Starting phenix.real_space_refine on Sun Mar 17 14:44:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szh_40916/03_2024/8szh_40916_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szh_40916/03_2024/8szh_40916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szh_40916/03_2024/8szh_40916.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szh_40916/03_2024/8szh_40916.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szh_40916/03_2024/8szh_40916_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szh_40916/03_2024/8szh_40916_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.051 sd= 0.156 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 P 4 5.49 5 S 108 5.16 5 C 11657 2.51 5 N 2968 2.21 5 O 3315 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 829": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18062 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 6579 Classifications: {'peptide': 835} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 32, 'TRANS': 802} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 5, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 6385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 812, 6385 Classifications: {'peptide': 812} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 31, 'TRANS': 780} Chain breaks: 3 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 54 Chain: "C" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1770 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "D" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2505 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ASN:plan1': 5, 'ARG:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 84 Chain: "E" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 408 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 144 Unusual residues: {' CA': 2, 'NAG': 1, 'PCW': 1, 'PO4': 1, 'SPM': 2, 'YP4': 1} Inner-chain residues flagged as termini: ['pdbres="TRP A 906 "'] Classifications: {'peptide': 1, 'undetermined': 8} Modifications used: {'COO': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 187 Unusual residues: {' CA': 2, 'CLR': 1, 'NAG': 2, 'PCW': 1, 'PO4': 1, 'SPM': 2, 'YP4': 1} Inner-chain residues flagged as termini: ['pdbres="TRP B1408 "'] Classifications: {'peptide': 1, 'undetermined': 10, 'water': 1} Modifications used: {'COO': 1} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 10.08, per 1000 atoms: 0.56 Number of scatterers: 18062 At special positions: 0 Unit cell: (91.9762, 114.536, 253.368, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 4 19.99 S 108 16.00 P 4 15.00 F 6 9.00 O 3315 8.00 N 2968 7.00 C 11657 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 449 " distance=2.03 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 562 " distance=2.03 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 568 " - pdb=" SG CYS A 582 " distance=2.03 Simple disulfide: pdb=" SG CYS A 585 " - pdb=" SG CYS A 598 " distance=2.03 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 765 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 449 " distance=2.03 Simple disulfide: pdb=" SG CYS B 542 " - pdb=" SG CYS B 562 " distance=2.03 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 582 " distance=2.03 Simple disulfide: pdb=" SG CYS B 585 " - pdb=" SG CYS B 598 " distance=2.03 Simple disulfide: pdb=" SG CYS B 677 " - pdb=" SG CYS B 765 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A 903 " - " ASN A 468 " " NAG B1404 " - " ASN B 468 " " NAG B1405 " - " ASN B 488 " " NAG F 1 " - " ASN A 488 " " NAG G 1 " - " ASN A 541 " " NAG H 1 " - " ASN B 541 " Time building additional restraints: 7.04 Conformation dependent library (CDL) restraints added in 3.3 seconds 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4270 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 70 helices and 21 sheets defined 38.2% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.18 Creating SS restraints... Processing helix chain 'A' and resid 65 through 82 removed outlier: 3.704A pdb=" N MET A 74 " --> pdb=" O TRP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 Processing helix chain 'A' and resid 116 through 123 removed outlier: 3.512A pdb=" N ASP A 121 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 159 removed outlier: 3.722A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 191 through 203 Processing helix chain 'A' and resid 219 through 232 Processing helix chain 'A' and resid 249 through 260 Processing helix chain 'A' and resid 273 through 286 Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 308 through 314 removed outlier: 4.987A pdb=" N HIS A 312 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL A 314 " --> pdb=" O PHE A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 336 removed outlier: 3.601A pdb=" N LYS A 336 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 356 Processing helix chain 'A' and resid 416 through 435 removed outlier: 3.600A pdb=" N ILE A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 465 Processing helix chain 'A' and resid 525 through 527 No H-bonds generated for 'chain 'A' and resid 525 through 527' Processing helix chain 'A' and resid 611 through 636 removed outlier: 4.248A pdb=" N ALA A 615 " --> pdb=" O PRO A 611 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 616 " --> pdb=" O PHE A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 645 Processing helix chain 'A' and resid 648 through 667 removed outlier: 4.072A pdb=" N SER A 665 " --> pdb=" O CYS A 661 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU A 666 " --> pdb=" O PHE A 662 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N PHE A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 706 removed outlier: 5.576A pdb=" N GLN A 681 " --> pdb=" O CYS A 677 " (cutoff:3.500A) Proline residue: A 682 - end of helix removed outlier: 3.909A pdb=" N CYS A 691 " --> pdb=" O SER A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 718 No H-bonds generated for 'chain 'A' and resid 715 through 718' Processing helix chain 'A' and resid 723 through 745 removed outlier: 4.589A pdb=" N MET A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N GLN A 735 " --> pdb=" O CYS A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 794 removed outlier: 3.964A pdb=" N LEU A 776 " --> pdb=" O ALA A 772 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE A 788 " --> pdb=" O ALA A 784 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE A 789 " --> pdb=" O ALA A 785 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER A 794 " --> pdb=" O PHE A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 820 removed outlier: 3.957A pdb=" N THR A 808 " --> pdb=" O ALA A 804 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE A 809 " --> pdb=" O LYS A 805 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE A 813 " --> pdb=" O PHE A 809 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE A 814 " --> pdb=" O SER A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 827 Processing helix chain 'A' and resid 832 through 861 removed outlier: 5.671A pdb=" N ASN A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LYS A 856 " --> pdb=" O ILE A 852 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR A 858 " --> pdb=" O PHE A 854 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 859 " --> pdb=" O ASN A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 878 removed outlier: 3.722A pdb=" N ARG A 873 " --> pdb=" O ILE A 869 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N CYS A 874 " --> pdb=" O GLU A 870 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ALA A 878 " --> pdb=" O CYS A 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 82 removed outlier: 3.683A pdb=" N LEU B 71 " --> pdb=" O GLY B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 88 No H-bonds generated for 'chain 'B' and resid 85 through 88' Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 116 through 123 Processing helix chain 'B' and resid 147 through 159 removed outlier: 3.680A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU B 159 " --> pdb=" O ASN B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 191 through 203 Processing helix chain 'B' and resid 219 through 232 removed outlier: 3.549A pdb=" N GLU B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 259 removed outlier: 3.563A pdb=" N VAL B 258 " --> pdb=" O HIS B 254 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 286 Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 308 through 314 removed outlier: 4.859A pdb=" N HIS B 312 " --> pdb=" O GLN B 309 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL B 314 " --> pdb=" O PHE B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 336 removed outlier: 3.697A pdb=" N LYS B 336 " --> pdb=" O GLU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 356 Processing helix chain 'B' and resid 401 through 403 No H-bonds generated for 'chain 'B' and resid 401 through 403' Processing helix chain 'B' and resid 417 through 435 removed outlier: 3.674A pdb=" N TYR B 421 " --> pdb=" O SER B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'B' and resid 452 through 454 No H-bonds generated for 'chain 'B' and resid 452 through 454' Processing helix chain 'B' and resid 457 through 465 Processing helix chain 'B' and resid 525 through 527 No H-bonds generated for 'chain 'B' and resid 525 through 527' Processing helix chain 'B' and resid 530 through 532 No H-bonds generated for 'chain 'B' and resid 530 through 532' Processing helix chain 'B' and resid 611 through 636 removed outlier: 3.820A pdb=" N LEU B 616 " --> pdb=" O PHE B 612 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE B 619 " --> pdb=" O ALA B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 645 Processing helix chain 'B' and resid 648 through 668 removed outlier: 3.935A pdb=" N TYR B 652 " --> pdb=" O ARG B 648 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU B 653 " --> pdb=" O GLU B 649 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER B 665 " --> pdb=" O CYS B 661 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LEU B 666 " --> pdb=" O PHE B 662 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N PHE B 667 " --> pdb=" O SER B 663 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N PHE B 668 " --> pdb=" O SER B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 698 removed outlier: 4.106A pdb=" N PHE B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS B 698 " --> pdb=" O CYS B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 703 No H-bonds generated for 'chain 'B' and resid 700 through 703' Processing helix chain 'B' and resid 725 through 745 removed outlier: 3.993A pdb=" N MET B 734 " --> pdb=" O LEU B 730 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLN B 735 " --> pdb=" O CYS B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 794 removed outlier: 3.940A pdb=" N PHE B 775 " --> pdb=" O MET B 771 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER B 794 " --> pdb=" O PHE B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 827 removed outlier: 3.541A pdb=" N ILE B 807 " --> pdb=" O GLU B 803 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR B 808 " --> pdb=" O ALA B 804 " (cutoff:3.500A) Proline residue: B 823 - end of helix Processing helix chain 'B' and resid 833 through 860 removed outlier: 3.608A pdb=" N ILE B 839 " --> pdb=" O ALA B 835 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA B 840 " --> pdb=" O VAL B 836 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE B 841 " --> pdb=" O GLU B 837 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ASN B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LYS B 856 " --> pdb=" O ILE B 852 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR B 858 " --> pdb=" O PHE B 854 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE B 859 " --> pdb=" O ASN B 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 32 removed outlier: 4.127A pdb=" N LYS C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 52 Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 212 through 215 removed outlier: 3.589A pdb=" N PHE C 215 " --> pdb=" O ILE C 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 212 through 215' Processing helix chain 'C' and resid 227 through 230 Processing helix chain 'C' and resid 242 through 254 removed outlier: 3.563A pdb=" N LYS C 248 " --> pdb=" O HIS C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 278 Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 296 through 310 removed outlier: 4.178A pdb=" N LEU C 310 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 351 Processing helix chain 'D' and resid 4 through 25 removed outlier: 3.945A pdb=" N ALA D 24 " --> pdb=" O ASP D 20 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N CYS D 25 " --> pdb=" O ALA D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 34 Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'E' and resid 9 through 23 Processing helix chain 'E' and resid 30 through 43 removed outlier: 3.548A pdb=" N ALA E 35 " --> pdb=" O SER E 31 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.512A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N PHE A 98 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 139 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N GLY A 35 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL A 141 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N LEU A 37 " --> pdb=" O VAL A 141 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 240 through 243 removed outlier: 9.447A pdb=" N GLU A 241 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR A 211 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N ILE A 243 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ALA A 213 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL A 266 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N ILE A 212 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL A 268 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N ALA A 214 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N PHE A 270 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE A 292 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N VAL A 269 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU A 294 " --> pdb=" O VAL A 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 318 through 321 removed outlier: 3.664A pdb=" N GLY A 509 " --> pdb=" O ILE A 491 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ASN A 493 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLU A 507 " --> pdb=" O ASN A 493 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N HIS A 495 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N PHE A 505 " --> pdb=" O HIS A 495 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 550 through 552 Processing sheet with id= E, first strand: chain 'A' and resid 589 through 591 Processing sheet with id= F, first strand: chain 'A' and resid 602 through 604 removed outlier: 3.833A pdb=" N ILE A 763 " --> pdb=" O GLU A 604 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 93 through 99 removed outlier: 6.238A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU B 34 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N PHE B 98 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLY B 35 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N VAL B 141 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LEU B 37 " --> pdb=" O VAL B 141 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 240 through 243 removed outlier: 9.603A pdb=" N GLU B 241 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR B 211 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N ILE B 243 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA B 213 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL B 266 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE B 212 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N VAL B 268 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ALA B 214 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N PHE B 270 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE B 292 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL B 269 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU B 294 " --> pdb=" O VAL B 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 318 through 321 removed outlier: 3.629A pdb=" N GLY B 509 " --> pdb=" O ILE B 491 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASN B 493 " --> pdb=" O GLU B 507 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N GLU B 507 " --> pdb=" O ASN B 493 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N HIS B 495 " --> pdb=" O PHE B 505 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N PHE B 505 " --> pdb=" O HIS B 495 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 468 through 470 Processing sheet with id= K, first strand: chain 'B' and resid 550 through 553 Processing sheet with id= L, first strand: chain 'B' and resid 589 through 591 Processing sheet with id= M, first strand: chain 'B' and resid 602 through 604 removed outlier: 3.675A pdb=" N ILE B 763 " --> pdb=" O GLU B 604 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 319 through 323 removed outlier: 6.796A pdb=" N ILE C 264 " --> pdb=" O TYR C 320 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N HIS C 322 " --> pdb=" O ILE C 264 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU C 266 " --> pdb=" O HIS C 322 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA C 220 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE C 189 " --> pdb=" O PHE C 196 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 111 through 113 removed outlier: 3.618A pdb=" N VAL D 112 " --> pdb=" O TYR D 124 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR D 124 " --> pdb=" O VAL D 112 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG D 137 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ASN D 125 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL D 135 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 178 through 181 removed outlier: 4.158A pdb=" N THR D 165 " --> pdb=" O SER D 161 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 187 through 192 removed outlier: 6.731A pdb=" N GLY D 202 " --> pdb=" O MET D 188 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LEU D 190 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL D 200 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU D 192 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N LEU D 198 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS D 209 " --> pdb=" O SER D 201 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLN D 220 " --> pdb=" O LEU D 210 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ASP D 212 " --> pdb=" O CYS D 218 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N CYS D 218 " --> pdb=" O ASP D 212 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 229 through 234 removed outlier: 6.754A pdb=" N GLY D 244 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE D 232 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA D 242 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N PHE D 234 " --> pdb=" O ALA D 240 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ALA D 240 " --> pdb=" O PHE D 234 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG D 251 " --> pdb=" O THR D 243 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N MET D 262 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ASP D 254 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLU D 260 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 306 through 308 removed outlier: 3.644A pdb=" N GLY D 306 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER D 275 " --> pdb=" O GLY D 288 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 46 through 51 removed outlier: 3.630A pdb=" N ARG D 46 " --> pdb=" O ASN D 340 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE D 338 " --> pdb=" O ARG D 48 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N THR D 50 " --> pdb=" O LEU D 336 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU D 336 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS D 317 " --> pdb=" O GLY D 330 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 58 through 61 removed outlier: 6.814A pdb=" N ALA D 73 " --> pdb=" O TYR D 59 " (cutoff:3.500A) 634 hydrogen bonds defined for protein. 1842 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.14 Time building geometry restraints manager: 7.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2908 1.32 - 1.45: 5213 1.45 - 1.58: 10195 1.58 - 1.71: 18 1.71 - 1.84: 136 Bond restraints: 18470 Sorted by residual: bond pdb=" C31 PCW B1403 " pdb=" O2 PCW B1403 " ideal model delta sigma weight residual 1.333 1.488 -0.155 2.00e-02 2.50e+03 6.03e+01 bond pdb=" C31 PCW A 902 " pdb=" O2 PCW A 902 " ideal model delta sigma weight residual 1.333 1.484 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" C31 PCW B1403 " pdb=" C32 PCW B1403 " ideal model delta sigma weight residual 1.502 1.604 -0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" C31 PCW A 902 " pdb=" C32 PCW A 902 " ideal model delta sigma weight residual 1.502 1.601 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" C16 PCW B1403 " pdb=" C17 PCW B1403 " ideal model delta sigma weight residual 1.523 1.622 -0.099 2.00e-02 2.50e+03 2.44e+01 ... (remaining 18465 not shown) Histogram of bond angle deviations from ideal: 95.26 - 106.81: 448 106.81 - 118.36: 13739 118.36 - 129.91: 10708 129.91 - 141.46: 130 141.46 - 153.02: 2 Bond angle restraints: 25027 Sorted by residual: angle pdb=" N ARG A 866 " pdb=" CA ARG A 866 " pdb=" C ARG A 866 " ideal model delta sigma weight residual 113.23 95.26 17.97 1.22e+00 6.72e-01 2.17e+02 angle pdb=" N ILE A 869 " pdb=" CA ILE A 869 " pdb=" C ILE A 869 " ideal model delta sigma weight residual 112.83 104.47 8.36 9.90e-01 1.02e+00 7.13e+01 angle pdb=" C18 PCW B1403 " pdb=" C19 PCW B1403 " pdb=" C20 PCW B1403 " ideal model delta sigma weight residual 127.82 153.02 -25.20 3.00e+00 1.11e-01 7.05e+01 angle pdb=" C18 PCW A 902 " pdb=" C19 PCW A 902 " pdb=" C20 PCW A 902 " ideal model delta sigma weight residual 127.82 152.59 -24.77 3.00e+00 1.11e-01 6.82e+01 angle pdb=" CA PHE A 862 " pdb=" C PHE A 862 " pdb=" O PHE A 862 " ideal model delta sigma weight residual 121.78 111.37 10.41 1.28e+00 6.10e-01 6.62e+01 ... (remaining 25022 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.04: 10156 20.04 - 40.08: 794 40.08 - 60.11: 112 60.11 - 80.15: 24 80.15 - 100.19: 14 Dihedral angle restraints: 11100 sinusoidal: 4505 harmonic: 6595 Sorted by residual: dihedral pdb=" CB CYS A 585 " pdb=" SG CYS A 585 " pdb=" SG CYS A 598 " pdb=" CB CYS A 598 " ideal model delta sinusoidal sigma weight residual -86.00 -172.13 86.13 1 1.00e+01 1.00e-02 8.95e+01 dihedral pdb=" CB CYS A 437 " pdb=" SG CYS A 437 " pdb=" SG CYS A 449 " pdb=" CB CYS A 449 " ideal model delta sinusoidal sigma weight residual 93.00 171.14 -78.14 1 1.00e+01 1.00e-02 7.63e+01 dihedral pdb=" CB CYS B 677 " pdb=" SG CYS B 677 " pdb=" SG CYS B 765 " pdb=" CB CYS B 765 " ideal model delta sinusoidal sigma weight residual -86.00 -41.20 -44.80 1 1.00e+01 1.00e-02 2.79e+01 ... (remaining 11097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.032: 2823 1.032 - 2.064: 0 2.064 - 3.095: 0 3.095 - 4.127: 0 4.127 - 5.159: 1 Chirality restraints: 2824 Sorted by residual: chirality pdb=" C2 PCW A 902 " pdb=" C1 PCW A 902 " pdb=" C3 PCW A 902 " pdb=" O2 PCW A 902 " both_signs ideal model delta sigma weight residual False -2.32 2.84 -5.16 2.00e-01 2.50e+01 6.65e+02 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.45 0.05 2.00e-02 2.50e+03 6.24e+00 chirality pdb=" C2 PCW B1403 " pdb=" C1 PCW B1403 " pdb=" C3 PCW B1403 " pdb=" O2 PCW B1403 " both_signs ideal model delta sigma weight residual False -2.32 -2.81 0.49 2.00e-01 2.50e+01 6.02e+00 ... (remaining 2821 not shown) Planarity restraints: 3148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " 0.198 2.00e-02 2.50e+03 1.63e-01 3.32e+02 pdb=" C7 NAG H 2 " -0.052 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " 0.143 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " -0.265 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 541 " -0.063 2.00e-02 2.50e+03 6.88e-02 5.92e+01 pdb=" CG ASN B 541 " 0.122 2.00e-02 2.50e+03 pdb=" OD1 ASN B 541 " -0.046 2.00e-02 2.50e+03 pdb=" ND2 ASN B 541 " 0.029 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 541 " -0.031 2.00e-02 2.50e+03 6.44e-02 4.15e+01 pdb=" CG ASN B 541 " 0.111 2.00e-02 2.50e+03 pdb=" OD1 ASN B 541 " -0.045 2.00e-02 2.50e+03 pdb=" ND2 ASN B 541 " -0.035 2.00e-02 2.50e+03 ... (remaining 3145 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1161 2.74 - 3.28: 16918 3.28 - 3.82: 27684 3.82 - 4.36: 33446 4.36 - 4.90: 59298 Nonbonded interactions: 138507 Sorted by model distance: nonbonded pdb=" OG SER D 331 " pdb=" OD1 ASP D 333 " model vdw 2.196 2.440 nonbonded pdb=" OD2 ASP A 238 " pdb=" OG SER A 262 " model vdw 2.208 2.440 nonbonded pdb=" O PHE B 668 " pdb=" OG SER B 834 " model vdw 2.220 2.440 nonbonded pdb=" O LEU B 87 " pdb=" NE2 GLN B 432 " model vdw 2.227 2.520 nonbonded pdb=" OE1 GLN B 253 " pdb=" NH2 ARG B 286 " model vdw 2.250 2.520 ... (remaining 138502 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 131 or (resid 132 through 135 and (name N or na \ me CA or name C or name O or name CB )) or resid 136 through 362 or resid 392 th \ rough 516 or (resid 517 and (name N or name CA or name C or name O or name CB )) \ or resid 518 through 586 or (resid 587 and (name N or name CA or name C or name \ O or name CB )) or resid 588 through 700 or (resid 701 and (name N or name CA o \ r name C or name O or name CB )) or resid 702 or (resid 703 and (name N or name \ CA or name C or name O or name CB )) or resid 704 through 706 or (resid 707 thro \ ugh 709 and (name N or name CA or name C or name O or name CB )) or resid 722 th \ rough 798 or (resid 799 and (name N or name CA or name C or name O or name CB )) \ or resid 800 through 861 or (resid 862 through 863 and (name N or name CA or na \ me C or name O or name CB )) or resid 864 through 865 or (resid 866 through 868 \ and (name N or name CA or name C or name O or name CB )) or resid 869 through 87 \ 0 or (resid 871 through 873 and (name N or name CA or name C or name O or name C \ B )) or resid 874 through 876 or resid 903 through 909)) selection = (chain 'B' and (resid 20 through 47 or (resid 48 and (name N or name CA or name \ C or name O or name CB )) or resid 49 through 124 or (resid 125 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 131 through 135 and (name N o \ r name CA or name C or name O or name CB )) or resid 136 through 361 or (resid 3 \ 62 and (name N or name CA or name C or name O or name CB )) or resid 392 through \ 498 or (resid 499 through 500 and (name N or name CA or name C or name O or nam \ e CB )) or resid 501 through 591 or (resid 592 and (name N or name CA or name C \ or name O or name CB )) or resid 593 through 867 or (resid 868 and (name N or na \ me CA or name C or name O or name CB )) or resid 869 through 876 or resid 1405 t \ hrough 1411)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 23.460 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 49.820 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 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 : 0.006 0.155 18470 Z= 0.390 Angle : 0.780 25.195 25027 Z= 0.440 Chirality : 0.110 5.159 2824 Planarity : 0.005 0.163 3142 Dihedral : 14.616 100.191 6776 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.18), residues: 2243 helix: 0.97 (0.18), residues: 882 sheet: -0.52 (0.27), residues: 379 loop : -1.16 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 719 HIS 0.006 0.001 HIS A 715 PHE 0.045 0.001 PHE B 612 TYR 0.042 0.002 TYR C 354 ARG 0.015 0.000 ARG A 886 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 1.700 Fit side-chains revert: symmetry clash REVERT: A 231 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7601 (mt-10) REVERT: B 336 LYS cc_start: 0.8430 (mmtm) cc_final: 0.8224 (mptt) REVERT: B 558 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7617 (mp0) REVERT: B 609 THR cc_start: 0.8789 (m) cc_final: 0.8389 (p) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.3406 time to fit residues: 127.7882 Evaluate side-chains 196 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 4.9990 chunk 169 optimal weight: 0.4980 chunk 94 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 175 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 203 optimal weight: 0.1980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN B 117 GLN ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.0807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18470 Z= 0.171 Angle : 0.494 6.264 25027 Z= 0.265 Chirality : 0.042 0.171 2824 Planarity : 0.004 0.047 3142 Dihedral : 8.789 89.774 2833 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.33 % Allowed : 6.57 % Favored : 92.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.18), residues: 2243 helix: 1.26 (0.18), residues: 883 sheet: -0.48 (0.27), residues: 386 loop : -1.08 (0.19), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 719 HIS 0.006 0.001 HIS B 766 PHE 0.016 0.001 PHE B 814 TYR 0.014 0.001 TYR C 230 ARG 0.005 0.000 ARG D 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 205 time to evaluate : 2.098 Fit side-chains revert: symmetry clash REVERT: A 231 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7475 (mt-10) REVERT: B 336 LYS cc_start: 0.8452 (mmtm) cc_final: 0.8221 (mptt) REVERT: B 558 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7612 (mp0) REVERT: B 612 PHE cc_start: 0.7527 (t80) cc_final: 0.7241 (t80) REVERT: D 197 ARG cc_start: 0.8218 (ttp-110) cc_final: 0.7859 (mtp85) outliers start: 25 outliers final: 15 residues processed: 216 average time/residue: 0.3386 time to fit residues: 108.5147 Evaluate side-chains 209 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 194 time to evaluate : 2.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 169 optimal weight: 0.6980 chunk 138 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 203 optimal weight: 0.4980 chunk 220 optimal weight: 6.9990 chunk 181 optimal weight: 1.9990 chunk 202 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 163 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 GLN ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18470 Z= 0.180 Angle : 0.479 5.741 25027 Z= 0.257 Chirality : 0.042 0.166 2824 Planarity : 0.004 0.047 3142 Dihedral : 8.146 88.804 2833 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.33 % Allowed : 9.29 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.18), residues: 2243 helix: 1.29 (0.18), residues: 887 sheet: -0.44 (0.27), residues: 381 loop : -1.09 (0.19), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 818 HIS 0.004 0.001 HIS B 429 PHE 0.017 0.001 PHE B 814 TYR 0.012 0.001 TYR A 421 ARG 0.005 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 201 time to evaluate : 1.967 Fit side-chains revert: symmetry clash REVERT: B 336 LYS cc_start: 0.8462 (mmtm) cc_final: 0.8226 (mptt) REVERT: B 558 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7617 (mp0) REVERT: B 753 ASN cc_start: 0.7849 (t0) cc_final: 0.7459 (t0) outliers start: 25 outliers final: 19 residues processed: 214 average time/residue: 0.3346 time to fit residues: 106.7876 Evaluate side-chains 211 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 192 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 105 optimal weight: 0.1980 chunk 22 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 chunk 216 optimal weight: 4.9990 chunk 106 optimal weight: 0.0020 chunk 193 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 GLN ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18470 Z= 0.234 Angle : 0.509 5.857 25027 Z= 0.273 Chirality : 0.043 0.177 2824 Planarity : 0.004 0.048 3142 Dihedral : 8.018 87.984 2833 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.98 % Allowed : 10.78 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.18), residues: 2243 helix: 1.29 (0.18), residues: 880 sheet: -0.43 (0.27), residues: 384 loop : -1.17 (0.19), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 818 HIS 0.005 0.001 HIS B 429 PHE 0.019 0.002 PHE A 789 TYR 0.013 0.001 TYR B 751 ARG 0.004 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 198 time to evaluate : 2.086 Fit side-chains revert: symmetry clash REVERT: A 789 PHE cc_start: 0.8171 (t80) cc_final: 0.7907 (t80) REVERT: B 336 LYS cc_start: 0.8479 (mmtm) cc_final: 0.8227 (mptt) REVERT: B 558 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7656 (mp0) REVERT: B 753 ASN cc_start: 0.7853 (t0) cc_final: 0.7542 (t0) REVERT: D 229 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8338 (mt) REVERT: D 234 PHE cc_start: 0.8588 (OUTLIER) cc_final: 0.8271 (m-80) outliers start: 37 outliers final: 23 residues processed: 223 average time/residue: 0.3348 time to fit residues: 111.1451 Evaluate side-chains 218 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 193 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 161 optimal weight: 3.9990 chunk 89 optimal weight: 0.0040 chunk 184 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 647 ASN B 117 GLN ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 18470 Z= 0.260 Angle : 0.521 6.614 25027 Z= 0.279 Chirality : 0.043 0.182 2824 Planarity : 0.004 0.048 3142 Dihedral : 8.009 88.184 2833 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.24 % Allowed : 11.59 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.18), residues: 2243 helix: 1.22 (0.18), residues: 881 sheet: -0.43 (0.27), residues: 377 loop : -1.22 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 818 HIS 0.005 0.001 HIS B 429 PHE 0.019 0.002 PHE A 444 TYR 0.012 0.001 TYR A 421 ARG 0.005 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 187 time to evaluate : 1.925 Fit side-chains revert: symmetry clash REVERT: A 789 PHE cc_start: 0.8165 (t80) cc_final: 0.7908 (t80) REVERT: B 117 GLN cc_start: 0.7313 (tm130) cc_final: 0.7037 (tm-30) REVERT: B 336 LYS cc_start: 0.8490 (mmtm) cc_final: 0.8224 (mptt) REVERT: B 558 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7631 (mp0) REVERT: B 697 VAL cc_start: 0.7685 (t) cc_final: 0.7380 (t) REVERT: B 753 ASN cc_start: 0.7884 (t0) cc_final: 0.7553 (t0) REVERT: B 876 THR cc_start: 0.6161 (OUTLIER) cc_final: 0.5736 (m) REVERT: D 229 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8338 (mt) outliers start: 42 outliers final: 28 residues processed: 214 average time/residue: 0.3152 time to fit residues: 101.0661 Evaluate side-chains 217 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 187 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 876 THR Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 290 TYR Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain D residue 15 LYS Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 2.9990 chunk 194 optimal weight: 0.7980 chunk 42 optimal weight: 0.4980 chunk 127 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 216 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 113 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN B 432 GLN ** B 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS C 333 GLN D 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18470 Z= 0.182 Angle : 0.485 10.752 25027 Z= 0.259 Chirality : 0.042 0.166 2824 Planarity : 0.004 0.047 3142 Dihedral : 7.782 86.375 2833 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.98 % Allowed : 12.65 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.18), residues: 2243 helix: 1.33 (0.18), residues: 879 sheet: -0.44 (0.27), residues: 379 loop : -1.19 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 818 HIS 0.003 0.001 HIS B 429 PHE 0.016 0.001 PHE B 814 TYR 0.014 0.001 TYR C 230 ARG 0.006 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 193 time to evaluate : 2.196 Fit side-chains revert: symmetry clash REVERT: A 789 PHE cc_start: 0.8200 (t80) cc_final: 0.7929 (t80) REVERT: B 336 LYS cc_start: 0.8464 (mmtm) cc_final: 0.8198 (mptt) REVERT: B 558 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7667 (mp0) REVERT: B 697 VAL cc_start: 0.7667 (t) cc_final: 0.7314 (t) REVERT: B 753 ASN cc_start: 0.7958 (t0) cc_final: 0.7638 (t0) REVERT: B 876 THR cc_start: 0.6090 (OUTLIER) cc_final: 0.5671 (m) REVERT: D 229 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8294 (mt) outliers start: 37 outliers final: 30 residues processed: 217 average time/residue: 0.3340 time to fit residues: 107.7385 Evaluate side-chains 220 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 188 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 876 THR Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 290 TYR Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 chunk 121 optimal weight: 0.0970 chunk 215 optimal weight: 1.9990 chunk 135 optimal weight: 0.0870 chunk 131 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.2362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 754 GLN B 117 GLN ** B 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS C 333 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18470 Z= 0.280 Angle : 0.541 9.429 25027 Z= 0.288 Chirality : 0.044 0.185 2824 Planarity : 0.004 0.051 3142 Dihedral : 7.863 87.399 2833 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.40 % Allowed : 12.65 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.18), residues: 2243 helix: 1.18 (0.18), residues: 881 sheet: -0.44 (0.28), residues: 375 loop : -1.24 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 818 HIS 0.005 0.001 HIS B 429 PHE 0.027 0.002 PHE D 235 TYR 0.017 0.001 TYR B 751 ARG 0.006 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 185 time to evaluate : 1.955 Fit side-chains revert: symmetry clash REVERT: A 603 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8700 (mm) REVERT: B 117 GLN cc_start: 0.7314 (tm130) cc_final: 0.7048 (tm-30) REVERT: B 307 MET cc_start: 0.8841 (mtp) cc_final: 0.8618 (mtt) REVERT: B 336 LYS cc_start: 0.8494 (mmtm) cc_final: 0.8226 (mptt) REVERT: B 558 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7646 (mp0) REVERT: B 697 VAL cc_start: 0.7733 (t) cc_final: 0.7449 (t) REVERT: B 753 ASN cc_start: 0.7963 (t0) cc_final: 0.6907 (t0) REVERT: B 876 THR cc_start: 0.6094 (OUTLIER) cc_final: 0.5687 (m) REVERT: D 229 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8344 (mt) outliers start: 45 outliers final: 27 residues processed: 215 average time/residue: 0.3212 time to fit residues: 102.8436 Evaluate side-chains 213 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 183 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 769 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 876 THR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 290 TYR Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 1.9990 chunk 86 optimal weight: 0.0870 chunk 128 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 106 optimal weight: 0.0970 chunk 20 optimal weight: 3.9990 chunk 169 optimal weight: 0.0020 overall best weight: 0.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18470 Z= 0.137 Angle : 0.460 9.446 25027 Z= 0.245 Chirality : 0.041 0.152 2824 Planarity : 0.003 0.049 3142 Dihedral : 7.462 84.412 2833 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.76 % Allowed : 13.13 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.18), residues: 2243 helix: 1.43 (0.18), residues: 875 sheet: -0.44 (0.28), residues: 380 loop : -1.12 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 299 HIS 0.002 0.001 HIS B 766 PHE 0.022 0.001 PHE D 235 TYR 0.013 0.001 TYR C 230 ARG 0.007 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 182 time to evaluate : 2.133 Fit side-chains revert: symmetry clash REVERT: A 603 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8627 (mm) REVERT: A 789 PHE cc_start: 0.8237 (t80) cc_final: 0.7900 (t80) REVERT: B 336 LYS cc_start: 0.8435 (mmtm) cc_final: 0.8180 (mptt) REVERT: B 558 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7626 (mp0) REVERT: B 697 VAL cc_start: 0.7747 (t) cc_final: 0.7383 (t) REVERT: B 876 THR cc_start: 0.6084 (OUTLIER) cc_final: 0.5688 (m) REVERT: C 302 TYR cc_start: 0.6867 (t80) cc_final: 0.6323 (t80) REVERT: D 229 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8276 (mt) outliers start: 33 outliers final: 25 residues processed: 203 average time/residue: 0.3504 time to fit residues: 106.0459 Evaluate side-chains 211 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 183 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 876 THR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 290 TYR Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 0.5980 chunk 206 optimal weight: 2.9990 chunk 188 optimal weight: 0.0010 chunk 201 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 157 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 190 optimal weight: 0.4980 chunk 200 optimal weight: 0.8980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 754 GLN ** B 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18470 Z= 0.153 Angle : 0.461 9.169 25027 Z= 0.245 Chirality : 0.041 0.159 2824 Planarity : 0.004 0.049 3142 Dihedral : 7.328 83.484 2833 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.66 % Allowed : 13.35 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.18), residues: 2243 helix: 1.49 (0.18), residues: 874 sheet: -0.39 (0.28), residues: 381 loop : -1.12 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 299 HIS 0.003 0.001 HIS B 429 PHE 0.023 0.001 PHE D 235 TYR 0.012 0.001 TYR A 421 ARG 0.007 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 190 time to evaluate : 1.972 Fit side-chains revert: symmetry clash REVERT: A 603 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8648 (mm) REVERT: A 789 PHE cc_start: 0.8229 (t80) cc_final: 0.7916 (t80) REVERT: B 117 GLN cc_start: 0.7327 (tm-30) cc_final: 0.7065 (tm-30) REVERT: B 336 LYS cc_start: 0.8439 (mmtm) cc_final: 0.8190 (mptt) REVERT: B 558 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7646 (mp0) REVERT: B 697 VAL cc_start: 0.7783 (t) cc_final: 0.7415 (t) REVERT: B 876 THR cc_start: 0.6141 (OUTLIER) cc_final: 0.5750 (m) REVERT: C 302 TYR cc_start: 0.6842 (t80) cc_final: 0.6310 (t80) REVERT: D 229 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8299 (mt) outliers start: 31 outliers final: 21 residues processed: 209 average time/residue: 0.3203 time to fit residues: 99.5450 Evaluate side-chains 209 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 185 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 876 THR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 0.9980 chunk 212 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 223 optimal weight: 0.0370 chunk 205 optimal weight: 0.9980 chunk 177 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 137 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 647 ASN ** B 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18470 Z= 0.231 Angle : 0.507 8.970 25027 Z= 0.270 Chirality : 0.043 0.176 2824 Planarity : 0.004 0.054 3142 Dihedral : 7.472 84.487 2833 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.49 % Allowed : 13.83 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.18), residues: 2243 helix: 1.33 (0.18), residues: 879 sheet: -0.44 (0.28), residues: 380 loop : -1.15 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 818 HIS 0.005 0.001 HIS B 429 PHE 0.025 0.002 PHE D 235 TYR 0.013 0.001 TYR A 421 ARG 0.008 0.000 ARG B 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 183 time to evaluate : 2.043 Fit side-chains revert: symmetry clash REVERT: A 603 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8669 (mm) REVERT: A 789 PHE cc_start: 0.8211 (t80) cc_final: 0.7906 (t80) REVERT: B 117 GLN cc_start: 0.7335 (tm-30) cc_final: 0.7066 (tm-30) REVERT: B 336 LYS cc_start: 0.8468 (mmtm) cc_final: 0.8207 (mptt) REVERT: B 558 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7636 (mp0) REVERT: B 697 VAL cc_start: 0.7800 (t) cc_final: 0.7483 (t) REVERT: B 876 THR cc_start: 0.6134 (OUTLIER) cc_final: 0.5746 (m) REVERT: D 17 GLN cc_start: 0.7507 (tm-30) cc_final: 0.7298 (tt0) REVERT: D 229 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8309 (mt) outliers start: 28 outliers final: 24 residues processed: 201 average time/residue: 0.3435 time to fit residues: 103.4223 Evaluate side-chains 209 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 182 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 769 SER Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 876 THR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 0.7980 chunk 189 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 177 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 754 GLN ** B 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.087653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.072288 restraints weight = 37123.983| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.98 r_work: 0.2965 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18470 Z= 0.250 Angle : 0.524 8.766 25027 Z= 0.278 Chirality : 0.043 0.179 2824 Planarity : 0.004 0.056 3142 Dihedral : 7.606 84.521 2833 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.66 % Allowed : 13.72 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.18), residues: 2243 helix: 1.23 (0.18), residues: 879 sheet: -0.46 (0.28), residues: 379 loop : -1.17 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 818 HIS 0.005 0.001 HIS B 429 PHE 0.025 0.002 PHE D 235 TYR 0.012 0.001 TYR B 751 ARG 0.008 0.000 ARG B 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3994.48 seconds wall clock time: 72 minutes 52.59 seconds (4372.59 seconds total)