Starting phenix.real_space_refine on Thu Sep 18 22:42:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ari_43783/09_2025/9ari_43783.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ari_43783/09_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_43783/09_2025/9ari_43783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ari_43783/09_2025/9ari_43783.map" model { file = "/net/cci-nas-00/data/ceres_data/9ari_43783/09_2025/9ari_43783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ari_43783/09_2025/9ari_43783.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASN:plan1': 24, 'ARG:plan': 36, 'GLU:plan': 41, 'GLN:plan1': 25, 'PHE:plan': 5, 'HIS:plan': 11, 'ASP:plan': 24, 'TYR:plan': 9, 'TRP:plan': 1} 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: {'ASP:plan': 36, 'GLU:plan': 46, 'HIS:plan': 8, 'PHE:plan': 16, 'ARG:plan': 20, 'ASN:plan1': 18, 'GLN:plan1': 18, 'TYR:plan': 17, 'TRP:plan': 4} 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: {'ASN:plan1': 24, 'ARG:plan': 36, 'GLU:plan': 41, 'GLN:plan1': 25, 'PHE:plan': 5, 'HIS:plan': 11, 'ASP:plan': 24, 'TYR:plan': 9, 'TRP:plan': 1} 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: {'ASP:plan': 36, 'GLU:plan': 46, 'HIS:plan': 8, 'PHE:plan': 16, 'ARG:plan': 20, 'ASN:plan1': 18, 'GLN:plan1': 18, 'TYR:plan': 17, 'TRP:plan': 4} 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: 4.02, per 1000 atoms: 0.19 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: 1.93 Conformation dependent library (CDL) restraints added in 876.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.87 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: 3.86 Time building geometry restraints manager: 2.47 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: 0.03 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: 2.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 18.010 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.370 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.007 0.001 ARG C 651 TYR 0.022 0.001 TYR D 843 PHE 0.039 0.002 PHE A 429 TRP 0.043 0.001 TRP C 632 HIS 0.006 0.001 HIS A 801 Details of bonding type rmsd covalent geometry : bond 0.00690 (21156) covalent geometry : angle 1.12312 (29196) SS BOND : bond 0.25578 ( 18) SS BOND : angle 8.47346 ( 36) hydrogen bonds : bond 0.15092 ( 1036) hydrogen bonds : angle 6.74552 ( 3048) *********************** 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 : 0.748 Fit side-chains 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: 0.1105 time to fit residues: 104.3625 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 : 0.770 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.0030 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 0.0030 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 0.0970 overall best weight: 0.3800 ------------------------------------------------------------------------------- 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 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 245 ASN D 357 GLN D 615 ASN D 710 ASN D 775 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.181453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.148605 restraints weight = 44138.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.142321 restraints weight = 56466.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.140357 restraints weight = 45042.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.140876 restraints weight = 36930.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.141048 restraints weight = 28927.572| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21174 Z= 0.118 Angle : 0.591 7.262 29232 Z= 0.307 Chirality : 0.043 0.244 3782 Planarity : 0.004 0.052 3706 Dihedral : 7.023 75.334 3365 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 6.57 % Allowed : 16.55 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.15 (0.14), residues: 3148 helix: 0.46 (0.14), residues: 1336 sheet: -2.69 (0.22), residues: 422 loop : -2.98 (0.15), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 743 TYR 0.018 0.001 TYR C 599 PHE 0.030 0.001 PHE A 575 TRP 0.014 0.001 TRP B 494 HIS 0.002 0.001 HIS B 486 Details of bonding type rmsd covalent geometry : bond 0.00246 (21156) covalent geometry : angle 0.59073 (29196) SS BOND : bond 0.00736 ( 18) SS BOND : angle 0.97532 ( 36) hydrogen bonds : bond 0.03634 ( 1036) hydrogen bonds : angle 4.77301 ( 3048) *********************** 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 437 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 325 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 569 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7919 (ttm-80) REVERT: A 597 MET cc_start: 0.8408 (ttt) cc_final: 0.8159 (ttm) REVERT: A 775 PHE cc_start: 0.7785 (t80) cc_final: 0.7545 (t80) REVERT: A 801 HIS cc_start: 0.8957 (OUTLIER) cc_final: 0.8342 (t-90) REVERT: A 806 MET cc_start: 0.9157 (mmt) cc_final: 0.8630 (mmt) REVERT: B 186 ILE cc_start: 0.9075 (pt) cc_final: 0.8776 (tp) REVERT: B 232 CYS cc_start: 0.5991 (t) cc_final: 0.5416 (t) REVERT: B 240 ILE cc_start: 0.8065 (tp) cc_final: 0.7816 (mt) REVERT: B 357 GLN cc_start: 0.7269 (mt0) cc_final: 0.6301 (pp30) REVERT: B 433 THR cc_start: 0.8167 (OUTLIER) cc_final: 0.7855 (t) REVERT: B 467 LYS cc_start: 0.8633 (mmmt) cc_final: 0.8120 (mmtm) REVERT: B 476 TYR cc_start: 0.7893 (p90) cc_final: 0.7479 (p90) REVERT: B 480 LEU cc_start: 0.7705 (tp) cc_final: 0.7318 (tt) REVERT: B 782 GLN cc_start: 0.8417 (pp30) cc_final: 0.8213 (tm-30) REVERT: C 797 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.7669 (pt) REVERT: C 801 HIS cc_start: 0.8675 (OUTLIER) cc_final: 0.8421 (t-90) REVERT: D 99 PHE cc_start: 0.5885 (t80) cc_final: 0.5570 (t80) REVERT: D 467 LYS cc_start: 0.8576 (mmmt) cc_final: 0.8234 (mptt) REVERT: D 709 PHE cc_start: 0.7462 (OUTLIER) cc_final: 0.7064 (t80) REVERT: D 795 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9253 (tp) outliers start: 112 outliers final: 61 residues processed: 417 average time/residue: 0.1075 time to fit residues: 75.0100 Evaluate side-chains 354 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 286 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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 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 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 433 THR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 750 THR 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 576 MET 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 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 64 VAL 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 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 246 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 311 optimal weight: 7.9990 chunk 169 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 201 optimal weight: 1.9990 chunk 304 optimal weight: 9.9990 chunk 302 optimal weight: 9.9990 chunk 164 optimal weight: 50.0000 chunk 75 optimal weight: 0.6980 chunk 303 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 ASN C 748 HIS D 697 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.177219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.146242 restraints weight = 44068.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.140899 restraints weight = 55529.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.138769 restraints weight = 45641.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.138430 restraints weight = 44559.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.137628 restraints weight = 38326.619| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 21174 Z= 0.147 Angle : 0.598 8.075 29232 Z= 0.309 Chirality : 0.043 0.228 3782 Planarity : 0.004 0.053 3706 Dihedral : 6.127 71.938 3308 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 6.98 % Allowed : 16.84 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.15), residues: 3148 helix: 0.80 (0.14), residues: 1334 sheet: -2.34 (0.23), residues: 418 loop : -2.62 (0.15), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 743 TYR 0.015 0.001 TYR D 239 PHE 0.033 0.002 PHE A 579 TRP 0.010 0.001 TRP D 635 HIS 0.004 0.001 HIS B 486 Details of bonding type rmsd covalent geometry : bond 0.00333 (21156) covalent geometry : angle 0.59747 (29196) SS BOND : bond 0.00385 ( 18) SS BOND : angle 0.68918 ( 36) hydrogen bonds : bond 0.03856 ( 1036) hydrogen bonds : angle 4.42532 ( 3048) *********************** 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 406 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 287 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.7540 (pt) cc_final: 0.7123 (tp) REVERT: A 797 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8028 (tt) REVERT: A 801 HIS cc_start: 0.8881 (OUTLIER) cc_final: 0.8219 (t-90) REVERT: B 186 ILE cc_start: 0.9032 (pt) cc_final: 0.8634 (tp) REVERT: B 240 ILE cc_start: 0.7838 (tp) cc_final: 0.7594 (mt) REVERT: B 357 GLN cc_start: 0.7300 (mt0) cc_final: 0.6336 (pp30) REVERT: B 429 CYS cc_start: 0.4510 (OUTLIER) cc_final: 0.4220 (t) REVERT: B 467 LYS cc_start: 0.8651 (mmmt) cc_final: 0.8139 (mmtm) REVERT: B 476 TYR cc_start: 0.7974 (p90) cc_final: 0.7583 (p90) REVERT: C 91 LEU cc_start: 0.7624 (pt) cc_final: 0.7179 (tp) REVERT: C 775 PHE cc_start: 0.8359 (t80) cc_final: 0.7954 (t80) REVERT: C 797 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.7798 (pt) REVERT: C 801 HIS cc_start: 0.8830 (OUTLIER) cc_final: 0.8131 (t-90) REVERT: D 795 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9296 (tp) outliers start: 119 outliers final: 73 residues processed: 380 average time/residue: 0.1137 time to fit residues: 71.9103 Evaluate side-chains 348 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 269 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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 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 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 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 410 THR 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 513 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 660 VAL Chi-restraints excluded: chain B residue 671 PHE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 714 VAL 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 163 ILE 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 758 GLU 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 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 418 ILE Chi-restraints excluded: chain D residue 428 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 554 PHE Chi-restraints excluded: chain D residue 612 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 162 optimal weight: 9.9990 chunk 253 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 271 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 276 optimal weight: 8.9990 chunk 83 optimal weight: 40.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 697 ASN B 703 HIS D 703 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.167988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.136646 restraints weight = 44317.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.131851 restraints weight = 62662.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.128346 restraints weight = 64028.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.127636 restraints weight = 59369.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.126078 restraints weight = 54444.288| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.124 21174 Z= 0.471 Angle : 0.902 13.071 29232 Z= 0.486 Chirality : 0.053 0.310 3782 Planarity : 0.005 0.054 3706 Dihedral : 7.239 70.556 3300 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.17 % Favored : 89.71 % Rotamer: Outliers : 9.39 % Allowed : 17.19 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.25 (0.14), residues: 3148 helix: 0.16 (0.14), residues: 1332 sheet: -2.56 (0.23), residues: 428 loop : -2.86 (0.15), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 774 TYR 0.044 0.003 TYR C 668 PHE 0.060 0.004 PHE C 554 TRP 0.027 0.003 TRP D 559 HIS 0.007 0.002 HIS C 425 Details of bonding type rmsd covalent geometry : bond 0.01106 (21156) covalent geometry : angle 0.90161 (29196) SS BOND : bond 0.00685 ( 18) SS BOND : angle 1.07297 ( 36) hydrogen bonds : bond 0.06281 ( 1036) hydrogen bonds : angle 5.45779 ( 3048) *********************** 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 427 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 267 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.7669 (pt) cc_final: 0.7204 (tp) REVERT: A 776 ARG cc_start: 0.8366 (mmm-85) cc_final: 0.7672 (mmm-85) REVERT: A 801 HIS cc_start: 0.9056 (OUTLIER) cc_final: 0.8529 (t-90) REVERT: A 806 MET cc_start: 0.9131 (mmt) cc_final: 0.8783 (tpp) REVERT: B 186 ILE cc_start: 0.8977 (pt) cc_final: 0.8648 (tp) REVERT: B 240 ILE cc_start: 0.8025 (tp) cc_final: 0.7752 (mt) REVERT: B 429 CYS cc_start: 0.4728 (OUTLIER) cc_final: 0.4516 (t) REVERT: C 91 LEU cc_start: 0.7548 (pt) cc_final: 0.7105 (tp) REVERT: C 783 MET cc_start: 0.8638 (tpp) cc_final: 0.8258 (tpp) REVERT: C 801 HIS cc_start: 0.9048 (OUTLIER) cc_final: 0.8525 (t-90) outliers start: 160 outliers final: 108 residues processed: 400 average time/residue: 0.1135 time to fit residues: 76.8858 Evaluate side-chains 353 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 242 time to evaluate : 0.775 ------------------------------------------------------------------------------- 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 166 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 385 VAL 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 458 THR Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 535 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 591 VAL Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 629 TRP 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 769 THR 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 239 TYR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 429 CYS 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 567 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 647 THR 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 721 LEU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 163 ILE 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 452 VAL Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 569 ARG 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 669 THR 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 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 349 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 428 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 510 VAL 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 647 THR 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 781 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 37 optimal weight: 2.9990 chunk 274 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 94 optimal weight: 30.0000 chunk 147 optimal weight: 1.9990 chunk 254 optimal weight: 20.0000 chunk 42 optimal weight: 0.0000 chunk 46 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- 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 = 0.4353 r_free = 0.4353 target = 0.174072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.142044 restraints weight = 43578.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.135637 restraints weight = 56819.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.132990 restraints weight = 54155.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.132737 restraints weight = 49898.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.131518 restraints weight = 42048.084| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21174 Z= 0.149 Angle : 0.635 11.233 29232 Z= 0.327 Chirality : 0.044 0.195 3782 Planarity : 0.004 0.055 3706 Dihedral : 6.233 70.574 3292 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 6.57 % Allowed : 20.54 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.15), residues: 3148 helix: 0.74 (0.14), residues: 1328 sheet: -2.49 (0.23), residues: 424 loop : -2.58 (0.16), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 743 TYR 0.020 0.001 TYR D 239 PHE 0.025 0.002 PHE A 579 TRP 0.011 0.001 TRP D 607 HIS 0.004 0.001 HIS B 486 Details of bonding type rmsd covalent geometry : bond 0.00333 (21156) covalent geometry : angle 0.63518 (29196) SS BOND : bond 0.00363 ( 18) SS BOND : angle 0.77886 ( 36) hydrogen bonds : bond 0.04207 ( 1036) hydrogen bonds : angle 4.54648 ( 3048) *********************** 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 384 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 272 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.4227 (OUTLIER) cc_final: 0.3914 (mm) REVERT: A 91 LEU cc_start: 0.7822 (pt) cc_final: 0.7381 (tp) REVERT: A 549 GLU cc_start: 0.8300 (pp20) cc_final: 0.8061 (pp20) REVERT: A 767 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9184 (pp) REVERT: A 776 ARG cc_start: 0.8094 (mmm-85) cc_final: 0.7538 (mmm-85) REVERT: A 801 HIS cc_start: 0.8974 (OUTLIER) cc_final: 0.8330 (t-90) REVERT: B 186 ILE cc_start: 0.9045 (pt) cc_final: 0.8716 (tp) REVERT: B 240 ILE cc_start: 0.8060 (tp) cc_final: 0.7805 (mt) REVERT: B 467 LYS cc_start: 0.8504 (mmmm) cc_final: 0.7959 (mptt) REVERT: B 663 VAL cc_start: 0.6375 (OUTLIER) cc_final: 0.6172 (p) REVERT: B 795 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9182 (tm) REVERT: C 26 ILE cc_start: 0.4222 (OUTLIER) cc_final: 0.3959 (mm) REVERT: C 91 LEU cc_start: 0.7872 (pt) cc_final: 0.7474 (tp) REVERT: C 776 ARG cc_start: 0.8070 (mmm-85) cc_final: 0.7552 (mmm-85) REVERT: C 783 MET cc_start: 0.8457 (tpp) cc_final: 0.7842 (tpp) REVERT: C 801 HIS cc_start: 0.8996 (OUTLIER) cc_final: 0.8319 (t-90) REVERT: D 467 LYS cc_start: 0.8727 (mmmt) cc_final: 0.8180 (mptt) REVERT: D 702 MET cc_start: 0.6516 (mmt) cc_final: 0.6213 (mmt) REVERT: D 901 GLU cc_start: 0.4490 (mm-30) cc_final: 0.4242 (mm-30) outliers start: 112 outliers final: 72 residues processed: 364 average time/residue: 0.1171 time to fit residues: 72.0594 Evaluate side-chains 339 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 260 time to evaluate : 0.729 ------------------------------------------------------------------------------- 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 166 LEU 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 471 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 632 TRP Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 773 LEU 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 367 LEU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 536 VAL 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 756 VAL Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain C residue 26 ILE 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 383 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 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 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 793 VAL 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 64 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 268 THR 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 440 ILE 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 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 48 optimal weight: 0.5980 chunk 172 optimal weight: 10.0000 chunk 248 optimal weight: 40.0000 chunk 68 optimal weight: 5.9990 chunk 197 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 121 optimal weight: 0.4980 chunk 4 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 314 optimal weight: 0.8980 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 697 ASN D 184 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.174422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.145698 restraints weight = 44932.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.138943 restraints weight = 54050.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.135307 restraints weight = 63631.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.136180 restraints weight = 60781.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.134840 restraints weight = 45932.854| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 21174 Z= 0.224 Angle : 0.676 10.807 29232 Z= 0.351 Chirality : 0.046 0.240 3782 Planarity : 0.004 0.049 3706 Dihedral : 6.138 64.988 3288 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.97 % Favored : 89.96 % Rotamer: Outliers : 7.39 % Allowed : 20.60 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.15), residues: 3148 helix: 0.77 (0.14), residues: 1328 sheet: -2.19 (0.25), residues: 388 loop : -2.58 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 774 TYR 0.022 0.001 TYR D 239 PHE 0.028 0.002 PHE C 554 TRP 0.012 0.002 TRP B 559 HIS 0.004 0.001 HIS C 425 Details of bonding type rmsd covalent geometry : bond 0.00525 (21156) covalent geometry : angle 0.67570 (29196) SS BOND : bond 0.00413 ( 18) SS BOND : angle 0.87057 ( 36) hydrogen bonds : bond 0.04634 ( 1036) hydrogen bonds : angle 4.66250 ( 3048) *********************** 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 391 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 265 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.4057 (OUTLIER) cc_final: 0.3787 (mm) REVERT: A 91 LEU cc_start: 0.7683 (pt) cc_final: 0.7272 (tp) REVERT: A 549 GLU cc_start: 0.8263 (pp20) cc_final: 0.7929 (pp20) REVERT: A 776 ARG cc_start: 0.8112 (mmm-85) cc_final: 0.7526 (mmm-85) REVERT: A 801 HIS cc_start: 0.9019 (OUTLIER) cc_final: 0.8371 (t-90) REVERT: B 186 ILE cc_start: 0.8984 (pt) cc_final: 0.8644 (tp) REVERT: B 240 ILE cc_start: 0.8060 (tp) cc_final: 0.7797 (mt) REVERT: B 433 THR cc_start: 0.8335 (OUTLIER) cc_final: 0.8110 (t) REVERT: B 467 LYS cc_start: 0.8515 (mmmm) cc_final: 0.7913 (mmtm) REVERT: B 795 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9218 (tm) REVERT: C 26 ILE cc_start: 0.3887 (OUTLIER) cc_final: 0.3662 (mm) REVERT: C 91 LEU cc_start: 0.7546 (pt) cc_final: 0.7256 (tp) REVERT: C 549 GLU cc_start: 0.8267 (pp20) cc_final: 0.7957 (pp20) REVERT: C 767 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9146 (pp) REVERT: C 783 MET cc_start: 0.8590 (tpp) cc_final: 0.8367 (tpp) REVERT: D 467 LYS cc_start: 0.8758 (mmmt) cc_final: 0.8233 (mptt) REVERT: D 702 MET cc_start: 0.6464 (mmt) cc_final: 0.6172 (mmt) outliers start: 126 outliers final: 100 residues processed: 366 average time/residue: 0.1116 time to fit residues: 69.1597 Evaluate side-chains 356 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 250 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 329 CYS Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 383 VAL 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 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 632 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 712 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 786 ASP Chi-restraints excluded: chain A residue 794 SER 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 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 508 MET 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 641 ILE 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 721 LEU Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 795 LEU 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 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 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 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 632 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 710 VAL Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 786 ASP 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 138 optimal weight: 0.6980 chunk 190 optimal weight: 9.9990 chunk 282 optimal weight: 0.3980 chunk 137 optimal weight: 0.6980 chunk 236 optimal weight: 0.8980 chunk 290 optimal weight: 0.7980 chunk 21 optimal weight: 30.0000 chunk 239 optimal weight: 0.0060 chunk 117 optimal weight: 3.9990 chunk 300 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 697 ASN D 697 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.179804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.149575 restraints weight = 45487.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.141317 restraints weight = 58100.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.138754 restraints weight = 53342.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.139840 restraints weight = 43404.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.139182 restraints weight = 34201.118| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 21174 Z= 0.111 Angle : 0.596 12.318 29232 Z= 0.300 Chirality : 0.043 0.156 3782 Planarity : 0.004 0.049 3706 Dihedral : 5.584 59.326 3286 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 5.75 % Allowed : 22.48 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.15), residues: 3148 helix: 1.18 (0.15), residues: 1318 sheet: -2.02 (0.25), residues: 388 loop : -2.37 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 544 TYR 0.025 0.001 TYR D 239 PHE 0.019 0.001 PHE A 575 TRP 0.010 0.001 TRP B 197 HIS 0.002 0.001 HIS B 405 Details of bonding type rmsd covalent geometry : bond 0.00236 (21156) covalent geometry : angle 0.59576 (29196) SS BOND : bond 0.00328 ( 18) SS BOND : angle 0.71915 ( 36) hydrogen bonds : bond 0.03503 ( 1036) hydrogen bonds : angle 4.22271 ( 3048) *********************** 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 367 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 269 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.4260 (OUTLIER) cc_final: 0.4026 (mm) REVERT: A 91 LEU cc_start: 0.7880 (pt) cc_final: 0.7454 (tp) REVERT: A 767 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9114 (pp) REVERT: A 776 ARG cc_start: 0.7792 (mmm-85) cc_final: 0.7267 (mmm-85) REVERT: B 186 ILE cc_start: 0.9036 (pt) cc_final: 0.8736 (tp) REVERT: B 240 ILE cc_start: 0.8083 (tp) cc_final: 0.7842 (mt) REVERT: B 405 HIS cc_start: 0.6781 (t70) cc_final: 0.6364 (t70) REVERT: B 433 THR cc_start: 0.8273 (OUTLIER) cc_final: 0.8021 (t) REVERT: B 467 LYS cc_start: 0.8511 (mmmm) cc_final: 0.8104 (mptt) REVERT: B 795 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9264 (tt) REVERT: C 26 ILE cc_start: 0.4096 (OUTLIER) cc_final: 0.3889 (mm) REVERT: C 91 LEU cc_start: 0.7873 (pt) cc_final: 0.7497 (tp) REVERT: C 549 GLU cc_start: 0.8188 (pp20) cc_final: 0.7921 (pp20) REVERT: C 767 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9110 (pp) REVERT: C 775 PHE cc_start: 0.7701 (OUTLIER) cc_final: 0.7205 (m-80) REVERT: C 783 MET cc_start: 0.8253 (tpp) cc_final: 0.7974 (tpp) REVERT: D 467 LYS cc_start: 0.8693 (mmmt) cc_final: 0.8158 (mptt) REVERT: D 702 MET cc_start: 0.6405 (mmt) cc_final: 0.6087 (mmt) outliers start: 98 outliers final: 72 residues processed: 353 average time/residue: 0.1104 time to fit residues: 66.6420 Evaluate side-chains 334 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 255 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 372 TYR Chi-restraints excluded: chain A residue 374 ILE 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 583 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 773 LEU 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 268 THR 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 433 THR Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 795 LEU 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 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 583 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 589 LEU 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 767 LEU Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 775 PHE Chi-restraints excluded: chain C residue 813 TRP 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 428 THR Chi-restraints excluded: chain D residue 536 VAL 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 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 824 MET 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 47 optimal weight: 4.9990 chunk 165 optimal weight: 0.8980 chunk 198 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 134 optimal weight: 0.8980 chunk 90 optimal weight: 40.0000 chunk 77 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 72 optimal weight: 0.0970 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 697 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.181486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.151838 restraints weight = 45120.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.146524 restraints weight = 59143.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.146113 restraints weight = 45780.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.145168 restraints weight = 41300.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.144422 restraints weight = 35704.862| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21174 Z= 0.121 Angle : 0.602 12.108 29232 Z= 0.302 Chirality : 0.043 0.194 3782 Planarity : 0.004 0.049 3706 Dihedral : 5.123 58.307 3275 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 5.63 % Allowed : 22.48 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.15), residues: 3148 helix: 1.31 (0.15), residues: 1312 sheet: -1.79 (0.26), residues: 368 loop : -2.31 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 716 TYR 0.016 0.001 TYR D 239 PHE 0.021 0.001 PHE D 99 TRP 0.008 0.001 TRP B 197 HIS 0.002 0.001 HIS B 486 Details of bonding type rmsd covalent geometry : bond 0.00274 (21156) covalent geometry : angle 0.60126 (29196) SS BOND : bond 0.00329 ( 18) SS BOND : angle 1.23469 ( 36) hydrogen bonds : bond 0.03645 ( 1036) hydrogen bonds : angle 4.16408 ( 3048) *********************** 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 359 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 263 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.7335 (pt) cc_final: 0.7078 (tp) REVERT: A 767 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9100 (pp) REVERT: A 776 ARG cc_start: 0.7796 (mmm-85) cc_final: 0.7197 (mmm-85) REVERT: B 186 ILE cc_start: 0.8889 (pt) cc_final: 0.8602 (tp) REVERT: B 240 ILE cc_start: 0.7963 (tp) cc_final: 0.7737 (mt) REVERT: B 405 HIS cc_start: 0.6674 (t70) cc_final: 0.6253 (t70) REVERT: B 433 THR cc_start: 0.8446 (OUTLIER) cc_final: 0.8166 (t) REVERT: B 467 LYS cc_start: 0.8477 (mmmm) cc_final: 0.8110 (mptt) REVERT: C 549 GLU cc_start: 0.8257 (pp20) cc_final: 0.7999 (pp20) REVERT: C 767 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9091 (pp) REVERT: C 775 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.7332 (m-80) REVERT: D 467 LYS cc_start: 0.8695 (mmmt) cc_final: 0.8225 (mptt) REVERT: D 671 PHE cc_start: 0.6822 (OUTLIER) cc_final: 0.6159 (t80) REVERT: D 702 MET cc_start: 0.6201 (mmt) cc_final: 0.5924 (mmt) outliers start: 96 outliers final: 77 residues processed: 343 average time/residue: 0.1079 time to fit residues: 62.5176 Evaluate side-chains 336 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 254 time to evaluate : 0.775 ------------------------------------------------------------------------------- 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 240 ILE 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 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 589 LEU Chi-restraints excluded: chain A residue 636 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 813 TRP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 367 LEU 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 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 643 LEU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 756 VAL 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 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 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 583 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 634 VAL 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 767 LEU Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 775 PHE 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 428 THR Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 643 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 90 optimal weight: 50.0000 chunk 279 optimal weight: 3.9990 chunk 170 optimal weight: 7.9990 chunk 113 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 144 optimal weight: 9.9990 chunk 141 optimal weight: 0.0770 chunk 269 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 146 optimal weight: 9.9990 chunk 115 optimal weight: 0.4980 overall best weight: 1.6542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 697 ASN D 184 ASN D 697 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.179931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.151878 restraints weight = 44877.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.142644 restraints weight = 52521.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.140020 restraints weight = 60267.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.140276 restraints weight = 48810.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.140448 restraints weight = 38343.329| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 21174 Z= 0.159 Angle : 0.626 12.375 29232 Z= 0.318 Chirality : 0.044 0.180 3782 Planarity : 0.004 0.048 3706 Dihedral : 5.231 56.181 3275 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.67 % Favored : 91.26 % Rotamer: Outliers : 6.10 % Allowed : 21.54 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.15), residues: 3148 helix: 1.25 (0.15), residues: 1312 sheet: -1.70 (0.26), residues: 368 loop : -2.30 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 716 TYR 0.012 0.001 TYR B 479 PHE 0.023 0.001 PHE A 579 TRP 0.011 0.001 TRP B 796 HIS 0.003 0.001 HIS B 486 Details of bonding type rmsd covalent geometry : bond 0.00371 (21156) covalent geometry : angle 0.62453 (29196) SS BOND : bond 0.00376 ( 18) SS BOND : angle 1.21975 ( 36) hydrogen bonds : bond 0.03997 ( 1036) hydrogen bonds : angle 4.24868 ( 3048) *********************** 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 361 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 257 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.7536 (pt) cc_final: 0.7262 (tp) REVERT: A 767 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9150 (pp) REVERT: A 776 ARG cc_start: 0.7855 (mmm-85) cc_final: 0.7281 (mmm-85) REVERT: B 186 ILE cc_start: 0.8989 (pt) cc_final: 0.8628 (tp) REVERT: B 240 ILE cc_start: 0.8095 (tp) cc_final: 0.7856 (mt) REVERT: B 405 HIS cc_start: 0.6863 (t70) cc_final: 0.6483 (t70) REVERT: B 433 THR cc_start: 0.8476 (OUTLIER) cc_final: 0.8200 (t) REVERT: B 467 LYS cc_start: 0.8483 (mmmm) cc_final: 0.8163 (mptt) REVERT: B 476 TYR cc_start: 0.7639 (p90) cc_final: 0.7274 (p90) REVERT: C 767 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9090 (pp) REVERT: C 775 PHE cc_start: 0.7661 (OUTLIER) cc_final: 0.7260 (m-80) REVERT: C 783 MET cc_start: 0.8024 (tpp) cc_final: 0.7281 (ttm) REVERT: D 99 PHE cc_start: 0.6074 (t80) cc_final: 0.5618 (t80) REVERT: D 467 LYS cc_start: 0.8691 (mmmt) cc_final: 0.8220 (mptt) REVERT: D 480 LEU cc_start: 0.7948 (tp) cc_final: 0.7707 (tp) REVERT: D 702 MET cc_start: 0.6298 (mmt) cc_final: 0.6048 (mmt) outliers start: 104 outliers final: 88 residues processed: 344 average time/residue: 0.1036 time to fit residues: 60.3655 Evaluate side-chains 341 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 249 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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 583 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 677 VAL Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 773 LEU 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 268 THR 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 465 LEU Chi-restraints excluded: chain B residue 508 MET 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 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 756 VAL 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 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 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 583 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 634 VAL 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 767 LEU Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 775 PHE 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 428 THR Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 566 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 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 101 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 144 optimal weight: 8.9990 chunk 129 optimal weight: 6.9990 chunk 257 optimal weight: 0.0980 chunk 24 optimal weight: 9.9990 chunk 3 optimal weight: 50.0000 chunk 59 optimal weight: 0.6980 chunk 82 optimal weight: 50.0000 chunk 292 optimal weight: 0.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 697 ASN D 697 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.177750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.148807 restraints weight = 45229.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.143792 restraints weight = 57290.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.141181 restraints weight = 50122.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.139451 restraints weight = 50072.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.138610 restraints weight = 41901.156| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 21174 Z= 0.221 Angle : 0.680 13.201 29232 Z= 0.350 Chirality : 0.045 0.201 3782 Planarity : 0.004 0.047 3706 Dihedral : 5.502 56.785 3275 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.78 % Favored : 90.12 % Rotamer: Outliers : 5.81 % Allowed : 22.07 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.15), residues: 3148 helix: 1.05 (0.15), residues: 1314 sheet: -1.70 (0.26), residues: 382 loop : -2.28 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 716 TYR 0.013 0.001 TYR A 599 PHE 0.025 0.002 PHE A 554 TRP 0.014 0.002 TRP A 629 HIS 0.004 0.001 HIS B 486 Details of bonding type rmsd covalent geometry : bond 0.00520 (21156) covalent geometry : angle 0.67884 (29196) SS BOND : bond 0.00457 ( 18) SS BOND : angle 1.28427 ( 36) hydrogen bonds : bond 0.04569 ( 1036) hydrogen bonds : angle 4.48744 ( 3048) ********************** 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 349 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 250 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 776 ARG cc_start: 0.7910 (mmm-85) cc_final: 0.7368 (mmm-85) REVERT: B 186 ILE cc_start: 0.8905 (pt) cc_final: 0.8504 (tp) REVERT: B 240 ILE cc_start: 0.7973 (tp) cc_final: 0.7720 (mt) REVERT: B 433 THR cc_start: 0.8321 (OUTLIER) cc_final: 0.8051 (t) REVERT: B 467 LYS cc_start: 0.8488 (mmmm) cc_final: 0.8168 (mptt) REVERT: C 775 PHE cc_start: 0.7781 (OUTLIER) cc_final: 0.7417 (m-80) REVERT: D 467 LYS cc_start: 0.8685 (mmmt) cc_final: 0.8220 (mptt) REVERT: D 702 MET cc_start: 0.6336 (mmt) cc_final: 0.6095 (mmt) REVERT: B 901 GLU cc_start: 0.4599 (mm-30) cc_final: 0.4050 (mm-30) outliers start: 99 outliers final: 87 residues processed: 335 average time/residue: 0.1058 time to fit residues: 60.0399 Evaluate side-chains 338 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 249 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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 583 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 677 VAL Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 268 THR 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 465 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 566 LEU 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 756 VAL 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 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 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 583 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 634 VAL 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 775 PHE 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 428 THR Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain D residue 513 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 259 optimal weight: 10.0000 chunk 80 optimal weight: 50.0000 chunk 103 optimal weight: 9.9990 chunk 239 optimal weight: 0.0010 chunk 52 optimal weight: 1.9990 chunk 278 optimal weight: 0.0670 chunk 293 optimal weight: 0.0970 chunk 88 optimal weight: 9.9990 chunk 233 optimal weight: 4.9990 chunk 201 optimal weight: 0.9980 chunk 8 optimal weight: 50.0000 overall best weight: 0.6324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 697 ASN D 697 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.181653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.151603 restraints weight = 45223.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.144252 restraints weight = 58741.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.140687 restraints weight = 51658.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.141018 restraints weight = 45635.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.141202 restraints weight = 36048.144| |-----------------------------------------------------------------------------| r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.3979 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= 0.113 Angle : 0.613 13.572 29232 Z= 0.305 Chirality : 0.043 0.194 3782 Planarity : 0.004 0.050 3706 Dihedral : 5.190 56.797 3275 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 4.81 % Allowed : 23.30 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.15), residues: 3148 helix: 1.35 (0.15), residues: 1304 sheet: -1.46 (0.28), residues: 362 loop : -2.16 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 716 TYR 0.019 0.001 TYR D 239 PHE 0.027 0.001 PHE B 637 TRP 0.010 0.001 TRP B 197 HIS 0.003 0.001 HIS A 592 Details of bonding type rmsd covalent geometry : bond 0.00250 (21156) covalent geometry : angle 0.61232 (29196) SS BOND : bond 0.00320 ( 18) SS BOND : angle 1.15408 ( 36) hydrogen bonds : bond 0.03622 ( 1036) hydrogen bonds : angle 4.14731 ( 3048) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3257.03 seconds wall clock time: 56 minutes 45.92 seconds (3405.92 seconds total)