Starting phenix.real_space_refine on Wed Nov 19 08:29:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6b7n_7063/11_2025/6b7n_7063.cif Found real_map, /net/cci-nas-00/data/ceres_data/6b7n_7063/11_2025/6b7n_7063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6b7n_7063/11_2025/6b7n_7063.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6b7n_7063/11_2025/6b7n_7063.map" model { file = "/net/cci-nas-00/data/ceres_data/6b7n_7063/11_2025/6b7n_7063.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6b7n_7063/11_2025/6b7n_7063.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 14019 2.51 5 N 3609 2.21 5 O 4467 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22215 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 7139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 966, 7139 Classifications: {'peptide': 966} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 33, 'TRANS': 932} Unresolved non-hydrogen bonds: 312 Unresolved non-hydrogen angles: 382 Unresolved non-hydrogen dihedrals: 254 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 8, 'GLU:plan': 19, 'TYR:plan': 2, 'GLN:plan1': 7, 'ASP:plan': 7, 'HIS:plan': 2, 'ARG:plan': 14, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 242 Chain: "B" Number of atoms: 7139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 966, 7139 Classifications: {'peptide': 966} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 33, 'TRANS': 932} Unresolved non-hydrogen bonds: 312 Unresolved non-hydrogen angles: 382 Unresolved non-hydrogen dihedrals: 254 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 8, 'GLU:plan': 19, 'TYR:plan': 2, 'GLN:plan1': 7, 'ASP:plan': 7, 'HIS:plan': 2, 'ARG:plan': 14, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 242 Chain: "C" Number of atoms: 7139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 966, 7139 Classifications: {'peptide': 966} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 33, 'TRANS': 932} Unresolved non-hydrogen bonds: 312 Unresolved non-hydrogen angles: 382 Unresolved non-hydrogen dihedrals: 254 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 8, 'GLU:plan': 19, 'TYR:plan': 2, 'GLN:plan1': 7, 'ASP:plan': 7, 'HIS:plan': 2, 'ARG:plan': 14, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 242 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 5.84, per 1000 atoms: 0.26 Number of scatterers: 22215 At special positions: 0 Unit cell: (124.8, 119.6, 150.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 4467 8.00 N 3609 7.00 C 14019 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 181 " distance=2.03 Simple disulfide: pdb=" SG CYS A 260 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS A 335 " - pdb=" SG CYS A 378 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 352 " distance=2.04 Simple disulfide: pdb=" SG CYS A 361 " - pdb=" SG CYS A 386 " distance=2.03 Simple disulfide: pdb=" SG CYS A 433 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS A 532 " - pdb=" SG CYS A 545 " distance=2.03 Simple disulfide: pdb=" SG CYS A 597 " - pdb=" SG CYS A 619 " distance=2.03 Simple disulfide: pdb=" SG CYS A 602 " - pdb=" SG CYS A 608 " distance=2.02 Simple disulfide: pdb=" SG CYS A 699 " - pdb=" SG CYS A 710 " distance=2.03 Simple disulfide: pdb=" SG CYS A 901 " - pdb=" SG CYS A 912 " distance=2.04 Simple disulfide: pdb=" SG CYS A 951 " - pdb=" SG CYS A 997 " distance=2.04 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS B 116 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 181 " distance=2.03 Simple disulfide: pdb=" SG CYS B 260 " - pdb=" SG CYS B 270 " distance=2.03 Simple disulfide: pdb=" SG CYS B 335 " - pdb=" SG CYS B 378 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 352 " distance=2.04 Simple disulfide: pdb=" SG CYS B 361 " - pdb=" SG CYS B 386 " distance=2.03 Simple disulfide: pdb=" SG CYS B 433 " - pdb=" SG CYS B 484 " distance=2.03 Simple disulfide: pdb=" SG CYS B 532 " - pdb=" SG CYS B 545 " distance=2.03 Simple disulfide: pdb=" SG CYS B 597 " - pdb=" SG CYS B 619 " distance=2.03 Simple disulfide: pdb=" SG CYS B 602 " - pdb=" SG CYS B 608 " distance=2.02 Simple disulfide: pdb=" SG CYS B 699 " - pdb=" SG CYS B 710 " distance=2.03 Simple disulfide: pdb=" SG CYS B 901 " - pdb=" SG CYS B 912 " distance=2.04 Simple disulfide: pdb=" SG CYS B 951 " - pdb=" SG CYS B 997 " distance=2.04 Simple disulfide: pdb=" SG CYS C 93 " - pdb=" SG CYS C 116 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 181 " distance=2.03 Simple disulfide: pdb=" SG CYS C 260 " - pdb=" SG CYS C 270 " distance=2.03 Simple disulfide: pdb=" SG CYS C 335 " - pdb=" SG CYS C 378 " distance=2.03 Simple disulfide: pdb=" SG CYS C 349 " - pdb=" SG CYS C 352 " distance=2.04 Simple disulfide: pdb=" SG CYS C 361 " - pdb=" SG CYS C 386 " distance=2.03 Simple disulfide: pdb=" SG CYS C 433 " - pdb=" SG CYS C 484 " distance=2.03 Simple disulfide: pdb=" SG CYS C 532 " - pdb=" SG CYS C 545 " distance=2.02 Simple disulfide: pdb=" SG CYS C 597 " - pdb=" SG CYS C 619 " distance=2.03 Simple disulfide: pdb=" SG CYS C 602 " - pdb=" SG CYS C 608 " distance=2.02 Simple disulfide: pdb=" SG CYS C 699 " - pdb=" SG CYS C 710 " distance=2.03 Simple disulfide: pdb=" SG CYS C 901 " - pdb=" SG CYS C 912 " distance=2.04 Simple disulfide: pdb=" SG CYS C 951 " - pdb=" SG CYS C 997 " distance=2.04 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " NAG G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " NAG L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " NAG Q 3 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1205 " - " ASN A 184 " " NAG A1206 " - " ASN A 162 " " NAG A1207 " - " ASN A 251 " " NAG A1208 " - " ASN A 311 " " NAG A1209 " - " ASN A 472 " " NAG A1210 " - " ASN A 494 " " NAG A1211 " - " ASN A 661 " " NAG A1217 " - " ASN A1003 " " NAG B1205 " - " ASN B 184 " " NAG B1206 " - " ASN B 162 " " NAG B1207 " - " ASN B 251 " " NAG B1208 " - " ASN B 311 " " NAG B1209 " - " ASN B 472 " " NAG B1210 " - " ASN B 494 " " NAG B1211 " - " ASN B 661 " " NAG B1217 " - " ASN B1003 " " NAG C1205 " - " ASN C 184 " " NAG C1206 " - " ASN C 162 " " NAG C1207 " - " ASN C 251 " " NAG C1208 " - " ASN C 311 " " NAG C1209 " - " ASN C 472 " " NAG C1210 " - " ASN C 494 " " NAG C1211 " - " ASN C 661 " " NAG C1217 " - " ASN C1003 " " NAG D 1 " - " ASN A 241 " " NAG E 1 " - " ASN A 74 " " NAG F 1 " - " ASN A 788 " " NAG G 1 " - " ASN A 914 " " NAG H 1 " - " ASN A 526 " " NAG I 1 " - " ASN B 241 " " NAG J 1 " - " ASN B 74 " " NAG K 1 " - " ASN B 788 " " NAG L 1 " - " ASN B 914 " " NAG M 1 " - " ASN B 526 " " NAG N 1 " - " ASN C 241 " " NAG O 1 " - " ASN C 74 " " NAG P 1 " - " ASN C 788 " " NAG Q 1 " - " ASN C 914 " " NAG R 1 " - " ASN C 526 " Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 928.7 milliseconds 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5484 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 45 sheets defined 27.1% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 117 through 123 removed outlier: 4.263A pdb=" N VAL A 121 " --> pdb=" O GLY A 117 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS A 122 " --> pdb=" O GLY A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 169 Processing helix chain 'A' and resid 263 through 273 removed outlier: 3.565A pdb=" N ILE A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 removed outlier: 3.846A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY A 371 " --> pdb=" O ALA A 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 366 through 371' Processing helix chain 'A' and resid 596 through 602 Processing helix chain 'A' and resid 605 through 615 removed outlier: 3.725A pdb=" N TYR A 615 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 641 Processing helix chain 'A' and resid 644 through 650 Processing helix chain 'A' and resid 651 through 657 removed outlier: 6.126A pdb=" N THR A 654 " --> pdb=" O ALA A 651 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS A 657 " --> pdb=" O THR A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 682 Processing helix chain 'A' and resid 695 through 699 Processing helix chain 'A' and resid 707 through 714 Processing helix chain 'A' and resid 725 through 739 Processing helix chain 'A' and resid 740 through 742 No H-bonds generated for 'chain 'A' and resid 740 through 742' Processing helix chain 'A' and resid 752 through 765 Processing helix chain 'A' and resid 774 through 795 Processing helix chain 'A' and resid 805 through 835 removed outlier: 3.744A pdb=" N VAL A 810 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A 812 " --> pdb=" O ASN A 808 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN A 824 " --> pdb=" O VAL A 820 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLY A 825 " --> pdb=" O VAL A 821 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA A 827 " --> pdb=" O GLN A 823 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU A 828 " --> pdb=" O GLN A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 851 Processing helix chain 'A' and resid 854 through 902 removed outlier: 3.611A pdb=" N ALA A 858 " --> pdb=" O GLU A 854 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 902 " --> pdb=" O ILE A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 991 removed outlier: 3.981A pdb=" N ASP A 990 " --> pdb=" O ARG A 987 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE A 991 " --> pdb=" O GLN A 988 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 987 through 991' Processing helix chain 'A' and resid 1008 through 1013 Processing helix chain 'B' and resid 117 through 123 removed outlier: 4.263A pdb=" N VAL B 121 " --> pdb=" O GLY B 117 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS B 122 " --> pdb=" O GLY B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 169 Processing helix chain 'B' and resid 263 through 273 removed outlier: 3.566A pdb=" N ILE B 268 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 removed outlier: 3.844A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY B 371 " --> pdb=" O ALA B 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 366 through 371' Processing helix chain 'B' and resid 596 through 602 Processing helix chain 'B' and resid 605 through 615 removed outlier: 3.726A pdb=" N TYR B 615 " --> pdb=" O LEU B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 641 Processing helix chain 'B' and resid 644 through 650 Processing helix chain 'B' and resid 651 through 657 removed outlier: 6.125A pdb=" N THR B 654 " --> pdb=" O ALA B 651 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS B 657 " --> pdb=" O THR B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 682 Processing helix chain 'B' and resid 695 through 699 Processing helix chain 'B' and resid 707 through 714 Processing helix chain 'B' and resid 725 through 739 Processing helix chain 'B' and resid 740 through 742 No H-bonds generated for 'chain 'B' and resid 740 through 742' Processing helix chain 'B' and resid 752 through 765 Processing helix chain 'B' and resid 774 through 795 Processing helix chain 'B' and resid 805 through 835 removed outlier: 3.743A pdb=" N VAL B 810 " --> pdb=" O ALA B 806 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA B 811 " --> pdb=" O LEU B 807 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE B 812 " --> pdb=" O ASN B 808 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN B 824 " --> pdb=" O VAL B 820 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLY B 825 " --> pdb=" O VAL B 821 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA B 827 " --> pdb=" O GLN B 823 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU B 828 " --> pdb=" O GLN B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 851 Processing helix chain 'B' and resid 854 through 902 removed outlier: 3.610A pdb=" N ALA B 858 " --> pdb=" O GLU B 854 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL B 902 " --> pdb=" O ILE B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 991 removed outlier: 3.982A pdb=" N ASP B 990 " --> pdb=" O ARG B 987 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE B 991 " --> pdb=" O GLN B 988 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 987 through 991' Processing helix chain 'B' and resid 1008 through 1013 Processing helix chain 'C' and resid 117 through 123 removed outlier: 4.264A pdb=" N VAL C 121 " --> pdb=" O GLY C 117 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS C 122 " --> pdb=" O GLY C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 169 Processing helix chain 'C' and resid 263 through 273 removed outlier: 3.566A pdb=" N ILE C 268 " --> pdb=" O VAL C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 371 removed outlier: 3.844A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY C 371 " --> pdb=" O ALA C 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 366 through 371' Processing helix chain 'C' and resid 596 through 602 Processing helix chain 'C' and resid 605 through 615 removed outlier: 3.725A pdb=" N TYR C 615 " --> pdb=" O LEU C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 641 Processing helix chain 'C' and resid 644 through 650 Processing helix chain 'C' and resid 651 through 657 removed outlier: 6.125A pdb=" N THR C 654 " --> pdb=" O ALA C 651 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS C 657 " --> pdb=" O THR C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 682 Processing helix chain 'C' and resid 695 through 699 Processing helix chain 'C' and resid 707 through 714 Processing helix chain 'C' and resid 725 through 739 Processing helix chain 'C' and resid 740 through 742 No H-bonds generated for 'chain 'C' and resid 740 through 742' Processing helix chain 'C' and resid 752 through 765 Processing helix chain 'C' and resid 774 through 795 Processing helix chain 'C' and resid 805 through 835 removed outlier: 3.744A pdb=" N VAL C 810 " --> pdb=" O ALA C 806 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA C 811 " --> pdb=" O LEU C 807 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE C 812 " --> pdb=" O ASN C 808 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN C 824 " --> pdb=" O VAL C 820 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY C 825 " --> pdb=" O VAL C 821 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA C 827 " --> pdb=" O GLN C 823 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU C 828 " --> pdb=" O GLN C 824 " (cutoff:3.500A) Processing helix chain 'C' and resid 846 through 851 Processing helix chain 'C' and resid 854 through 902 removed outlier: 3.609A pdb=" N ALA C 858 " --> pdb=" O GLU C 854 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL C 902 " --> pdb=" O ILE C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 991 removed outlier: 3.980A pdb=" N ASP C 990 " --> pdb=" O ARG C 987 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE C 991 " --> pdb=" O GLN C 988 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 987 through 991' Processing helix chain 'C' and resid 1008 through 1013 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 85 removed outlier: 6.204A pdb=" N THR A 250 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ILE A 254 " --> pdb=" O THR A 250 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 91 removed outlier: 3.556A pdb=" N PHE A 237 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 91 removed outlier: 4.472A pdb=" N GLN A 205 " --> pdb=" O TYR A 201 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N PHE A 206 " --> pdb=" O LEU A 213 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 105 removed outlier: 3.677A pdb=" N LEU A 225 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 143 " --> pdb=" O PHE A 155 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY A 189 " --> pdb=" O CYS A 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 281 through 282 removed outlier: 6.441A pdb=" N GLN A 489 " --> pdb=" O ALA A 500 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ALA A 500 " --> pdb=" O GLN A 489 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE A 491 " --> pdb=" O VAL A 498 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 296 through 297 removed outlier: 3.632A pdb=" N THR A 434 " --> pdb=" O GLY A 445 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N TYR A 468 " --> pdb=" O VAL A 481 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER A 462 " --> pdb=" O GLY A 465 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU A 467 " --> pdb=" O PHE A 460 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE A 460 " --> pdb=" O LEU A 467 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.603A pdb=" N GLU A 344 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET A 372 " --> pdb=" O GLY A 416 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 333 through 335 removed outlier: 3.513A pdb=" N CYS A 386 " --> pdb=" O VAL A 406 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 353 through 356 removed outlier: 3.526A pdb=" N THR A 353 " --> pdb=" O THR A 393 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 537 through 539 removed outlier: 3.815A pdb=" N LEU A 537 " --> pdb=" O VAL A 544 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 569 through 574 Processing sheet with id=AB3, first strand: chain 'A' and resid 580 through 587 removed outlier: 3.613A pdb=" N VAL A 935 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY A 928 " --> pdb=" O ALA A 925 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 593 through 595 Processing sheet with id=AB5, first strand: chain 'A' and resid 949 through 952 Processing sheet with id=AB6, first strand: chain 'A' and resid 964 through 969 Processing sheet with id=AB7, first strand: chain 'B' and resid 80 through 85 removed outlier: 6.205A pdb=" N THR B 250 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ILE B 254 " --> pdb=" O THR B 250 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 90 through 91 removed outlier: 3.555A pdb=" N PHE B 237 " --> pdb=" O THR B 95 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 90 through 91 removed outlier: 4.472A pdb=" N GLN B 205 " --> pdb=" O TYR B 201 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N PHE B 206 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 101 through 105 removed outlier: 3.677A pdb=" N LEU B 225 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B 143 " --> pdb=" O PHE B 155 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU B 151 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY B 189 " --> pdb=" O CYS B 181 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 281 through 282 removed outlier: 6.443A pdb=" N GLN B 489 " --> pdb=" O ALA B 500 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ALA B 500 " --> pdb=" O GLN B 489 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE B 491 " --> pdb=" O VAL B 498 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 296 through 297 removed outlier: 3.631A pdb=" N THR B 434 " --> pdb=" O GLY B 445 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N TYR B 468 " --> pdb=" O VAL B 481 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER B 462 " --> pdb=" O GLY B 465 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LEU B 467 " --> pdb=" O PHE B 460 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE B 460 " --> pdb=" O LEU B 467 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.602A pdb=" N GLU B 344 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET B 372 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 333 through 335 removed outlier: 3.514A pdb=" N CYS B 386 " --> pdb=" O VAL B 406 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 353 through 356 removed outlier: 3.525A pdb=" N THR B 353 " --> pdb=" O THR B 393 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 537 through 539 removed outlier: 3.815A pdb=" N LEU B 537 " --> pdb=" O VAL B 544 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 569 through 574 Processing sheet with id=AC9, first strand: chain 'B' and resid 580 through 587 removed outlier: 3.612A pdb=" N VAL B 935 " --> pdb=" O SER B 580 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY B 928 " --> pdb=" O ALA B 925 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 593 through 595 Processing sheet with id=AD2, first strand: chain 'B' and resid 949 through 952 Processing sheet with id=AD3, first strand: chain 'B' and resid 964 through 969 Processing sheet with id=AD4, first strand: chain 'C' and resid 80 through 85 removed outlier: 6.203A pdb=" N THR C 250 " --> pdb=" O ILE C 254 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ILE C 254 " --> pdb=" O THR C 250 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 90 through 91 removed outlier: 3.556A pdb=" N PHE C 237 " --> pdb=" O THR C 95 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 90 through 91 removed outlier: 4.472A pdb=" N GLN C 205 " --> pdb=" O TYR C 201 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N PHE C 206 " --> pdb=" O LEU C 213 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 101 through 105 removed outlier: 3.676A pdb=" N LEU C 225 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL C 143 " --> pdb=" O PHE C 155 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU C 151 " --> pdb=" O GLY C 147 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY C 189 " --> pdb=" O CYS C 181 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 281 through 282 removed outlier: 6.442A pdb=" N GLN C 489 " --> pdb=" O ALA C 500 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ALA C 500 " --> pdb=" O GLN C 489 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE C 491 " --> pdb=" O VAL C 498 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 296 through 297 removed outlier: 3.633A pdb=" N THR C 434 " --> pdb=" O GLY C 445 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N TYR C 468 " --> pdb=" O VAL C 481 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER C 462 " --> pdb=" O GLY C 465 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU C 467 " --> pdb=" O PHE C 460 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE C 460 " --> pdb=" O LEU C 467 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.603A pdb=" N GLU C 344 " --> pdb=" O VAL C 308 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET C 372 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 333 through 335 removed outlier: 3.514A pdb=" N CYS C 386 " --> pdb=" O VAL C 406 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 353 through 356 removed outlier: 3.526A pdb=" N THR C 353 " --> pdb=" O THR C 393 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 537 through 539 removed outlier: 3.816A pdb=" N LEU C 537 " --> pdb=" O VAL C 544 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 569 through 574 Processing sheet with id=AE6, first strand: chain 'C' and resid 580 through 587 removed outlier: 3.612A pdb=" N VAL C 935 " --> pdb=" O SER C 580 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY C 928 " --> pdb=" O ALA C 925 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 593 through 595 Processing sheet with id=AE8, first strand: chain 'C' and resid 949 through 952 Processing sheet with id=AE9, first strand: chain 'C' and resid 964 through 969 888 hydrogen bonds defined for protein. 2439 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: 5.38 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6630 1.33 - 1.46: 5433 1.46 - 1.58: 10383 1.58 - 1.71: 0 1.71 - 1.83: 162 Bond restraints: 22608 Sorted by residual: bond pdb=" C1 NAG L 3 " pdb=" O5 NAG L 3 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.38e+00 bond pdb=" C1 NAG G 3 " pdb=" O5 NAG G 3 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.38e+00 bond pdb=" C1 NAG Q 3 " pdb=" O5 NAG Q 3 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.97e+00 bond pdb=" C1 NAG B1210 " pdb=" O5 NAG B1210 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.55e+00 bond pdb=" CA PRO A 192 " pdb=" C PRO A 192 " ideal model delta sigma weight residual 1.517 1.501 0.016 6.70e-03 2.23e+04 5.48e+00 ... (remaining 22603 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.34: 30660 4.34 - 8.69: 248 8.69 - 13.03: 49 13.03 - 17.38: 0 17.38 - 21.72: 3 Bond angle restraints: 30960 Sorted by residual: angle pdb=" CA LEU B 467 " pdb=" CB LEU B 467 " pdb=" CG LEU B 467 " ideal model delta sigma weight residual 116.30 138.02 -21.72 3.50e+00 8.16e-02 3.85e+01 angle pdb=" CA LEU A 467 " pdb=" CB LEU A 467 " pdb=" CG LEU A 467 " ideal model delta sigma weight residual 116.30 138.00 -21.70 3.50e+00 8.16e-02 3.85e+01 angle pdb=" CA LEU C 467 " pdb=" CB LEU C 467 " pdb=" CG LEU C 467 " ideal model delta sigma weight residual 116.30 137.98 -21.68 3.50e+00 8.16e-02 3.84e+01 angle pdb=" C LEU B 994 " pdb=" N THR B 995 " pdb=" CA THR B 995 " ideal model delta sigma weight residual 121.54 133.31 -11.77 1.91e+00 2.74e-01 3.80e+01 angle pdb=" C LEU A 994 " pdb=" N THR A 995 " pdb=" CA THR A 995 " ideal model delta sigma weight residual 121.54 133.30 -11.76 1.91e+00 2.74e-01 3.79e+01 ... (remaining 30955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 13446 17.80 - 35.60: 562 35.60 - 53.40: 173 53.40 - 71.21: 27 71.21 - 89.01: 18 Dihedral angle restraints: 14226 sinusoidal: 5724 harmonic: 8502 Sorted by residual: dihedral pdb=" CA LEU A 556 " pdb=" C LEU A 556 " pdb=" N GLN A 557 " pdb=" CA GLN A 557 " ideal model delta harmonic sigma weight residual 180.00 126.53 53.47 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" CA LEU B 556 " pdb=" C LEU B 556 " pdb=" N GLN B 557 " pdb=" CA GLN B 557 " ideal model delta harmonic sigma weight residual 180.00 126.55 53.45 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" CA LEU C 556 " pdb=" C LEU C 556 " pdb=" N GLN C 557 " pdb=" CA GLN C 557 " ideal model delta harmonic sigma weight residual 180.00 126.60 53.40 0 5.00e+00 4.00e-02 1.14e+02 ... (remaining 14223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 3793 0.118 - 0.236: 178 0.236 - 0.355: 25 0.355 - 0.473: 6 0.473 - 0.591: 6 Chirality restraints: 4008 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 526 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.73e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN C 526 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.95e+00 chirality pdb=" C1 NAG A1217 " pdb=" ND2 ASN A1003 " pdb=" C2 NAG A1217 " pdb=" O5 NAG A1217 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.87e+00 ... (remaining 4005 not shown) Planarity restraints: 3912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 358 " -0.016 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C THR A 358 " 0.057 2.00e-02 2.50e+03 pdb=" O THR A 358 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP A 359 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 358 " -0.016 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C THR B 358 " 0.057 2.00e-02 2.50e+03 pdb=" O THR B 358 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP B 359 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 358 " -0.016 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C THR C 358 " 0.057 2.00e-02 2.50e+03 pdb=" O THR C 358 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP C 359 " -0.019 2.00e-02 2.50e+03 ... (remaining 3909 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1365 2.72 - 3.26: 22344 3.26 - 3.81: 36242 3.81 - 4.35: 42158 4.35 - 4.90: 72173 Nonbonded interactions: 174282 Sorted by model distance: nonbonded pdb=" OG SER B 442 " pdb=" OD1 ASP C 848 " model vdw 2.171 3.040 nonbonded pdb=" OG SER C 462 " pdb=" O GLY C 465 " model vdw 2.191 3.040 nonbonded pdb=" OG SER B 462 " pdb=" O GLY B 465 " model vdw 2.192 3.040 nonbonded pdb=" OG SER A 462 " pdb=" O GLY A 465 " model vdw 2.193 3.040 nonbonded pdb=" OG SER A 959 " pdb=" OG1 THR B 768 " model vdw 2.215 3.040 ... (remaining 174277 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' } ncs_group { reference = chain 'G' selection = chain 'L' selection = chain 'Q' } 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: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.390 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 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 : 0.008 0.130 22704 Z= 0.390 Angle : 1.210 21.719 31209 Z= 0.601 Chirality : 0.066 0.591 4008 Planarity : 0.008 0.073 3873 Dihedral : 11.304 77.905 8625 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.41 % Allowed : 12.07 % Favored : 87.52 % Rotamer: Outliers : 0.78 % Allowed : 4.02 % Favored : 95.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.75 % 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: -4.33 (0.13), residues: 2892 helix: -2.00 (0.15), residues: 684 sheet: -2.86 (0.19), residues: 588 loop : -3.39 (0.13), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 84 TYR 0.038 0.003 TYR B 226 PHE 0.038 0.004 PHE B 839 TRP 0.008 0.003 TRP A 973 HIS 0.011 0.004 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00845 (22608) covalent geometry : angle 1.13946 (30960) SS BOND : bond 0.00519 ( 39) SS BOND : angle 2.38146 ( 78) hydrogen bonds : bond 0.20252 ( 882) hydrogen bonds : angle 9.82268 ( 2439) link_BETA1-4 : bond 0.00697 ( 18) link_BETA1-4 : angle 3.29685 ( 54) link_NAG-ASN : bond 0.00930 ( 39) link_NAG-ASN : angle 6.17026 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.721 Fit side-chains REVERT: A 218 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8938 (tp) REVERT: A 731 MET cc_start: 0.8826 (mtm) cc_final: 0.8588 (mtm) REVERT: B 731 MET cc_start: 0.8699 (mtm) cc_final: 0.8404 (mtm) REVERT: C 104 MET cc_start: 0.8437 (ptp) cc_final: 0.8127 (ptp) REVERT: C 372 MET cc_start: 0.8224 (tpp) cc_final: 0.7981 (tpp) outliers start: 18 outliers final: 1 residues processed: 101 average time/residue: 0.1547 time to fit residues: 25.2860 Evaluate side-chains 56 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain B residue 365 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.0050 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN A 87 GLN A 126 HIS A 331 ASN A 489 GLN A 557 GLN A 639 ASN A 767 GLN A 895 GLN A 939 ASN A 968 GLN A1011 ASN B 65 ASN B 87 GLN B 126 HIS B 331 ASN B 402 GLN B 557 GLN B 767 GLN B 895 GLN B 939 ASN B 968 GLN B1011 ASN C 65 ASN C 87 GLN C 126 HIS C 331 ASN C 557 GLN C 639 ASN C 847 GLN C 895 GLN C 939 ASN C 968 GLN C1011 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.049535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.041916 restraints weight = 118278.239| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 4.11 r_work: 0.2922 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22704 Z= 0.148 Angle : 0.811 19.635 31209 Z= 0.398 Chirality : 0.047 0.416 4008 Planarity : 0.005 0.052 3873 Dihedral : 9.196 59.381 4279 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.41 % Allowed : 10.17 % Favored : 89.42 % Rotamer: Outliers : 1.47 % Allowed : 6.44 % Favored : 92.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: -3.08 (0.15), residues: 2892 helix: 0.41 (0.19), residues: 678 sheet: -2.76 (0.20), residues: 537 loop : -3.00 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 888 TYR 0.020 0.001 TYR A 226 PHE 0.018 0.002 PHE B 839 TRP 0.011 0.002 TRP A 973 HIS 0.005 0.001 HIS C 421 Details of bonding type rmsd covalent geometry : bond 0.00297 (22608) covalent geometry : angle 0.77483 (30960) SS BOND : bond 0.00425 ( 39) SS BOND : angle 1.17822 ( 78) hydrogen bonds : bond 0.04748 ( 882) hydrogen bonds : angle 6.28826 ( 2439) link_BETA1-4 : bond 0.00710 ( 18) link_BETA1-4 : angle 1.72993 ( 54) link_NAG-ASN : bond 0.00687 ( 39) link_NAG-ASN : angle 3.78915 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 62 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: A 218 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8980 (tp) REVERT: A 358 THR cc_start: 0.8336 (OUTLIER) cc_final: 0.8126 (m) REVERT: B 731 MET cc_start: 0.9291 (mtm) cc_final: 0.9079 (mtm) REVERT: C 718 MET cc_start: 0.9090 (mtp) cc_final: 0.8802 (mtm) outliers start: 34 outliers final: 12 residues processed: 96 average time/residue: 0.1297 time to fit residues: 22.0791 Evaluate side-chains 66 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 994 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 240 optimal weight: 7.9990 chunk 98 optimal weight: 0.5980 chunk 219 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 140 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 120 optimal weight: 0.0970 chunk 17 optimal weight: 7.9990 chunk 277 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN A 402 GLN A 489 GLN A 639 ASN B 309 GLN ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 GLN C 639 ASN ** C 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 767 GLN ** C 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.048893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.041152 restraints weight = 118951.168| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 4.12 r_work: 0.2899 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 22704 Z= 0.163 Angle : 0.754 12.762 31209 Z= 0.371 Chirality : 0.047 0.425 4008 Planarity : 0.004 0.050 3873 Dihedral : 8.335 59.898 4279 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.41 % Allowed : 11.10 % Favored : 88.49 % Rotamer: Outliers : 1.90 % Allowed : 7.39 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % 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: -2.42 (0.16), residues: 2892 helix: 1.50 (0.20), residues: 675 sheet: -2.24 (0.20), residues: 609 loop : -2.87 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 888 TYR 0.023 0.002 TYR C 226 PHE 0.022 0.002 PHE B 577 TRP 0.006 0.001 TRP A 973 HIS 0.007 0.001 HIS A 421 Details of bonding type rmsd covalent geometry : bond 0.00353 (22608) covalent geometry : angle 0.72520 (30960) SS BOND : bond 0.00455 ( 39) SS BOND : angle 1.07437 ( 78) hydrogen bonds : bond 0.04354 ( 882) hydrogen bonds : angle 5.61191 ( 2439) link_BETA1-4 : bond 0.00429 ( 18) link_BETA1-4 : angle 1.73323 ( 54) link_NAG-ASN : bond 0.00525 ( 39) link_NAG-ASN : angle 3.24309 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 55 time to evaluate : 0.897 Fit side-chains REVERT: A 218 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8969 (tp) REVERT: A 372 MET cc_start: 0.9240 (ttm) cc_final: 0.8875 (ttm) REVERT: A 771 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8251 (mm) REVERT: A 980 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8189 (mtm) REVERT: C 718 MET cc_start: 0.9084 (mtp) cc_final: 0.8736 (mtm) REVERT: C 771 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8288 (mm) outliers start: 44 outliers final: 26 residues processed: 96 average time/residue: 0.1250 time to fit residues: 21.4960 Evaluate side-chains 82 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 52 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 602 CYS Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 980 MET Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 597 CYS Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 597 CYS Chi-restraints excluded: chain C residue 602 CYS Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 994 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 109 optimal weight: 7.9990 chunk 264 optimal weight: 2.9990 chunk 218 optimal weight: 9.9990 chunk 135 optimal weight: 4.9990 chunk 272 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 259 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 174 optimal weight: 7.9990 chunk 143 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 HIS ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 639 ASN ** C 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.047787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.040035 restraints weight = 119687.452| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 4.08 r_work: 0.2858 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 22704 Z= 0.207 Angle : 0.766 15.042 31209 Z= 0.376 Chirality : 0.047 0.433 4008 Planarity : 0.004 0.049 3873 Dihedral : 7.956 59.161 4279 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.41 % Allowed : 10.89 % Favored : 88.69 % Rotamer: Outliers : 2.85 % Allowed : 8.26 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -2.15 (0.16), residues: 2892 helix: 1.96 (0.20), residues: 675 sheet: -2.21 (0.20), residues: 606 loop : -2.76 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 978 TYR 0.024 0.002 TYR C 226 PHE 0.023 0.002 PHE B 839 TRP 0.005 0.001 TRP A 973 HIS 0.007 0.002 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.00452 (22608) covalent geometry : angle 0.73851 (30960) SS BOND : bond 0.00454 ( 39) SS BOND : angle 1.21601 ( 78) hydrogen bonds : bond 0.04347 ( 882) hydrogen bonds : angle 5.41861 ( 2439) link_BETA1-4 : bond 0.00477 ( 18) link_BETA1-4 : angle 1.68201 ( 54) link_NAG-ASN : bond 0.00491 ( 39) link_NAG-ASN : angle 3.15811 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 52 time to evaluate : 0.854 Fit side-chains REVERT: A 249 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.8916 (pp) REVERT: A 372 MET cc_start: 0.9306 (ttm) cc_final: 0.8904 (ttm) REVERT: A 733 THR cc_start: 0.9261 (OUTLIER) cc_final: 0.9021 (m) REVERT: A 771 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8227 (mm) REVERT: B 86 TYR cc_start: 0.9312 (OUTLIER) cc_final: 0.8719 (m-80) REVERT: C 372 MET cc_start: 0.8950 (ttm) cc_final: 0.8480 (ttm) REVERT: C 718 MET cc_start: 0.9122 (mtp) cc_final: 0.8674 (mtm) outliers start: 66 outliers final: 28 residues processed: 113 average time/residue: 0.1191 time to fit residues: 24.5449 Evaluate side-chains 84 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 52 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 602 CYS Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 354 MET Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 597 CYS Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 597 CYS Chi-restraints excluded: chain C residue 602 CYS Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 994 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 230 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 269 optimal weight: 10.0000 chunk 215 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 64 optimal weight: 0.0980 chunk 189 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 775 GLN ** 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 = 0.3189 r_free = 0.3189 target = 0.046361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.038676 restraints weight = 119865.626| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 4.03 r_work: 0.2803 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 22704 Z= 0.296 Angle : 0.836 13.800 31209 Z= 0.409 Chirality : 0.048 0.447 4008 Planarity : 0.004 0.051 3873 Dihedral : 8.017 57.879 4275 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.41 % Allowed : 11.76 % Favored : 87.83 % Rotamer: Outliers : 3.50 % Allowed : 8.91 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % 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: -2.09 (0.16), residues: 2892 helix: 1.95 (0.20), residues: 675 sheet: -2.15 (0.21), residues: 561 loop : -2.70 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 978 TYR 0.029 0.002 TYR B 226 PHE 0.032 0.002 PHE B 839 TRP 0.005 0.001 TRP A 973 HIS 0.010 0.002 HIS C 236 Details of bonding type rmsd covalent geometry : bond 0.00650 (22608) covalent geometry : angle 0.80856 (30960) SS BOND : bond 0.00397 ( 39) SS BOND : angle 1.40654 ( 78) hydrogen bonds : bond 0.04665 ( 882) hydrogen bonds : angle 5.54088 ( 2439) link_BETA1-4 : bond 0.00366 ( 18) link_BETA1-4 : angle 1.80821 ( 54) link_NAG-ASN : bond 0.00461 ( 39) link_NAG-ASN : angle 3.28557 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 52 time to evaluate : 0.914 Fit side-chains REVERT: A 249 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9068 (pp) REVERT: A 372 MET cc_start: 0.9323 (ttm) cc_final: 0.8937 (ttm) REVERT: A 733 THR cc_start: 0.9398 (OUTLIER) cc_final: 0.9185 (m) REVERT: A 771 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8217 (mm) REVERT: A 980 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8305 (mtm) REVERT: B 86 TYR cc_start: 0.9262 (OUTLIER) cc_final: 0.8841 (m-80) REVERT: B 516 ILE cc_start: 0.9298 (OUTLIER) cc_final: 0.8995 (mp) REVERT: B 930 PHE cc_start: 0.8953 (OUTLIER) cc_final: 0.6813 (p90) REVERT: C 372 MET cc_start: 0.8914 (ttm) cc_final: 0.8503 (ttm) REVERT: C 388 MET cc_start: 0.9543 (OUTLIER) cc_final: 0.9029 (mtp) REVERT: C 718 MET cc_start: 0.9121 (mtp) cc_final: 0.8667 (mtm) outliers start: 81 outliers final: 48 residues processed: 125 average time/residue: 0.1192 time to fit residues: 27.0245 Evaluate side-chains 107 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 51 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 602 CYS Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 930 PHE Chi-restraints excluded: chain A residue 980 MET Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 597 CYS Chi-restraints excluded: chain B residue 912 CYS Chi-restraints excluded: chain B residue 930 PHE Chi-restraints excluded: chain B residue 932 MET Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 597 CYS Chi-restraints excluded: chain C residue 602 CYS Chi-restraints excluded: chain C residue 912 CYS Chi-restraints excluded: chain C residue 930 PHE Chi-restraints excluded: chain C residue 950 ILE Chi-restraints excluded: chain C residue 994 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 194 optimal weight: 0.3980 chunk 179 optimal weight: 4.9990 chunk 40 optimal weight: 0.0970 chunk 192 optimal weight: 9.9990 chunk 209 optimal weight: 6.9990 chunk 245 optimal weight: 0.9990 chunk 286 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 chunk 224 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 HIS ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 605 ASN ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 605 ASN C 639 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.048399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.040683 restraints weight = 118515.883| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 4.07 r_work: 0.2883 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22704 Z= 0.129 Angle : 0.709 11.211 31209 Z= 0.347 Chirality : 0.046 0.436 4008 Planarity : 0.004 0.051 3873 Dihedral : 7.366 59.378 4275 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.41 % Allowed : 10.20 % Favored : 89.38 % Rotamer: Outliers : 2.29 % Allowed : 10.94 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -1.85 (0.16), residues: 2892 helix: 2.26 (0.20), residues: 675 sheet: -1.85 (0.21), residues: 558 loop : -2.67 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 357 TYR 0.014 0.001 TYR A 226 PHE 0.022 0.002 PHE A 839 TRP 0.007 0.001 TRP A 973 HIS 0.007 0.001 HIS A 421 Details of bonding type rmsd covalent geometry : bond 0.00266 (22608) covalent geometry : angle 0.68242 (30960) SS BOND : bond 0.00369 ( 39) SS BOND : angle 1.04021 ( 78) hydrogen bonds : bond 0.03934 ( 882) hydrogen bonds : angle 5.17224 ( 2439) link_BETA1-4 : bond 0.00642 ( 18) link_BETA1-4 : angle 1.43032 ( 54) link_NAG-ASN : bond 0.00692 ( 39) link_NAG-ASN : angle 3.05060 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 56 time to evaluate : 0.939 Fit side-chains REVERT: A 249 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.8890 (pp) REVERT: A 316 MET cc_start: 0.8794 (mtp) cc_final: 0.8516 (mtp) REVERT: A 733 THR cc_start: 0.9253 (OUTLIER) cc_final: 0.9006 (m) REVERT: A 771 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8192 (mm) REVERT: B 86 TYR cc_start: 0.9200 (OUTLIER) cc_final: 0.8827 (m-80) REVERT: C 372 MET cc_start: 0.8936 (ttm) cc_final: 0.8638 (ttm) REVERT: C 718 MET cc_start: 0.9086 (mtp) cc_final: 0.8626 (mtm) outliers start: 53 outliers final: 30 residues processed: 102 average time/residue: 0.1260 time to fit residues: 23.1791 Evaluate side-chains 86 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 52 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 602 CYS Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 912 CYS Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 597 CYS Chi-restraints excluded: chain B residue 912 CYS Chi-restraints excluded: chain B residue 932 MET Chi-restraints excluded: chain B residue 950 ILE Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 602 CYS Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 950 ILE Chi-restraints excluded: chain C residue 994 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 0.7980 chunk 188 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 256 optimal weight: 10.0000 chunk 267 optimal weight: 2.9990 chunk 212 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 236 optimal weight: 0.7980 chunk 178 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 639 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.048653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.040922 restraints weight = 118126.289| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 4.10 r_work: 0.2887 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22704 Z= 0.125 Angle : 0.694 11.199 31209 Z= 0.339 Chirality : 0.045 0.432 4008 Planarity : 0.004 0.049 3873 Dihedral : 7.110 59.724 4275 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.41 % Allowed : 10.17 % Favored : 89.42 % Rotamer: Outliers : 2.16 % Allowed : 11.41 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -1.71 (0.16), residues: 2892 helix: 2.44 (0.20), residues: 675 sheet: -1.73 (0.21), residues: 546 loop : -2.62 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 888 TYR 0.015 0.001 TYR C 105 PHE 0.018 0.001 PHE B 839 TRP 0.007 0.001 TRP A 973 HIS 0.006 0.001 HIS A 421 Details of bonding type rmsd covalent geometry : bond 0.00262 (22608) covalent geometry : angle 0.66568 (30960) SS BOND : bond 0.00436 ( 39) SS BOND : angle 1.13135 ( 78) hydrogen bonds : bond 0.03773 ( 882) hydrogen bonds : angle 5.03336 ( 2439) link_BETA1-4 : bond 0.00467 ( 18) link_BETA1-4 : angle 1.47572 ( 54) link_NAG-ASN : bond 0.00513 ( 39) link_NAG-ASN : angle 3.04789 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 55 time to evaluate : 0.914 Fit side-chains REVERT: A 249 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.8999 (pp) REVERT: A 316 MET cc_start: 0.8804 (mtp) cc_final: 0.8520 (mtp) REVERT: A 733 THR cc_start: 0.9232 (OUTLIER) cc_final: 0.8993 (m) REVERT: A 980 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.8399 (mtm) REVERT: B 86 TYR cc_start: 0.9173 (OUTLIER) cc_final: 0.8862 (m-80) REVERT: B 718 MET cc_start: 0.9041 (mtp) cc_final: 0.8670 (mtm) REVERT: C 372 MET cc_start: 0.8901 (ttm) cc_final: 0.8602 (ttm) outliers start: 50 outliers final: 32 residues processed: 99 average time/residue: 0.1226 time to fit residues: 22.1879 Evaluate side-chains 90 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 54 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 602 CYS Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 912 CYS Chi-restraints excluded: chain A residue 930 PHE Chi-restraints excluded: chain A residue 980 MET Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 597 CYS Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain B residue 932 MET Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 597 CYS Chi-restraints excluded: chain C residue 602 CYS Chi-restraints excluded: chain C residue 912 CYS Chi-restraints excluded: chain C residue 950 ILE Chi-restraints excluded: chain C residue 994 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 192 optimal weight: 9.9990 chunk 228 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 chunk 223 optimal weight: 0.0000 chunk 100 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 6 optimal weight: 0.0370 chunk 140 optimal weight: 3.9990 chunk 194 optimal weight: 0.4980 chunk 280 optimal weight: 0.8980 overall best weight: 0.4862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 HIS ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 HIS C 639 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.049549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.041746 restraints weight = 117381.345| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 4.27 r_work: 0.2912 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 22704 Z= 0.108 Angle : 0.678 11.012 31209 Z= 0.331 Chirality : 0.045 0.427 4008 Planarity : 0.004 0.048 3873 Dihedral : 6.772 57.733 4275 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.47 % Favored : 90.11 % Rotamer: Outliers : 2.08 % Allowed : 11.37 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -1.58 (0.16), residues: 2892 helix: 2.58 (0.20), residues: 675 sheet: -1.62 (0.22), residues: 546 loop : -2.57 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 908 TYR 0.014 0.001 TYR A 226 PHE 0.019 0.001 PHE B 577 TRP 0.007 0.001 TRP A 973 HIS 0.006 0.001 HIS A 421 Details of bonding type rmsd covalent geometry : bond 0.00214 (22608) covalent geometry : angle 0.65014 (30960) SS BOND : bond 0.00429 ( 39) SS BOND : angle 1.28119 ( 78) hydrogen bonds : bond 0.03541 ( 882) hydrogen bonds : angle 4.86303 ( 2439) link_BETA1-4 : bond 0.00549 ( 18) link_BETA1-4 : angle 1.41936 ( 54) link_NAG-ASN : bond 0.00559 ( 39) link_NAG-ASN : angle 2.96011 ( 117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 57 time to evaluate : 0.927 Fit side-chains REVERT: A 249 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.8747 (pp) REVERT: A 316 MET cc_start: 0.8869 (mtp) cc_final: 0.8581 (mtp) REVERT: A 733 THR cc_start: 0.9057 (OUTLIER) cc_final: 0.8804 (m) REVERT: A 980 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8374 (mtm) REVERT: B 86 TYR cc_start: 0.9115 (OUTLIER) cc_final: 0.8854 (m-80) REVERT: C 372 MET cc_start: 0.8920 (ttm) cc_final: 0.8561 (ttm) outliers start: 48 outliers final: 30 residues processed: 100 average time/residue: 0.1288 time to fit residues: 23.1295 Evaluate side-chains 88 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 54 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 980 MET Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 597 CYS Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain B residue 932 MET Chi-restraints excluded: chain B residue 950 ILE Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 597 CYS Chi-restraints excluded: chain C residue 692 VAL Chi-restraints excluded: chain C residue 912 CYS Chi-restraints excluded: chain C residue 950 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 182 optimal weight: 7.9990 chunk 180 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 223 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 256 optimal weight: 7.9990 chunk 284 optimal weight: 0.0770 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 236 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 605 ASN ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 639 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.049135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.041284 restraints weight = 118483.961| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 4.29 r_work: 0.2896 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22704 Z= 0.125 Angle : 0.683 11.199 31209 Z= 0.332 Chirality : 0.045 0.430 4008 Planarity : 0.004 0.049 3873 Dihedral : 6.683 58.433 4275 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.61 % Favored : 89.97 % Rotamer: Outliers : 2.33 % Allowed : 11.28 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.16), residues: 2892 helix: 2.66 (0.20), residues: 675 sheet: -1.56 (0.22), residues: 546 loop : -2.53 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 908 TYR 0.016 0.001 TYR A 226 PHE 0.018 0.001 PHE B 577 TRP 0.006 0.001 TRP B 973 HIS 0.006 0.001 HIS A 421 Details of bonding type rmsd covalent geometry : bond 0.00265 (22608) covalent geometry : angle 0.65463 (30960) SS BOND : bond 0.00397 ( 39) SS BOND : angle 1.33933 ( 78) hydrogen bonds : bond 0.03548 ( 882) hydrogen bonds : angle 4.83895 ( 2439) link_BETA1-4 : bond 0.00414 ( 18) link_BETA1-4 : angle 1.48473 ( 54) link_NAG-ASN : bond 0.00504 ( 39) link_NAG-ASN : angle 2.94574 ( 117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 54 time to evaluate : 0.906 Fit side-chains REVERT: A 249 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8711 (pp) REVERT: A 316 MET cc_start: 0.8891 (mtp) cc_final: 0.8603 (mtp) REVERT: A 733 THR cc_start: 0.9089 (OUTLIER) cc_final: 0.8837 (m) REVERT: A 980 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.8416 (mtm) REVERT: B 86 TYR cc_start: 0.9089 (OUTLIER) cc_final: 0.8835 (m-80) REVERT: B 372 MET cc_start: 0.8944 (ttm) cc_final: 0.8584 (ttm) REVERT: C 372 MET cc_start: 0.9179 (ttm) cc_final: 0.8781 (ttm) REVERT: C 718 MET cc_start: 0.9038 (mtp) cc_final: 0.8639 (mtm) outliers start: 54 outliers final: 38 residues processed: 102 average time/residue: 0.1247 time to fit residues: 23.1345 Evaluate side-chains 97 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 55 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 602 CYS Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 912 CYS Chi-restraints excluded: chain A residue 980 MET Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 597 CYS Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain B residue 932 MET Chi-restraints excluded: chain B residue 950 ILE Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 597 CYS Chi-restraints excluded: chain C residue 602 CYS Chi-restraints excluded: chain C residue 692 VAL Chi-restraints excluded: chain C residue 912 CYS Chi-restraints excluded: chain C residue 944 VAL Chi-restraints excluded: chain C residue 950 ILE Chi-restraints excluded: chain C residue 994 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 226 optimal weight: 0.9990 chunk 232 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 274 optimal weight: 1.9990 chunk 140 optimal weight: 7.9990 chunk 4 optimal weight: 0.0970 chunk 266 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 147 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 639 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.048987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.041128 restraints weight = 118622.417| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 4.28 r_work: 0.2890 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22704 Z= 0.132 Angle : 0.684 11.173 31209 Z= 0.332 Chirality : 0.045 0.428 4008 Planarity : 0.004 0.049 3873 Dihedral : 6.625 59.009 4275 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.44 % Favored : 90.15 % Rotamer: Outliers : 1.95 % Allowed : 11.67 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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 (0.16), residues: 2892 helix: 2.66 (0.20), residues: 678 sheet: -1.37 (0.22), residues: 546 loop : -2.52 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 908 TYR 0.016 0.001 TYR A 226 PHE 0.024 0.002 PHE B 577 TRP 0.007 0.001 TRP A 973 HIS 0.006 0.001 HIS A 421 Details of bonding type rmsd covalent geometry : bond 0.00281 (22608) covalent geometry : angle 0.65684 (30960) SS BOND : bond 0.00392 ( 39) SS BOND : angle 1.20421 ( 78) hydrogen bonds : bond 0.03584 ( 882) hydrogen bonds : angle 4.78844 ( 2439) link_BETA1-4 : bond 0.00415 ( 18) link_BETA1-4 : angle 1.50068 ( 54) link_NAG-ASN : bond 0.00493 ( 39) link_NAG-ASN : angle 2.94907 ( 117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 53 time to evaluate : 0.805 Fit side-chains REVERT: A 249 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8715 (pp) REVERT: A 316 MET cc_start: 0.8894 (mtp) cc_final: 0.8613 (mtp) REVERT: A 729 MET cc_start: 0.9170 (mtp) cc_final: 0.8853 (mtm) REVERT: A 733 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8825 (m) REVERT: A 980 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8469 (mtm) REVERT: B 372 MET cc_start: 0.8976 (ttm) cc_final: 0.8601 (ttm) REVERT: C 354 MET cc_start: 0.9145 (ptp) cc_final: 0.8826 (ptp) REVERT: C 372 MET cc_start: 0.9144 (ttm) cc_final: 0.8760 (ttm) outliers start: 45 outliers final: 37 residues processed: 92 average time/residue: 0.1240 time to fit residues: 20.4508 Evaluate side-chains 93 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 53 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 602 CYS Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 912 CYS Chi-restraints excluded: chain A residue 980 MET Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 597 CYS Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain B residue 932 MET Chi-restraints excluded: chain B residue 950 ILE Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 597 CYS Chi-restraints excluded: chain C residue 602 CYS Chi-restraints excluded: chain C residue 692 VAL Chi-restraints excluded: chain C residue 912 CYS Chi-restraints excluded: chain C residue 944 VAL Chi-restraints excluded: chain C residue 950 ILE Chi-restraints excluded: chain C residue 980 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 36 optimal weight: 10.0000 chunk 155 optimal weight: 7.9990 chunk 205 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 214 optimal weight: 9.9990 chunk 143 optimal weight: 0.8980 chunk 60 optimal weight: 0.2980 chunk 82 optimal weight: 7.9990 chunk 51 optimal weight: 0.0370 chunk 70 optimal weight: 0.0270 chunk 234 optimal weight: 7.9990 overall best weight: 1.2518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 GLN ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 557 GLN C 639 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.049133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.041248 restraints weight = 118460.201| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 4.28 r_work: 0.2895 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22704 Z= 0.125 Angle : 0.675 11.121 31209 Z= 0.328 Chirality : 0.045 0.427 4008 Planarity : 0.004 0.049 3873 Dihedral : 6.554 58.263 4275 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.51 % Favored : 90.08 % Rotamer: Outliers : 2.08 % Allowed : 11.63 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -1.40 (0.16), residues: 2892 helix: 2.68 (0.20), residues: 678 sheet: -1.35 (0.22), residues: 546 loop : -2.50 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 908 TYR 0.016 0.001 TYR A 226 PHE 0.027 0.001 PHE B 577 TRP 0.007 0.001 TRP A 973 HIS 0.006 0.001 HIS A 421 Details of bonding type rmsd covalent geometry : bond 0.00263 (22608) covalent geometry : angle 0.64840 (30960) SS BOND : bond 0.00384 ( 39) SS BOND : angle 1.20681 ( 78) hydrogen bonds : bond 0.03535 ( 882) hydrogen bonds : angle 4.76993 ( 2439) link_BETA1-4 : bond 0.00391 ( 18) link_BETA1-4 : angle 1.45135 ( 54) link_NAG-ASN : bond 0.00499 ( 39) link_NAG-ASN : angle 2.88399 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3617.87 seconds wall clock time: 63 minutes 36.58 seconds (3816.58 seconds total)