Starting phenix.real_space_refine on Sun Jul 5 13:30:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dit_46918/07_2026/9dit_46918.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dit_46918/07_2026/9dit_46918.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dit_46918/07_2026/9dit_46918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dit_46918/07_2026/9dit_46918.map" model { file = "/net/cci-nas-00/data/ceres_data/9dit_46918/07_2026/9dit_46918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dit_46918/07_2026/9dit_46918.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 8 9.91 5 K 5 8.98 5 Mg 4 5.21 5 S 172 5.16 5 C 18328 2.51 5 N 4588 2.21 5 O 5116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 136 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28221 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7051 Classifications: {'peptide': 899} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 35, 'TRANS': 863} Chain breaks: 5 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'ARG:plan': 7, 'ASN:plan1': 3, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 72 Chain: "B" Number of atoms: 7051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7051 Classifications: {'peptide': 899} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 35, 'TRANS': 863} Chain breaks: 5 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'ARG:plan': 7, 'ASN:plan1': 3, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 72 Chain: "C" Number of atoms: 7051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7051 Classifications: {'peptide': 899} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 35, 'TRANS': 863} Chain breaks: 5 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'ARG:plan': 7, 'ASN:plan1': 3, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 72 Chain: "D" Number of atoms: 7051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7051 Classifications: {'peptide': 899} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 35, 'TRANS': 863} Chain breaks: 5 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'ARG:plan': 7, 'ASN:plan1': 3, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 72 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 1 Ad-hoc single atom residues: {' K': 1, ' CA': 2} Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain breaks: 3 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 1 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 1 Ad-hoc single atom residues: {' K': 4, ' CA': 2} Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain breaks: 6 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 1 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Time building chain proxies: 6.44, per 1000 atoms: 0.23 Number of scatterers: 28221 At special positions: 0 Unit cell: (149.883, 148.82, 123.308, 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 8 19.99 K 5 19.00 S 172 16.00 Mg 4 11.99 O 5116 8.00 N 4588 7.00 C 18328 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.3 seconds 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6784 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 24 sheets defined 59.2% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 15 through 44 removed outlier: 4.016A pdb=" N PHE A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A 23 " --> pdb=" O PHE A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 93 Processing helix chain 'A' and resid 96 through 123 Processing helix chain 'A' and resid 136 through 160 Processing helix chain 'A' and resid 162 through 167 Processing helix chain 'A' and resid 169 through 177 Processing helix chain 'A' and resid 178 through 188 removed outlier: 4.002A pdb=" N ILE A 186 " --> pdb=" O SER A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 204 removed outlier: 3.779A pdb=" N PHE A 197 " --> pdb=" O GLY A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 213 Processing helix chain 'A' and resid 218 through 249 Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 262 through 275 Processing helix chain 'A' and resid 286 through 317 removed outlier: 4.812A pdb=" N GLY A 302 " --> pdb=" O MET A 298 " (cutoff:3.500A) Proline residue: A 309 - end of helix Processing helix chain 'A' and resid 341 through 353 Processing helix chain 'A' and resid 373 through 383 Processing helix chain 'A' and resid 396 through 403 Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'A' and resid 421 through 440 Processing helix chain 'A' and resid 452 through 460 removed outlier: 4.333A pdb=" N ALA A 456 " --> pdb=" O TYR A 452 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TYR A 457 " --> pdb=" O HIS A 453 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU A 458 " --> pdb=" O ASN A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'A' and resid 475 through 489 removed outlier: 3.647A pdb=" N LEU A 488 " --> pdb=" O ALA A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 500 removed outlier: 3.810A pdb=" N LEU A 499 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE A 500 " --> pdb=" O MET A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 523 Processing helix chain 'A' and resid 532 through 536 Processing helix chain 'A' and resid 539 through 550 Processing helix chain 'A' and resid 592 through 602 removed outlier: 3.612A pdb=" N VAL A 596 " --> pdb=" O SER A 592 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ARG A 598 " --> pdb=" O GLU A 594 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ALA A 599 " --> pdb=" O GLU A 595 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE A 600 " --> pdb=" O VAL A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 616 Processing helix chain 'A' and resid 617 through 621 removed outlier: 4.114A pdb=" N CYS A 621 " --> pdb=" O LYS A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 725 Processing helix chain 'A' and resid 728 through 735 Processing helix chain 'A' and resid 756 through 761 Processing helix chain 'A' and resid 762 through 765 Processing helix chain 'A' and resid 769 through 773 Processing helix chain 'A' and resid 781 through 793 removed outlier: 3.877A pdb=" N ARG A 787 " --> pdb=" O ASP A 783 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LYS A 790 " --> pdb=" O HIS A 786 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N THR A 791 " --> pdb=" O ARG A 787 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 792 " --> pdb=" O GLU A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 814 Processing helix chain 'A' and resid 815 through 819 removed outlier: 3.508A pdb=" N CYS A 819 " --> pdb=" O ILE A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 852 Processing helix chain 'A' and resid 882 through 886 Processing helix chain 'A' and resid 894 through 902 removed outlier: 3.790A pdb=" N GLN A 899 " --> pdb=" O SER A 896 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASP A 902 " --> pdb=" O GLN A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 915 Processing helix chain 'A' and resid 916 through 921 Processing helix chain 'A' and resid 926 through 931 Processing helix chain 'A' and resid 932 through 940 Processing helix chain 'A' and resid 940 through 952 removed outlier: 3.620A pdb=" N LEU A 944 " --> pdb=" O ASN A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 965 Processing helix chain 'A' and resid 975 through 980 Processing helix chain 'A' and resid 981 through 984 removed outlier: 3.947A pdb=" N ARG A 984 " --> pdb=" O ASN A 981 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 981 through 984' Processing helix chain 'A' and resid 997 through 1002 removed outlier: 3.552A pdb=" N GLY A1001 " --> pdb=" O LEU A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1018 Processing helix chain 'B' and resid 15 through 44 removed outlier: 4.017A pdb=" N PHE B 19 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER B 23 " --> pdb=" O PHE B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 93 Processing helix chain 'B' and resid 96 through 123 Processing helix chain 'B' and resid 136 through 160 Processing helix chain 'B' and resid 162 through 167 Processing helix chain 'B' and resid 169 through 177 Processing helix chain 'B' and resid 178 through 188 removed outlier: 4.002A pdb=" N ILE B 186 " --> pdb=" O SER B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 204 removed outlier: 3.779A pdb=" N PHE B 197 " --> pdb=" O GLY B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'B' and resid 218 through 249 Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 262 through 275 Processing helix chain 'B' and resid 286 through 317 removed outlier: 4.812A pdb=" N GLY B 302 " --> pdb=" O MET B 298 " (cutoff:3.500A) Proline residue: B 309 - end of helix Processing helix chain 'B' and resid 341 through 353 Processing helix chain 'B' and resid 373 through 383 Processing helix chain 'B' and resid 396 through 403 Processing helix chain 'B' and resid 404 through 408 Processing helix chain 'B' and resid 421 through 440 Processing helix chain 'B' and resid 452 through 460 removed outlier: 4.334A pdb=" N ALA B 456 " --> pdb=" O TYR B 452 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TYR B 457 " --> pdb=" O HIS B 453 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU B 458 " --> pdb=" O ASN B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 469 Processing helix chain 'B' and resid 475 through 489 removed outlier: 3.647A pdb=" N LEU B 488 " --> pdb=" O ALA B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 500 removed outlier: 3.810A pdb=" N LEU B 499 " --> pdb=" O LEU B 495 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE B 500 " --> pdb=" O MET B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 523 Processing helix chain 'B' and resid 532 through 536 Processing helix chain 'B' and resid 539 through 550 Processing helix chain 'B' and resid 592 through 602 removed outlier: 3.613A pdb=" N VAL B 596 " --> pdb=" O SER B 592 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ARG B 598 " --> pdb=" O GLU B 594 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ALA B 599 " --> pdb=" O GLU B 595 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE B 600 " --> pdb=" O VAL B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 616 Processing helix chain 'B' and resid 617 through 621 removed outlier: 4.114A pdb=" N CYS B 621 " --> pdb=" O LYS B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 725 Processing helix chain 'B' and resid 728 through 735 Processing helix chain 'B' and resid 756 through 761 Processing helix chain 'B' and resid 762 through 765 Processing helix chain 'B' and resid 769 through 773 Processing helix chain 'B' and resid 781 through 793 removed outlier: 3.877A pdb=" N ARG B 787 " --> pdb=" O ASP B 783 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LYS B 790 " --> pdb=" O HIS B 786 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N THR B 791 " --> pdb=" O ARG B 787 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 792 " --> pdb=" O GLU B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 814 Processing helix chain 'B' and resid 815 through 819 removed outlier: 3.509A pdb=" N CYS B 819 " --> pdb=" O ILE B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 852 Processing helix chain 'B' and resid 882 through 886 Processing helix chain 'B' and resid 894 through 902 removed outlier: 3.789A pdb=" N GLN B 899 " --> pdb=" O SER B 896 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASP B 902 " --> pdb=" O GLN B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 915 Processing helix chain 'B' and resid 916 through 921 Processing helix chain 'B' and resid 926 through 931 Processing helix chain 'B' and resid 932 through 940 Processing helix chain 'B' and resid 940 through 952 removed outlier: 3.620A pdb=" N LEU B 944 " --> pdb=" O ASN B 940 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 965 Processing helix chain 'B' and resid 975 through 980 Processing helix chain 'B' and resid 981 through 984 removed outlier: 3.947A pdb=" N ARG B 984 " --> pdb=" O ASN B 981 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 981 through 984' Processing helix chain 'B' and resid 997 through 1002 removed outlier: 3.553A pdb=" N GLY B1001 " --> pdb=" O LEU B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1005 through 1018 Processing helix chain 'C' and resid 15 through 44 removed outlier: 4.016A pdb=" N PHE C 19 " --> pdb=" O GLN C 15 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER C 23 " --> pdb=" O PHE C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 93 Processing helix chain 'C' and resid 96 through 123 Processing helix chain 'C' and resid 136 through 160 Processing helix chain 'C' and resid 162 through 167 Processing helix chain 'C' and resid 169 through 177 Processing helix chain 'C' and resid 178 through 188 removed outlier: 4.001A pdb=" N ILE C 186 " --> pdb=" O SER C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 204 removed outlier: 3.779A pdb=" N PHE C 197 " --> pdb=" O GLY C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 213 Processing helix chain 'C' and resid 218 through 249 Processing helix chain 'C' and resid 250 through 254 Processing helix chain 'C' and resid 262 through 275 Processing helix chain 'C' and resid 286 through 317 removed outlier: 4.812A pdb=" N GLY C 302 " --> pdb=" O MET C 298 " (cutoff:3.500A) Proline residue: C 309 - end of helix Processing helix chain 'C' and resid 341 through 353 Processing helix chain 'C' and resid 373 through 383 Processing helix chain 'C' and resid 396 through 403 Processing helix chain 'C' and resid 404 through 408 Processing helix chain 'C' and resid 421 through 440 Processing helix chain 'C' and resid 452 through 460 removed outlier: 4.334A pdb=" N ALA C 456 " --> pdb=" O TYR C 452 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TYR C 457 " --> pdb=" O HIS C 453 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU C 458 " --> pdb=" O ASN C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 469 Processing helix chain 'C' and resid 475 through 489 removed outlier: 3.647A pdb=" N LEU C 488 " --> pdb=" O ALA C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 500 removed outlier: 3.811A pdb=" N LEU C 499 " --> pdb=" O LEU C 495 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE C 500 " --> pdb=" O MET C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 523 Processing helix chain 'C' and resid 532 through 536 Processing helix chain 'C' and resid 539 through 550 Processing helix chain 'C' and resid 592 through 602 removed outlier: 3.613A pdb=" N VAL C 596 " --> pdb=" O SER C 592 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ARG C 598 " --> pdb=" O GLU C 594 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ALA C 599 " --> pdb=" O GLU C 595 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE C 600 " --> pdb=" O VAL C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 616 Processing helix chain 'C' and resid 617 through 621 removed outlier: 4.114A pdb=" N CYS C 621 " --> pdb=" O LYS C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 725 Processing helix chain 'C' and resid 728 through 735 Processing helix chain 'C' and resid 756 through 761 Processing helix chain 'C' and resid 762 through 765 Processing helix chain 'C' and resid 769 through 773 Processing helix chain 'C' and resid 781 through 793 removed outlier: 3.877A pdb=" N ARG C 787 " --> pdb=" O ASP C 783 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LYS C 790 " --> pdb=" O HIS C 786 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N THR C 791 " --> pdb=" O ARG C 787 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU C 792 " --> pdb=" O GLU C 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 807 through 814 Processing helix chain 'C' and resid 815 through 819 removed outlier: 3.508A pdb=" N CYS C 819 " --> pdb=" O ILE C 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 839 through 852 Processing helix chain 'C' and resid 882 through 886 Processing helix chain 'C' and resid 894 through 902 removed outlier: 3.790A pdb=" N GLN C 899 " --> pdb=" O SER C 896 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASP C 902 " --> pdb=" O GLN C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 915 Processing helix chain 'C' and resid 916 through 921 Processing helix chain 'C' and resid 926 through 931 Processing helix chain 'C' and resid 932 through 940 Processing helix chain 'C' and resid 940 through 952 removed outlier: 3.619A pdb=" N LEU C 944 " --> pdb=" O ASN C 940 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 965 Processing helix chain 'C' and resid 975 through 980 Processing helix chain 'C' and resid 981 through 984 removed outlier: 3.947A pdb=" N ARG C 984 " --> pdb=" O ASN C 981 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 981 through 984' Processing helix chain 'C' and resid 997 through 1002 removed outlier: 3.551A pdb=" N GLY C1001 " --> pdb=" O LEU C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1018 Processing helix chain 'D' and resid 15 through 44 removed outlier: 4.017A pdb=" N PHE D 19 " --> pdb=" O GLN D 15 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER D 23 " --> pdb=" O PHE D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 93 Processing helix chain 'D' and resid 96 through 123 Processing helix chain 'D' and resid 136 through 160 Processing helix chain 'D' and resid 162 through 167 Processing helix chain 'D' and resid 169 through 177 Processing helix chain 'D' and resid 178 through 188 removed outlier: 4.003A pdb=" N ILE D 186 " --> pdb=" O SER D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 204 removed outlier: 3.779A pdb=" N PHE D 197 " --> pdb=" O GLY D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 213 Processing helix chain 'D' and resid 218 through 249 Processing helix chain 'D' and resid 250 through 254 Processing helix chain 'D' and resid 262 through 275 Processing helix chain 'D' and resid 286 through 317 removed outlier: 4.813A pdb=" N GLY D 302 " --> pdb=" O MET D 298 " (cutoff:3.500A) Proline residue: D 309 - end of helix Processing helix chain 'D' and resid 341 through 353 Processing helix chain 'D' and resid 373 through 383 Processing helix chain 'D' and resid 396 through 403 Processing helix chain 'D' and resid 404 through 408 Processing helix chain 'D' and resid 421 through 440 Processing helix chain 'D' and resid 452 through 460 removed outlier: 4.333A pdb=" N ALA D 456 " --> pdb=" O TYR D 452 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TYR D 457 " --> pdb=" O HIS D 453 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU D 458 " --> pdb=" O ASN D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 469 Processing helix chain 'D' and resid 475 through 489 removed outlier: 3.648A pdb=" N LEU D 488 " --> pdb=" O ALA D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 491 through 500 removed outlier: 3.810A pdb=" N LEU D 499 " --> pdb=" O LEU D 495 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE D 500 " --> pdb=" O MET D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 523 Processing helix chain 'D' and resid 532 through 536 Processing helix chain 'D' and resid 539 through 550 Processing helix chain 'D' and resid 592 through 602 removed outlier: 3.613A pdb=" N VAL D 596 " --> pdb=" O SER D 592 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ARG D 598 " --> pdb=" O GLU D 594 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ALA D 599 " --> pdb=" O GLU D 595 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE D 600 " --> pdb=" O VAL D 596 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 616 Processing helix chain 'D' and resid 617 through 621 removed outlier: 4.113A pdb=" N CYS D 621 " --> pdb=" O LYS D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 725 Processing helix chain 'D' and resid 728 through 735 Processing helix chain 'D' and resid 756 through 761 Processing helix chain 'D' and resid 762 through 765 Processing helix chain 'D' and resid 769 through 773 Processing helix chain 'D' and resid 781 through 793 removed outlier: 3.877A pdb=" N ARG D 787 " --> pdb=" O ASP D 783 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LYS D 790 " --> pdb=" O HIS D 786 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N THR D 791 " --> pdb=" O ARG D 787 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU D 792 " --> pdb=" O GLU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 807 through 814 Processing helix chain 'D' and resid 815 through 819 removed outlier: 3.508A pdb=" N CYS D 819 " --> pdb=" O ILE D 816 " (cutoff:3.500A) Processing helix chain 'D' and resid 839 through 852 Processing helix chain 'D' and resid 882 through 886 Processing helix chain 'D' and resid 894 through 902 removed outlier: 3.789A pdb=" N GLN D 899 " --> pdb=" O SER D 896 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASP D 902 " --> pdb=" O GLN D 899 " (cutoff:3.500A) Processing helix chain 'D' and resid 912 through 915 Processing helix chain 'D' and resid 916 through 921 Processing helix chain 'D' and resid 926 through 931 Processing helix chain 'D' and resid 932 through 940 Processing helix chain 'D' and resid 940 through 952 removed outlier: 3.620A pdb=" N LEU D 944 " --> pdb=" O ASN D 940 " (cutoff:3.500A) Processing helix chain 'D' and resid 956 through 965 Processing helix chain 'D' and resid 975 through 980 Processing helix chain 'D' and resid 981 through 984 removed outlier: 3.947A pdb=" N ARG D 984 " --> pdb=" O ASN D 981 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 981 through 984' Processing helix chain 'D' and resid 997 through 1002 removed outlier: 3.552A pdb=" N GLY D1001 " --> pdb=" O LEU D 997 " (cutoff:3.500A) Processing helix chain 'D' and resid 1005 through 1018 Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 130 Processing sheet with id=AA2, first strand: chain 'A' and resid 387 through 391 removed outlier: 4.583A pdb=" N GLY A 338 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N HIS A 333 " --> pdb=" O ALA A 410 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N LEU A 412 " --> pdb=" O HIS A 333 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL A 335 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU A 414 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N CYS A 337 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 525 through 530 removed outlier: 7.020A pdb=" N GLN A 585 " --> pdb=" O ILE A 558 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE A 558 " --> pdb=" O GLN A 585 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N PHE A 587 " --> pdb=" O LEU A 556 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 708 through 709 Processing sheet with id=AA5, first strand: chain 'A' and resid 798 through 802 removed outlier: 6.503A pdb=" N THR A 776 " --> pdb=" O SER A 799 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LEU A 801 " --> pdb=" O THR A 776 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE A 778 " --> pdb=" O LEU A 801 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL A 741 " --> pdb=" O ILE A 777 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL A 779 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL A 743 " --> pdb=" O VAL A 779 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL A 742 " --> pdb=" O VAL A 823 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N VAL A 825 " --> pdb=" O VAL A 742 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N CYS A 744 " --> pdb=" O VAL A 825 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N SER A 826 " --> pdb=" O GLU A 891 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N PHE A 925 " --> pdb=" O LEU A 888 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N THR A 890 " --> pdb=" O PHE A 925 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 986 through 991 removed outlier: 6.638A pdb=" N GLN A1058 " --> pdb=" O LEU A1024 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU A1024 " --> pdb=" O GLN A1058 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TYR A1060 " --> pdb=" O ILE A1022 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AA8, first strand: chain 'B' and resid 387 through 391 removed outlier: 6.465A pdb=" N VAL B 334 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU B 367 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL B 336 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N HIS B 333 " --> pdb=" O ALA B 410 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N LEU B 412 " --> pdb=" O HIS B 333 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL B 335 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N LEU B 414 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N CYS B 337 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 525 through 530 removed outlier: 7.020A pdb=" N GLN B 585 " --> pdb=" O ILE B 558 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE B 558 " --> pdb=" O GLN B 585 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N PHE B 587 " --> pdb=" O LEU B 556 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 708 through 709 Processing sheet with id=AB2, first strand: chain 'B' and resid 798 through 802 removed outlier: 6.504A pdb=" N THR B 776 " --> pdb=" O SER B 799 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LEU B 801 " --> pdb=" O THR B 776 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE B 778 " --> pdb=" O LEU B 801 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL B 741 " --> pdb=" O ILE B 777 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL B 779 " --> pdb=" O VAL B 741 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL B 743 " --> pdb=" O VAL B 779 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL B 742 " --> pdb=" O VAL B 823 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N VAL B 825 " --> pdb=" O VAL B 742 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N CYS B 744 " --> pdb=" O VAL B 825 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N SER B 826 " --> pdb=" O GLU B 891 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N PHE B 925 " --> pdb=" O LEU B 888 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N THR B 890 " --> pdb=" O PHE B 925 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 986 through 991 removed outlier: 6.637A pdb=" N GLN B1058 " --> pdb=" O LEU B1024 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU B1024 " --> pdb=" O GLN B1058 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TYR B1060 " --> pdb=" O ILE B1022 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 128 through 130 Processing sheet with id=AB5, first strand: chain 'C' and resid 387 through 391 removed outlier: 4.583A pdb=" N GLY C 338 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N HIS C 333 " --> pdb=" O ALA C 410 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N LEU C 412 " --> pdb=" O HIS C 333 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL C 335 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N LEU C 414 " --> pdb=" O VAL C 335 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N CYS C 337 " --> pdb=" O LEU C 414 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 525 through 530 removed outlier: 7.021A pdb=" N GLN C 585 " --> pdb=" O ILE C 558 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE C 558 " --> pdb=" O GLN C 585 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N PHE C 587 " --> pdb=" O LEU C 556 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AB8, first strand: chain 'C' and resid 798 through 802 removed outlier: 6.504A pdb=" N THR C 776 " --> pdb=" O SER C 799 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LEU C 801 " --> pdb=" O THR C 776 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE C 778 " --> pdb=" O LEU C 801 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL C 741 " --> pdb=" O ILE C 777 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL C 779 " --> pdb=" O VAL C 741 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL C 743 " --> pdb=" O VAL C 779 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL C 742 " --> pdb=" O VAL C 823 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N VAL C 825 " --> pdb=" O VAL C 742 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N CYS C 744 " --> pdb=" O VAL C 825 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N SER C 826 " --> pdb=" O GLU C 891 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N PHE C 925 " --> pdb=" O LEU C 888 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N THR C 890 " --> pdb=" O PHE C 925 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 986 through 991 removed outlier: 6.638A pdb=" N GLN C1058 " --> pdb=" O LEU C1024 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU C1024 " --> pdb=" O GLN C1058 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TYR C1060 " --> pdb=" O ILE C1022 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 128 through 130 Processing sheet with id=AC2, first strand: chain 'D' and resid 387 through 391 removed outlier: 4.583A pdb=" N GLY D 338 " --> pdb=" O LEU D 367 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N HIS D 333 " --> pdb=" O ALA D 410 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N LEU D 412 " --> pdb=" O HIS D 333 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL D 335 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU D 414 " --> pdb=" O VAL D 335 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N CYS D 337 " --> pdb=" O LEU D 414 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 525 through 530 removed outlier: 7.020A pdb=" N GLN D 585 " --> pdb=" O ILE D 558 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE D 558 " --> pdb=" O GLN D 585 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N PHE D 587 " --> pdb=" O LEU D 556 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 708 through 709 Processing sheet with id=AC5, first strand: chain 'D' and resid 798 through 802 removed outlier: 6.503A pdb=" N THR D 776 " --> pdb=" O SER D 799 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LEU D 801 " --> pdb=" O THR D 776 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE D 778 " --> pdb=" O LEU D 801 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL D 741 " --> pdb=" O ILE D 777 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL D 779 " --> pdb=" O VAL D 741 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL D 743 " --> pdb=" O VAL D 779 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL D 742 " --> pdb=" O VAL D 823 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N VAL D 825 " --> pdb=" O VAL D 742 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N CYS D 744 " --> pdb=" O VAL D 825 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N SER D 826 " --> pdb=" O GLU D 891 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N PHE D 925 " --> pdb=" O LEU D 888 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N THR D 890 " --> pdb=" O PHE D 925 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 986 through 991 removed outlier: 6.639A pdb=" N GLN D1058 " --> pdb=" O LEU D1024 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU D1024 " --> pdb=" O GLN D1058 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TYR D1060 " --> pdb=" O ILE D1022 " (cutoff:3.500A) 1484 hydrogen bonds defined for protein. 3960 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: 6.60 Time building geometry restraints manager: 3.31 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: 5220 1.32 - 1.45: 7445 1.45 - 1.57: 15963 1.57 - 1.70: 0 1.70 - 1.82: 260 Bond restraints: 28888 Sorted by residual: bond pdb=" CA ARG B 986 " pdb=" C ARG B 986 " ideal model delta sigma weight residual 1.522 1.473 0.050 1.20e-02 6.94e+03 1.71e+01 bond pdb=" CA ARG D 986 " pdb=" C ARG D 986 " ideal model delta sigma weight residual 1.522 1.473 0.049 1.20e-02 6.94e+03 1.67e+01 bond pdb=" CA ARG A 986 " pdb=" C ARG A 986 " ideal model delta sigma weight residual 1.522 1.474 0.049 1.20e-02 6.94e+03 1.66e+01 bond pdb=" CA ARG C 986 " pdb=" C ARG C 986 " ideal model delta sigma weight residual 1.522 1.474 0.048 1.20e-02 6.94e+03 1.63e+01 bond pdb=" CA ARG A 720 " pdb=" C ARG A 720 " ideal model delta sigma weight residual 1.518 1.481 0.036 9.60e-03 1.09e+04 1.44e+01 ... (remaining 28883 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 26040 1.55 - 3.09: 10533 3.09 - 4.64: 2344 4.64 - 6.18: 355 6.18 - 7.73: 28 Bond angle restraints: 39300 Sorted by residual: angle pdb=" CA ASP B 910 " pdb=" CB ASP B 910 " pdb=" CG ASP B 910 " ideal model delta sigma weight residual 112.60 118.37 -5.77 1.00e+00 1.00e+00 3.33e+01 angle pdb=" CA ASP D 910 " pdb=" CB ASP D 910 " pdb=" CG ASP D 910 " ideal model delta sigma weight residual 112.60 118.36 -5.76 1.00e+00 1.00e+00 3.32e+01 angle pdb=" CA ASP C 910 " pdb=" CB ASP C 910 " pdb=" CG ASP C 910 " ideal model delta sigma weight residual 112.60 118.35 -5.75 1.00e+00 1.00e+00 3.31e+01 angle pdb=" CA ASP A 910 " pdb=" CB ASP A 910 " pdb=" CG ASP A 910 " ideal model delta sigma weight residual 112.60 118.35 -5.75 1.00e+00 1.00e+00 3.31e+01 angle pdb=" CA ASP B 895 " pdb=" CB ASP B 895 " pdb=" CG ASP B 895 " ideal model delta sigma weight residual 112.60 117.95 -5.35 1.00e+00 1.00e+00 2.86e+01 ... (remaining 39295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 15848 17.93 - 35.85: 868 35.85 - 53.78: 116 53.78 - 71.70: 52 71.70 - 89.63: 40 Dihedral angle restraints: 16924 sinusoidal: 6432 harmonic: 10492 Sorted by residual: dihedral pdb=" CA ASP B 904 " pdb=" C ASP B 904 " pdb=" N ASP B 905 " pdb=" CA ASP B 905 " ideal model delta harmonic sigma weight residual 180.00 -151.90 -28.10 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA ASP D 904 " pdb=" C ASP D 904 " pdb=" N ASP D 905 " pdb=" CA ASP D 905 " ideal model delta harmonic sigma weight residual -180.00 -151.90 -28.10 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA ASP A 904 " pdb=" C ASP A 904 " pdb=" N ASP A 905 " pdb=" CA ASP A 905 " ideal model delta harmonic sigma weight residual -180.00 -151.90 -28.10 0 5.00e+00 4.00e-02 3.16e+01 ... (remaining 16921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 2977 0.088 - 0.177: 1301 0.177 - 0.265: 175 0.265 - 0.354: 31 0.354 - 0.442: 12 Chirality restraints: 4496 Sorted by residual: chirality pdb=" CA LEU C 458 " pdb=" N LEU C 458 " pdb=" C LEU C 458 " pdb=" CB LEU C 458 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.88e+00 chirality pdb=" CA LEU A 458 " pdb=" N LEU A 458 " pdb=" C LEU A 458 " pdb=" CB LEU A 458 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.84e+00 chirality pdb=" CA LEU D 458 " pdb=" N LEU D 458 " pdb=" C LEU D 458 " pdb=" CB LEU D 458 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.81e+00 ... (remaining 4493 not shown) Planarity restraints: 4968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 167 " -0.123 2.00e-02 2.50e+03 6.23e-02 9.71e+01 pdb=" CG TRP B 167 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP B 167 " 0.050 2.00e-02 2.50e+03 pdb=" CD2 TRP B 167 " 0.038 2.00e-02 2.50e+03 pdb=" NE1 TRP B 167 " 0.035 2.00e-02 2.50e+03 pdb=" CE2 TRP B 167 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP B 167 " 0.091 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 167 " -0.067 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 167 " 0.029 2.00e-02 2.50e+03 pdb=" CH2 TRP B 167 " -0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 167 " 0.123 2.00e-02 2.50e+03 6.23e-02 9.70e+01 pdb=" CG TRP C 167 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP C 167 " -0.049 2.00e-02 2.50e+03 pdb=" CD2 TRP C 167 " -0.038 2.00e-02 2.50e+03 pdb=" NE1 TRP C 167 " -0.035 2.00e-02 2.50e+03 pdb=" CE2 TRP C 167 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP C 167 " -0.091 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 167 " 0.067 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 167 " -0.029 2.00e-02 2.50e+03 pdb=" CH2 TRP C 167 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 167 " 0.122 2.00e-02 2.50e+03 6.22e-02 9.67e+01 pdb=" CG TRP D 167 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TRP D 167 " -0.049 2.00e-02 2.50e+03 pdb=" CD2 TRP D 167 " -0.039 2.00e-02 2.50e+03 pdb=" NE1 TRP D 167 " -0.036 2.00e-02 2.50e+03 pdb=" CE2 TRP D 167 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP D 167 " -0.091 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 167 " 0.067 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 167 " -0.029 2.00e-02 2.50e+03 pdb=" CH2 TRP D 167 " 0.066 2.00e-02 2.50e+03 ... (remaining 4965 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.54: 76 2.54 - 3.19: 25889 3.19 - 3.84: 53670 3.84 - 4.49: 78193 4.49 - 5.14: 125975 Nonbonded interactions: 283803 Sorted by model distance: nonbonded pdb=" OE2 GLU B 328 " pdb="MG MG B1101 " model vdw 1.894 2.170 nonbonded pdb=" OE2 GLU C 328 " pdb="MG MG C1105 " model vdw 1.894 2.170 nonbonded pdb=" OE2 GLU A 328 " pdb="MG MG A1102 " model vdw 1.894 2.170 nonbonded pdb=" OE2 GLU D 328 " pdb="MG MG D1101 " model vdw 1.895 2.170 nonbonded pdb=" OE2 GLU C 363 " pdb="MG MG C1105 " model vdw 1.967 2.170 ... (remaining 283798 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 14 through 1065) selection = (chain 'B' and resid 14 through 1065) selection = (chain 'C' and resid 14 through 1065) selection = (chain 'D' and resid 14 through 1065) } 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 27.670 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.040 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:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 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 : 0.012 0.050 28888 Z= 0.715 Angle : 1.680 7.729 39300 Z= 1.131 Chirality : 0.092 0.442 4496 Planarity : 0.012 0.070 4968 Dihedral : 12.935 89.630 10140 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.60 % Allowed : 4.21 % Favored : 95.19 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.14), residues: 3548 helix: -1.06 (0.11), residues: 1812 sheet: 0.28 (0.27), residues: 412 loop : 0.07 (0.18), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 196 TYR 0.111 0.015 TYR D 938 PHE 0.097 0.012 PHE D 500 TRP 0.123 0.022 TRP B 167 HIS 0.010 0.003 HIS D 453 Details of bonding type rmsd/Z covalent geometry : bond 0.01181 / 0.72 (28888) covalent geometry : angle 1.68005 / 1.13 (39300) hydrogen bonds : bond 0.17289 / 11.35 ( 1484) hydrogen bonds : angle 7.34410 / 5.32 ( 3960) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 1.133 Fit side-chains REVERT: A 81 MET cc_start: 0.8635 (mmt) cc_final: 0.8332 (mmt) REVERT: A 502 MET cc_start: 0.9444 (mmm) cc_final: 0.8991 (mmt) REVERT: A 960 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8718 (mt-10) REVERT: B 81 MET cc_start: 0.8664 (mmt) cc_final: 0.8369 (mmt) REVERT: B 204 MET cc_start: 0.9296 (mtp) cc_final: 0.9072 (mtm) REVERT: B 502 MET cc_start: 0.9490 (mmm) cc_final: 0.9193 (mmt) REVERT: C 204 MET cc_start: 0.9293 (mtp) cc_final: 0.9071 (mtm) REVERT: C 502 MET cc_start: 0.9579 (mmm) cc_final: 0.8873 (mmt) REVERT: D 81 MET cc_start: 0.8639 (mmt) cc_final: 0.8342 (mmt) REVERT: D 204 MET cc_start: 0.9302 (mtp) cc_final: 0.9084 (mtm) REVERT: D 502 MET cc_start: 0.9575 (mmm) cc_final: 0.8853 (mmt) outliers start: 18 outliers final: 3 residues processed: 134 average time/residue: 0.6920 time to fit residues: 109.3899 Evaluate side-chains 98 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 95 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain D residue 209 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 3.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 ASN A 416 ASN A 424 GLN A 438 ASN A1046 ASN B 398 ASN B 416 ASN B 438 ASN B1046 ASN C 398 ASN C 416 ASN C 424 GLN C 438 ASN C1046 ASN D 398 ASN D 416 ASN D 424 GLN D 438 ASN D1046 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.060602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.045327 restraints weight = 81102.803| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 3.43 r_work: 0.2532 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 28888 Z= 0.227 Angle : 0.622 8.277 39300 Z= 0.329 Chirality : 0.045 0.151 4496 Planarity : 0.004 0.040 4968 Dihedral : 5.474 62.281 3854 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.60 % Allowed : 6.30 % Favored : 93.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.15), residues: 3548 helix: 0.33 (0.12), residues: 1828 sheet: 0.13 (0.25), residues: 452 loop : 0.84 (0.19), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 808 TYR 0.012 0.002 TYR C 914 PHE 0.022 0.002 PHE C 500 TRP 0.020 0.002 TRP A 514 HIS 0.008 0.001 HIS A 607 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.23 (28888) covalent geometry : angle 0.62177 / 0.33 (39300) hydrogen bonds : bond 0.05475 / 3.61 ( 1484) hydrogen bonds : angle 5.00751 / 3.60 ( 3960) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 1.110 Fit side-chains REVERT: A 496 MET cc_start: 0.9125 (tpp) cc_final: 0.8867 (tpt) REVERT: A 542 GLU cc_start: 0.9273 (OUTLIER) cc_final: 0.8872 (mp0) REVERT: B 502 MET cc_start: 0.9524 (mmm) cc_final: 0.8668 (mmt) REVERT: B 542 GLU cc_start: 0.9289 (OUTLIER) cc_final: 0.8886 (mp0) REVERT: C 81 MET cc_start: 0.8785 (mmt) cc_final: 0.8545 (mmt) REVERT: C 502 MET cc_start: 0.9539 (mmm) cc_final: 0.8646 (mmt) REVERT: C 542 GLU cc_start: 0.9289 (OUTLIER) cc_final: 0.8887 (mp0) REVERT: D 542 GLU cc_start: 0.9274 (OUTLIER) cc_final: 0.8861 (mp0) outliers start: 18 outliers final: 0 residues processed: 109 average time/residue: 0.7811 time to fit residues: 98.5941 Evaluate side-chains 93 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain C residue 542 GLU Chi-restraints excluded: chain D residue 542 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 145 optimal weight: 30.0000 chunk 354 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 319 optimal weight: 8.9990 chunk 271 optimal weight: 9.9990 chunk 130 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 59 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 268 optimal weight: 7.9990 chunk 257 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 GLN B 15 GLN B 424 GLN C 15 GLN D 15 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.062348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.047261 restraints weight = 80476.926| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 3.43 r_work: 0.2588 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28888 Z= 0.118 Angle : 0.513 7.050 39300 Z= 0.264 Chirality : 0.041 0.136 4496 Planarity : 0.003 0.042 4968 Dihedral : 4.712 55.249 3848 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.66 % Allowed : 6.53 % Favored : 92.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.15), residues: 3548 helix: 0.75 (0.12), residues: 1828 sheet: 0.17 (0.25), residues: 452 loop : 1.00 (0.19), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 757 TYR 0.009 0.001 TYR C 268 PHE 0.016 0.001 PHE C 500 TRP 0.015 0.001 TRP D 514 HIS 0.004 0.001 HIS A 607 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (28888) covalent geometry : angle 0.51338 / 0.26 (39300) hydrogen bonds : bond 0.04316 / 2.86 ( 1484) hydrogen bonds : angle 4.51384 / 3.25 ( 3960) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 1.068 Fit side-chains REVERT: A 81 MET cc_start: 0.8755 (mmt) cc_final: 0.8350 (mpm) REVERT: A 496 MET cc_start: 0.8940 (tpp) cc_final: 0.8711 (tpt) REVERT: B 81 MET cc_start: 0.8736 (mmt) cc_final: 0.8433 (mpm) REVERT: C 81 MET cc_start: 0.8714 (mmt) cc_final: 0.8475 (mmt) REVERT: D 81 MET cc_start: 0.8736 (mmt) cc_final: 0.8432 (mpm) outliers start: 20 outliers final: 1 residues processed: 113 average time/residue: 0.6845 time to fit residues: 91.8374 Evaluate side-chains 93 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 947 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 26 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 328 optimal weight: 6.9990 chunk 251 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 194 optimal weight: 5.9990 chunk 196 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 51 optimal weight: 0.0870 chunk 43 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 overall best weight: 2.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.061498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.046249 restraints weight = 80424.992| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 3.43 r_work: 0.2561 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 28888 Z= 0.155 Angle : 0.514 8.476 39300 Z= 0.260 Chirality : 0.041 0.148 4496 Planarity : 0.003 0.041 4968 Dihedral : 4.404 47.840 3848 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.16 % Allowed : 6.90 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.15), residues: 3548 helix: 0.90 (0.12), residues: 1844 sheet: 0.23 (0.27), residues: 424 loop : 0.97 (0.19), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 757 TYR 0.010 0.001 TYR D 268 PHE 0.017 0.001 PHE C 500 TRP 0.013 0.001 TRP C 514 HIS 0.003 0.001 HIS A 607 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (28888) covalent geometry : angle 0.51405 / 0.26 (39300) hydrogen bonds : bond 0.04234 / 2.81 ( 1484) hydrogen bonds : angle 4.35375 / 3.13 ( 3960) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 90 time to evaluate : 0.981 Fit side-chains REVERT: A 81 MET cc_start: 0.8667 (mmt) cc_final: 0.8365 (mmt) REVERT: A 519 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.8923 (mmm) REVERT: A 542 GLU cc_start: 0.9301 (OUTLIER) cc_final: 0.8908 (mp0) REVERT: A 912 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8389 (pm20) REVERT: B 496 MET cc_start: 0.9236 (OUTLIER) cc_final: 0.8973 (ttm) REVERT: B 542 GLU cc_start: 0.9308 (OUTLIER) cc_final: 0.8880 (mp0) REVERT: B 912 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8352 (pm20) REVERT: C 81 MET cc_start: 0.8694 (mmt) cc_final: 0.8394 (mmt) REVERT: C 542 GLU cc_start: 0.9313 (OUTLIER) cc_final: 0.8885 (mp0) REVERT: C 912 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8359 (pm20) REVERT: D 81 MET cc_start: 0.8671 (mmt) cc_final: 0.8418 (mmt) REVERT: D 496 MET cc_start: 0.9231 (OUTLIER) cc_final: 0.8945 (ttm) REVERT: D 542 GLU cc_start: 0.9305 (OUTLIER) cc_final: 0.8880 (mp0) REVERT: D 912 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8322 (pm20) outliers start: 35 outliers final: 4 residues processed: 116 average time/residue: 0.7407 time to fit residues: 100.4513 Evaluate side-chains 104 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain B residue 912 GLU Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 542 GLU Chi-restraints excluded: chain C residue 912 GLU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 542 GLU Chi-restraints excluded: chain D residue 912 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 131 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 271 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 260 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 296 optimal weight: 1.9990 chunk 214 optimal weight: 9.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.061880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.046821 restraints weight = 80190.249| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 3.43 r_work: 0.2578 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28888 Z= 0.133 Angle : 0.497 8.982 39300 Z= 0.249 Chirality : 0.041 0.141 4496 Planarity : 0.003 0.041 4968 Dihedral : 4.185 40.567 3848 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.56 % Allowed : 6.96 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.15), residues: 3548 helix: 0.96 (0.12), residues: 1876 sheet: 0.21 (0.27), residues: 428 loop : 1.01 (0.19), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 948 TYR 0.009 0.001 TYR A 938 PHE 0.013 0.001 PHE C 500 TRP 0.011 0.001 TRP A 514 HIS 0.002 0.001 HIS A 607 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (28888) covalent geometry : angle 0.49716 / 0.25 (39300) hydrogen bonds : bond 0.04006 / 2.65 ( 1484) hydrogen bonds : angle 4.24466 / 3.06 ( 3960) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 94 time to evaluate : 1.182 Fit side-chains REVERT: A 496 MET cc_start: 0.9009 (tpp) cc_final: 0.8806 (tpt) REVERT: A 542 GLU cc_start: 0.9311 (OUTLIER) cc_final: 0.8916 (mp0) REVERT: A 912 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8383 (pm20) REVERT: B 81 MET cc_start: 0.8700 (mmt) cc_final: 0.8407 (mpm) REVERT: B 496 MET cc_start: 0.9276 (OUTLIER) cc_final: 0.8991 (ttm) REVERT: B 542 GLU cc_start: 0.9321 (OUTLIER) cc_final: 0.8885 (mp0) REVERT: B 912 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8300 (pm20) REVERT: C 542 GLU cc_start: 0.9327 (OUTLIER) cc_final: 0.8890 (mp0) REVERT: C 912 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8340 (pm20) REVERT: D 81 MET cc_start: 0.8690 (mmt) cc_final: 0.8360 (mmt) REVERT: D 496 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.8962 (ttm) REVERT: D 542 GLU cc_start: 0.9328 (OUTLIER) cc_final: 0.8896 (mp0) REVERT: D 912 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8349 (pm20) outliers start: 47 outliers final: 5 residues processed: 134 average time/residue: 0.6439 time to fit residues: 102.6526 Evaluate side-chains 106 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain B residue 912 GLU Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 511 MET Chi-restraints excluded: chain C residue 542 GLU Chi-restraints excluded: chain C residue 912 GLU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 542 GLU Chi-restraints excluded: chain D residue 912 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 5 optimal weight: 6.9990 chunk 336 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 276 optimal weight: 2.9990 chunk 277 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 chunk 322 optimal weight: 10.0000 chunk 333 optimal weight: 0.8980 chunk 224 optimal weight: 0.2980 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.061609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.046486 restraints weight = 80565.693| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 3.41 r_work: 0.2570 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 28888 Z= 0.146 Angle : 0.500 9.079 39300 Z= 0.252 Chirality : 0.041 0.143 4496 Planarity : 0.003 0.042 4968 Dihedral : 4.083 35.054 3848 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.09 % Allowed : 8.49 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.15), residues: 3548 helix: 1.03 (0.13), residues: 1876 sheet: 0.09 (0.25), residues: 464 loop : 0.98 (0.19), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 520 TYR 0.009 0.001 TYR C 938 PHE 0.014 0.001 PHE B 500 TRP 0.011 0.001 TRP C 514 HIS 0.003 0.001 HIS B 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (28888) covalent geometry : angle 0.50011 / 0.25 (39300) hydrogen bonds : bond 0.03995 / 2.65 ( 1484) hydrogen bonds : angle 4.23510 / 3.05 ( 3960) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 93 time to evaluate : 0.739 Fit side-chains REVERT: A 81 MET cc_start: 0.8708 (mmt) cc_final: 0.8475 (mpm) REVERT: A 542 GLU cc_start: 0.9310 (OUTLIER) cc_final: 0.8919 (mp0) REVERT: A 912 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8402 (pm20) REVERT: B 81 MET cc_start: 0.8690 (mmt) cc_final: 0.8399 (mpm) REVERT: B 496 MET cc_start: 0.9284 (OUTLIER) cc_final: 0.9067 (ttm) REVERT: B 519 MET cc_start: 0.9008 (mmm) cc_final: 0.8600 (mmm) REVERT: B 542 GLU cc_start: 0.9324 (OUTLIER) cc_final: 0.8900 (mp0) REVERT: B 912 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8313 (pm20) REVERT: B 947 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8747 (tp) REVERT: C 81 MET cc_start: 0.8717 (mmt) cc_final: 0.8403 (mpm) REVERT: C 542 GLU cc_start: 0.9334 (OUTLIER) cc_final: 0.8910 (mp0) REVERT: C 912 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8304 (pm20) REVERT: C 915 MET cc_start: 0.9253 (tpt) cc_final: 0.9041 (tpt) REVERT: D 496 MET cc_start: 0.9271 (OUTLIER) cc_final: 0.9023 (ttm) REVERT: D 519 MET cc_start: 0.9104 (mmm) cc_final: 0.8877 (mmm) REVERT: D 542 GLU cc_start: 0.9328 (OUTLIER) cc_final: 0.8902 (mp0) REVERT: D 912 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8301 (pm20) REVERT: D 915 MET cc_start: 0.9257 (tpt) cc_final: 0.8906 (tpt) REVERT: D 947 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8743 (tp) outliers start: 33 outliers final: 10 residues processed: 116 average time/residue: 0.6922 time to fit residues: 93.6432 Evaluate side-chains 111 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain B residue 890 THR Chi-restraints excluded: chain B residue 912 GLU Chi-restraints excluded: chain B residue 947 ILE Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 542 GLU Chi-restraints excluded: chain C residue 890 THR Chi-restraints excluded: chain C residue 912 GLU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 542 GLU Chi-restraints excluded: chain D residue 912 GLU Chi-restraints excluded: chain D residue 947 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 178 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 175 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 235 optimal weight: 10.0000 chunk 326 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 252 optimal weight: 4.9990 chunk 179 optimal weight: 5.9990 chunk 350 optimal weight: 10.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.061419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.046238 restraints weight = 80456.727| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 3.43 r_work: 0.2563 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 28888 Z= 0.158 Angle : 0.506 9.510 39300 Z= 0.254 Chirality : 0.041 0.144 4496 Planarity : 0.003 0.042 4968 Dihedral : 4.016 30.329 3848 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.26 % Allowed : 8.92 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.15), residues: 3548 helix: 1.05 (0.13), residues: 1876 sheet: 0.07 (0.25), residues: 464 loop : 0.96 (0.19), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 808 TYR 0.010 0.001 TYR A 914 PHE 0.019 0.001 PHE C 500 TRP 0.012 0.001 TRP D 514 HIS 0.003 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (28888) covalent geometry : angle 0.50642 / 0.25 (39300) hydrogen bonds : bond 0.04034 / 2.68 ( 1484) hydrogen bonds : angle 4.22304 / 3.04 ( 3960) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 92 time to evaluate : 1.113 Fit side-chains revert: symmetry clash REVERT: A 542 GLU cc_start: 0.9314 (OUTLIER) cc_final: 0.8923 (mp0) REVERT: A 912 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8328 (pm20) REVERT: B 81 MET cc_start: 0.8733 (mmt) cc_final: 0.8395 (mmt) REVERT: B 502 MET cc_start: 0.9211 (mmt) cc_final: 0.8639 (mmt) REVERT: B 542 GLU cc_start: 0.9322 (OUTLIER) cc_final: 0.8905 (mp0) REVERT: B 912 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8377 (pm20) REVERT: B 947 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8771 (tp) REVERT: C 81 MET cc_start: 0.8725 (mmt) cc_final: 0.8409 (mpm) REVERT: C 519 MET cc_start: 0.9098 (mmm) cc_final: 0.8638 (mmm) REVERT: C 542 GLU cc_start: 0.9330 (OUTLIER) cc_final: 0.8908 (mp0) REVERT: C 912 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8335 (pm20) REVERT: C 915 MET cc_start: 0.9313 (tpt) cc_final: 0.8968 (tpt) REVERT: C 947 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8732 (tp) REVERT: D 81 MET cc_start: 0.8710 (mmt) cc_final: 0.8382 (mpm) REVERT: D 496 MET cc_start: 0.9308 (OUTLIER) cc_final: 0.9052 (ttm) REVERT: D 519 MET cc_start: 0.9101 (mmm) cc_final: 0.8751 (mmm) REVERT: D 542 GLU cc_start: 0.9325 (OUTLIER) cc_final: 0.8906 (mp0) REVERT: D 912 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8316 (pm20) REVERT: D 915 MET cc_start: 0.9255 (tpt) cc_final: 0.8794 (tpt) REVERT: D 947 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8754 (tp) outliers start: 38 outliers final: 15 residues processed: 122 average time/residue: 0.7437 time to fit residues: 106.0167 Evaluate side-chains 116 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain B residue 890 THR Chi-restraints excluded: chain B residue 912 GLU Chi-restraints excluded: chain B residue 947 ILE Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 542 GLU Chi-restraints excluded: chain C residue 890 THR Chi-restraints excluded: chain C residue 912 GLU Chi-restraints excluded: chain C residue 947 ILE Chi-restraints excluded: chain C residue 1043 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 511 MET Chi-restraints excluded: chain D residue 542 GLU Chi-restraints excluded: chain D residue 890 THR Chi-restraints excluded: chain D residue 912 GLU Chi-restraints excluded: chain D residue 947 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 137 optimal weight: 10.0000 chunk 296 optimal weight: 4.9990 chunk 234 optimal weight: 10.0000 chunk 123 optimal weight: 4.9990 chunk 352 optimal weight: 0.7980 chunk 202 optimal weight: 5.9990 chunk 235 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 chunk 133 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 250 optimal weight: 0.9980 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.061717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.046569 restraints weight = 80697.676| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 3.42 r_work: 0.2574 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28888 Z= 0.143 Angle : 0.507 10.523 39300 Z= 0.254 Chirality : 0.041 0.141 4496 Planarity : 0.003 0.042 4968 Dihedral : 3.969 27.074 3848 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.06 % Allowed : 9.45 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.15), residues: 3548 helix: 1.09 (0.13), residues: 1876 sheet: 0.03 (0.25), residues: 464 loop : 0.93 (0.19), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 984 TYR 0.010 0.001 TYR A 914 PHE 0.016 0.001 PHE C 500 TRP 0.011 0.001 TRP D 514 HIS 0.003 0.001 HIS D 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (28888) covalent geometry : angle 0.50721 / 0.25 (39300) hydrogen bonds : bond 0.03962 / 2.63 ( 1484) hydrogen bonds : angle 4.19888 / 3.03 ( 3960) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 89 time to evaluate : 0.963 Fit side-chains revert: symmetry clash REVERT: A 542 GLU cc_start: 0.9318 (OUTLIER) cc_final: 0.8930 (mp0) REVERT: A 912 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8339 (pm20) REVERT: B 502 MET cc_start: 0.9196 (mmt) cc_final: 0.8640 (mmt) REVERT: B 542 GLU cc_start: 0.9322 (OUTLIER) cc_final: 0.8912 (mp0) REVERT: B 912 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8326 (pm20) REVERT: B 947 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8757 (tp) REVERT: C 81 MET cc_start: 0.8714 (mmt) cc_final: 0.8399 (mpm) REVERT: C 519 MET cc_start: 0.9135 (mmm) cc_final: 0.8823 (mmm) REVERT: C 542 GLU cc_start: 0.9335 (OUTLIER) cc_final: 0.8945 (mp0) REVERT: C 912 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8308 (pm20) REVERT: C 947 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8765 (tp) REVERT: D 81 MET cc_start: 0.8707 (mmt) cc_final: 0.8383 (mpm) REVERT: D 496 MET cc_start: 0.9301 (OUTLIER) cc_final: 0.9093 (ttm) REVERT: D 519 MET cc_start: 0.9115 (mmm) cc_final: 0.8760 (mmm) REVERT: D 542 GLU cc_start: 0.9334 (OUTLIER) cc_final: 0.8926 (mp0) REVERT: D 912 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8306 (pm20) REVERT: D 915 MET cc_start: 0.9264 (tpt) cc_final: 0.8790 (tpt) REVERT: D 947 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8751 (tp) outliers start: 32 outliers final: 14 residues processed: 114 average time/residue: 0.7491 time to fit residues: 98.9046 Evaluate side-chains 115 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain B residue 912 GLU Chi-restraints excluded: chain B residue 947 ILE Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 298 MET Chi-restraints excluded: chain C residue 542 GLU Chi-restraints excluded: chain C residue 890 THR Chi-restraints excluded: chain C residue 912 GLU Chi-restraints excluded: chain C residue 947 ILE Chi-restraints excluded: chain C residue 1043 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 542 GLU Chi-restraints excluded: chain D residue 890 THR Chi-restraints excluded: chain D residue 912 GLU Chi-restraints excluded: chain D residue 947 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 220 optimal weight: 4.9990 chunk 288 optimal weight: 10.0000 chunk 315 optimal weight: 2.9990 chunk 284 optimal weight: 6.9990 chunk 328 optimal weight: 0.9990 chunk 294 optimal weight: 8.9990 chunk 320 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 311 optimal weight: 0.8980 chunk 194 optimal weight: 0.9980 chunk 145 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 HIS ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 HIS ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.062773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.047604 restraints weight = 79769.853| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 3.40 r_work: 0.2603 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 28888 Z= 0.109 Angle : 0.488 10.411 39300 Z= 0.244 Chirality : 0.040 0.140 4496 Planarity : 0.003 0.042 4968 Dihedral : 3.883 22.895 3848 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.80 % Allowed : 9.81 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.15), residues: 3548 helix: 1.30 (0.13), residues: 1836 sheet: 0.06 (0.25), residues: 464 loop : 1.06 (0.19), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 520 TYR 0.011 0.001 TYR A 914 PHE 0.014 0.001 PHE C 500 TRP 0.011 0.001 TRP B 514 HIS 0.002 0.000 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (28888) covalent geometry : angle 0.48818 / 0.24 (39300) hydrogen bonds : bond 0.03748 / 2.48 ( 1484) hydrogen bonds : angle 4.14440 / 2.99 ( 3960) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 1.125 Fit side-chains REVERT: A 542 GLU cc_start: 0.9330 (OUTLIER) cc_final: 0.8975 (mp0) REVERT: A 912 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8064 (pm20) REVERT: B 496 MET cc_start: 0.9265 (OUTLIER) cc_final: 0.9053 (ttm) REVERT: B 502 MET cc_start: 0.9205 (mmt) cc_final: 0.8630 (mmt) REVERT: B 542 GLU cc_start: 0.9338 (OUTLIER) cc_final: 0.8981 (mp0) REVERT: B 912 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8332 (pm20) REVERT: B 947 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8708 (tp) REVERT: C 81 MET cc_start: 0.8698 (mmt) cc_final: 0.8390 (mpm) REVERT: C 542 GLU cc_start: 0.9349 (OUTLIER) cc_final: 0.8976 (mp0) REVERT: C 912 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8310 (pm20) REVERT: C 915 MET cc_start: 0.9199 (mmp) cc_final: 0.8921 (tpt) REVERT: C 947 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8739 (tp) REVERT: D 81 MET cc_start: 0.8694 (mmt) cc_final: 0.8374 (mpm) REVERT: D 496 MET cc_start: 0.9250 (OUTLIER) cc_final: 0.9034 (ttm) REVERT: D 542 GLU cc_start: 0.9329 (OUTLIER) cc_final: 0.8965 (mp0) REVERT: D 912 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8279 (pm20) outliers start: 24 outliers final: 4 residues processed: 113 average time/residue: 0.7445 time to fit residues: 98.0063 Evaluate side-chains 107 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain B residue 890 THR Chi-restraints excluded: chain B residue 912 GLU Chi-restraints excluded: chain B residue 947 ILE Chi-restraints excluded: chain C residue 542 GLU Chi-restraints excluded: chain C residue 912 GLU Chi-restraints excluded: chain C residue 947 ILE Chi-restraints excluded: chain C residue 1043 VAL Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 542 GLU Chi-restraints excluded: chain D residue 890 THR Chi-restraints excluded: chain D residue 912 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 201 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 271 optimal weight: 10.0000 chunk 256 optimal weight: 4.9990 chunk 204 optimal weight: 0.0870 chunk 82 optimal weight: 9.9990 chunk 147 optimal weight: 6.9990 chunk 202 optimal weight: 2.9990 chunk 340 optimal weight: 8.9990 chunk 246 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 overall best weight: 1.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 897 ASN C 243 HIS ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 897 ASN ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.063051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.047687 restraints weight = 80097.116| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 3.44 r_work: 0.2608 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28888 Z= 0.114 Angle : 0.501 9.311 39300 Z= 0.248 Chirality : 0.040 0.217 4496 Planarity : 0.003 0.042 4968 Dihedral : 3.857 29.688 3848 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.66 % Allowed : 9.98 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.15), residues: 3548 helix: 1.32 (0.13), residues: 1836 sheet: 0.08 (0.25), residues: 464 loop : 1.01 (0.19), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 520 TYR 0.017 0.001 TYR B 914 PHE 0.016 0.001 PHE C 492 TRP 0.012 0.001 TRP A 80 HIS 0.002 0.000 HIS C 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (28888) covalent geometry : angle 0.50064 / 0.25 (39300) hydrogen bonds : bond 0.03759 / 2.48 ( 1484) hydrogen bonds : angle 4.12393 / 2.97 ( 3960) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 1.090 Fit side-chains REVERT: A 204 MET cc_start: 0.9040 (mmm) cc_final: 0.8793 (mmm) REVERT: A 542 GLU cc_start: 0.9340 (OUTLIER) cc_final: 0.8988 (mp0) REVERT: A 912 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7802 (pm20) REVERT: A 915 MET cc_start: 0.8064 (mmm) cc_final: 0.7796 (mmp) REVERT: B 204 MET cc_start: 0.8982 (mmm) cc_final: 0.8744 (mmm) REVERT: B 496 MET cc_start: 0.9260 (OUTLIER) cc_final: 0.9039 (ttm) REVERT: B 502 MET cc_start: 0.9179 (mmt) cc_final: 0.8611 (mmt) REVERT: B 542 GLU cc_start: 0.9315 (OUTLIER) cc_final: 0.8968 (mp0) REVERT: B 912 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8302 (pm20) REVERT: B 947 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8675 (tp) REVERT: C 81 MET cc_start: 0.8670 (mmt) cc_final: 0.8367 (mpm) REVERT: C 204 MET cc_start: 0.9039 (mmm) cc_final: 0.8814 (mmm) REVERT: C 519 MET cc_start: 0.9114 (mmm) cc_final: 0.8810 (tpp) REVERT: C 542 GLU cc_start: 0.9331 (OUTLIER) cc_final: 0.8971 (mp0) REVERT: C 912 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8280 (pm20) REVERT: D 81 MET cc_start: 0.8667 (mmt) cc_final: 0.8351 (mpm) REVERT: D 204 MET cc_start: 0.9041 (mmm) cc_final: 0.8799 (mmm) REVERT: D 496 MET cc_start: 0.9291 (OUTLIER) cc_final: 0.9054 (ttm) REVERT: D 542 GLU cc_start: 0.9329 (OUTLIER) cc_final: 0.8957 (mp0) REVERT: D 912 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8304 (pm20) REVERT: D 947 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8761 (tp) outliers start: 20 outliers final: 7 residues processed: 108 average time/residue: 0.8016 time to fit residues: 100.2297 Evaluate side-chains 113 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain B residue 890 THR Chi-restraints excluded: chain B residue 912 GLU Chi-restraints excluded: chain B residue 947 ILE Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 542 GLU Chi-restraints excluded: chain C residue 912 GLU Chi-restraints excluded: chain C residue 1043 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 542 GLU Chi-restraints excluded: chain D residue 890 THR Chi-restraints excluded: chain D residue 912 GLU Chi-restraints excluded: chain D residue 947 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 278 optimal weight: 3.9990 chunk 121 optimal weight: 0.7980 chunk 42 optimal weight: 10.0000 chunk 236 optimal weight: 6.9990 chunk 220 optimal weight: 10.0000 chunk 312 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 326 optimal weight: 6.9990 chunk 49 optimal weight: 0.3980 chunk 54 optimal weight: 4.9990 chunk 293 optimal weight: 0.0370 overall best weight: 2.0462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.062946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.047862 restraints weight = 80590.754| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 3.42 r_work: 0.2594 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28888 Z= 0.132 Angle : 0.512 13.628 39300 Z= 0.253 Chirality : 0.040 0.244 4496 Planarity : 0.003 0.042 4968 Dihedral : 3.877 35.794 3848 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.70 % Allowed : 10.08 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.15), residues: 3548 helix: 1.32 (0.13), residues: 1836 sheet: 0.08 (0.25), residues: 464 loop : 0.98 (0.19), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 808 TYR 0.015 0.001 TYR D 914 PHE 0.019 0.001 PHE C 492 TRP 0.013 0.001 TRP A 80 HIS 0.002 0.001 HIS C 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (28888) covalent geometry : angle 0.51244 / 0.25 (39300) hydrogen bonds : bond 0.03836 / 2.52 ( 1484) hydrogen bonds : angle 4.12975 / 2.97 ( 3960) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5798.48 seconds wall clock time: 100 minutes 37.95 seconds (6037.95 seconds total)