Starting phenix.real_space_refine on Wed Jun 18 06:27:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ari_43783/06_2025/9ari_43783.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ari_43783/06_2025/9ari_43783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ari_43783/06_2025/9ari_43783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ari_43783/06_2025/9ari_43783.map" model { file = "/net/cci-nas-00/data/ceres_data/9ari_43783/06_2025/9ari_43783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ari_43783/06_2025/9ari_43783.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 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: 4 Type Number sf(0) Gaussians S 88 5.16 5 C 13348 2.51 5 N 3454 2.21 5 O 3866 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20756 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 801, 5296 Classifications: {'peptide': 801} Incomplete info: {'truncation_to_alanine': 251} Link IDs: {'PTRANS': 36, 'TRANS': 764} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1059 Unresolved non-hydrogen angles: 1295 Unresolved non-hydrogen dihedrals: 890 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 25, 'ASP:plan': 24, 'TYR:plan': 9, 'ASN:plan1': 24, 'TRP:plan': 1, 'HIS:plan': 11, 'PHE:plan': 5, 'GLU:plan': 41, 'ARG:plan': 36} Unresolved non-hydrogen planarities: 745 Chain: "B" Number of atoms: 5072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 5072 Classifications: {'peptide': 787} Incomplete info: {'truncation_to_alanine': 277} Link IDs: {'PTRANS': 28, 'TRANS': 758} Chain breaks: 2 Unresolved non-hydrogen bonds: 1194 Unresolved non-hydrogen angles: 1481 Unresolved non-hydrogen dihedrals: 1034 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 18, 'ASP:plan': 36, 'TYR:plan': 17, 'ASN:plan1': 18, 'TRP:plan': 4, 'HIS:plan': 8, 'PHE:plan': 16, 'GLU:plan': 46, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 809 Chain: "C" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 801, 5296 Classifications: {'peptide': 801} Incomplete info: {'truncation_to_alanine': 251} Link IDs: {'PTRANS': 36, 'TRANS': 764} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1059 Unresolved non-hydrogen angles: 1295 Unresolved non-hydrogen dihedrals: 890 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 25, 'ASP:plan': 24, 'TYR:plan': 9, 'ASN:plan1': 24, 'TRP:plan': 1, 'HIS:plan': 11, 'PHE:plan': 5, 'GLU:plan': 41, 'ARG:plan': 36} Unresolved non-hydrogen planarities: 745 Chain: "D" Number of atoms: 5072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 5072 Classifications: {'peptide': 787} Incomplete info: {'truncation_to_alanine': 277} Link IDs: {'PTRANS': 28, 'TRANS': 758} Chain breaks: 2 Unresolved non-hydrogen bonds: 1194 Unresolved non-hydrogen angles: 1481 Unresolved non-hydrogen dihedrals: 1034 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 18, 'ASP:plan': 36, 'TYR:plan': 17, 'ASN:plan1': 18, 'TRP:plan': 4, 'HIS:plan': 8, 'PHE:plan': 16, 'GLU:plan': 46, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 809 Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 12.73, per 1000 atoms: 0.61 Number of scatterers: 20756 At special positions: 0 Unit cell: (146.59, 129.47, 180.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 88 16.00 O 3866 8.00 N 3454 7.00 C 13348 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS A 457 " - pdb=" SG CYS A 476 " distance=2.75 Simple disulfide: pdb=" SG CYS A 765 " - pdb=" SG CYS A 819 " distance=2.03 Simple disulfide: pdb=" SG CYS A 831 " - pdb=" SG CYS D 557 " distance=1.96 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.02 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 557 " - pdb=" SG CYS C 831 " distance=1.67 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 329 " distance=2.03 Simple disulfide: pdb=" SG CYS C 441 " - pdb=" SG CYS C 475 " distance=2.03 Simple disulfide: pdb=" SG CYS C 457 " - pdb=" SG CYS C 476 " distance=2.75 Simple disulfide: pdb=" SG CYS C 765 " - pdb=" SG CYS C 819 " distance=2.03 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " distance=2.03 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: 5.45 Conformation dependent library (CDL) restraints added in 3.1 seconds 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5936 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 34 sheets defined 42.9% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.85 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 70 through 83 Processing helix chain 'A' and resid 103 through 113 removed outlier: 4.269A pdb=" N VAL A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 129 removed outlier: 3.793A pdb=" N TYR A 128 " --> pdb=" O ARG A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 156 removed outlier: 4.071A pdb=" N GLN A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 Processing helix chain 'A' and resid 225 through 234 removed outlier: 3.720A pdb=" N GLU A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 260 Processing helix chain 'A' and resid 272 through 275 removed outlier: 3.567A pdb=" N ILE A 275 " --> pdb=" O GLU A 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 272 through 275' Processing helix chain 'A' and resid 276 through 281 Processing helix chain 'A' and resid 297 through 317 Processing helix chain 'A' and resid 337 through 349 removed outlier: 3.906A pdb=" N LEU A 341 " --> pdb=" O LYS A 337 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER A 349 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 492 Processing helix chain 'A' and resid 521 through 529 removed outlier: 3.640A pdb=" N GLY A 529 " --> pdb=" O GLU A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 605 removed outlier: 3.711A pdb=" N SER A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 634 Processing helix chain 'A' and resid 647 through 676 removed outlier: 3.715A pdb=" N MET A 655 " --> pdb=" O ARG A 651 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP A 657 " --> pdb=" O LEU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 695 removed outlier: 3.572A pdb=" N ARG A 694 " --> pdb=" O ASP A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 717 removed outlier: 3.798A pdb=" N GLN A 717 " --> pdb=" O TYR A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 729 removed outlier: 3.571A pdb=" N THR A 722 " --> pdb=" O VAL A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 744 Processing helix chain 'A' and resid 754 through 762 Processing helix chain 'A' and resid 787 through 803 removed outlier: 4.038A pdb=" N GLN A 791 " --> pdb=" O SER A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 814 Processing helix chain 'A' and resid 834 through 862 removed outlier: 4.145A pdb=" N PHE A 853 " --> pdb=" O ILE A 849 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A 862 " --> pdb=" O TYR A 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 57 removed outlier: 4.290A pdb=" N GLU B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 removed outlier: 3.546A pdb=" N ARG B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 119 Processing helix chain 'B' and resid 149 through 164 Processing helix chain 'B' and resid 178 through 191 Processing helix chain 'B' and resid 209 through 222 Processing helix chain 'B' and resid 233 through 248 Processing helix chain 'B' and resid 259 through 264 Processing helix chain 'B' and resid 288 through 311 Processing helix chain 'B' and resid 324 through 330 Processing helix chain 'B' and resid 334 through 340 removed outlier: 4.107A pdb=" N TYR B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 472 Processing helix chain 'B' and resid 495 through 503 Processing helix chain 'B' and resid 516 through 523 removed outlier: 4.312A pdb=" N VAL B 522 " --> pdb=" O GLU B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 580 removed outlier: 3.621A pdb=" N TRP B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR B 579 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 614 Processing helix chain 'B' and resid 625 through 656 removed outlier: 3.826A pdb=" N GLN B 656 " --> pdb=" O ALA B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 699 Processing helix chain 'B' and resid 700 through 709 Processing helix chain 'B' and resid 713 through 723 Processing helix chain 'B' and resid 733 through 743 Processing helix chain 'B' and resid 772 through 786 Processing helix chain 'B' and resid 787 through 797 removed outlier: 3.675A pdb=" N GLU B 791 " --> pdb=" O GLY B 787 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA B 794 " --> pdb=" O GLU B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 844 removed outlier: 3.513A pdb=" N TRP B 844 " --> pdb=" O HIS B 840 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 50 Processing helix chain 'C' and resid 70 through 85 removed outlier: 3.738A pdb=" N SER C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 113 removed outlier: 4.268A pdb=" N VAL C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 129 removed outlier: 3.793A pdb=" N TYR C 128 " --> pdb=" O ARG C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 156 removed outlier: 4.071A pdb=" N GLN C 147 " --> pdb=" O PRO C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 185 Processing helix chain 'C' and resid 225 through 234 removed outlier: 3.720A pdb=" N GLU C 231 " --> pdb=" O ALA C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 260 Processing helix chain 'C' and resid 272 through 275 removed outlier: 3.566A pdb=" N ILE C 275 " --> pdb=" O GLU C 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 272 through 275' Processing helix chain 'C' and resid 276 through 281 Processing helix chain 'C' and resid 297 through 317 Processing helix chain 'C' and resid 337 through 349 removed outlier: 3.906A pdb=" N LEU C 341 " --> pdb=" O LYS C 337 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER C 349 " --> pdb=" O VAL C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 492 Processing helix chain 'C' and resid 521 through 529 removed outlier: 3.640A pdb=" N GLY C 529 " --> pdb=" O GLU C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 605 removed outlier: 3.710A pdb=" N SER C 605 " --> pdb=" O LEU C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 634 Processing helix chain 'C' and resid 647 through 676 removed outlier: 3.715A pdb=" N MET C 655 " --> pdb=" O ARG C 651 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP C 657 " --> pdb=" O LEU C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 695 removed outlier: 3.572A pdb=" N ARG C 694 " --> pdb=" O ASP C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 717 removed outlier: 3.799A pdb=" N GLN C 717 " --> pdb=" O TYR C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 718 through 729 removed outlier: 3.571A pdb=" N THR C 722 " --> pdb=" O VAL C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 744 Processing helix chain 'C' and resid 754 through 762 Processing helix chain 'C' and resid 787 through 803 removed outlier: 4.037A pdb=" N GLN C 791 " --> pdb=" O SER C 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 814 Processing helix chain 'C' and resid 834 through 862 removed outlier: 4.145A pdb=" N PHE C 853 " --> pdb=" O ILE C 849 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS C 862 " --> pdb=" O TYR C 858 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 57 removed outlier: 4.290A pdb=" N GLU D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 92 removed outlier: 3.545A pdb=" N ARG D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 119 Processing helix chain 'D' and resid 149 through 164 Processing helix chain 'D' and resid 178 through 191 Processing helix chain 'D' and resid 209 through 222 Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 259 through 264 Processing helix chain 'D' and resid 288 through 311 Processing helix chain 'D' and resid 324 through 330 Processing helix chain 'D' and resid 334 through 340 removed outlier: 4.108A pdb=" N TYR D 338 " --> pdb=" O MET D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 472 Processing helix chain 'D' and resid 495 through 503 Processing helix chain 'D' and resid 516 through 523 removed outlier: 4.312A pdb=" N VAL D 522 " --> pdb=" O GLU D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 580 removed outlier: 3.621A pdb=" N TRP D 559 " --> pdb=" O SER D 555 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR D 579 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 614 Processing helix chain 'D' and resid 625 through 656 removed outlier: 3.825A pdb=" N GLN D 656 " --> pdb=" O ALA D 652 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 699 Processing helix chain 'D' and resid 700 through 709 Processing helix chain 'D' and resid 713 through 723 Processing helix chain 'D' and resid 733 through 743 Processing helix chain 'D' and resid 772 through 786 Processing helix chain 'D' and resid 787 through 797 removed outlier: 3.675A pdb=" N GLU D 791 " --> pdb=" O GLY D 787 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA D 794 " --> pdb=" O GLU D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 819 through 844 removed outlier: 3.513A pdb=" N TRP D 844 " --> pdb=" O HIS D 840 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 33 Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 92 removed outlier: 6.423A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 138 " --> pdb=" O VAL A 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 164 through 166 removed outlier: 3.634A pdb=" N LEU A 242 " --> pdb=" O LEU A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 292 removed outlier: 6.925A pdb=" N ASN A 376 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLN A 384 " --> pdb=" O ASN A 376 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A 394 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN A 389 " --> pdb=" O HIS A 392 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 360 through 361 removed outlier: 3.778A pdb=" N GLU A 360 " --> pdb=" O LYS A 368 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 421 through 422 removed outlier: 3.755A pdb=" N VAL A 422 " --> pdb=" O MET A 533 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET A 783 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU A 549 " --> pdb=" O MET A 783 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 431 through 433 Processing sheet with id=AA8, first strand: chain 'A' and resid 702 through 703 removed outlier: 7.022A pdb=" N ALA A 703 " --> pdb=" O ILE A 751 " (cutoff:3.500A) removed outlier: 9.628A pdb=" N ASP A 753 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE A 750 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 562 " --> pdb=" O PHE A 750 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TRP A 752 " --> pdb=" O THR A 560 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR A 560 " --> pdb=" O TRP A 752 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 69 removed outlier: 7.328A pdb=" N MET B 73 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU B 41 " --> pdb=" O MET B 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 66 through 69 removed outlier: 7.461A pdb=" N GLY B 36 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N VAL B 97 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ALA B 38 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N PHE B 99 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE B 40 " --> pdb=" O PHE B 99 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LEU B 124 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL B 97 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE B 144 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 198 through 205 removed outlier: 8.346A pdb=" N PHE B 169 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 9.521A pdb=" N LEU B 203 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE B 171 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N LEU B 205 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N THR B 173 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE B 227 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE B 228 " --> pdb=" O ILE B 257 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 278 through 281 removed outlier: 6.854A pdb=" N ILE B 364 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL B 376 " --> pdb=" O ILE B 364 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 379 through 380 Processing sheet with id=AB5, first strand: chain 'B' and resid 405 through 408 Processing sheet with id=AB6, first strand: chain 'B' and resid 434 through 438 removed outlier: 3.736A pdb=" N VAL B 434 " --> pdb=" O CYS B 457 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS B 455 " --> pdb=" O CYS B 436 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS B 438 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE B 453 " --> pdb=" O LYS B 438 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 508 through 509 removed outlier: 3.603A pdb=" N ALA B 509 " --> pdb=" O ALA B 765 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 730 through 732 removed outlier: 3.624A pdb=" N TYR B 731 " --> pdb=" O SER B 535 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 26 through 33 Processing sheet with id=AC1, first strand: chain 'C' and resid 90 through 92 removed outlier: 6.423A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU C 138 " --> pdb=" O VAL C 118 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 164 through 166 removed outlier: 3.633A pdb=" N LEU C 242 " --> pdb=" O LEU C 269 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 290 through 292 removed outlier: 6.925A pdb=" N ASN C 376 " --> pdb=" O GLN C 384 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLN C 384 " --> pdb=" O ASN C 376 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE C 394 " --> pdb=" O ILE C 387 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN C 389 " --> pdb=" O HIS C 392 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 360 through 361 removed outlier: 3.779A pdb=" N GLU C 360 " --> pdb=" O LYS C 368 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 421 through 422 removed outlier: 3.755A pdb=" N VAL C 422 " --> pdb=" O MET C 533 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET C 783 " --> pdb=" O GLU C 549 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU C 549 " --> pdb=" O MET C 783 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 431 through 433 Processing sheet with id=AC7, first strand: chain 'C' and resid 702 through 703 removed outlier: 7.022A pdb=" N ALA C 703 " --> pdb=" O ILE C 751 " (cutoff:3.500A) removed outlier: 9.628A pdb=" N ASP C 753 " --> pdb=" O ALA C 703 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE C 750 " --> pdb=" O LEU C 562 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU C 562 " --> pdb=" O PHE C 750 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TRP C 752 " --> pdb=" O THR C 560 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR C 560 " --> pdb=" O TRP C 752 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 66 through 69 removed outlier: 7.328A pdb=" N MET D 73 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU D 41 " --> pdb=" O MET D 73 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 66 through 69 removed outlier: 7.461A pdb=" N GLY D 36 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N VAL D 97 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ALA D 38 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N PHE D 99 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE D 40 " --> pdb=" O PHE D 99 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N LEU D 124 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL D 97 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE D 144 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 198 through 205 removed outlier: 8.346A pdb=" N PHE D 169 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 9.521A pdb=" N LEU D 203 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE D 171 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N LEU D 205 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR D 173 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE D 227 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE D 228 " --> pdb=" O ILE D 257 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 278 through 281 removed outlier: 6.855A pdb=" N ILE D 364 " --> pdb=" O VAL D 376 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL D 376 " --> pdb=" O ILE D 364 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 379 through 380 Processing sheet with id=AD4, first strand: chain 'D' and resid 405 through 408 Processing sheet with id=AD5, first strand: chain 'D' and resid 434 through 438 removed outlier: 3.736A pdb=" N VAL D 434 " --> pdb=" O CYS D 457 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS D 455 " --> pdb=" O CYS D 436 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS D 438 " --> pdb=" O ILE D 453 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE D 453 " --> pdb=" O LYS D 438 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 508 through 509 removed outlier: 3.603A pdb=" N ALA D 509 " --> pdb=" O ALA D 765 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 730 through 732 removed outlier: 3.624A pdb=" N TYR D 731 " --> pdb=" O SER D 535 " (cutoff:3.500A) 1044 hydrogen bonds defined for protein. 3048 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.39 Time building geometry restraints manager: 6.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 3398 1.25 - 1.39: 4826 1.39 - 1.54: 12337 1.54 - 1.68: 459 1.68 - 1.82: 136 Bond restraints: 21156 Sorted by residual: bond pdb=" C THR C 669 " pdb=" O THR C 669 " ideal model delta sigma weight residual 1.236 1.110 0.126 1.26e-02 6.30e+03 1.00e+02 bond pdb=" C THR A 669 " pdb=" O THR A 669 " ideal model delta sigma weight residual 1.236 1.111 0.126 1.26e-02 6.30e+03 9.96e+01 bond pdb=" C ASN A 671 " pdb=" O ASN A 671 " ideal model delta sigma weight residual 1.236 1.124 0.113 1.15e-02 7.56e+03 9.62e+01 bond pdb=" C ASN C 671 " pdb=" O ASN C 671 " ideal model delta sigma weight residual 1.236 1.124 0.113 1.15e-02 7.56e+03 9.60e+01 bond pdb=" C ALA C 670 " pdb=" O ALA C 670 " ideal model delta sigma weight residual 1.236 1.132 0.105 1.15e-02 7.56e+03 8.27e+01 ... (remaining 21151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.72: 28848 4.72 - 9.44: 301 9.44 - 14.16: 38 14.16 - 18.89: 7 18.89 - 23.61: 2 Bond angle restraints: 29196 Sorted by residual: angle pdb=" C PHE A 479 " pdb=" CA PHE A 479 " pdb=" CB PHE A 479 " ideal model delta sigma weight residual 110.88 87.27 23.61 1.57e+00 4.06e-01 2.26e+02 angle pdb=" C PHE C 479 " pdb=" CA PHE C 479 " pdb=" CB PHE C 479 " ideal model delta sigma weight residual 110.88 87.29 23.59 1.57e+00 4.06e-01 2.26e+02 angle pdb=" C LEU C 635 " pdb=" N LEU C 636 " pdb=" CA LEU C 636 " ideal model delta sigma weight residual 122.95 106.94 16.01 1.66e+00 3.63e-01 9.30e+01 angle pdb=" N ILE C 797 " pdb=" CA ILE C 797 " pdb=" CB ILE C 797 " ideal model delta sigma weight residual 110.54 123.10 -12.56 1.36e+00 5.41e-01 8.53e+01 angle pdb=" N ILE A 797 " pdb=" CA ILE A 797 " pdb=" CB ILE A 797 " ideal model delta sigma weight residual 110.54 123.09 -12.55 1.36e+00 5.41e-01 8.52e+01 ... (remaining 29191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.34: 11482 14.34 - 28.68: 531 28.68 - 43.02: 205 43.02 - 57.35: 52 57.35 - 71.69: 8 Dihedral angle restraints: 12278 sinusoidal: 3120 harmonic: 9158 Sorted by residual: dihedral pdb=" C PHE A 479 " pdb=" N PHE A 479 " pdb=" CA PHE A 479 " pdb=" CB PHE A 479 " ideal model delta harmonic sigma weight residual -122.60 -93.55 -29.05 0 2.50e+00 1.60e-01 1.35e+02 dihedral pdb=" C PHE C 479 " pdb=" N PHE C 479 " pdb=" CA PHE C 479 " pdb=" CB PHE C 479 " ideal model delta harmonic sigma weight residual -122.60 -93.59 -29.01 0 2.50e+00 1.60e-01 1.35e+02 dihedral pdb=" C ASN B 615 " pdb=" N ASN B 615 " pdb=" CA ASN B 615 " pdb=" CB ASN B 615 " ideal model delta harmonic sigma weight residual -122.60 -150.52 27.92 0 2.50e+00 1.60e-01 1.25e+02 ... (remaining 12275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.225: 3707 0.225 - 0.450: 59 0.450 - 0.675: 10 0.675 - 0.900: 4 0.900 - 1.125: 2 Chirality restraints: 3782 Sorted by residual: chirality pdb=" CA ASN B 615 " pdb=" N ASN B 615 " pdb=" C ASN B 615 " pdb=" CB ASN B 615 " both_signs ideal model delta sigma weight residual False 2.51 1.39 1.13 2.00e-01 2.50e+01 3.16e+01 chirality pdb=" CA ASN D 615 " pdb=" N ASN D 615 " pdb=" C ASN D 615 " pdb=" CB ASN D 615 " both_signs ideal model delta sigma weight residual False 2.51 1.39 1.12 2.00e-01 2.50e+01 3.16e+01 chirality pdb=" CA PHE C 675 " pdb=" N PHE C 675 " pdb=" C PHE C 675 " pdb=" CB PHE C 675 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.24e+01 ... (remaining 3779 not shown) Planarity restraints: 3706 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 830 " 0.029 2.00e-02 2.50e+03 6.07e-02 3.68e+01 pdb=" C THR C 830 " -0.105 2.00e-02 2.50e+03 pdb=" O THR C 830 " 0.040 2.00e-02 2.50e+03 pdb=" N CYS C 831 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 830 " 0.029 2.00e-02 2.50e+03 6.04e-02 3.65e+01 pdb=" C THR A 830 " -0.104 2.00e-02 2.50e+03 pdb=" O THR A 830 " 0.040 2.00e-02 2.50e+03 pdb=" N CYS A 831 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 616 " -0.027 2.00e-02 2.50e+03 5.76e-02 3.32e+01 pdb=" C ASN B 616 " 0.100 2.00e-02 2.50e+03 pdb=" O ASN B 616 " -0.039 2.00e-02 2.50e+03 pdb=" N SER B 617 " -0.034 2.00e-02 2.50e+03 ... (remaining 3703 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 67 2.43 - 3.05: 14056 3.05 - 3.67: 30282 3.67 - 4.28: 39833 4.28 - 4.90: 65322 Nonbonded interactions: 149560 Sorted by model distance: nonbonded pdb=" O LEU D 513 " pdb=" CG2 THR D 514 " model vdw 1.816 3.460 nonbonded pdb=" O LEU B 513 " pdb=" CG2 THR B 514 " model vdw 1.816 3.460 nonbonded pdb=" O GLY A 459 " pdb=" N ASN A 461 " model vdw 1.891 3.120 nonbonded pdb=" O GLY C 459 " pdb=" N ASN C 461 " model vdw 1.891 3.120 nonbonded pdb=" OG SER A 638 " pdb=" N GLY A 639 " model vdw 1.961 3.120 ... (remaining 149555 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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 group one per residue 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: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.820 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 49.310 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.100 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:3.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 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 : 0.010 0.721 21174 Z= 0.610 Angle : 1.161 29.798 29232 Z= 0.754 Chirality : 0.075 1.125 3782 Planarity : 0.007 0.063 3706 Dihedral : 10.705 71.692 6288 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.86 % Favored : 92.88 % Rotamer: Outliers : 9.33 % Allowed : 8.80 % Favored : 81.87 % Cbeta Deviations : 1.52 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.13), residues: 3148 helix: -0.70 (0.13), residues: 1350 sheet: -3.15 (0.21), residues: 414 loop : -3.47 (0.14), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP C 632 HIS 0.006 0.001 HIS A 801 PHE 0.039 0.002 PHE A 429 TYR 0.022 0.001 TYR D 843 ARG 0.007 0.001 ARG C 651 Details of bonding type rmsd hydrogen bonds : bond 0.15092 ( 1036) hydrogen bonds : angle 6.74552 ( 3048) SS BOND : bond 0.25578 ( 18) SS BOND : angle 8.47346 ( 36) covalent geometry : bond 0.00690 (21156) covalent geometry : angle 1.12312 (29196) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 430 time to evaluate : 2.129 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 546 GLN cc_start: 0.8359 (mm-40) cc_final: 0.7952 (pp30) REVERT: A 597 MET cc_start: 0.8061 (ttt) cc_final: 0.7525 (ttm) REVERT: A 783 MET cc_start: 0.7913 (tpp) cc_final: 0.7591 (tpp) REVERT: A 801 HIS cc_start: 0.9323 (OUTLIER) cc_final: 0.8852 (t-90) REVERT: B 184 ASN cc_start: 0.8790 (m110) cc_final: 0.8587 (m-40) REVERT: B 232 CYS cc_start: 0.6404 (t) cc_final: 0.5849 (t) REVERT: B 467 LYS cc_start: 0.8577 (mmmt) cc_final: 0.8231 (mptt) REVERT: B 480 LEU cc_start: 0.7577 (tp) cc_final: 0.7241 (tt) REVERT: B 782 GLN cc_start: 0.8326 (pp30) cc_final: 0.8054 (tm-30) REVERT: C 546 GLN cc_start: 0.8553 (mm-40) cc_final: 0.7882 (pp30) REVERT: C 801 HIS cc_start: 0.9303 (OUTLIER) cc_final: 0.8455 (t-90) REVERT: D 467 LYS cc_start: 0.8627 (mmmt) cc_final: 0.8002 (mmtm) REVERT: D 782 GLN cc_start: 0.8435 (pp30) cc_final: 0.8090 (tm-30) REVERT: D 795 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9247 (tp) outliers start: 159 outliers final: 68 residues processed: 568 average time/residue: 0.2499 time to fit residues: 233.5366 Evaluate side-chains 365 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 294 time to evaluate : 2.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 431 TYR Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 475 CYS Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 565 LYS Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 831 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 475 CYS Chi-restraints excluded: chain C residue 493 PHE Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 632 TRP Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 794 SER Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 813 TRP Chi-restraints excluded: chain C residue 831 CYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 824 MET Chi-restraints excluded: chain D residue 834 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 266 optimal weight: 20.0000 chunk 239 optimal weight: 50.0000 chunk 132 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 161 optimal weight: 20.0000 chunk 127 optimal weight: 0.7980 chunk 247 optimal weight: 50.0000 chunk 95 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 184 optimal weight: 5.9990 chunk 286 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 498 HIS A 577 GLN A 792 GLN B 357 GLN B 615 ASN B 710 ASN B 775 GLN C 159 ASN C 498 HIS C 577 GLN C 748 HIS C 792 GLN D 357 GLN D 615 ASN D 710 ASN D 775 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.179344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.145588 restraints weight = 43945.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.136057 restraints weight = 57013.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.133871 restraints weight = 44107.929| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21174 Z= 0.129 Angle : 0.602 7.532 29232 Z= 0.314 Chirality : 0.043 0.222 3782 Planarity : 0.004 0.052 3706 Dihedral : 7.073 75.254 3365 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 7.04 % Allowed : 16.20 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.14), residues: 3148 helix: 0.44 (0.14), residues: 1336 sheet: -2.70 (0.22), residues: 422 loop : -2.93 (0.15), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 494 HIS 0.005 0.001 HIS B 486 PHE 0.032 0.002 PHE A 575 TYR 0.018 0.001 TYR C 599 ARG 0.008 0.001 ARG C 743 Details of bonding type rmsd hydrogen bonds : bond 0.03789 ( 1036) hydrogen bonds : angle 4.73616 ( 3048) SS BOND : bond 0.00900 ( 18) SS BOND : angle 0.98683 ( 36) covalent geometry : bond 0.00287 (21156) covalent geometry : angle 0.60131 (29196) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 318 time to evaluate : 2.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 569 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7950 (ttm-80) REVERT: A 775 PHE cc_start: 0.7830 (t80) cc_final: 0.7603 (t80) REVERT: A 801 HIS cc_start: 0.9007 (OUTLIER) cc_final: 0.8334 (t-90) REVERT: B 186 ILE cc_start: 0.9175 (pt) cc_final: 0.8874 (tp) REVERT: B 232 CYS cc_start: 0.6268 (t) cc_final: 0.5613 (t) REVERT: B 240 ILE cc_start: 0.8204 (tp) cc_final: 0.7948 (mt) REVERT: B 357 GLN cc_start: 0.7263 (mt0) cc_final: 0.6301 (pp30) REVERT: B 429 CYS cc_start: 0.4694 (OUTLIER) cc_final: 0.4315 (t) REVERT: B 467 LYS cc_start: 0.8658 (mmmt) cc_final: 0.8232 (mptt) REVERT: B 476 TYR cc_start: 0.7992 (p90) cc_final: 0.7562 (p90) REVERT: B 782 GLN cc_start: 0.8456 (pp30) cc_final: 0.8232 (tm-30) REVERT: C 797 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.7687 (pt) REVERT: C 801 HIS cc_start: 0.8893 (OUTLIER) cc_final: 0.8166 (t-90) REVERT: D 99 PHE cc_start: 0.6273 (t80) cc_final: 0.5963 (t80) REVERT: D 433 THR cc_start: 0.8339 (OUTLIER) cc_final: 0.8065 (t) REVERT: D 467 LYS cc_start: 0.8609 (mmmt) cc_final: 0.8232 (mptt) REVERT: D 709 PHE cc_start: 0.7489 (OUTLIER) cc_final: 0.7270 (t80) REVERT: D 795 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9291 (tp) outliers start: 120 outliers final: 62 residues processed: 414 average time/residue: 0.2486 time to fit residues: 171.3120 Evaluate side-chains 350 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 280 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 569 ARG Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 714 PHE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 632 TRP Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 813 TRP Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 709 PHE Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 841 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 283 optimal weight: 7.9990 chunk 255 optimal weight: 20.0000 chunk 118 optimal weight: 8.9990 chunk 284 optimal weight: 4.9990 chunk 173 optimal weight: 0.0980 chunk 125 optimal weight: 3.9990 chunk 186 optimal weight: 0.0020 chunk 55 optimal weight: 3.9990 chunk 83 optimal weight: 30.0000 chunk 171 optimal weight: 5.9990 chunk 1 optimal weight: 30.0000 overall best weight: 2.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 703 HIS C 748 HIS D 697 ASN D 703 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.173578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.141485 restraints weight = 43408.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.135930 restraints weight = 58151.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.135104 restraints weight = 67657.722| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 21174 Z= 0.226 Angle : 0.663 8.356 29232 Z= 0.350 Chirality : 0.046 0.265 3782 Planarity : 0.004 0.057 3706 Dihedral : 6.477 73.880 3308 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.69 % Favored : 92.28 % Rotamer: Outliers : 7.63 % Allowed : 17.19 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.15), residues: 3148 helix: 0.62 (0.14), residues: 1326 sheet: -2.47 (0.23), residues: 420 loop : -2.73 (0.15), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 559 HIS 0.006 0.001 HIS B 486 PHE 0.036 0.002 PHE A 579 TYR 0.013 0.001 TYR C 668 ARG 0.004 0.001 ARG C 743 Details of bonding type rmsd hydrogen bonds : bond 0.04611 ( 1036) hydrogen bonds : angle 4.72407 ( 3048) SS BOND : bond 0.00450 ( 18) SS BOND : angle 0.73994 ( 36) covalent geometry : bond 0.00535 (21156) covalent geometry : angle 0.66325 (29196) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 277 time to evaluate : 2.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.7402 (pt) cc_final: 0.7119 (tp) REVERT: A 797 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.7700 (pt) REVERT: A 801 HIS cc_start: 0.8996 (OUTLIER) cc_final: 0.8353 (t-90) REVERT: B 186 ILE cc_start: 0.8929 (pt) cc_final: 0.8580 (tp) REVERT: B 240 ILE cc_start: 0.7798 (tp) cc_final: 0.7546 (mt) REVERT: B 467 LYS cc_start: 0.8724 (mmmt) cc_final: 0.8259 (mptt) REVERT: C 91 LEU cc_start: 0.7523 (pt) cc_final: 0.7094 (tp) REVERT: C 797 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.7684 (pt) REVERT: C 801 HIS cc_start: 0.8962 (OUTLIER) cc_final: 0.8299 (t-90) REVERT: D 99 PHE cc_start: 0.5845 (t80) cc_final: 0.5395 (t80) REVERT: D 357 GLN cc_start: 0.7785 (mt0) cc_final: 0.7365 (pp30) REVERT: D 433 THR cc_start: 0.8330 (OUTLIER) cc_final: 0.8063 (t) REVERT: D 739 MET cc_start: 0.6968 (mtt) cc_final: 0.6764 (mtt) REVERT: D 795 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9223 (tt) outliers start: 130 outliers final: 92 residues processed: 382 average time/residue: 0.2781 time to fit residues: 177.9048 Evaluate side-chains 354 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 256 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 714 PHE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 632 TRP Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 813 TRP Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 824 MET Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 841 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 24 optimal weight: 0.9990 chunk 106 optimal weight: 7.9990 chunk 158 optimal weight: 60.0000 chunk 134 optimal weight: 0.4980 chunk 272 optimal weight: 20.0000 chunk 214 optimal weight: 0.9990 chunk 303 optimal weight: 2.9990 chunk 242 optimal weight: 1.9990 chunk 239 optimal weight: 30.0000 chunk 69 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 ASN B 697 ASN D 184 ASN D 697 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.175383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.145189 restraints weight = 44085.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.138795 restraints weight = 48920.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.133813 restraints weight = 54519.832| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21174 Z= 0.148 Angle : 0.593 7.450 29232 Z= 0.308 Chirality : 0.043 0.202 3782 Planarity : 0.004 0.049 3706 Dihedral : 6.249 71.692 3304 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 7.81 % Allowed : 18.02 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.15), residues: 3148 helix: 0.90 (0.14), residues: 1334 sheet: -2.35 (0.23), residues: 428 loop : -2.57 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 197 HIS 0.004 0.001 HIS B 486 PHE 0.024 0.002 PHE A 579 TYR 0.010 0.001 TYR A 599 ARG 0.003 0.000 ARG C 743 Details of bonding type rmsd hydrogen bonds : bond 0.03883 ( 1036) hydrogen bonds : angle 4.38629 ( 3048) SS BOND : bond 0.00401 ( 18) SS BOND : angle 0.70608 ( 36) covalent geometry : bond 0.00341 (21156) covalent geometry : angle 0.59324 (29196) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 276 time to evaluate : 2.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.7581 (pt) cc_final: 0.7217 (tp) REVERT: A 783 MET cc_start: 0.8724 (tpp) cc_final: 0.8470 (tpt) REVERT: A 797 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8074 (tt) REVERT: A 801 HIS cc_start: 0.8973 (OUTLIER) cc_final: 0.8322 (t-90) REVERT: A 806 MET cc_start: 0.9187 (mmt) cc_final: 0.8902 (mpp) REVERT: B 186 ILE cc_start: 0.8969 (pt) cc_final: 0.8641 (tp) REVERT: B 240 ILE cc_start: 0.7875 (tp) cc_final: 0.7616 (mt) REVERT: B 433 THR cc_start: 0.8289 (OUTLIER) cc_final: 0.8022 (t) REVERT: B 467 LYS cc_start: 0.8672 (mmmt) cc_final: 0.8140 (mmtm) REVERT: C 91 LEU cc_start: 0.7668 (pt) cc_final: 0.7338 (tp) REVERT: C 783 MET cc_start: 0.8170 (tpp) cc_final: 0.7734 (ttm) REVERT: C 801 HIS cc_start: 0.8905 (OUTLIER) cc_final: 0.8232 (t-90) REVERT: D 99 PHE cc_start: 0.6123 (t80) cc_final: 0.5734 (t80) REVERT: D 357 GLN cc_start: 0.7713 (mt0) cc_final: 0.7357 (pp30) REVERT: D 433 THR cc_start: 0.8252 (OUTLIER) cc_final: 0.7986 (t) REVERT: D 467 LYS cc_start: 0.8771 (mmmt) cc_final: 0.8250 (mptt) REVERT: D 795 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9184 (tt) outliers start: 133 outliers final: 86 residues processed: 387 average time/residue: 0.2712 time to fit residues: 173.5465 Evaluate side-chains 353 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 261 time to evaluate : 2.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 632 TRP Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 813 TRP Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 697 ASN Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 841 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 68 optimal weight: 3.9990 chunk 21 optimal weight: 30.0000 chunk 237 optimal weight: 10.0000 chunk 138 optimal weight: 0.0670 chunk 45 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 286 optimal weight: 2.9990 chunk 33 optimal weight: 40.0000 chunk 279 optimal weight: 3.9990 chunk 216 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 overall best weight: 1.1520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 697 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.178547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.149232 restraints weight = 45375.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.144079 restraints weight = 57010.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.141921 restraints weight = 56636.981| |-----------------------------------------------------------------------------| r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21174 Z= 0.129 Angle : 0.587 9.921 29232 Z= 0.299 Chirality : 0.043 0.183 3782 Planarity : 0.004 0.046 3706 Dihedral : 5.891 66.255 3298 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 7.75 % Allowed : 19.07 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.15), residues: 3148 helix: 1.11 (0.14), residues: 1326 sheet: -2.22 (0.23), residues: 428 loop : -2.41 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 197 HIS 0.003 0.001 HIS B 486 PHE 0.021 0.001 PHE A 579 TYR 0.010 0.001 TYR B 699 ARG 0.007 0.001 ARG D 696 Details of bonding type rmsd hydrogen bonds : bond 0.03648 ( 1036) hydrogen bonds : angle 4.21833 ( 3048) SS BOND : bond 0.00344 ( 18) SS BOND : angle 0.65632 ( 36) covalent geometry : bond 0.00295 (21156) covalent geometry : angle 0.58680 (29196) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 268 time to evaluate : 2.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.3924 (OUTLIER) cc_final: 0.3632 (mm) REVERT: A 91 LEU cc_start: 0.7294 (pt) cc_final: 0.7032 (tp) REVERT: A 419 LEU cc_start: 0.8391 (mt) cc_final: 0.8189 (mt) REVERT: A 532 ASP cc_start: 0.8546 (t70) cc_final: 0.8333 (t0) REVERT: A 587 VAL cc_start: 0.7871 (OUTLIER) cc_final: 0.7617 (p) REVERT: A 776 ARG cc_start: 0.7881 (mmm-85) cc_final: 0.7236 (mmm-85) REVERT: A 794 SER cc_start: 0.9354 (OUTLIER) cc_final: 0.8948 (t) REVERT: A 797 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8078 (tt) REVERT: A 801 HIS cc_start: 0.8874 (OUTLIER) cc_final: 0.8240 (t-90) REVERT: B 186 ILE cc_start: 0.8893 (pt) cc_final: 0.8531 (tp) REVERT: B 240 ILE cc_start: 0.7792 (tp) cc_final: 0.7552 (mt) REVERT: B 467 LYS cc_start: 0.8639 (mmmt) cc_final: 0.8221 (mmtm) REVERT: B 476 TYR cc_start: 0.7793 (p90) cc_final: 0.7430 (p90) REVERT: C 26 ILE cc_start: 0.3950 (OUTLIER) cc_final: 0.3705 (mm) REVERT: C 91 LEU cc_start: 0.7377 (pt) cc_final: 0.7139 (tp) REVERT: D 99 PHE cc_start: 0.5982 (t80) cc_final: 0.5678 (t80) REVERT: D 357 GLN cc_start: 0.7502 (mt0) cc_final: 0.7208 (pp30) REVERT: D 433 THR cc_start: 0.8249 (OUTLIER) cc_final: 0.7976 (t) REVERT: D 467 LYS cc_start: 0.8731 (mmmt) cc_final: 0.8242 (mptt) REVERT: D 795 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9199 (tt) outliers start: 132 outliers final: 89 residues processed: 377 average time/residue: 0.2617 time to fit residues: 166.0889 Evaluate side-chains 349 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 252 time to evaluate : 2.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 632 TRP Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 714 PHE Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 813 TRP Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 824 MET Chi-restraints excluded: chain D residue 841 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 149 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 272 optimal weight: 30.0000 chunk 246 optimal weight: 0.2980 chunk 117 optimal weight: 2.9990 chunk 235 optimal weight: 0.7980 chunk 189 optimal weight: 50.0000 chunk 221 optimal weight: 0.8980 chunk 140 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 184 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.179132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.150299 restraints weight = 45246.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.146837 restraints weight = 56058.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.144106 restraints weight = 54006.923| |-----------------------------------------------------------------------------| r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21174 Z= 0.120 Angle : 0.579 8.652 29232 Z= 0.293 Chirality : 0.043 0.173 3782 Planarity : 0.004 0.044 3706 Dihedral : 5.603 59.298 3290 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 7.10 % Allowed : 19.66 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.15), residues: 3148 helix: 1.23 (0.15), residues: 1326 sheet: -1.93 (0.24), residues: 408 loop : -2.35 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 197 HIS 0.003 0.001 HIS C 801 PHE 0.018 0.001 PHE A 579 TYR 0.010 0.001 TYR D 699 ARG 0.002 0.000 ARG A 776 Details of bonding type rmsd hydrogen bonds : bond 0.03522 ( 1036) hydrogen bonds : angle 4.13216 ( 3048) SS BOND : bond 0.00307 ( 18) SS BOND : angle 0.63925 ( 36) covalent geometry : bond 0.00272 (21156) covalent geometry : angle 0.57851 (29196) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 261 time to evaluate : 2.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.3944 (OUTLIER) cc_final: 0.3726 (mm) REVERT: A 91 LEU cc_start: 0.7106 (pt) cc_final: 0.6901 (tp) REVERT: A 534 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8624 (mm) REVERT: A 587 VAL cc_start: 0.7731 (OUTLIER) cc_final: 0.7481 (p) REVERT: A 776 ARG cc_start: 0.7897 (mmm-85) cc_final: 0.7274 (mmm-85) REVERT: A 794 SER cc_start: 0.9355 (OUTLIER) cc_final: 0.8993 (t) REVERT: B 186 ILE cc_start: 0.8845 (pt) cc_final: 0.8480 (tp) REVERT: B 240 ILE cc_start: 0.7677 (tp) cc_final: 0.7444 (mt) REVERT: B 433 THR cc_start: 0.8292 (OUTLIER) cc_final: 0.8011 (t) REVERT: B 467 LYS cc_start: 0.8629 (mmmt) cc_final: 0.8233 (mptt) REVERT: C 775 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.7294 (m-80) REVERT: C 783 MET cc_start: 0.8091 (tpp) cc_final: 0.7611 (ttm) REVERT: C 806 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8683 (mpp) REVERT: D 99 PHE cc_start: 0.6004 (t80) cc_final: 0.5693 (t80) REVERT: D 357 GLN cc_start: 0.7320 (mt0) cc_final: 0.6913 (pp30) REVERT: D 433 THR cc_start: 0.8398 (OUTLIER) cc_final: 0.8131 (t) REVERT: D 467 LYS cc_start: 0.8757 (mmmt) cc_final: 0.8222 (mptt) REVERT: D 702 MET cc_start: 0.6199 (mmt) cc_final: 0.5925 (mmt) REVERT: D 795 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9153 (tt) outliers start: 121 outliers final: 90 residues processed: 363 average time/residue: 0.2538 time to fit residues: 155.5225 Evaluate side-chains 350 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 251 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 775 PHE Chi-restraints excluded: chain C residue 806 MET Chi-restraints excluded: chain C residue 813 TRP Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 824 MET Chi-restraints excluded: chain D residue 841 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 282 optimal weight: 9.9990 chunk 312 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 258 optimal weight: 20.0000 chunk 262 optimal weight: 30.0000 chunk 92 optimal weight: 7.9990 chunk 287 optimal weight: 2.9990 chunk 111 optimal weight: 30.0000 chunk 243 optimal weight: 7.9990 chunk 134 optimal weight: 0.6980 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 697 ASN B 767 GLN D 697 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.172166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.142778 restraints weight = 45072.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.139974 restraints weight = 60240.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.134936 restraints weight = 64033.504| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.101 21174 Z= 0.376 Angle : 0.796 10.368 29232 Z= 0.423 Chirality : 0.049 0.254 3782 Planarity : 0.005 0.046 3706 Dihedral : 6.064 59.567 3281 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.23 % Favored : 89.68 % Rotamer: Outliers : 8.16 % Allowed : 19.60 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.15), residues: 3148 helix: 0.73 (0.14), residues: 1316 sheet: -1.96 (0.25), residues: 392 loop : -2.53 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 559 HIS 0.009 0.002 HIS A 801 PHE 0.041 0.003 PHE A 554 TYR 0.027 0.002 TYR C 668 ARG 0.007 0.001 ARG D 774 Details of bonding type rmsd hydrogen bonds : bond 0.05443 ( 1036) hydrogen bonds : angle 4.95959 ( 3048) SS BOND : bond 0.00612 ( 18) SS BOND : angle 1.48311 ( 36) covalent geometry : bond 0.00877 (21156) covalent geometry : angle 0.79438 (29196) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 243 time to evaluate : 2.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.3916 (OUTLIER) cc_final: 0.3687 (mm) REVERT: A 91 LEU cc_start: 0.7431 (pt) cc_final: 0.7118 (tp) REVERT: B 186 ILE cc_start: 0.8890 (pt) cc_final: 0.8558 (tp) REVERT: B 240 ILE cc_start: 0.7934 (tp) cc_final: 0.7672 (mt) REVERT: B 433 THR cc_start: 0.8323 (OUTLIER) cc_final: 0.8043 (t) REVERT: B 467 LYS cc_start: 0.8700 (mmmt) cc_final: 0.8286 (mptt) REVERT: C 806 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8546 (mpp) REVERT: D 357 GLN cc_start: 0.7659 (mt0) cc_final: 0.7376 (pp30) REVERT: D 433 THR cc_start: 0.8339 (OUTLIER) cc_final: 0.8061 (t) REVERT: D 702 MET cc_start: 0.6360 (mmt) cc_final: 0.6043 (mmt) REVERT: D 795 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9202 (tt) REVERT: D 901 GLU cc_start: 0.5105 (mm-30) cc_final: 0.4835 (mm-30) outliers start: 139 outliers final: 105 residues processed: 359 average time/residue: 0.2557 time to fit residues: 155.1874 Evaluate side-chains 345 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 235 time to evaluate : 2.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 431 TYR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 629 TRP Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 767 GLN Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 493 PHE Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 806 MET Chi-restraints excluded: chain C residue 813 TRP Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 824 MET Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 841 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 224 optimal weight: 8.9990 chunk 46 optimal weight: 20.0000 chunk 266 optimal weight: 3.9990 chunk 198 optimal weight: 0.9990 chunk 275 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 208 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 197 optimal weight: 10.0000 chunk 209 optimal weight: 0.2980 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 697 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.177401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.148165 restraints weight = 45071.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.140991 restraints weight = 60226.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.139439 restraints weight = 55832.898| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 21174 Z= 0.227 Angle : 0.690 12.973 29232 Z= 0.358 Chirality : 0.045 0.196 3782 Planarity : 0.004 0.047 3706 Dihedral : 5.816 58.841 3281 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.77 % Favored : 91.20 % Rotamer: Outliers : 7.69 % Allowed : 19.72 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.15), residues: 3148 helix: 0.93 (0.15), residues: 1310 sheet: -1.88 (0.25), residues: 392 loop : -2.48 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 559 HIS 0.006 0.001 HIS C 801 PHE 0.026 0.002 PHE C 554 TYR 0.016 0.001 TYR A 599 ARG 0.004 0.001 ARG C 716 Details of bonding type rmsd hydrogen bonds : bond 0.04583 ( 1036) hydrogen bonds : angle 4.63845 ( 3048) SS BOND : bond 0.00456 ( 18) SS BOND : angle 1.25698 ( 36) covalent geometry : bond 0.00533 (21156) covalent geometry : angle 0.68876 (29196) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 252 time to evaluate : 2.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.3823 (OUTLIER) cc_final: 0.3590 (mm) REVERT: A 91 LEU cc_start: 0.7620 (pt) cc_final: 0.7290 (tp) REVERT: A 776 ARG cc_start: 0.7994 (mmm-85) cc_final: 0.7367 (mmm-85) REVERT: B 186 ILE cc_start: 0.8983 (pt) cc_final: 0.8665 (tp) REVERT: B 240 ILE cc_start: 0.8016 (tp) cc_final: 0.7766 (mt) REVERT: B 433 THR cc_start: 0.8372 (OUTLIER) cc_final: 0.8108 (t) REVERT: B 467 LYS cc_start: 0.8580 (mmmt) cc_final: 0.8249 (mptt) REVERT: C 775 PHE cc_start: 0.7659 (OUTLIER) cc_final: 0.7204 (m-80) REVERT: C 783 MET cc_start: 0.8225 (tpp) cc_final: 0.7837 (ttm) REVERT: C 806 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8623 (mpp) REVERT: D 433 THR cc_start: 0.8375 (OUTLIER) cc_final: 0.8120 (t) REVERT: D 467 LYS cc_start: 0.8701 (mmmt) cc_final: 0.8249 (mptt) REVERT: D 702 MET cc_start: 0.6305 (mmt) cc_final: 0.6060 (mmt) REVERT: B 901 GLU cc_start: 0.4582 (mm-30) cc_final: 0.4156 (mm-30) REVERT: D 901 GLU cc_start: 0.4597 (mm-30) cc_final: 0.4300 (mm-30) outliers start: 131 outliers final: 107 residues processed: 358 average time/residue: 0.2785 time to fit residues: 172.3956 Evaluate side-chains 351 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 239 time to evaluate : 2.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 239 TYR Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 629 TRP Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 775 PHE Chi-restraints excluded: chain C residue 806 MET Chi-restraints excluded: chain C residue 813 TRP Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 671 PHE Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 824 MET Chi-restraints excluded: chain D residue 841 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 183 optimal weight: 20.0000 chunk 261 optimal weight: 0.4980 chunk 97 optimal weight: 6.9990 chunk 221 optimal weight: 8.9990 chunk 303 optimal weight: 8.9990 chunk 84 optimal weight: 0.0870 chunk 271 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 chunk 61 optimal weight: 0.1980 chunk 224 optimal weight: 20.0000 chunk 126 optimal weight: 0.9990 overall best weight: 1.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS B 184 ASN B 697 ASN C 162 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.179574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.150582 restraints weight = 45229.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.146449 restraints weight = 57727.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.144859 restraints weight = 47028.603| |-----------------------------------------------------------------------------| r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21174 Z= 0.155 Angle : 0.621 9.349 29232 Z= 0.318 Chirality : 0.044 0.169 3782 Planarity : 0.004 0.049 3706 Dihedral : 5.515 58.053 3279 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 6.92 % Allowed : 20.72 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.15), residues: 3148 helix: 1.15 (0.15), residues: 1310 sheet: -1.55 (0.26), residues: 364 loop : -2.46 (0.16), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 607 HIS 0.004 0.001 HIS C 801 PHE 0.019 0.002 PHE B 99 TYR 0.012 0.001 TYR A 599 ARG 0.004 0.000 ARG C 716 Details of bonding type rmsd hydrogen bonds : bond 0.04035 ( 1036) hydrogen bonds : angle 4.37508 ( 3048) SS BOND : bond 0.00352 ( 18) SS BOND : angle 1.16972 ( 36) covalent geometry : bond 0.00359 (21156) covalent geometry : angle 0.62021 (29196) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 244 time to evaluate : 2.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 776 ARG cc_start: 0.7953 (mmm-85) cc_final: 0.7278 (mmm-85) REVERT: A 783 MET cc_start: 0.8124 (tpp) cc_final: 0.7724 (ttm) REVERT: B 186 ILE cc_start: 0.8771 (pt) cc_final: 0.8459 (tp) REVERT: B 240 ILE cc_start: 0.7798 (tp) cc_final: 0.7560 (mt) REVERT: B 405 HIS cc_start: 0.6774 (t70) cc_final: 0.6434 (t70) REVERT: B 433 THR cc_start: 0.8348 (OUTLIER) cc_final: 0.8083 (t) REVERT: B 467 LYS cc_start: 0.8586 (mmmt) cc_final: 0.8218 (mptt) REVERT: C 775 PHE cc_start: 0.7835 (OUTLIER) cc_final: 0.7347 (m-80) REVERT: C 776 ARG cc_start: 0.7571 (mmm-85) cc_final: 0.6840 (mmm-85) REVERT: C 783 MET cc_start: 0.8241 (tpp) cc_final: 0.7819 (ttm) REVERT: D 433 THR cc_start: 0.8389 (OUTLIER) cc_final: 0.8125 (t) REVERT: D 467 LYS cc_start: 0.8660 (mmmt) cc_final: 0.8209 (mptt) REVERT: D 702 MET cc_start: 0.6205 (mmt) cc_final: 0.5959 (mmt) REVERT: B 901 GLU cc_start: 0.4191 (mm-30) cc_final: 0.3899 (mm-30) outliers start: 118 outliers final: 107 residues processed: 342 average time/residue: 0.2566 time to fit residues: 150.4129 Evaluate side-chains 349 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 239 time to evaluate : 2.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 775 PHE Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 813 TRP Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 750 THR Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 824 MET Chi-restraints excluded: chain D residue 841 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 145 optimal weight: 9.9990 chunk 165 optimal weight: 10.0000 chunk 281 optimal weight: 2.9990 chunk 108 optimal weight: 0.3980 chunk 69 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 273 optimal weight: 20.0000 chunk 277 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 697 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.179152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.150364 restraints weight = 45146.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.144873 restraints weight = 58619.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.142672 restraints weight = 48316.804| |-----------------------------------------------------------------------------| r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21174 Z= 0.173 Angle : 0.636 9.447 29232 Z= 0.326 Chirality : 0.044 0.168 3782 Planarity : 0.004 0.049 3706 Dihedral : 5.499 56.438 3279 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 6.81 % Allowed : 20.72 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.15), residues: 3148 helix: 1.18 (0.15), residues: 1312 sheet: -1.58 (0.26), residues: 384 loop : -2.39 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 559 HIS 0.005 0.001 HIS C 801 PHE 0.023 0.002 PHE A 579 TYR 0.012 0.001 TYR A 599 ARG 0.003 0.000 ARG D 774 Details of bonding type rmsd hydrogen bonds : bond 0.04173 ( 1036) hydrogen bonds : angle 4.37327 ( 3048) SS BOND : bond 0.00374 ( 18) SS BOND : angle 1.18213 ( 36) covalent geometry : bond 0.00406 (21156) covalent geometry : angle 0.63543 (29196) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 243 time to evaluate : 2.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 776 ARG cc_start: 0.7881 (mmm-85) cc_final: 0.7221 (mmm-85) REVERT: B 186 ILE cc_start: 0.8843 (pt) cc_final: 0.8507 (tp) REVERT: B 240 ILE cc_start: 0.7901 (tp) cc_final: 0.7656 (mt) REVERT: B 405 HIS cc_start: 0.6897 (t70) cc_final: 0.6591 (t70) REVERT: B 433 THR cc_start: 0.8397 (OUTLIER) cc_final: 0.8136 (t) REVERT: B 467 LYS cc_start: 0.8613 (mmmt) cc_final: 0.8205 (mptt) REVERT: C 775 PHE cc_start: 0.7824 (OUTLIER) cc_final: 0.7264 (m-80) REVERT: C 783 MET cc_start: 0.8171 (tpp) cc_final: 0.7777 (ttm) REVERT: D 433 THR cc_start: 0.8421 (OUTLIER) cc_final: 0.8158 (t) REVERT: D 467 LYS cc_start: 0.8650 (mmmt) cc_final: 0.8155 (mptt) REVERT: D 702 MET cc_start: 0.6144 (mmt) cc_final: 0.5918 (mmt) REVERT: B 901 GLU cc_start: 0.4348 (mm-30) cc_final: 0.4043 (mm-30) REVERT: D 901 GLU cc_start: 0.4185 (mm-30) cc_final: 0.3901 (mm-30) outliers start: 116 outliers final: 104 residues processed: 341 average time/residue: 0.2678 time to fit residues: 156.5769 Evaluate side-chains 345 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 238 time to evaluate : 2.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 629 TRP Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 629 TRP Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 775 PHE Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 813 TRP Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 750 THR Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 824 MET Chi-restraints excluded: chain D residue 841 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 110 optimal weight: 0.7980 chunk 183 optimal weight: 20.0000 chunk 146 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 chunk 285 optimal weight: 0.7980 chunk 258 optimal weight: 6.9990 chunk 40 optimal weight: 0.0040 chunk 22 optimal weight: 0.0970 chunk 89 optimal weight: 50.0000 chunk 49 optimal weight: 0.7980 chunk 187 optimal weight: 2.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 ASN B 697 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.183061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.153238 restraints weight = 45625.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.147496 restraints weight = 58947.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.143295 restraints weight = 50785.959| |-----------------------------------------------------------------------------| r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21174 Z= 0.108 Angle : 0.596 12.714 29232 Z= 0.298 Chirality : 0.043 0.180 3782 Planarity : 0.004 0.050 3706 Dihedral : 5.154 56.767 3279 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 4.87 % Allowed : 22.71 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.15), residues: 3148 helix: 1.43 (0.15), residues: 1314 sheet: -1.44 (0.27), residues: 362 loop : -2.29 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 629 HIS 0.002 0.001 HIS C 425 PHE 0.028 0.001 PHE D 637 TYR 0.011 0.001 TYR D 479 ARG 0.002 0.000 ARG B 519 Details of bonding type rmsd hydrogen bonds : bond 0.03355 ( 1036) hydrogen bonds : angle 4.07850 ( 3048) SS BOND : bond 0.00266 ( 18) SS BOND : angle 1.10641 ( 36) covalent geometry : bond 0.00236 (21156) covalent geometry : angle 0.59490 (29196) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6765.49 seconds wall clock time: 117 minutes 14.87 seconds (7034.87 seconds total)