 3.736A pdb=" N ARG D 322 " --> pdb=" O GLY D 318 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE D 324 " --> pdb=" O VAL D 320 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL D 325 " --> pdb=" O GLU D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.638A pdb=" N ILE D 353 " --> pdb=" O PRO D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 359 removed outlier: 3.871A pdb=" N ARG D 359 " --> pdb=" O ALA D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 382 removed outlier: 3.808A pdb=" N GLU D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN D 382 " --> pdb=" O LEU D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 400 removed outlier: 4.133A pdb=" N VAL D 399 " --> pdb=" O ASP D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 428 removed outlier: 3.655A pdb=" N ALA D 412 " --> pdb=" O GLY D 408 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN D 421 " --> pdb=" O GLU D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 444 Processing helix chain 'D' and resid 448 through 459 removed outlier: 3.582A pdb=" N PHE D 452 " --> pdb=" O THR D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 499 removed outlier: 3.885A pdb=" N ARG D 487 " --> pdb=" O GLU D 483 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU D 488 " --> pdb=" O ASP D 484 " (cutoff:3.500A) removed outlier: 4.444A 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 507 Processing helix chain 'D' and resid 523 through 535 removed outlier: 3.623A pdb=" N CYS D 535 " --> pdb=" O ILE D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 553 removed outlier: 4.307A pdb=" N MET D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TRP D 551 " --> pdb=" O LEU D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 569 removed outlier: 3.923A pdb=" N GLU D 561 " --> pdb=" O ALA D 557 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE D 562 " --> pdb=" O ASN D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 587 Processing helix chain 'D' and resid 599 through 610 removed outlier: 3.505A pdb=" N GLY D 610 " --> pdb=" O THR D 606 " (cutoff:3.500A) 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 661 removed outlier: 3.808A pdb=" N VAL D 654 " --> pdb=" O GLU D 650 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 679 removed outlier: 4.155A pdb=" N LEU D 675 " --> pdb=" O ASP D 671 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR D 679 " --> pdb=" O LEU D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 707 removed outlier: 4.308A pdb=" N ILE D 707 " --> pdb=" O ILE D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 740 removed outlier: 3.799A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 743 No H-bonds generated for 'chain 'D' and resid 741 through 743' Processing helix chain 'D' and resid 748 through 764 removed outlier: 3.648A pdb=" N ARG D 753 " --> pdb=" O ASP D 749 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LYS D 754 " --> pdb=" O ASN D 750 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR D 755 " --> pdb=" O ASP D 751 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU D 756 " --> pdb=" O ILE D 752 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE D 758 " --> pdb=" O LYS D 754 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 50 removed outlier: 3.852A pdb=" N MET E 46 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASP E 47 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU E 49 " --> pdb=" O LYS E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 93 Processing helix chain 'E' and resid 130 through 135 Processing helix chain 'E' and resid 202 through 206 removed outlier: 4.058A pdb=" N ILE E 206 " --> pdb=" O TYR E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 226 removed outlier: 3.671A pdb=" N GLN E 215 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE E 216 " --> pdb=" O GLN E 212 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLU E 221 " --> pdb=" O LYS E 217 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix removed outlier: 3.680A pdb=" N HIS E 226 " --> pdb=" O LEU E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 233 removed outlier: 4.024A pdb=" N LYS E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 261 Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 281 through 296 removed outlier: 3.645A pdb=" N ALA E 293 " --> pdb=" O ALA E 289 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU E 294 " --> pdb=" O PHE E 290 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 334 removed outlier: 3.736A pdb=" N ARG E 322 " --> pdb=" O GLY E 318 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE E 324 " --> pdb=" O VAL E 320 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.638A pdb=" N ILE E 353 " --> pdb=" O PRO E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 359 removed outlier: 3.872A pdb=" N ARG E 359 " --> pdb=" O ALA E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 382 removed outlier: 3.808A pdb=" N GLU E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN E 382 " --> pdb=" O LEU E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 400 removed outlier: 4.134A pdb=" N VAL E 399 " --> pdb=" O ASP E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 428 removed outlier: 3.655A pdb=" N ALA E 412 " --> pdb=" O GLY E 408 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN E 421 " --> pdb=" O GLU E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 444 Processing helix chain 'E' and resid 448 through 459 removed outlier: 3.582A pdb=" N PHE E 452 " --> pdb=" O THR E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 482 through 499 removed outlier: 3.885A pdb=" N ARG E 487 " --> pdb=" O GLU E 483 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU E 488 " --> pdb=" O ASP E 484 " (cutoff:3.500A) removed outlier: 4.443A 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 507 Processing helix chain 'E' and resid 523 through 535 removed outlier: 3.625A pdb=" N CYS E 535 " --> pdb=" O ILE E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 553 removed outlier: 4.306A pdb=" N MET E 550 " --> pdb=" O GLU E 546 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TRP E 551 " --> pdb=" O LEU E 547 " (cutoff:3.500A) Processing helix chain 'E' and resid 557 through 569 removed outlier: 3.922A pdb=" N GLU E 561 " --> pdb=" O ALA E 557 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE E 562 " --> pdb=" O ASN E 558 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 587 Processing helix chain 'E' and resid 599 through 610 removed outlier: 3.505A pdb=" N GLY E 610 " --> pdb=" O THR E 606 " (cutoff:3.500A) Processing helix chain 'E' and resid 625 through 629 Processing helix chain 'E' and resid 630 through 634 Processing helix chain 'E' and resid 649 through 661 removed outlier: 3.808A pdb=" N VAL E 654 " --> pdb=" O GLU E 650 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 671 through 679 removed outlier: 4.155A pdb=" N LEU E 675 " --> pdb=" O ASP E 671 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR E 679 " --> pdb=" O LEU E 675 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 707 removed outlier: 4.309A pdb=" N ILE E 707 " --> pdb=" O ILE E 703 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 740 removed outlier: 3.799A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 741 through 743 No H-bonds generated for 'chain 'E' and resid 741 through 743' Processing helix chain 'E' and resid 748 through 764 removed outlier: 3.647A pdb=" N ARG E 753 " --> pdb=" O ASP E 749 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS E 754 " --> pdb=" O ASN E 750 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N TYR E 755 " --> pdb=" O ASP E 751 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU E 756 " --> pdb=" O ILE E 752 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE E 758 " --> pdb=" O LYS E 754 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 50 removed outlier: 3.852A pdb=" N MET F 46 " --> pdb=" O SER F 42 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASP F 47 " --> pdb=" O GLN F 43 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU F 49 " --> pdb=" O LYS F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 93 Processing helix chain 'F' and resid 130 through 135 Processing helix chain 'F' and resid 202 through 206 removed outlier: 4.058A pdb=" N ILE F 206 " --> pdb=" O TYR F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 226 removed outlier: 3.671A pdb=" N GLN F 215 " --> pdb=" O LYS F 211 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE F 216 " --> pdb=" O GLN F 212 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU F 221 " --> pdb=" O LYS F 217 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix removed outlier: 3.680A pdb=" N HIS F 226 " --> pdb=" O LEU F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 233 removed outlier: 4.024A pdb=" N LYS F 231 " --> pdb=" O PRO F 227 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU F 232 " --> pdb=" O ALA F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 261 Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 281 through 296 removed outlier: 3.646A pdb=" N ALA F 293 " --> pdb=" O ALA F 289 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU F 294 " --> pdb=" O PHE F 290 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN F 296 " --> pdb=" O GLU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 334 removed outlier: 3.736A pdb=" N ARG F 322 " --> pdb=" O GLY F 318 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE F 324 " --> pdb=" O VAL F 320 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL F 325 " --> pdb=" O GLU F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 353 removed outlier: 3.638A pdb=" N ILE F 353 " --> pdb=" O PRO F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 359 removed outlier: 3.872A pdb=" N ARG F 359 " --> pdb=" O ALA F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 382 removed outlier: 3.808A pdb=" N GLU F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN F 382 " --> pdb=" O LEU F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 400 removed outlier: 4.134A pdb=" N VAL F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 428 removed outlier: 3.654A pdb=" N ALA F 412 " --> pdb=" O GLY F 408 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN F 421 " --> pdb=" O GLU F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 444 Processing helix chain 'F' and resid 448 through 459 removed outlier: 3.583A pdb=" N PHE F 452 " --> pdb=" O THR F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 499 removed outlier: 3.885A pdb=" N ARG F 487 " --> pdb=" O GLU F 483 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU F 488 " --> pdb=" O ASP F 484 " (cutoff:3.500A) removed outlier: 4.443A 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 507 Processing helix chain 'F' and resid 523 through 535 removed outlier: 3.624A pdb=" N CYS F 535 " --> pdb=" O ILE F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 553 removed outlier: 4.306A pdb=" N MET F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TRP F 551 " --> pdb=" O LEU F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 569 removed outlier: 3.923A pdb=" N GLU F 561 " --> pdb=" O ALA F 557 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE F 562 " --> pdb=" O ASN F 558 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 587 Processing helix chain 'F' and resid 599 through 610 removed outlier: 3.505A pdb=" N GLY F 610 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 625 through 629 Processing helix chain 'F' and resid 630 through 634 Processing helix chain 'F' and resid 649 through 661 removed outlier: 3.808A pdb=" N VAL F 654 " --> pdb=" O GLU F 650 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 671 through 679 removed outlier: 4.155A pdb=" N LEU F 675 " --> pdb=" O ASP F 671 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR F 679 " --> pdb=" O LEU F 675 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 707 removed outlier: 4.307A pdb=" N ILE F 707 " --> pdb=" O ILE F 703 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 740 removed outlier: 3.800A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 741 through 743 No H-bonds generated for 'chain 'F' and resid 741 through 743' Processing helix chain 'F' and resid 748 through 764 removed outlier: 3.648A pdb=" N ARG F 753 " --> pdb=" O ASP F 749 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LYS F 754 " --> pdb=" O ASN F 750 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TYR F 755 " --> pdb=" O ASP F 751 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU F 756 " --> pdb=" O ILE F 752 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE F 758 " --> pdb=" O LYS F 754 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 40 removed outlier: 5.489A pdb=" N VAL A 39 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N CYS A 69 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL A 57 " --> pdb=" O CYS A 69 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR A 56 " --> pdb=" O CYS A 105 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS A 60 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N SER A 101 " --> pdb=" O LYS A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 269 removed outlier: 6.134A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG A 365 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 389 through 390 removed outlier: 8.172A pdb=" N LYS A 389 " --> pdb=" O VAL A 447 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 539 removed outlier: 6.842A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL A 514 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 643 " --> pdb=" O LEU A 515 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 39 through 40 removed outlier: 5.489A pdb=" N VAL B 39 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N CYS B 69 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL B 57 " --> pdb=" O CYS B 69 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR B 56 " --> pdb=" O CYS B 105 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS B 60 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N SER B 101 " --> pdb=" O LYS B 60 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 265 through 269 removed outlier: 6.136A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG B 365 " --> pdb=" O GLY B 240 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 389 through 390 removed outlier: 8.172A pdb=" N LYS B 389 " --> pdb=" O VAL B 447 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 538 through 539 removed outlier: 6.842A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL B 514 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 643 " --> pdb=" O LEU B 515 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 39 through 40 removed outlier: 5.488A pdb=" N VAL C 39 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N CYS C 69 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL C 57 " --> pdb=" O CYS C 69 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR C 56 " --> pdb=" O CYS C 105 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS C 60 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N SER C 101 " --> pdb=" O LYS C 60 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 265 through 269 removed outlier: 6.134A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG C 365 " --> pdb=" O GLY C 240 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 389 through 390 removed outlier: 8.173A pdb=" N LYS C 389 " --> pdb=" O VAL C 447 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 538 through 539 removed outlier: 6.843A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL C 514 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE C 643 " --> pdb=" O LEU C 515 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 39 through 40 removed outlier: 5.489A pdb=" N VAL D 39 " --> pdb=" O LEU D 72 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N CYS D 69 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL D 57 " --> pdb=" O CYS D 69 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR D 56 " --> pdb=" O CYS D 105 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS D 60 " --> pdb=" O SER D 101 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N SER D 101 " --> pdb=" O LYS D 60 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 265 through 269 removed outlier: 6.134A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG D 365 " --> pdb=" O GLY D 240 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 389 through 390 removed outlier: 8.172A pdb=" N LYS D 389 " --> pdb=" O VAL D 447 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 538 through 539 removed outlier: 6.842A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL D 514 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE D 643 " --> pdb=" O LEU D 515 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 39 through 40 removed outlier: 5.489A pdb=" N VAL E 39 " --> pdb=" O LEU E 72 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N CYS E 69 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL E 57 " --> pdb=" O CYS E 69 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR E 56 " --> pdb=" O CYS E 105 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS E 60 " --> pdb=" O SER E 101 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N SER E 101 " --> pdb=" O LYS E 60 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 265 through 269 removed outlier: 6.133A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG E 365 " --> pdb=" O GLY E 240 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 389 through 390 removed outlier: 8.171A pdb=" N LYS E 389 " --> pdb=" O VAL E 447 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 538 through 539 removed outlier: 6.842A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL E 514 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE E 643 " --> pdb=" O LEU E 515 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 39 through 40 removed outlier: 5.489A pdb=" N VAL F 39 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N CYS F 69 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL F 57 " --> pdb=" O CYS F 69 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR F 56 " --> pdb=" O CYS F 105 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS F 60 " --> pdb=" O SER F 101 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N SER F 101 " --> pdb=" O LYS F 60 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 265 through 269 removed outlier: 6.135A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 389 through 390 removed outlier: 8.172A pdb=" N LYS F 389 " --> pdb=" O VAL F 447 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'F' and resid 538 through 539 removed outlier: 6.842A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL F 514 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE F 643 " --> pdb=" O LEU F 515 " (cutoff:3.500A) 1080 hydrogen bonds defined for protein. 3078 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.74 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11963 1.34 - 1.46: 5602 1.46 - 1.58: 17595 1.58 - 1.69: 36 1.69 - 1.81: 288 Bond restraints: 35484 Sorted by residual: bond pdb=" C4 ADP E1001 " pdb=" C5 ADP E1001 " ideal model delta sigma weight residual 1.490 1.439 0.051 2.00e-02 2.50e+03 6.47e+00 bond pdb=" C4 ADP B1001 " pdb=" C5 ADP B1001 " ideal model delta sigma weight residual 1.490 1.439 0.051 2.00e-02 2.50e+03 6.47e+00 bond pdb=" C4 ADP A1001 " pdb=" C5 ADP A1001 " ideal model delta sigma weight residual 1.490 1.441 0.049 2.00e-02 2.50e+03 6.12e+00 bond pdb=" C4 ADP C1001 " pdb=" C5 ADP C1001 " ideal model delta sigma weight residual 1.490 1.441 0.049 2.00e-02 2.50e+03 6.08e+00 bond pdb=" C4 ADP D1001 " pdb=" C5 ADP D1001 " ideal model delta sigma weight residual 1.490 1.441 0.049 2.00e-02 2.50e+03 5.96e+00 ... (remaining 35479 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 46982 2.21 - 4.42: 787 4.42 - 6.63: 174 6.63 - 8.84: 15 8.84 - 11.05: 18 Bond angle restraints: 47976 Sorted by residual: angle pdb=" CA GLN B 473 " pdb=" CB GLN B 473 " pdb=" CG GLN B 473 " ideal model delta sigma weight residual 114.10 124.78 -10.68 2.00e+00 2.50e-01 2.85e+01 angle pdb=" CA GLN F 473 " pdb=" CB GLN F 473 " pdb=" CG GLN F 473 " ideal model delta sigma weight residual 114.10 124.73 -10.63 2.00e+00 2.50e-01 2.83e+01 angle pdb=" CA GLN D 473 " pdb=" CB GLN D 473 " pdb=" CG GLN D 473 " ideal model delta sigma weight residual 114.10 124.73 -10.63 2.00e+00 2.50e-01 2.83e+01 angle pdb=" CA GLN A 473 " pdb=" CB GLN A 473 " pdb=" CG GLN A 473 " ideal model delta sigma weight residual 114.10 124.72 -10.62 2.00e+00 2.50e-01 2.82e+01 angle pdb=" CA GLN E 473 " pdb=" CB GLN E 473 " pdb=" CG GLN E 473 " ideal model delta sigma weight residual 114.10 124.72 -10.62 2.00e+00 2.50e-01 2.82e+01 ... (remaining 47971 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.21: 21333 32.21 - 64.42: 549 64.42 - 96.63: 48 96.63 - 128.84: 6 128.84 - 161.05: 6 Dihedral angle restraints: 21942 sinusoidal: 9258 harmonic: 12684 Sorted by residual: dihedral pdb=" C5' ADP E1001 " pdb=" O5' ADP E1001 " pdb=" PA ADP E1001 " pdb=" O2A ADP E1001 " ideal model delta sinusoidal sigma weight residual 300.00 138.96 161.05 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" C5' ADP B1001 " pdb=" O5' ADP B1001 " pdb=" PA ADP B1001 " pdb=" O2A ADP B1001 " ideal model delta sinusoidal sigma weight residual 300.00 139.42 160.58 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" C5' ADP D1001 " pdb=" O5' ADP D1001 " pdb=" PA ADP D1001 " pdb=" O2A ADP D1001 " ideal model delta sinusoidal sigma weight residual 300.00 143.97 156.03 1 2.00e+01 2.50e-03 4.59e+01 ... (remaining 21939 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 3393 0.037 - 0.074: 1410 0.074 - 0.111: 487 0.111 - 0.149: 80 0.149 - 0.186: 6 Chirality restraints: 5376 Sorted by residual: chirality pdb=" CG LEU D 381 " pdb=" CB LEU D 381 " pdb=" CD1 LEU D 381 " pdb=" CD2 LEU D 381 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.62e-01 chirality pdb=" CG LEU E 381 " pdb=" CB LEU E 381 " pdb=" CD1 LEU E 381 " pdb=" CD2 LEU E 381 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.35e-01 chirality pdb=" CG LEU B 381 " pdb=" CB LEU B 381 " pdb=" CD1 LEU B 381 " pdb=" CD2 LEU B 381 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.32e-01 ... (remaining 5373 not shown) Planarity restraints: 6306 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 349 " -0.167 9.50e-02 1.11e+02 7.50e-02 3.66e+00 pdb=" NE ARG A 349 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 349 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 349 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 349 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 349 " -0.167 9.50e-02 1.11e+02 7.49e-02 3.66e+00 pdb=" NE ARG E 349 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG E 349 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG E 349 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG E 349 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 349 " -0.166 9.50e-02 1.11e+02 7.45e-02 3.61e+00 pdb=" NE ARG C 349 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG C 349 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG C 349 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 349 " -0.003 2.00e-02 2.50e+03 ... (remaining 6303 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 7809 2.79 - 3.32: 32367 3.32 - 3.84: 55665 3.84 - 4.37: 63522 4.37 - 4.90: 106874 Nonbonded interactions: 266237 Sorted by model distance: nonbonded pdb=" CA GLY E 250 " pdb=" O2A ADP E1001 " model vdw 2.259 3.440 nonbonded pdb=" OG1 THR A 448 " pdb=" OD1 ASP A 450 " model vdw 2.270 3.040 nonbonded pdb=" CA GLY B 250 " pdb=" O2A ADP B1001 " model vdw 2.270 3.440 nonbonded pdb=" OG1 THR B 448 " pdb=" OD1 ASP B 450 " model vdw 2.270 3.040 nonbonded pdb=" OG1 THR D 448 " pdb=" OD1 ASP D 450 " model vdw 2.270 3.040 ... (remaining 266232 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.070 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: 0.050 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 30.400 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 35484 Z= 0.191 Angle : 0.746 11.050 47976 Z= 0.397 Chirality : 0.044 0.186 5376 Planarity : 0.004 0.075 6306 Dihedral : 14.610 161.046 13722 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.76 % Favored : 95.96 % Rotamer: Outliers : 0.03 % Allowed : 0.96 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.12), residues: 4386 helix: -0.80 (0.13), residues: 1620 sheet: 0.43 (0.24), residues: 504 loop : -1.70 (0.12), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 753 TYR 0.015 0.002 TYR D 203 PHE 0.016 0.001 PHE F 516 TRP 0.016 0.002 TRP F 454 HIS 0.006 0.001 HIS E 317 Details of bonding type rmsd covalent geometry : bond 0.00380 (35484) covalent geometry : angle 0.74576 (47976) hydrogen bonds : bond 0.25608 ( 1080) hydrogen bonds : angle 6.85229 ( 3078) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 736 time to evaluate : 1.254 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 301 ILE cc_start: 0.6558 (mt) cc_final: 0.6309 (mt) REVERT: A 330 THR cc_start: 0.7339 (m) cc_final: 0.7109 (p) REVERT: A 354 ASP cc_start: 0.8006 (t0) cc_final: 0.7738 (t0) REVERT: A 508 MET cc_start: 0.6103 (tmm) cc_final: 0.5793 (ttt) REVERT: B 301 ILE cc_start: 0.6185 (mt) cc_final: 0.5955 (mt) REVERT: B 330 THR cc_start: 0.7284 (m) cc_final: 0.7035 (p) REVERT: B 354 ASP cc_start: 0.7946 (t0) cc_final: 0.7342 (t0) REVERT: B 540 ILE cc_start: 0.6678 (mt) cc_final: 0.6328 (mm) REVERT: C 301 ILE cc_start: 0.6114 (mt) cc_final: 0.5848 (mt) REVERT: C 330 THR cc_start: 0.7368 (m) cc_final: 0.7052 (p) REVERT: C 341 VAL cc_start: 0.7006 (p) cc_final: 0.6690 (p) REVERT: D 99 VAL cc_start: 0.8467 (m) cc_final: 0.8135 (p) REVERT: D 301 ILE cc_start: 0.6121 (mt) cc_final: 0.5832 (mt) REVERT: D 330 THR cc_start: 0.7598 (m) cc_final: 0.7291 (p) REVERT: D 540 ILE cc_start: 0.6572 (mt) cc_final: 0.6062 (mm) REVERT: E 301 ILE cc_start: 0.6270 (mt) cc_final: 0.5960 (mt) REVERT: E 330 THR cc_start: 0.7300 (m) cc_final: 0.7063 (p) REVERT: E 354 ASP cc_start: 0.7922 (t0) cc_final: 0.7358 (t0) REVERT: E 540 ILE cc_start: 0.6855 (mt) cc_final: 0.6498 (mm) REVERT: E 558 ASN cc_start: 0.6400 (m-40) cc_final: 0.6173 (m-40) REVERT: F 69 CYS cc_start: 0.8706 (t) cc_final: 0.8497 (m) REVERT: F 99 VAL cc_start: 0.8279 (m) cc_final: 0.8070 (p) REVERT: F 301 ILE cc_start: 0.6393 (mt) cc_final: 0.6034 (mt) REVERT: F 330 THR cc_start: 0.7600 (m) cc_final: 0.7341 (p) REVERT: F 354 ASP cc_start: 0.7922 (t0) cc_final: 0.7623 (t70) outliers start: 1 outliers final: 0 residues processed: 736 average time/residue: 0.2022 time to fit residues: 245.2946 Evaluate side-chains 421 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 421 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.0070 chunk 401 optimal weight: 3.9990 chunk 424 optimal weight: 0.5980 overall best weight: 0.8602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 317 HIS B 36 ASN B 317 HIS C 36 ASN D 36 ASN E 36 ASN E 317 HIS F 36 ASN F 317 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.137301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.097979 restraints weight = 80884.879| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 4.03 r_work: 0.3243 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35484 Z= 0.146 Angle : 0.681 9.073 47976 Z= 0.324 Chirality : 0.047 0.163 5376 Planarity : 0.005 0.060 6306 Dihedral : 7.794 137.130 4920 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.20 % Favored : 95.53 % Rotamer: Outliers : 1.38 % Allowed : 9.80 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.13), residues: 4386 helix: -0.49 (0.13), residues: 1662 sheet: 0.32 (0.25), residues: 486 loop : -1.46 (0.13), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 225 TYR 0.008 0.001 TYR F 244 PHE 0.018 0.002 PHE B 516 TRP 0.023 0.002 TRP A 454 HIS 0.005 0.001 HIS D 499 Details of bonding type rmsd covalent geometry : bond 0.00325 (35484) covalent geometry : angle 0.68082 (47976) hydrogen bonds : bond 0.03945 ( 1080) hydrogen bonds : angle 4.96056 ( 3078) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 478 time to evaluate : 1.320 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 26 LEU cc_start: 0.7044 (tp) cc_final: 0.6672 (tt) REVERT: A 301 ILE cc_start: 0.6916 (mt) cc_final: 0.6687 (mt) REVERT: A 354 ASP cc_start: 0.8458 (t0) cc_final: 0.8197 (t0) REVERT: A 388 MET cc_start: 0.7846 (ppp) cc_final: 0.7421 (ppp) REVERT: A 508 MET cc_start: 0.6398 (tmm) cc_final: 0.6120 (ttt) REVERT: B 99 VAL cc_start: 0.8592 (m) cc_final: 0.8346 (p) REVERT: B 354 ASP cc_start: 0.8490 (t0) cc_final: 0.8228 (t0) REVERT: B 388 MET cc_start: 0.7882 (ppp) cc_final: 0.6952 (ppp) REVERT: B 508 MET cc_start: 0.6278 (ttt) cc_final: 0.6014 (ttt) REVERT: C 84 MET cc_start: 0.8442 (tpp) cc_final: 0.7946 (tpt) REVERT: C 99 VAL cc_start: 0.8576 (m) cc_final: 0.8287 (p) REVERT: C 317 HIS cc_start: 0.8371 (m90) cc_final: 0.7784 (m90) REVERT: C 330 THR cc_start: 0.7609 (m) cc_final: 0.7408 (p) REVERT: C 388 MET cc_start: 0.7815 (ppp) cc_final: 0.7164 (ppp) REVERT: C 546 GLU cc_start: 0.8105 (tt0) cc_final: 0.7898 (tm-30) REVERT: D 26 LEU cc_start: 0.7265 (tp) cc_final: 0.6912 (tt) REVERT: D 84 MET cc_start: 0.8386 (tpt) cc_final: 0.8097 (tpt) REVERT: D 99 VAL cc_start: 0.8444 (m) cc_final: 0.8145 (p) REVERT: D 216 ILE cc_start: 0.8051 (mm) cc_final: 0.7754 (mm) REVERT: D 301 ILE cc_start: 0.6597 (mt) cc_final: 0.6301 (mt) REVERT: D 317 HIS cc_start: 0.8326 (m90) cc_final: 0.7758 (m-70) REVERT: D 330 THR cc_start: 0.7806 (m) cc_final: 0.7594 (p) REVERT: D 388 MET cc_start: 0.7656 (ppp) cc_final: 0.7303 (ppp) REVERT: D 508 MET cc_start: 0.6352 (ttt) cc_final: 0.6077 (ttt) REVERT: E 354 ASP cc_start: 0.8441 (t0) cc_final: 0.8155 (t0) REVERT: E 388 MET cc_start: 0.7980 (ppp) cc_final: 0.6520 (ppp) REVERT: E 508 MET cc_start: 0.6317 (ttt) cc_final: 0.6016 (ttt) REVERT: E 546 GLU cc_start: 0.8079 (tt0) cc_final: 0.7868 (tm-30) REVERT: F 26 LEU cc_start: 0.6727 (tp) cc_final: 0.6395 (tt) REVERT: F 301 ILE cc_start: 0.6791 (mt) cc_final: 0.6503 (mt) REVERT: F 388 MET cc_start: 0.7714 (ppp) cc_final: 0.7330 (ppp) REVERT: F 426 LYS cc_start: 0.7762 (ttmt) cc_final: 0.7338 (tmtt) REVERT: F 546 GLU cc_start: 0.8187 (tt0) cc_final: 0.7964 (tm-30) outliers start: 52 outliers final: 30 residues processed: 507 average time/residue: 0.1973 time to fit residues: 167.4779 Evaluate side-chains 409 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 379 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 550 MET Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 547 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 288 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 chunk 178 optimal weight: 0.0020 chunk 275 optimal weight: 3.9990 chunk 157 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 319 optimal weight: 2.9990 chunk 217 optimal weight: 8.9990 chunk 354 optimal weight: 1.9990 chunk 1 optimal weight: 30.0000 chunk 340 optimal weight: 0.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 HIS A 490 GLN A 558 ASN A 616 ASN B 490 GLN B 558 ASN B 616 ASN C 490 GLN C 558 ASN C 616 ASN D 406 HIS D 490 GLN D 558 ASN D 616 ASN E 490 GLN E 616 ASN F 490 GLN F 616 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.132585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.092687 restraints weight = 78944.296| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 4.26 r_work: 0.3137 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.5224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 35484 Z= 0.201 Angle : 0.700 9.308 47976 Z= 0.344 Chirality : 0.048 0.200 5376 Planarity : 0.005 0.089 6306 Dihedral : 7.481 115.285 4920 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.49 % Favored : 95.37 % Rotamer: Outliers : 2.72 % Allowed : 11.98 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.13), residues: 4386 helix: -0.72 (0.12), residues: 1806 sheet: -0.21 (0.25), residues: 420 loop : -1.33 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 287 TYR 0.018 0.001 TYR E 495 PHE 0.037 0.002 PHE D 516 TRP 0.034 0.003 TRP B 454 HIS 0.005 0.001 HIS F 384 Details of bonding type rmsd covalent geometry : bond 0.00439 (35484) covalent geometry : angle 0.69964 (47976) hydrogen bonds : bond 0.04518 ( 1080) hydrogen bonds : angle 4.61920 ( 3078) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 344 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 ASN cc_start: 0.8639 (m-40) cc_final: 0.8385 (m-40) REVERT: A 388 MET cc_start: 0.8275 (ppp) cc_final: 0.7910 (ppp) REVERT: A 508 MET cc_start: 0.7759 (tmm) cc_final: 0.7136 (ttt) REVERT: A 564 ASP cc_start: 0.8433 (m-30) cc_final: 0.8140 (m-30) REVERT: A 678 MET cc_start: 0.8921 (tpp) cc_final: 0.8696 (tpp) REVERT: B 84 MET cc_start: 0.7866 (tpt) cc_final: 0.7249 (tpt) REVERT: B 388 MET cc_start: 0.8103 (ppp) cc_final: 0.6986 (ppp) REVERT: B 508 MET cc_start: 0.7363 (ttt) cc_final: 0.7133 (ttt) REVERT: C 84 MET cc_start: 0.8303 (tpp) cc_final: 0.8081 (tpt) REVERT: C 241 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.7965 (mt) REVERT: C 317 HIS cc_start: 0.8382 (m90) cc_final: 0.7923 (m-70) REVERT: C 388 MET cc_start: 0.8261 (ppp) cc_final: 0.7751 (ppp) REVERT: C 426 LYS cc_start: 0.8040 (ttmt) cc_final: 0.7634 (tmtt) REVERT: C 547 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8798 (tp) REVERT: D 26 LEU cc_start: 0.7480 (tp) cc_final: 0.7065 (tt) REVERT: D 317 HIS cc_start: 0.8528 (OUTLIER) cc_final: 0.7840 (m-70) REVERT: D 388 MET cc_start: 0.8099 (ppp) cc_final: 0.7763 (ppp) REVERT: D 508 MET cc_start: 0.7580 (ttt) cc_final: 0.7195 (ttt) REVERT: D 560 ARG cc_start: 0.7082 (OUTLIER) cc_final: 0.6774 (mmm-85) REVERT: D 678 MET cc_start: 0.9113 (tpp) cc_final: 0.8897 (tpp) REVERT: E 84 MET cc_start: 0.7509 (tpt) cc_final: 0.6940 (tpp) REVERT: E 317 HIS cc_start: 0.8432 (OUTLIER) cc_final: 0.7758 (m90) REVERT: E 417 GLU cc_start: 0.8262 (pt0) cc_final: 0.8012 (pt0) REVERT: E 508 MET cc_start: 0.7385 (ttt) cc_final: 0.7096 (ttt) REVERT: E 547 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8824 (tp) REVERT: E 564 ASP cc_start: 0.8349 (m-30) cc_final: 0.8068 (m-30) REVERT: F 317 HIS cc_start: 0.7966 (m90) cc_final: 0.7173 (m170) REVERT: F 387 ASN cc_start: 0.8536 (p0) cc_final: 0.8256 (m-40) REVERT: F 388 MET cc_start: 0.8339 (ppp) cc_final: 0.7309 (ppp) REVERT: F 426 LYS cc_start: 0.7871 (ttmt) cc_final: 0.7459 (tmtt) REVERT: F 547 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8915 (tp) REVERT: F 560 ARG cc_start: 0.7092 (mmm-85) cc_final: 0.6694 (mmm-85) REVERT: F 564 ASP cc_start: 0.8390 (m-30) cc_final: 0.7913 (m-30) outliers start: 102 outliers final: 39 residues processed: 415 average time/residue: 0.2019 time to fit residues: 139.9777 Evaluate side-chains 312 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 266 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 317 HIS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 560 ARG Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 317 HIS Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 728 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 226 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 chunk 309 optimal weight: 5.9990 chunk 243 optimal weight: 6.9990 chunk 420 optimal weight: 0.5980 chunk 293 optimal weight: 20.0000 chunk 288 optimal weight: 4.9990 chunk 208 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 356 optimal weight: 5.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 HIS A 735 HIS B 384 HIS B 735 HIS C 384 HIS C 558 ASN C 735 HIS D 384 HIS E 384 HIS E 735 HIS F 36 ASN F 735 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.123246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.077505 restraints weight = 76216.468| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 3.93 r_work: 0.2831 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.7986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.150 35484 Z= 0.311 Angle : 0.780 10.347 47976 Z= 0.386 Chirality : 0.051 0.204 5376 Planarity : 0.006 0.070 6306 Dihedral : 7.904 134.575 4920 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.92 % Favored : 94.94 % Rotamer: Outliers : 2.98 % Allowed : 12.57 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.13), residues: 4386 helix: -0.81 (0.12), residues: 1812 sheet: -0.43 (0.26), residues: 408 loop : -1.20 (0.14), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 210 TYR 0.069 0.002 TYR A 203 PHE 0.035 0.003 PHE D 516 TRP 0.016 0.002 TRP C 454 HIS 0.005 0.001 HIS D 404 Details of bonding type rmsd covalent geometry : bond 0.00723 (35484) covalent geometry : angle 0.77977 (47976) hydrogen bonds : bond 0.04148 ( 1080) hydrogen bonds : angle 4.75488 ( 3078) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 258 time to evaluate : 1.181 Fit side-chains REVERT: A 317 HIS cc_start: 0.8509 (OUTLIER) cc_final: 0.7870 (m90) REVERT: A 388 MET cc_start: 0.8650 (ppp) cc_final: 0.7947 (ptt) REVERT: A 426 LYS cc_start: 0.8194 (ttmt) cc_final: 0.7766 (tmtt) REVERT: A 516 PHE cc_start: 0.9351 (OUTLIER) cc_final: 0.8314 (p90) REVERT: A 580 ASP cc_start: 0.9256 (p0) cc_final: 0.9020 (p0) REVERT: B 317 HIS cc_start: 0.8531 (OUTLIER) cc_final: 0.7741 (m90) REVERT: B 388 MET cc_start: 0.8482 (ppp) cc_final: 0.7543 (ppp) REVERT: B 426 LYS cc_start: 0.8340 (ttmt) cc_final: 0.7948 (tmtt) REVERT: B 516 PHE cc_start: 0.9440 (OUTLIER) cc_final: 0.8819 (p90) REVERT: C 84 MET cc_start: 0.8008 (tpp) cc_final: 0.7550 (tpt) REVERT: C 244 TYR cc_start: 0.8033 (m-80) cc_final: 0.7516 (m-80) REVERT: C 317 HIS cc_start: 0.8593 (OUTLIER) cc_final: 0.8005 (m-70) REVERT: C 388 MET cc_start: 0.8644 (ppp) cc_final: 0.7952 (ppp) REVERT: C 404 HIS cc_start: 0.7619 (OUTLIER) cc_final: 0.7337 (p-80) REVERT: C 426 LYS cc_start: 0.8285 (ttmt) cc_final: 0.7947 (tmtt) REVERT: C 516 PHE cc_start: 0.9360 (OUTLIER) cc_final: 0.8468 (p90) REVERT: D 26 LEU cc_start: 0.7356 (tp) cc_final: 0.6859 (tt) REVERT: D 305 GLU cc_start: 0.7600 (pp20) cc_final: 0.7240 (pp20) REVERT: D 317 HIS cc_start: 0.8629 (m90) cc_final: 0.7981 (m-70) REVERT: D 387 ASN cc_start: 0.9288 (m-40) cc_final: 0.9002 (t0) REVERT: D 388 MET cc_start: 0.8676 (ppp) cc_final: 0.7935 (ptt) REVERT: D 426 LYS cc_start: 0.8242 (ttmt) cc_final: 0.7801 (tmtt) REVERT: D 516 PHE cc_start: 0.9307 (OUTLIER) cc_final: 0.7922 (p90) REVERT: E 84 MET cc_start: 0.7684 (tpt) cc_final: 0.6960 (tpt) REVERT: E 317 HIS cc_start: 0.8642 (OUTLIER) cc_final: 0.8135 (m90) REVERT: E 388 MET cc_start: 0.8590 (ppp) cc_final: 0.8121 (ptt) REVERT: E 426 LYS cc_start: 0.8331 (ttmt) cc_final: 0.7939 (tmtt) REVERT: E 516 PHE cc_start: 0.9408 (OUTLIER) cc_final: 0.8709 (p90) REVERT: F 84 MET cc_start: 0.7968 (tpt) cc_final: 0.7640 (tpt) REVERT: F 317 HIS cc_start: 0.8109 (m90) cc_final: 0.7316 (m-70) REVERT: F 388 MET cc_start: 0.8598 (ppp) cc_final: 0.7591 (ptt) REVERT: F 426 LYS cc_start: 0.8212 (ttmt) cc_final: 0.7826 (tmtt) REVERT: F 516 PHE cc_start: 0.9350 (OUTLIER) cc_final: 0.8564 (p90) REVERT: F 561 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8378 (mp0) outliers start: 112 outliers final: 53 residues processed: 343 average time/residue: 0.1901 time to fit residues: 110.9601 Evaluate side-chains 281 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 216 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 516 PHE Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 516 PHE Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 516 PHE Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 317 HIS Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 516 PHE Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 516 PHE Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 728 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 163 optimal weight: 0.0570 chunk 418 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 305 optimal weight: 9.9990 chunk 28 optimal weight: 0.2980 chunk 77 optimal weight: 10.0000 chunk 297 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 400 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 183 optimal weight: 5.9990 overall best weight: 1.0502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 GLN D 406 HIS E 348 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.124868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.079282 restraints weight = 76058.326| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 3.85 r_work: 0.2878 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.8076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 35484 Z= 0.131 Angle : 0.592 7.644 47976 Z= 0.286 Chirality : 0.046 0.156 5376 Planarity : 0.004 0.057 6306 Dihedral : 7.464 139.459 4920 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.13 % Favored : 95.74 % Rotamer: Outliers : 2.26 % Allowed : 14.27 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.13), residues: 4386 helix: -0.57 (0.12), residues: 1830 sheet: -0.26 (0.26), residues: 414 loop : -1.15 (0.14), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 210 TYR 0.021 0.001 TYR E 203 PHE 0.021 0.001 PHE D 516 TRP 0.009 0.001 TRP B 454 HIS 0.003 0.001 HIS D 384 Details of bonding type rmsd covalent geometry : bond 0.00304 (35484) covalent geometry : angle 0.59171 (47976) hydrogen bonds : bond 0.03263 ( 1080) hydrogen bonds : angle 4.39917 ( 3078) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 242 time to evaluate : 1.283 Fit side-chains REVERT: A 317 HIS cc_start: 0.8501 (OUTLIER) cc_final: 0.7818 (m-70) REVERT: A 388 MET cc_start: 0.8645 (ppp) cc_final: 0.7850 (ptt) REVERT: A 426 LYS cc_start: 0.8197 (ttmt) cc_final: 0.7767 (tmtt) REVERT: A 516 PHE cc_start: 0.9222 (OUTLIER) cc_final: 0.8199 (p90) REVERT: A 561 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8314 (mp0) REVERT: B 317 HIS cc_start: 0.8350 (OUTLIER) cc_final: 0.7544 (m-70) REVERT: B 388 MET cc_start: 0.8350 (ppp) cc_final: 0.7567 (ppp) REVERT: B 426 LYS cc_start: 0.8297 (ttmt) cc_final: 0.7925 (tmtt) REVERT: B 516 PHE cc_start: 0.9211 (OUTLIER) cc_final: 0.8715 (p90) REVERT: C 84 MET cc_start: 0.8169 (tpp) cc_final: 0.7777 (tpt) REVERT: C 244 TYR cc_start: 0.8062 (m-80) cc_final: 0.7526 (m-80) REVERT: C 317 HIS cc_start: 0.8457 (OUTLIER) cc_final: 0.7876 (m-70) REVERT: C 388 MET cc_start: 0.8534 (ppp) cc_final: 0.7838 (ppp) REVERT: C 426 LYS cc_start: 0.8241 (ttmt) cc_final: 0.7913 (tmtt) REVERT: C 516 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.8542 (p90) REVERT: D 26 LEU cc_start: 0.7556 (tp) cc_final: 0.7051 (tt) REVERT: D 305 GLU cc_start: 0.7509 (pp20) cc_final: 0.7185 (pp20) REVERT: D 317 HIS cc_start: 0.8617 (m90) cc_final: 0.7821 (m-70) REVERT: D 388 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.7901 (ptt) REVERT: D 426 LYS cc_start: 0.8274 (ttmt) cc_final: 0.7795 (tmtt) REVERT: E 317 HIS cc_start: 0.8511 (OUTLIER) cc_final: 0.7639 (m-70) REVERT: E 426 LYS cc_start: 0.8320 (ttmt) cc_final: 0.7935 (tmtt) REVERT: E 516 PHE cc_start: 0.9206 (OUTLIER) cc_final: 0.8691 (p90) REVERT: F 84 MET cc_start: 0.7758 (tpt) cc_final: 0.7405 (tpt) REVERT: F 317 HIS cc_start: 0.8012 (m90) cc_final: 0.7073 (m-70) REVERT: F 382 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.7994 (mp-120) REVERT: F 388 MET cc_start: 0.8385 (ppp) cc_final: 0.7705 (ptt) REVERT: F 426 LYS cc_start: 0.8190 (ttmt) cc_final: 0.7793 (tmtt) REVERT: F 516 PHE cc_start: 0.9163 (OUTLIER) cc_final: 0.8714 (p90) outliers start: 85 outliers final: 47 residues processed: 305 average time/residue: 0.1901 time to fit residues: 99.2605 Evaluate side-chains 271 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 212 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 516 PHE Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 516 PHE Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 317 HIS Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 516 PHE Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 382 GLN Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 516 PHE Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 728 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 97 optimal weight: 0.5980 chunk 168 optimal weight: 0.8980 chunk 153 optimal weight: 9.9990 chunk 406 optimal weight: 4.9990 chunk 341 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 72 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 313 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 227 optimal weight: 0.7980 overall best weight: 1.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 624 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.123360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.077553 restraints weight = 76119.178| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 3.86 r_work: 0.2842 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.8530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 35484 Z= 0.167 Angle : 0.597 7.199 47976 Z= 0.290 Chirality : 0.046 0.158 5376 Planarity : 0.004 0.056 6306 Dihedral : 7.375 145.067 4920 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.47 % Favored : 95.39 % Rotamer: Outliers : 2.66 % Allowed : 14.91 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.13), residues: 4386 helix: -0.35 (0.12), residues: 1830 sheet: 0.03 (0.25), residues: 456 loop : -1.11 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 560 TYR 0.014 0.001 TYR F 244 PHE 0.026 0.001 PHE D 516 TRP 0.008 0.001 TRP E 454 HIS 0.004 0.001 HIS A 384 Details of bonding type rmsd covalent geometry : bond 0.00387 (35484) covalent geometry : angle 0.59746 (47976) hydrogen bonds : bond 0.03158 ( 1080) hydrogen bonds : angle 4.26258 ( 3078) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 229 time to evaluate : 1.311 Fit side-chains revert: symmetry clash REVERT: A 69 CYS cc_start: 0.9232 (m) cc_final: 0.8938 (m) REVERT: A 317 HIS cc_start: 0.8415 (OUTLIER) cc_final: 0.7732 (m-70) REVERT: A 388 MET cc_start: 0.8645 (ppp) cc_final: 0.7941 (ptt) REVERT: A 426 LYS cc_start: 0.8294 (ttmt) cc_final: 0.7841 (tmtt) REVERT: A 508 MET cc_start: 0.8700 (tmm) cc_final: 0.8320 (ttt) REVERT: A 516 PHE cc_start: 0.9264 (OUTLIER) cc_final: 0.8340 (p90) REVERT: A 561 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8324 (mp0) REVERT: B 317 HIS cc_start: 0.8280 (OUTLIER) cc_final: 0.7521 (m-70) REVERT: B 388 MET cc_start: 0.8434 (ppp) cc_final: 0.8146 (ptt) REVERT: B 426 LYS cc_start: 0.8362 (ttmt) cc_final: 0.7959 (tmtt) REVERT: B 466 GLU cc_start: 0.7728 (pm20) cc_final: 0.7282 (mp0) REVERT: B 516 PHE cc_start: 0.9198 (OUTLIER) cc_final: 0.8709 (p90) REVERT: C 84 MET cc_start: 0.8192 (tpp) cc_final: 0.7745 (tpt) REVERT: C 317 HIS cc_start: 0.8386 (OUTLIER) cc_final: 0.7860 (m-70) REVERT: C 388 MET cc_start: 0.8612 (ppp) cc_final: 0.7882 (ppp) REVERT: C 426 LYS cc_start: 0.8340 (ttmt) cc_final: 0.8052 (tmtt) REVERT: C 516 PHE cc_start: 0.9159 (OUTLIER) cc_final: 0.8353 (p90) REVERT: D 26 LEU cc_start: 0.7328 (tp) cc_final: 0.6789 (tt) REVERT: D 305 GLU cc_start: 0.7657 (pp20) cc_final: 0.7412 (pp20) REVERT: D 317 HIS cc_start: 0.8393 (m90) cc_final: 0.7799 (m-70) REVERT: D 388 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.7981 (ptt) REVERT: D 426 LYS cc_start: 0.8282 (ttmt) cc_final: 0.7793 (tmtt) REVERT: E 244 TYR cc_start: 0.7948 (m-80) cc_final: 0.7682 (m-80) REVERT: E 317 HIS cc_start: 0.8340 (OUTLIER) cc_final: 0.7581 (m-70) REVERT: E 426 LYS cc_start: 0.8359 (ttmt) cc_final: 0.7982 (tmtt) REVERT: E 516 PHE cc_start: 0.9157 (OUTLIER) cc_final: 0.8655 (p90) REVERT: F 244 TYR cc_start: 0.7697 (m-80) cc_final: 0.7238 (m-80) REVERT: F 317 HIS cc_start: 0.7917 (m90) cc_final: 0.7038 (m-70) REVERT: F 382 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.7909 (mp-120) REVERT: F 388 MET cc_start: 0.8457 (ppp) cc_final: 0.7795 (ptt) REVERT: F 426 LYS cc_start: 0.8190 (ttmt) cc_final: 0.7810 (tmtt) REVERT: F 516 PHE cc_start: 0.9147 (OUTLIER) cc_final: 0.8592 (p90) outliers start: 100 outliers final: 65 residues processed: 307 average time/residue: 0.1835 time to fit residues: 95.9737 Evaluate side-chains 296 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 219 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 516 PHE Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 516 PHE Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 317 HIS Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 516 PHE Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 382 GLN Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 516 PHE Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 728 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 60 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 289 optimal weight: 0.9990 chunk 87 optimal weight: 20.0000 chunk 246 optimal weight: 0.6980 chunk 268 optimal weight: 2.9990 chunk 219 optimal weight: 20.0000 chunk 233 optimal weight: 10.0000 chunk 284 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 13 optimal weight: 20.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 558 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.121673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.075565 restraints weight = 75828.050| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.88 r_work: 0.2803 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.9131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 35484 Z= 0.199 Angle : 0.624 11.145 47976 Z= 0.303 Chirality : 0.047 0.162 5376 Planarity : 0.004 0.060 6306 Dihedral : 7.359 139.185 4920 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.01 % Favored : 95.85 % Rotamer: Outliers : 2.85 % Allowed : 15.23 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.13), residues: 4386 helix: -0.26 (0.12), residues: 1830 sheet: -0.02 (0.25), residues: 456 loop : -1.06 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG E 144 TYR 0.018 0.001 TYR E 138 PHE 0.028 0.001 PHE D 516 TRP 0.008 0.001 TRP E 454 HIS 0.004 0.001 HIS A 384 Details of bonding type rmsd covalent geometry : bond 0.00462 (35484) covalent geometry : angle 0.62418 (47976) hydrogen bonds : bond 0.03270 ( 1080) hydrogen bonds : angle 4.26005 ( 3078) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 240 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 CYS cc_start: 0.9275 (m) cc_final: 0.9049 (m) REVERT: A 317 HIS cc_start: 0.8344 (OUTLIER) cc_final: 0.7764 (m-70) REVERT: A 388 MET cc_start: 0.8584 (ppp) cc_final: 0.8121 (ptt) REVERT: A 426 LYS cc_start: 0.8305 (ttmt) cc_final: 0.7879 (tmtt) REVERT: A 516 PHE cc_start: 0.9257 (OUTLIER) cc_final: 0.8390 (p90) REVERT: B 84 MET cc_start: 0.8064 (tpt) cc_final: 0.7853 (tpt) REVERT: B 317 HIS cc_start: 0.8320 (OUTLIER) cc_final: 0.7561 (m-70) REVERT: B 382 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8230 (mp10) REVERT: B 388 MET cc_start: 0.8428 (ppp) cc_final: 0.8136 (ptt) REVERT: B 426 LYS cc_start: 0.8385 (ttmt) cc_final: 0.8031 (tmtt) REVERT: B 516 PHE cc_start: 0.9280 (OUTLIER) cc_final: 0.8743 (p90) REVERT: C 84 MET cc_start: 0.8189 (tpp) cc_final: 0.7691 (tpt) REVERT: C 317 HIS cc_start: 0.8454 (OUTLIER) cc_final: 0.7884 (m-70) REVERT: C 382 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8084 (mp-120) REVERT: C 388 MET cc_start: 0.8510 (ppp) cc_final: 0.7710 (ptt) REVERT: C 426 LYS cc_start: 0.8406 (ttmt) cc_final: 0.8073 (tmtt) REVERT: C 516 PHE cc_start: 0.9223 (OUTLIER) cc_final: 0.8200 (p90) REVERT: D 26 LEU cc_start: 0.7556 (tp) cc_final: 0.6981 (tt) REVERT: D 84 MET cc_start: 0.8002 (tpt) cc_final: 0.7632 (tpt) REVERT: D 175 ILE cc_start: -0.0803 (OUTLIER) cc_final: -0.1135 (tp) REVERT: D 317 HIS cc_start: 0.8460 (OUTLIER) cc_final: 0.7896 (m-70) REVERT: D 388 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8234 (ptt) REVERT: D 426 LYS cc_start: 0.8326 (ttmt) cc_final: 0.7931 (tmtt) REVERT: D 516 PHE cc_start: 0.9289 (OUTLIER) cc_final: 0.8036 (p90) REVERT: E 84 MET cc_start: 0.7596 (tpt) cc_final: 0.7135 (tpt) REVERT: E 244 TYR cc_start: 0.8096 (m-80) cc_final: 0.7721 (m-80) REVERT: E 317 HIS cc_start: 0.8347 (OUTLIER) cc_final: 0.7567 (m-70) REVERT: E 382 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.8268 (mp10) REVERT: E 426 LYS cc_start: 0.8430 (ttmt) cc_final: 0.8031 (tmtt) REVERT: E 516 PHE cc_start: 0.9234 (OUTLIER) cc_final: 0.8670 (p90) REVERT: E 561 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8282 (mp0) REVERT: F 26 LEU cc_start: 0.7424 (tp) cc_final: 0.6882 (tt) REVERT: F 317 HIS cc_start: 0.7935 (m90) cc_final: 0.7039 (m-70) REVERT: F 382 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8086 (mp-120) REVERT: F 388 MET cc_start: 0.8437 (ppp) cc_final: 0.7824 (ptt) REVERT: F 426 LYS cc_start: 0.8375 (ttmt) cc_final: 0.7987 (tmtt) REVERT: F 516 PHE cc_start: 0.9209 (OUTLIER) cc_final: 0.8512 (p90) outliers start: 107 outliers final: 71 residues processed: 324 average time/residue: 0.1875 time to fit residues: 104.9066 Evaluate side-chains 315 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 226 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 382 GLN Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 516 PHE Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 382 GLN Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 516 PHE Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 317 HIS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 516 PHE Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 317 HIS Chi-restraints excluded: chain E residue 321 GLU Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 382 GLN Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 516 PHE Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 382 GLN Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 516 PHE Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 647 LEU Chi-restraints excluded: chain F residue 728 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 394 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 407 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 160 optimal weight: 30.0000 chunk 66 optimal weight: 0.8980 chunk 73 optimal weight: 20.0000 chunk 86 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 558 ASN ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 735 HIS E 490 GLN E 494 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.120057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.074211 restraints weight = 74461.618| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.79 r_work: 0.2746 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.9590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 35484 Z= 0.242 Angle : 0.668 11.084 47976 Z= 0.326 Chirality : 0.048 0.197 5376 Planarity : 0.005 0.064 6306 Dihedral : 7.558 146.505 4920 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.24 % Favored : 95.62 % Rotamer: Outliers : 2.90 % Allowed : 15.89 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.13), residues: 4386 helix: -0.25 (0.12), residues: 1830 sheet: -0.08 (0.24), residues: 474 loop : -1.03 (0.14), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 144 TYR 0.023 0.002 TYR A 244 PHE 0.028 0.002 PHE D 516 TRP 0.009 0.001 TRP E 454 HIS 0.006 0.001 HIS C 384 Details of bonding type rmsd covalent geometry : bond 0.00561 (35484) covalent geometry : angle 0.66762 (47976) hydrogen bonds : bond 0.03456 ( 1080) hydrogen bonds : angle 4.32155 ( 3078) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 223 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.7712 (tp) cc_final: 0.7279 (tt) REVERT: A 69 CYS cc_start: 0.9258 (m) cc_final: 0.9041 (m) REVERT: A 317 HIS cc_start: 0.8442 (OUTLIER) cc_final: 0.7845 (m-70) REVERT: A 388 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8274 (ptt) REVERT: A 426 LYS cc_start: 0.8447 (ttmt) cc_final: 0.8005 (tmtt) REVERT: A 516 PHE cc_start: 0.9297 (OUTLIER) cc_final: 0.8391 (p90) REVERT: A 580 ASP cc_start: 0.9208 (p0) cc_final: 0.8948 (p0) REVERT: B 84 MET cc_start: 0.7882 (tpt) cc_final: 0.7648 (tpt) REVERT: B 317 HIS cc_start: 0.8487 (OUTLIER) cc_final: 0.7642 (m-70) REVERT: B 382 GLN cc_start: 0.9153 (OUTLIER) cc_final: 0.8251 (mp10) REVERT: B 388 MET cc_start: 0.8438 (ppp) cc_final: 0.8165 (ptt) REVERT: B 426 LYS cc_start: 0.8425 (ttmt) cc_final: 0.8024 (tmtt) REVERT: B 516 PHE cc_start: 0.9313 (OUTLIER) cc_final: 0.8701 (p90) REVERT: C 317 HIS cc_start: 0.8568 (OUTLIER) cc_final: 0.7924 (m-70) REVERT: C 332 MET cc_start: 0.8806 (ttp) cc_final: 0.8526 (tpp) REVERT: C 382 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8016 (mp-120) REVERT: C 388 MET cc_start: 0.8563 (ppp) cc_final: 0.7831 (ptt) REVERT: C 404 HIS cc_start: 0.7533 (OUTLIER) cc_final: 0.7322 (p-80) REVERT: C 426 LYS cc_start: 0.8454 (ttmt) cc_final: 0.8085 (tmtt) REVERT: C 516 PHE cc_start: 0.9254 (OUTLIER) cc_final: 0.8229 (p90) REVERT: D 26 LEU cc_start: 0.7552 (tp) cc_final: 0.6989 (tt) REVERT: D 84 MET cc_start: 0.7697 (tpt) cc_final: 0.7309 (tpt) REVERT: D 175 ILE cc_start: 0.0308 (OUTLIER) cc_final: -0.0099 (tp) REVERT: D 305 GLU cc_start: 0.7677 (pp20) cc_final: 0.7402 (pp20) REVERT: D 317 HIS cc_start: 0.8573 (OUTLIER) cc_final: 0.7933 (m-70) REVERT: D 388 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8336 (ptt) REVERT: D 426 LYS cc_start: 0.8461 (ttmt) cc_final: 0.8075 (tmtt) REVERT: D 516 PHE cc_start: 0.9312 (OUTLIER) cc_final: 0.7965 (p90) REVERT: E 244 TYR cc_start: 0.8252 (m-80) cc_final: 0.7912 (m-80) REVERT: E 273 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8252 (pm20) REVERT: E 317 HIS cc_start: 0.8431 (OUTLIER) cc_final: 0.7579 (m-70) REVERT: E 382 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8308 (mp10) REVERT: E 516 PHE cc_start: 0.9277 (OUTLIER) cc_final: 0.8649 (p90) REVERT: E 561 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8391 (mp0) REVERT: F 26 LEU cc_start: 0.7335 (tp) cc_final: 0.6745 (tt) REVERT: F 317 HIS cc_start: 0.8020 (m90) cc_final: 0.7101 (m-70) REVERT: F 382 GLN cc_start: 0.9124 (OUTLIER) cc_final: 0.8094 (mp-120) REVERT: F 388 MET cc_start: 0.8489 (ppp) cc_final: 0.7987 (ptt) REVERT: F 426 LYS cc_start: 0.8455 (ttmt) cc_final: 0.8057 (tmtt) REVERT: F 516 PHE cc_start: 0.9224 (OUTLIER) cc_final: 0.8434 (p90) outliers start: 109 outliers final: 77 residues processed: 307 average time/residue: 0.1921 time to fit residues: 101.5138 Evaluate side-chains 311 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 213 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 382 GLN Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 516 PHE Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 382 GLN Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 516 PHE Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 317 HIS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 516 PHE Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain E residue 277 LYS Chi-restraints excluded: chain E residue 317 HIS Chi-restraints excluded: chain E residue 321 GLU Chi-restraints excluded: chain E residue 382 GLN Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 516 PHE Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 382 GLN Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 516 PHE Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 647 LEU Chi-restraints excluded: chain F residue 728 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 400 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 188 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 436 optimal weight: 4.9990 chunk 21 optimal weight: 0.0870 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 533 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.121211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.076241 restraints weight = 73959.020| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 4.00 r_work: 0.2779 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.9720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 35484 Z= 0.160 Angle : 0.615 10.946 47976 Z= 0.296 Chirality : 0.046 0.211 5376 Planarity : 0.004 0.054 6306 Dihedral : 7.361 141.310 4920 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.76 % Favored : 96.10 % Rotamer: Outliers : 2.58 % Allowed : 16.32 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.13), residues: 4386 helix: -0.15 (0.12), residues: 1836 sheet: -0.11 (0.25), residues: 414 loop : -0.90 (0.14), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 377 TYR 0.020 0.001 TYR B 138 PHE 0.032 0.001 PHE B 771 TRP 0.008 0.001 TRP E 454 HIS 0.004 0.001 HIS A 384 Details of bonding type rmsd covalent geometry : bond 0.00374 (35484) covalent geometry : angle 0.61472 (47976) hydrogen bonds : bond 0.03076 ( 1080) hydrogen bonds : angle 4.22377 ( 3078) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 223 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.7742 (tp) cc_final: 0.7326 (tt) REVERT: A 69 CYS cc_start: 0.9313 (m) cc_final: 0.9065 (m) REVERT: A 317 HIS cc_start: 0.8348 (OUTLIER) cc_final: 0.7805 (m-70) REVERT: A 388 MET cc_start: 0.8642 (ppp) cc_final: 0.8326 (ptt) REVERT: A 516 PHE cc_start: 0.9214 (OUTLIER) cc_final: 0.8308 (p90) REVERT: A 580 ASP cc_start: 0.9161 (p0) cc_final: 0.8917 (p0) REVERT: B 84 MET cc_start: 0.8066 (tpt) cc_final: 0.7804 (tpt) REVERT: B 317 HIS cc_start: 0.8406 (OUTLIER) cc_final: 0.7631 (m-70) REVERT: B 382 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.8276 (mp10) REVERT: B 388 MET cc_start: 0.8468 (ppp) cc_final: 0.8218 (ptt) REVERT: B 516 PHE cc_start: 0.9203 (OUTLIER) cc_final: 0.8644 (p90) REVERT: B 614 LYS cc_start: 0.8695 (mttm) cc_final: 0.8399 (mmmt) REVERT: C 84 MET cc_start: 0.7875 (tpt) cc_final: 0.7513 (tpt) REVERT: C 317 HIS cc_start: 0.8468 (OUTLIER) cc_final: 0.7873 (m-70) REVERT: C 332 MET cc_start: 0.8715 (ttp) cc_final: 0.8505 (tpp) REVERT: C 382 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8043 (mp-120) REVERT: C 388 MET cc_start: 0.8544 (ppp) cc_final: 0.8163 (ptt) REVERT: C 426 LYS cc_start: 0.8452 (ttmt) cc_final: 0.8067 (tmtt) REVERT: C 449 MET cc_start: 0.8648 (tpp) cc_final: 0.8375 (tpp) REVERT: C 516 PHE cc_start: 0.9159 (OUTLIER) cc_final: 0.8349 (p90) REVERT: D 26 LEU cc_start: 0.7501 (tp) cc_final: 0.6921 (tt) REVERT: D 175 ILE cc_start: 0.0526 (OUTLIER) cc_final: 0.0110 (tp) REVERT: D 305 GLU cc_start: 0.7633 (pp20) cc_final: 0.7337 (pp20) REVERT: D 317 HIS cc_start: 0.8490 (m90) cc_final: 0.7902 (m-70) REVERT: D 388 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8387 (ptt) REVERT: D 426 LYS cc_start: 0.8460 (ttmt) cc_final: 0.8064 (tmtt) REVERT: D 516 PHE cc_start: 0.9232 (OUTLIER) cc_final: 0.7962 (p90) REVERT: E 84 MET cc_start: 0.8004 (tpt) cc_final: 0.7682 (tpt) REVERT: E 244 TYR cc_start: 0.8226 (m-80) cc_final: 0.7892 (m-80) REVERT: E 273 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8231 (pm20) REVERT: E 317 HIS cc_start: 0.8382 (OUTLIER) cc_final: 0.7638 (m-70) REVERT: E 382 GLN cc_start: 0.9184 (OUTLIER) cc_final: 0.8332 (mp10) REVERT: E 516 PHE cc_start: 0.9167 (OUTLIER) cc_final: 0.8673 (p90) REVERT: E 561 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8363 (mp0) REVERT: F 26 LEU cc_start: 0.7441 (tp) cc_final: 0.6861 (tt) REVERT: F 317 HIS cc_start: 0.7950 (m170) cc_final: 0.6996 (m-70) REVERT: F 382 GLN cc_start: 0.9110 (OUTLIER) cc_final: 0.8105 (mp-120) REVERT: F 388 MET cc_start: 0.8513 (ppp) cc_final: 0.7982 (ptt) REVERT: F 426 LYS cc_start: 0.8479 (ttmt) cc_final: 0.8051 (tmtt) REVERT: F 516 PHE cc_start: 0.9132 (OUTLIER) cc_final: 0.8470 (p90) outliers start: 97 outliers final: 68 residues processed: 301 average time/residue: 0.1885 time to fit residues: 97.9864 Evaluate side-chains 296 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 210 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 382 GLN Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 516 PHE Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 382 GLN Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 516 PHE Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 516 PHE Chi-restraints excluded: chain D residue 533 ASN Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain E residue 277 LYS Chi-restraints excluded: chain E residue 317 HIS Chi-restraints excluded: chain E residue 321 GLU Chi-restraints excluded: chain E residue 382 GLN Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 516 PHE Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 382 GLN Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 516 PHE Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 728 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 183 optimal weight: 0.4980 chunk 129 optimal weight: 0.7980 chunk 310 optimal weight: 4.9990 chunk 78 optimal weight: 30.0000 chunk 222 optimal weight: 1.9990 chunk 385 optimal weight: 1.9990 chunk 320 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 338 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.121119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.075920 restraints weight = 75457.579| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.92 r_work: 0.2786 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.9802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 35484 Z= 0.151 Angle : 0.620 11.197 47976 Z= 0.297 Chirality : 0.046 0.222 5376 Planarity : 0.004 0.056 6306 Dihedral : 7.311 140.336 4920 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.20 % Favored : 95.67 % Rotamer: Outliers : 2.48 % Allowed : 16.43 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.13), residues: 4386 helix: -0.09 (0.12), residues: 1836 sheet: -0.06 (0.25), residues: 414 loop : -0.87 (0.14), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 338 TYR 0.023 0.001 TYR A 203 PHE 0.023 0.001 PHE B 771 TRP 0.008 0.001 TRP F 454 HIS 0.004 0.001 HIS A 384 Details of bonding type rmsd covalent geometry : bond 0.00354 (35484) covalent geometry : angle 0.61977 (47976) hydrogen bonds : bond 0.03020 ( 1080) hydrogen bonds : angle 4.19542 ( 3078) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 217 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.7714 (tp) cc_final: 0.7290 (tt) REVERT: A 69 CYS cc_start: 0.9246 (m) cc_final: 0.9018 (m) REVERT: A 317 HIS cc_start: 0.8292 (OUTLIER) cc_final: 0.7780 (m-70) REVERT: A 388 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8247 (ptt) REVERT: A 426 LYS cc_start: 0.8404 (ttmt) cc_final: 0.7942 (tmtt) REVERT: A 516 PHE cc_start: 0.9199 (OUTLIER) cc_final: 0.8358 (p90) REVERT: A 580 ASP cc_start: 0.9176 (p0) cc_final: 0.8932 (p0) REVERT: B 317 HIS cc_start: 0.8411 (OUTLIER) cc_final: 0.7657 (m-70) REVERT: B 382 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.8295 (mp10) REVERT: B 388 MET cc_start: 0.8415 (ppp) cc_final: 0.8188 (ptt) REVERT: B 516 PHE cc_start: 0.9185 (OUTLIER) cc_final: 0.8687 (p90) REVERT: C 317 HIS cc_start: 0.8453 (OUTLIER) cc_final: 0.7818 (m-70) REVERT: C 332 MET cc_start: 0.8746 (ttp) cc_final: 0.8538 (tpp) REVERT: C 382 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8000 (mp-120) REVERT: C 388 MET cc_start: 0.8547 (ppp) cc_final: 0.8131 (ptt) REVERT: C 426 LYS cc_start: 0.8486 (ttmt) cc_final: 0.8090 (tmtt) REVERT: C 516 PHE cc_start: 0.9144 (OUTLIER) cc_final: 0.8312 (p90) REVERT: D 26 LEU cc_start: 0.7524 (tp) cc_final: 0.6948 (tt) REVERT: D 175 ILE cc_start: 0.0643 (OUTLIER) cc_final: 0.0317 (tp) REVERT: D 305 GLU cc_start: 0.7601 (pp20) cc_final: 0.7299 (pp20) REVERT: D 317 HIS cc_start: 0.8501 (OUTLIER) cc_final: 0.7877 (m-70) REVERT: D 388 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8394 (ptt) REVERT: D 516 PHE cc_start: 0.9213 (OUTLIER) cc_final: 0.7901 (p90) REVERT: E 84 MET cc_start: 0.7913 (tpt) cc_final: 0.7711 (tpt) REVERT: E 244 TYR cc_start: 0.8213 (m-80) cc_final: 0.7810 (m-80) REVERT: E 273 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8190 (pm20) REVERT: E 317 HIS cc_start: 0.8315 (OUTLIER) cc_final: 0.7612 (m-70) REVERT: E 382 GLN cc_start: 0.9186 (OUTLIER) cc_final: 0.8330 (mp10) REVERT: E 516 PHE cc_start: 0.9142 (OUTLIER) cc_final: 0.8608 (p90) REVERT: E 561 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8382 (mp0) REVERT: F 26 LEU cc_start: 0.7357 (tp) cc_final: 0.6765 (tt) REVERT: F 84 MET cc_start: 0.7185 (tpt) cc_final: 0.6948 (tpt) REVERT: F 317 HIS cc_start: 0.7990 (m170) cc_final: 0.7029 (m-70) REVERT: F 382 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8045 (mp-120) REVERT: F 388 MET cc_start: 0.8503 (ppp) cc_final: 0.7950 (ptt) REVERT: F 426 LYS cc_start: 0.8461 (ttmt) cc_final: 0.8044 (tmtt) REVERT: F 516 PHE cc_start: 0.9102 (OUTLIER) cc_final: 0.8413 (p90) REVERT: F 614 LYS cc_start: 0.8676 (mttm) cc_final: 0.8371 (mmmt) outliers start: 93 outliers final: 65 residues processed: 292 average time/residue: 0.1898 time to fit residues: 95.1201 Evaluate side-chains 289 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 204 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 382 GLN Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 516 PHE Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 382 GLN Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 516 PHE Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 317 HIS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 516 PHE Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain E residue 277 LYS Chi-restraints excluded: chain E residue 317 HIS Chi-restraints excluded: chain E residue 321 GLU Chi-restraints excluded: chain E residue 382 GLN Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 516 PHE Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 382 GLN Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 516 PHE Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 728 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 96 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 269 optimal weight: 3.9990 chunk 409 optimal weight: 0.9980 chunk 283 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 288 optimal weight: 0.9980 chunk 332 optimal weight: 9.9990 chunk 142 optimal weight: 1.9990 chunk 422 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 533 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.121141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.076176 restraints weight = 75411.996| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.93 r_work: 0.2804 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.9907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 35484 Z= 0.145 Angle : 0.612 11.258 47976 Z= 0.292 Chirality : 0.046 0.219 5376 Planarity : 0.004 0.054 6306 Dihedral : 7.237 137.754 4920 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.76 % Favored : 96.10 % Rotamer: Outliers : 2.61 % Allowed : 16.19 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.13), residues: 4386 helix: -0.04 (0.12), residues: 1836 sheet: 0.02 (0.25), residues: 426 loop : -0.84 (0.14), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 338 TYR 0.016 0.001 TYR F 244 PHE 0.042 0.001 PHE B 674 TRP 0.014 0.001 TRP F 454 HIS 0.003 0.001 HIS C 384 Details of bonding type rmsd covalent geometry : bond 0.00340 (35484) covalent geometry : angle 0.61246 (47976) hydrogen bonds : bond 0.02982 ( 1080) hydrogen bonds : angle 4.16290 ( 3078) =============================================================================== Job complete usr+sys time: 8649.87 seconds wall clock time: 148 minutes 30.90 seconds (8910.90 seconds total)