Starting phenix.real_space_refine on Sun Sep 13 09:55:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6b7n_7063/09_2026/6b7n_7063.cif Found real_map, /net/cci-nas-00/data/ceres_data/6b7n_7063/09_2026/6b7n_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 { model { file = "/net/cci-nas-00/data/ceres_data/6b7n_7063/09_2026/6b7n_7063.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6b7n_7063/09_2026/6b7n_7063.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6b7n_7063/09_2026/6b7n_7063.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6b7n_7063/09_2026/6b7n_7063.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6b7n_7063/09_2026/6b7n_7063.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6b7n_7063/09_2026/6b7n_7063.map" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 8 Time building chain proxies: 4.76, per 1000 atoms: 0.21 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: 1.77 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.91 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: 5.46 Time building geometry restraints manager: 2.39 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: 12413 17.80 - 35.60: 470 35.60 - 53.40: 117 53.40 - 71.21: 11 71.21 - 89.01: 18 Dihedral angle restraints: 13029 sinusoidal: 4527 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 13026 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: 1.440 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.040 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.070 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 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 : 10.774 77.905 7428 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/Z covalent geometry : bond 0.00845 / 0.39 (22608) covalent geometry : angle 1.13946 / 0.59 (30960) SS BOND : bond 0.00519 / 0.38 ( 39) SS BOND : angle 2.38146 / 1.62 ( 78) hydrogen bonds : bond 0.20252 / 13.95 ( 882) hydrogen bonds : angle 9.82268 / 6.85 ( 2439) link_BETA1-4 : bond 0.00697 / 0.37 ( 18) link_BETA1-4 : angle 3.29685 / 2.13 ( 54) link_NAG-ASN : bond 0.00930 / 0.68 ( 39) link_NAG-ASN : angle 6.17026 / 3.96 ( 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 : 0.829 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: 0.1538 time to fit residues: 25.5128 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 : 0.836 ------------------------------------------------------------------------------- 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... A 65 ASN A 87 GLN A 126 HIS A 331 ASN A 402 GLN 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 402 GLN 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: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.049475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.041878 restraints weight = 118291.210| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 4.10 r_work: 0.2921 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1411 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= 0.148 Angle : 0.818 19.555 31209 Z= 0.401 Chirality : 0.048 0.411 4008 Planarity : 0.005 0.053 3873 Dihedral : 7.255 51.797 3082 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.41 % Allowed : 10.37 % Favored : 89.21 % Rotamer: Outliers : 1.51 % Allowed : 6.53 % Favored : 91.96 % 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: -3.10 (0.15), residues: 2892 helix: 0.36 (0.19), residues: 678 sheet: -2.77 (0.20), residues: 537 loop : -3.00 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 888 TYR 0.020 0.001 TYR A 226 PHE 0.019 0.002 PHE B 839 TRP 0.011 0.002 TRP A 973 HIS 0.005 0.001 HIS A 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.15 (22608) covalent geometry : angle 0.78133 / 0.39 (30960) SS BOND : bond 0.00431 / 0.28 ( 39) SS BOND : angle 1.18637 / 0.81 ( 78) hydrogen bonds : bond 0.04831 / 3.25 ( 882) hydrogen bonds : angle 6.35041 / 4.43 ( 2439) link_BETA1-4 : bond 0.00635 / 0.36 ( 18) link_BETA1-4 : angle 1.71333 / 1.22 ( 54) link_NAG-ASN : bond 0.00676 / 0.47 ( 39) link_NAG-ASN : angle 3.80964 / 2.49 ( 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: 35 poor density : 61 time to evaluate : 0.762 Fit side-chains revert: symmetry clash REVERT: A 218 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8980 (tp) REVERT: A 358 THR cc_start: 0.8347 (OUTLIER) cc_final: 0.8141 (m) REVERT: B 388 MET cc_start: 0.8987 (ptp) cc_final: 0.8784 (ptp) REVERT: B 731 MET cc_start: 0.9252 (mtm) cc_final: 0.9034 (mtm) REVERT: C 718 MET cc_start: 0.9084 (mtp) cc_final: 0.8796 (mtm) outliers start: 35 outliers final: 12 residues processed: 95 average time/residue: 0.1229 time to fit residues: 20.8410 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 : 0.642 ------------------------------------------------------------------------------- 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: 4.9990 chunk 98 optimal weight: 6.9990 chunk 219 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 chunk 116 optimal weight: 0.9980 chunk 12 optimal weight: 9.9990 chunk 140 optimal weight: 0.7980 chunk 30 optimal weight: 10.0000 chunk 120 optimal weight: 0.0270 chunk 17 optimal weight: 7.9990 chunk 277 optimal weight: 6.9990 overall best weight: 2.5642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.048189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.040476 restraints weight = 119681.842| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 4.10 r_work: 0.2875 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 22704 Z= 0.208 Angle : 0.783 11.675 31209 Z= 0.386 Chirality : 0.047 0.415 4008 Planarity : 0.004 0.051 3873 Dihedral : 6.898 49.970 3082 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.41 % Allowed : 10.86 % Favored : 88.73 % Rotamer: Outliers : 1.86 % Allowed : 7.31 % Favored : 90.83 % 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: -2.49 (0.15), residues: 2892 helix: 1.38 (0.20), residues: 678 sheet: -2.35 (0.20), residues: 606 loop : -2.86 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 888 TYR 0.026 0.002 TYR A 226 PHE 0.022 0.002 PHE B 577 TRP 0.007 0.001 TRP A 973 HIS 0.007 0.001 HIS A 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.21 (22608) covalent geometry : angle 0.75287 / 0.38 (30960) SS BOND : bond 0.00454 / 0.27 ( 39) SS BOND : angle 1.13321 / 0.78 ( 78) hydrogen bonds : bond 0.04538 / 3.04 ( 882) hydrogen bonds : angle 5.77822 / 4.06 ( 2439) link_BETA1-4 : bond 0.00376 / 0.21 ( 18) link_BETA1-4 : angle 1.72056 / 1.15 ( 54) link_NAG-ASN : bond 0.00510 / 0.35 ( 39) link_NAG-ASN : angle 3.37978 / 2.24 ( 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 95 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 52 time to evaluate : 0.837 Fit side-chains REVERT: A 218 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8981 (tp) REVERT: A 372 MET cc_start: 0.9259 (ttm) cc_final: 0.8887 (ttm) REVERT: A 771 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8174 (mm) REVERT: B 388 MET cc_start: 0.9299 (ptp) cc_final: 0.9094 (ptp) REVERT: C 372 MET cc_start: 0.8967 (tpp) cc_final: 0.8765 (ttm) REVERT: C 718 MET cc_start: 0.9099 (mtp) cc_final: 0.8748 (mtm) REVERT: C 771 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8308 (mm) outliers start: 43 outliers final: 28 residues processed: 93 average time/residue: 0.1149 time to fit residues: 19.1001 Evaluate side-chains 83 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 52 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 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 365 LEU Chi-restraints excluded: chain B residue 393 THR 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 789 ILE 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: 6.9990 chunk 264 optimal weight: 0.9990 chunk 218 optimal weight: 7.9990 chunk 135 optimal weight: 4.9990 chunk 272 optimal weight: 5.9990 chunk 177 optimal weight: 0.8980 chunk 259 optimal weight: 0.7980 chunk 91 optimal weight: 0.0670 chunk 122 optimal weight: 8.9990 chunk 174 optimal weight: 6.9990 chunk 143 optimal weight: 9.9990 overall best weight: 1.5522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 HIS A 309 GLN ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 GLN C 639 ASN ** C 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.048875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.041143 restraints weight = 118535.221| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 4.10 r_work: 0.2898 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22704 Z= 0.144 Angle : 0.721 12.791 31209 Z= 0.354 Chirality : 0.046 0.418 4008 Planarity : 0.004 0.049 3873 Dihedral : 6.510 48.568 3082 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.41 % Allowed : 10.51 % Favored : 89.07 % Rotamer: Outliers : 2.29 % Allowed : 8.39 % Favored : 89.32 % 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: -2.14 (0.16), residues: 2892 helix: 1.97 (0.20), residues: 675 sheet: -2.06 (0.21), residues: 582 loop : -2.82 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 357 TYR 0.019 0.001 TYR C 226 PHE 0.021 0.002 PHE B 839 TRP 0.007 0.001 TRP A 973 HIS 0.006 0.001 HIS A 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (22608) covalent geometry : angle 0.69420 / 0.35 (30960) SS BOND : bond 0.00385 / 0.25 ( 39) SS BOND : angle 1.00677 / 0.69 ( 78) hydrogen bonds : bond 0.04010 / 2.68 ( 882) hydrogen bonds : angle 5.37416 / 3.78 ( 2439) link_BETA1-4 : bond 0.00471 / 0.25 ( 18) link_BETA1-4 : angle 1.46858 / 1.03 ( 54) link_NAG-ASN : bond 0.00529 / 0.36 ( 39) link_NAG-ASN : angle 3.10309 / 2.08 ( 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 109 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 56 time to evaluate : 0.818 Fit side-chains REVERT: A 249 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9028 (pp) REVERT: A 316 MET cc_start: 0.8718 (mtp) cc_final: 0.8449 (mtp) REVERT: A 733 THR cc_start: 0.9215 (OUTLIER) cc_final: 0.8945 (m) REVERT: A 980 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.8310 (mtm) REVERT: B 388 MET cc_start: 0.9321 (ptp) cc_final: 0.8737 (ptp) REVERT: C 372 MET cc_start: 0.8933 (tpp) cc_final: 0.8325 (ttm) REVERT: C 391 ILE cc_start: 0.9429 (OUTLIER) cc_final: 0.9192 (pt) REVERT: C 718 MET cc_start: 0.9080 (mtp) cc_final: 0.8743 (mtm) REVERT: C 731 MET cc_start: 0.9401 (mtm) cc_final: 0.9101 (ttm) REVERT: C 932 MET cc_start: 0.9443 (mtp) cc_final: 0.9228 (mtm) outliers start: 53 outliers final: 29 residues processed: 104 average time/residue: 0.1207 time to fit residues: 22.8737 Evaluate side-chains 86 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 53 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 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 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 358 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 391 ILE 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 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: 2.9990 chunk 4 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 269 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 chunk 183 optimal weight: 4.9990 chunk 67 optimal weight: 0.1980 chunk 64 optimal weight: 1.9990 chunk 189 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 HIS ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 GLN ** C 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 639 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.049365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.041639 restraints weight = 117381.517| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 4.10 r_work: 0.2915 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22704 Z= 0.124 Angle : 0.695 10.901 31209 Z= 0.341 Chirality : 0.046 0.413 4008 Planarity : 0.004 0.048 3873 Dihedral : 6.133 48.997 3078 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.41 % Allowed : 10.34 % Favored : 89.25 % Rotamer: Outliers : 2.64 % Allowed : 8.95 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -1.92 (0.16), residues: 2892 helix: 2.22 (0.20), residues: 675 sheet: -1.90 (0.21), residues: 582 loop : -2.72 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 357 TYR 0.017 0.001 TYR B 226 PHE 0.019 0.001 PHE B 839 TRP 0.005 0.001 TRP A 973 HIS 0.005 0.001 HIS A 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (22608) covalent geometry : angle 0.66970 / 0.34 (30960) SS BOND : bond 0.00377 / 0.25 ( 39) SS BOND : angle 0.97886 / 0.67 ( 78) hydrogen bonds : bond 0.03780 / 2.54 ( 882) hydrogen bonds : angle 5.12353 / 3.60 ( 2439) link_BETA1-4 : bond 0.00480 / 0.28 ( 18) link_BETA1-4 : angle 1.41175 / 0.95 ( 54) link_NAG-ASN : bond 0.00541 / 0.37 ( 39) link_NAG-ASN : angle 2.96209 / 1.98 ( 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 119 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 58 time to evaluate : 0.689 Fit side-chains REVERT: A 249 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.8981 (pp) REVERT: A 316 MET cc_start: 0.8750 (mtp) cc_final: 0.8431 (mtp) REVERT: A 733 THR cc_start: 0.9158 (OUTLIER) cc_final: 0.8882 (m) REVERT: A 980 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8137 (mtm) REVERT: B 86 TYR cc_start: 0.9279 (OUTLIER) cc_final: 0.8704 (m-80) REVERT: B 388 MET cc_start: 0.9315 (ptp) cc_final: 0.9099 (ptm) REVERT: B 980 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8429 (mtm) REVERT: C 372 MET cc_start: 0.8950 (tpp) cc_final: 0.8425 (ttm) REVERT: C 388 MET cc_start: 0.9299 (OUTLIER) cc_final: 0.8639 (mtp) REVERT: C 391 ILE cc_start: 0.9409 (OUTLIER) cc_final: 0.9169 (pt) REVERT: C 718 MET cc_start: 0.9085 (mtp) cc_final: 0.8636 (mtm) REVERT: C 771 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8282 (mm) outliers start: 61 outliers final: 30 residues processed: 109 average time/residue: 0.1178 time to fit residues: 23.3160 Evaluate side-chains 91 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 53 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 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 733 THR 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 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 733 THR Chi-restraints excluded: chain B residue 932 MET Chi-restraints excluded: chain B residue 980 MET 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 388 MET Chi-restraints excluded: chain C residue 391 ILE 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 733 THR Chi-restraints excluded: chain C residue 771 LEU 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: 7.9990 chunk 179 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 chunk 209 optimal weight: 9.9990 chunk 245 optimal weight: 4.9990 chunk 286 optimal weight: 9.9990 chunk 108 optimal weight: 0.9990 chunk 224 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 116 optimal weight: 0.6980 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 421 HIS ** 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 = 0.3225 r_free = 0.3225 target = 0.047432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.039693 restraints weight = 120025.042| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 4.08 r_work: 0.2840 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 22704 Z= 0.229 Angle : 0.774 12.116 31209 Z= 0.377 Chirality : 0.047 0.432 4008 Planarity : 0.004 0.048 3873 Dihedral : 6.348 49.603 3078 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.41 % Allowed : 10.62 % Favored : 88.97 % Rotamer: Outliers : 2.90 % Allowed : 9.55 % Favored : 87.55 % 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: -1.85 (0.16), residues: 2892 helix: 2.26 (0.20), residues: 675 sheet: -1.88 (0.21), residues: 552 loop : -2.66 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 401 TYR 0.022 0.002 TYR C 226 PHE 0.026 0.002 PHE B 839 TRP 0.005 0.001 TRP A 973 HIS 0.008 0.002 HIS C 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.23 (22608) covalent geometry : angle 0.74763 / 0.37 (30960) SS BOND : bond 0.00394 / 0.26 ( 39) SS BOND : angle 1.22091 / 0.83 ( 78) hydrogen bonds : bond 0.04301 / 2.87 ( 882) hydrogen bonds : angle 5.23891 / 3.69 ( 2439) link_BETA1-4 : bond 0.00387 / 0.21 ( 18) link_BETA1-4 : angle 1.72020 / 1.14 ( 54) link_NAG-ASN : bond 0.00504 / 0.34 ( 39) link_NAG-ASN : angle 3.06007 / 2.03 ( 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 119 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 52 time to evaluate : 0.886 Fit side-chains REVERT: A 249 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.8937 (pp) REVERT: A 316 MET cc_start: 0.8776 (mtp) cc_final: 0.8520 (mtp) REVERT: A 372 MET cc_start: 0.9318 (ttm) cc_final: 0.8935 (ttm) REVERT: A 733 THR cc_start: 0.9360 (OUTLIER) cc_final: 0.9133 (m) REVERT: A 980 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8434 (mtm) REVERT: B 86 TYR cc_start: 0.9227 (OUTLIER) cc_final: 0.8840 (m-80) REVERT: B 388 MET cc_start: 0.9413 (ptp) cc_final: 0.9131 (ptm) REVERT: B 980 MET cc_start: 0.9194 (OUTLIER) cc_final: 0.8555 (mtm) REVERT: C 372 MET cc_start: 0.8981 (tpp) cc_final: 0.8255 (ttm) REVERT: C 391 ILE cc_start: 0.9431 (OUTLIER) cc_final: 0.9177 (pt) REVERT: C 718 MET cc_start: 0.9129 (mtp) cc_final: 0.8681 (mtm) REVERT: C 731 MET cc_start: 0.9386 (mtm) cc_final: 0.8977 (ttm) REVERT: C 771 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8171 (mm) outliers start: 67 outliers final: 40 residues processed: 109 average time/residue: 0.1142 time to fit residues: 22.7640 Evaluate side-chains 98 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 51 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 113 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 441 VAL 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 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 107 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 191 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 932 MET Chi-restraints excluded: chain B residue 980 MET 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 113 THR Chi-restraints excluded: chain C residue 308 VAL 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 388 MET Chi-restraints excluded: chain C residue 391 ILE 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 771 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 5.9990 chunk 188 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 chunk 170 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 256 optimal weight: 10.0000 chunk 267 optimal weight: 10.0000 chunk 212 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 236 optimal weight: 6.9990 chunk 178 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 421 HIS ** 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 = 0.3245 r_free = 0.3245 target = 0.048116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.040362 restraints weight = 118175.128| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 4.07 r_work: 0.2871 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22704 Z= 0.159 Angle : 0.712 11.363 31209 Z= 0.347 Chirality : 0.046 0.430 4008 Planarity : 0.004 0.050 3873 Dihedral : 6.154 49.380 3078 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.41 % Allowed : 10.48 % Favored : 89.11 % Rotamer: Outliers : 2.68 % Allowed : 10.25 % Favored : 87.07 % 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: -1.75 (0.16), residues: 2892 helix: 2.39 (0.20), residues: 675 sheet: -1.78 (0.21), residues: 549 loop : -2.63 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 888 TYR 0.017 0.001 TYR A 226 PHE 0.023 0.002 PHE B 839 TRP 0.006 0.001 TRP A 973 HIS 0.006 0.001 HIS A 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (22608) covalent geometry : angle 0.68708 / 0.34 (30960) SS BOND : bond 0.00347 / 0.23 ( 39) SS BOND : angle 1.02446 / 0.70 ( 78) hydrogen bonds : bond 0.03966 / 2.64 ( 882) hydrogen bonds : angle 5.08676 / 3.58 ( 2439) link_BETA1-4 : bond 0.00385 / 0.21 ( 18) link_BETA1-4 : angle 1.42833 / 0.97 ( 54) link_NAG-ASN : bond 0.00507 / 0.35 ( 39) link_NAG-ASN : angle 2.94131 / 1.96 ( 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 115 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 53 time to evaluate : 0.591 Fit side-chains REVERT: A 249 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.8868 (pp) REVERT: A 316 MET cc_start: 0.8816 (mtp) cc_final: 0.8553 (mtp) REVERT: A 354 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8202 (mtm) REVERT: A 372 MET cc_start: 0.9307 (ttm) cc_final: 0.9011 (ttm) REVERT: A 733 THR cc_start: 0.9286 (OUTLIER) cc_final: 0.9043 (m) REVERT: A 980 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8335 (mtm) REVERT: B 86 TYR cc_start: 0.9204 (OUTLIER) cc_final: 0.8869 (m-80) REVERT: B 930 PHE cc_start: 0.8808 (OUTLIER) cc_final: 0.7015 (p90) REVERT: B 980 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.8493 (mtm) REVERT: C 372 MET cc_start: 0.8926 (tpp) cc_final: 0.8427 (ttm) REVERT: C 388 MET cc_start: 0.9382 (OUTLIER) cc_final: 0.8792 (mtp) REVERT: C 391 ILE cc_start: 0.9399 (OUTLIER) cc_final: 0.9151 (pt) REVERT: C 718 MET cc_start: 0.9110 (mtp) cc_final: 0.8654 (mtm) REVERT: C 771 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8210 (mm) outliers start: 62 outliers final: 39 residues processed: 107 average time/residue: 0.1072 time to fit residues: 20.7736 Evaluate side-chains 100 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 51 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 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 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 191 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 912 CYS Chi-restraints excluded: chain B residue 930 PHE Chi-restraints excluded: chain B residue 932 MET Chi-restraints excluded: chain B residue 950 ILE Chi-restraints excluded: chain B residue 980 MET Chi-restraints excluded: chain B residue 999 VAL 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 104 MET Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 308 VAL 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 388 MET Chi-restraints excluded: chain C residue 391 ILE 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 733 THR Chi-restraints excluded: chain C residue 771 LEU 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: 0.0670 chunk 47 optimal weight: 0.0570 chunk 223 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 142 optimal weight: 9.9990 chunk 6 optimal weight: 0.0370 chunk 140 optimal weight: 6.9990 chunk 194 optimal weight: 0.4980 chunk 280 optimal weight: 7.9990 overall best weight: 0.2314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 HIS B 455 HIS ** C 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 HIS C 639 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.050528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.042768 restraints weight = 116687.442| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 4.12 r_work: 0.2950 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 22704 Z= 0.108 Angle : 0.676 10.758 31209 Z= 0.331 Chirality : 0.045 0.411 4008 Planarity : 0.004 0.048 3873 Dihedral : 5.749 49.477 3078 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.27 % Favored : 90.32 % Rotamer: Outliers : 1.90 % Allowed : 11.15 % Favored : 86.94 % 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: -1.60 (0.16), residues: 2892 helix: 2.50 (0.20), residues: 675 sheet: -1.60 (0.22), residues: 546 loop : -2.56 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 908 TYR 0.019 0.001 TYR B 61 PHE 0.017 0.001 PHE B 155 TRP 0.008 0.002 TRP B 396 HIS 0.007 0.001 HIS C 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.11 (22608) covalent geometry : angle 0.65288 / 0.33 (30960) SS BOND : bond 0.00367 / 0.24 ( 39) SS BOND : angle 0.92571 / 0.62 ( 78) hydrogen bonds : bond 0.03401 / 2.29 ( 882) hydrogen bonds : angle 4.81504 / 3.38 ( 2439) link_BETA1-4 : bond 0.00531 / 0.29 ( 18) link_BETA1-4 : angle 1.32441 / 0.91 ( 54) link_NAG-ASN : bond 0.00586 / 0.40 ( 39) link_NAG-ASN : angle 2.80162 / 1.86 ( 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 103 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 59 time to evaluate : 0.864 Fit side-chains REVERT: A 249 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.8812 (pp) REVERT: A 316 MET cc_start: 0.8796 (mtp) cc_final: 0.8549 (mtp) REVERT: A 354 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8226 (mtm) REVERT: A 733 THR cc_start: 0.9055 (OUTLIER) cc_final: 0.8730 (m) REVERT: A 980 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8453 (mtm) REVERT: B 86 TYR cc_start: 0.9121 (OUTLIER) cc_final: 0.8844 (m-80) REVERT: B 354 MET cc_start: 0.8958 (mtp) cc_final: 0.8575 (mtm) REVERT: B 372 MET cc_start: 0.9028 (ttm) cc_final: 0.8728 (ttm) REVERT: B 980 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8360 (mtm) REVERT: C 372 MET cc_start: 0.8782 (tpp) cc_final: 0.8542 (ttm) REVERT: C 391 ILE cc_start: 0.9367 (OUTLIER) cc_final: 0.9084 (pt) REVERT: C 731 MET cc_start: 0.9269 (mtm) cc_final: 0.8866 (ttm) outliers start: 44 outliers final: 25 residues processed: 95 average time/residue: 0.1183 time to fit residues: 20.2770 Evaluate side-chains 87 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 55 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 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 602 CYS Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 950 ILE 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 406 VAL Chi-restraints excluded: chain B residue 597 CYS Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain B residue 912 CYS Chi-restraints excluded: chain B residue 932 MET Chi-restraints excluded: chain B residue 980 MET 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 358 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 391 ILE 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 950 ILE Chi-restraints excluded: chain C residue 994 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 182 optimal weight: 0.9990 chunk 180 optimal weight: 0.5980 chunk 110 optimal weight: 4.9990 chunk 223 optimal weight: 1.9990 chunk 136 optimal weight: 8.9990 chunk 256 optimal weight: 8.9990 chunk 284 optimal weight: 0.7980 chunk 33 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 236 optimal weight: 1.9990 chunk 169 optimal weight: 6.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 421 HIS ** 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 = 0.3298 r_free = 0.3298 target = 0.049587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.041703 restraints weight = 118235.436| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 4.30 r_work: 0.2910 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22704 Z= 0.127 Angle : 0.670 10.959 31209 Z= 0.326 Chirality : 0.045 0.412 4008 Planarity : 0.004 0.047 3873 Dihedral : 5.700 48.385 3078 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.58 % Favored : 90.01 % Rotamer: Outliers : 1.99 % Allowed : 11.24 % Favored : 86.77 % 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: -1.47 (0.16), residues: 2892 helix: 2.65 (0.20), residues: 675 sheet: -1.38 (0.22), residues: 531 loop : -2.55 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 401 TYR 0.017 0.001 TYR A 226 PHE 0.015 0.001 PHE B 839 TRP 0.006 0.001 TRP B 973 HIS 0.007 0.001 HIS C 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (22608) covalent geometry : angle 0.64670 / 0.32 (30960) SS BOND : bond 0.00314 / 0.21 ( 39) SS BOND : angle 0.86830 / 0.59 ( 78) hydrogen bonds : bond 0.03491 / 2.35 ( 882) hydrogen bonds : angle 4.77855 / 3.36 ( 2439) link_BETA1-4 : bond 0.00367 / 0.20 ( 18) link_BETA1-4 : angle 1.38404 / 0.93 ( 54) link_NAG-ASN : bond 0.00488 / 0.33 ( 39) link_NAG-ASN : angle 2.74441 / 1.81 ( 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 101 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 55 time to evaluate : 0.687 Fit side-chains REVERT: A 249 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.8713 (pp) REVERT: A 316 MET cc_start: 0.8860 (mtp) cc_final: 0.8576 (mtp) REVERT: A 354 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8130 (mtm) REVERT: A 733 THR cc_start: 0.9044 (OUTLIER) cc_final: 0.8790 (m) REVERT: A 980 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8389 (mtm) REVERT: B 86 TYR cc_start: 0.9089 (OUTLIER) cc_final: 0.8851 (m-80) REVERT: B 372 MET cc_start: 0.8977 (ttm) cc_final: 0.8619 (ttm) REVERT: B 980 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8335 (mtm) REVERT: C 357 ARG cc_start: 0.8618 (mmm160) cc_final: 0.8219 (mmp80) REVERT: C 372 MET cc_start: 0.9042 (tpp) cc_final: 0.8479 (ttm) REVERT: C 391 ILE cc_start: 0.9214 (OUTLIER) cc_final: 0.8968 (pt) REVERT: C 718 MET cc_start: 0.9135 (mtp) cc_final: 0.8757 (mtm) outliers start: 46 outliers final: 27 residues processed: 92 average time/residue: 0.1200 time to fit residues: 19.6606 Evaluate side-chains 89 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 55 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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 467 LEU Chi-restraints excluded: chain A residue 602 CYS Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 950 ILE 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 912 CYS Chi-restraints excluded: chain B residue 932 MET Chi-restraints excluded: chain B residue 980 MET Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain B residue 999 VAL 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 145 VAL Chi-restraints excluded: chain C residue 206 PHE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 391 ILE 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 950 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 226 optimal weight: 3.9990 chunk 232 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 274 optimal weight: 0.9980 chunk 140 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 266 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 147 optimal weight: 10.0000 chunk 145 optimal weight: 5.9990 chunk 130 optimal weight: 0.4980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 421 HIS ** 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 = 0.048638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.040873 restraints weight = 118679.138| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 4.09 r_work: 0.2882 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22704 Z= 0.175 Angle : 0.707 11.329 31209 Z= 0.343 Chirality : 0.046 0.419 4008 Planarity : 0.004 0.047 3873 Dihedral : 5.837 48.398 3078 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.41 % Favored : 90.18 % Rotamer: Outliers : 1.77 % Allowed : 11.41 % Favored : 86.81 % 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: -1.45 (0.16), residues: 2892 helix: 2.64 (0.20), residues: 678 sheet: -1.38 (0.22), residues: 546 loop : -2.53 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 401 TYR 0.017 0.001 TYR A 226 PHE 0.019 0.002 PHE B 839 TRP 0.006 0.001 TRP A 973 HIS 0.006 0.001 HIS A 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.18 (22608) covalent geometry : angle 0.68289 / 0.34 (30960) SS BOND : bond 0.00447 / 0.32 ( 39) SS BOND : angle 1.13028 / 0.74 ( 78) hydrogen bonds : bond 0.03769 / 2.52 ( 882) hydrogen bonds : angle 4.86206 / 3.41 ( 2439) link_BETA1-4 : bond 0.00327 / 0.18 ( 18) link_BETA1-4 : angle 1.49870 / 1.00 ( 54) link_NAG-ASN : bond 0.00454 / 0.31 ( 39) link_NAG-ASN : angle 2.80716 / 1.86 ( 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 95 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 54 time to evaluate : 0.693 Fit side-chains REVERT: A 249 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.8856 (pp) REVERT: A 316 MET cc_start: 0.8795 (mtp) cc_final: 0.8509 (mtp) REVERT: A 354 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8216 (mtm) REVERT: A 733 THR cc_start: 0.9225 (OUTLIER) cc_final: 0.8952 (m) REVERT: A 980 MET cc_start: 0.9128 (OUTLIER) cc_final: 0.8526 (mtm) REVERT: B 372 MET cc_start: 0.8968 (ttm) cc_final: 0.8625 (ttm) REVERT: B 980 MET cc_start: 0.9130 (OUTLIER) cc_final: 0.8552 (mtm) REVERT: C 372 MET cc_start: 0.9197 (tpp) cc_final: 0.8478 (ttm) REVERT: C 391 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.9111 (pt) REVERT: C 718 MET cc_start: 0.9167 (mtp) cc_final: 0.8820 (mtm) REVERT: C 731 MET cc_start: 0.9326 (mtm) cc_final: 0.8937 (ttm) outliers start: 41 outliers final: 30 residues processed: 88 average time/residue: 0.1205 time to fit residues: 19.4137 Evaluate side-chains 89 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 53 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 441 VAL 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 980 MET Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 191 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 912 CYS Chi-restraints excluded: chain B residue 932 MET Chi-restraints excluded: chain B residue 980 MET Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain B residue 999 VAL 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 145 VAL Chi-restraints excluded: chain C residue 206 PHE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 391 ILE 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 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 36 optimal weight: 9.9990 chunk 155 optimal weight: 6.9990 chunk 205 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 214 optimal weight: 8.9990 chunk 143 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 51 optimal weight: 0.0060 chunk 70 optimal weight: 4.9990 chunk 234 optimal weight: 4.9990 overall best weight: 4.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 421 HIS ** 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 = 0.3200 r_free = 0.3200 target = 0.046554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.038828 restraints weight = 120128.171| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 4.04 r_work: 0.2814 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 22704 Z= 0.291 Angle : 0.819 14.849 31209 Z= 0.397 Chirality : 0.048 0.442 4008 Planarity : 0.004 0.048 3873 Dihedral : 6.299 49.313 3078 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.41 % Allowed : 11.34 % Favored : 88.24 % Rotamer: Outliers : 2.16 % Allowed : 11.11 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -1.62 (0.16), residues: 2892 helix: 2.33 (0.20), residues: 678 sheet: -1.62 (0.21), residues: 576 loop : -2.50 (0.16), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 978 TYR 0.028 0.002 TYR A 226 PHE 0.029 0.002 PHE B 839 TRP 0.007 0.001 TRP C 396 HIS 0.010 0.002 HIS C 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.29 (22608) covalent geometry : angle 0.79509 / 0.39 (30960) SS BOND : bond 0.00329 / 0.22 ( 39) SS BOND : angle 1.53546 / 0.99 ( 78) hydrogen bonds : bond 0.04504 / 3.00 ( 882) hydrogen bonds : angle 5.25444 / 3.69 ( 2439) link_BETA1-4 : bond 0.00315 / 0.18 ( 18) link_BETA1-4 : angle 1.75840 / 1.15 ( 54) link_NAG-ASN : bond 0.00460 / 0.30 ( 39) link_NAG-ASN : angle 2.96690 / 1.98 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3588.19 seconds wall clock time: 63 minutes 11.46 seconds (3791.46 seconds total)