Starting phenix.real_space_refine on Mon Sep 14 06:25:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xcn_22128/09_2026/6xcn_22128.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xcn_22128/09_2026/6xcn_22128.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6xcn_22128/09_2026/6xcn_22128.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xcn_22128/09_2026/6xcn_22128.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xcn_22128/09_2026/6xcn_22128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xcn_22128/09_2026/6xcn_22128.map" model { file = "/net/cci-nas-00/data/ceres_data/6xcn_22128/09_2026/6xcn_22128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xcn_22128/09_2026/6xcn_22128.cif" } resolution = 3.66 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= 0.004 sd= 0.024 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 123 5.16 5 C 18228 2.51 5 N 4680 2.21 5 O 5631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 192 residue(s): 0.21s 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: 28662 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 7581 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 985, 7578 Classifications: {'peptide': 985} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 48, 'TRANS': 936} Chain breaks: 11 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 5, 'ASN:plan1': 4, 'GLU:plan': 9, 'GLN:plan1': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 84 Conformer: "B" Number of residues, atoms: 985, 7578 Classifications: {'peptide': 985} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 48, 'TRANS': 936} Chain breaks: 11 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 5, 'ASN:plan1': 4, 'GLU:plan': 9, 'GLN:plan1': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 84 bond proxies already assigned to first conformer: 7742 Chain: "C" Number of atoms: 7581 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 985, 7578 Classifications: {'peptide': 985} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 48, 'TRANS': 936} Chain breaks: 11 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 5, 'ASN:plan1': 4, 'GLU:plan': 9, 'GLN:plan1': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 84 Conformer: "B" Number of residues, atoms: 985, 7578 Classifications: {'peptide': 985} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 48, 'TRANS': 936} Chain breaks: 11 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 5, 'ASN:plan1': 4, 'GLU:plan': 9, 'GLN:plan1': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 84 bond proxies already assigned to first conformer: 7742 Chain: "E" Number of atoms: 7581 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 985, 7578 Classifications: {'peptide': 985} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 48, 'TRANS': 936} Chain breaks: 11 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 5, 'ASN:plan1': 4, 'GLU:plan': 9, 'GLN:plan1': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 84 Conformer: "B" Number of residues, atoms: 985, 7578 Classifications: {'peptide': 985} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 48, 'TRANS': 936} Chain breaks: 11 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 5, 'ASN:plan1': 4, 'GLU:plan': 9, 'GLN:plan1': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 84 bond proxies already assigned to first conformer: 7742 Chain: "B" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 890 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "F" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 890 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "H" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 890 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "D" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 810 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "G" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 810 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "L" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 810 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "S" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "T" 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: "U" 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: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "W" 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: "X" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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: "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 Chain: "E" 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: 10.97, per 1000 atoms: 0.38 Number of scatterers: 28662 At special positions: 0 Unit cell: (133.76, 139.612, 219.868, 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 123 16.00 O 5631 8.00 N 4680 7.00 C 18228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.02 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.02 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.02 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.02 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 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 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " BETA1-6 " NAG N 1 " - " FUC N 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG S 1 " - " FUC S 3 " " NAG X 1 " - " FUC X 3 " NAG-ASN " NAG A1305 " - " ASN A 61 " " NAG A1306 " - " ASN A 122 " " NAG A1307 " - " ASN A 165 " " NAG A1308 " - " ASN A 234 " " NAG A1309 " - " ASN A 282 " " NAG A1310 " - " ASN A 603 " " NAG A1311 " - " ASN A 616 " " NAG A1312 " - " ASN A 709 " " NAG C1305 " - " ASN C 61 " " NAG C1306 " - " ASN C 122 " " NAG C1307 " - " ASN C 165 " " NAG C1308 " - " ASN C 234 " " NAG C1309 " - " ASN C 282 " " NAG C1310 " - " ASN C 603 " " NAG C1311 " - " ASN C 616 " " NAG C1312 " - " ASN C 709 " " NAG E1305 " - " ASN E 61 " " NAG E1306 " - " ASN E 122 " " NAG E1307 " - " ASN E 165 " " NAG E1308 " - " ASN E 234 " " NAG E1309 " - " ASN E 282 " " NAG E1310 " - " ASN E 603 " " NAG E1311 " - " ASN E 616 " " NAG E1312 " - " ASN E 709 " " NAG I 1 " - " ASN A 331 " " NAG J 1 " - " ASN A 343 " " NAG K 1 " - " ASN A 717 " " NAG M 1 " - " ASN A 801 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN C 331 " " NAG P 1 " - " ASN C 343 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1134 " " NAG T 1 " - " ASN E 331 " " NAG U 1 " - " ASN E 343 " " NAG V 1 " - " ASN E 717 " " NAG W 1 " - " ASN E 801 " " NAG X 1 " - " ASN E1134 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 2.2 seconds 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6732 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 69 sheets defined 21.9% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.746A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.397A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.581A pdb=" N VAL A 407 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.128A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.154A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.171A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.539A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.745A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.399A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.581A pdb=" N VAL C 407 " --> pdb=" O ARG C 403 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.128A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.154A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.171A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.539A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 303 Processing helix chain 'E' and resid 337 through 343 removed outlier: 3.745A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 370 removed outlier: 4.398A pdb=" N LEU E 368 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 410 removed outlier: 3.581A pdb=" N VAL E 407 " --> pdb=" O ARG E 403 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG E 408 " --> pdb=" O GLY E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 502 through 506 Processing helix chain 'E' and resid 737 through 743 Processing helix chain 'E' and resid 746 through 754 Processing helix chain 'E' and resid 755 through 757 No H-bonds generated for 'chain 'E' and resid 755 through 757' Processing helix chain 'E' and resid 758 through 783 removed outlier: 4.128A pdb=" N ASP E 775 " --> pdb=" O ALA E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 825 Processing helix chain 'E' and resid 866 through 885 Processing helix chain 'E' and resid 886 through 890 Processing helix chain 'E' and resid 897 through 908 Processing helix chain 'E' and resid 912 through 919 removed outlier: 4.154A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 941 Processing helix chain 'E' and resid 942 through 944 No H-bonds generated for 'chain 'E' and resid 942 through 944' Processing helix chain 'E' and resid 945 through 965 Processing helix chain 'E' and resid 966 through 968 No H-bonds generated for 'chain 'E' and resid 966 through 968' Processing helix chain 'E' and resid 976 through 984 Processing helix chain 'E' and resid 985 through 1033 removed outlier: 5.171A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) Processing helix chain 'E' and resid 1140 through 1147 removed outlier: 4.539A pdb=" N GLU E1144 " --> pdb=" O PRO E1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'H' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.563A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.271A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 10.769A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 9.470A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 49 removed outlier: 6.795A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 52 through 55 removed outlier: 3.853A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.783A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 128 through 129 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.765A pdb=" N TYR A 313 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.209A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.983A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.466A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.270A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY A 667 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 719 Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 719 removed outlier: 7.024A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB9, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.803A pdb=" N ILE A 788 " --> pdb=" O ASN E 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1123 Processing sheet with id=AC2, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.563A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.272A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 10.769A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 9.469A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 48 through 49 removed outlier: 6.795A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 52 through 55 removed outlier: 3.854A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.783A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 128 through 129 Processing sheet with id=AC8, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.765A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.209A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 357 through 358 removed outlier: 3.983A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.466A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.270A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY C 667 " --> pdb=" O ILE C 670 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 702 through 704 Processing sheet with id=AD6, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AD7, first strand: chain 'C' and resid 718 through 719 Processing sheet with id=AD8, first strand: chain 'C' and resid 718 through 719 removed outlier: 7.025A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE1, first strand: chain 'C' and resid 1120 through 1123 Processing sheet with id=AE2, first strand: chain 'E' and resid 29 through 31 removed outlier: 3.563A pdb=" N SER E 60 " --> pdb=" O SER E 31 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 36 through 37 removed outlier: 7.271A pdb=" N VAL E 36 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 10.768A pdb=" N LEU E 223 " --> pdb=" O HIS E 207 " (cutoff:3.500A) removed outlier: 9.469A pdb=" N HIS E 207 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N SER E 205 " --> pdb=" O PRO E 225 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL E 227 " --> pdb=" O ILE E 203 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN E 188 " --> pdb=" O GLU E 96 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 48 through 49 removed outlier: 6.795A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 52 through 55 removed outlier: 3.853A pdb=" N ASP E 53 " --> pdb=" O ARG E 273 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 84 through 85 removed outlier: 3.783A pdb=" N ILE E 105 " --> pdb=" O GLN E 239 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AE8, first strand: chain 'E' and resid 311 through 319 removed outlier: 3.765A pdb=" N TYR E 313 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL E 595 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASN E 317 " --> pdb=" O GLY E 593 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N GLY E 593 " --> pdb=" O ASN E 317 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 324 through 328 removed outlier: 4.209A pdb=" N GLU E 324 " --> pdb=" O CYS E 538 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR E 553 " --> pdb=" O ASP E 586 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLY E 566 " --> pdb=" O ASP E 574 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 357 through 358 removed outlier: 3.984A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.466A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AF4, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.270A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY E 667 " --> pdb=" O ILE E 670 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ALA E 672 " --> pdb=" O PRO E 665 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 711 through 715 Processing sheet with id=AF6, first strand: chain 'E' and resid 718 through 719 Processing sheet with id=AF7, first strand: chain 'E' and resid 718 through 719 removed outlier: 7.025A pdb=" N GLY E1059 " --> pdb=" O SER E1055 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N SER E1055 " --> pdb=" O GLY E1059 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL E1061 " --> pdb=" O PRO E1053 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU E1063 " --> pdb=" O SER E1051 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N SER E1051 " --> pdb=" O LEU E1063 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL E1065 " --> pdb=" O LEU E1049 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 734 through 736 Processing sheet with id=AF9, first strand: chain 'E' and resid 1120 through 1123 Processing sheet with id=AG1, first strand: chain 'B' and resid 57 through 58 removed outlier: 3.580A pdb=" N TYR B 58 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N TYR B 102 " --> pdb=" O ARG B 94 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 68 through 70 Processing sheet with id=AG3, first strand: chain 'F' and resid 57 through 58 removed outlier: 3.581A pdb=" N TYR F 58 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N TYR F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 68 through 70 Processing sheet with id=AG5, first strand: chain 'H' and resid 57 through 58 removed outlier: 3.580A pdb=" N TYR H 58 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N TYR H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 68 through 70 Processing sheet with id=AG7, first strand: chain 'D' and resid 9 through 11 removed outlier: 5.733A pdb=" N TRP D 35 " --> pdb=" O MET D 47 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'D' and resid 9 through 11 Processing sheet with id=AG9, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AH1, first strand: chain 'G' and resid 9 through 11 removed outlier: 5.733A pdb=" N TRP G 35 " --> pdb=" O MET G 47 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 9 through 11 Processing sheet with id=AH3, first strand: chain 'G' and resid 19 through 24 Processing sheet with id=AH4, first strand: chain 'L' and resid 9 through 11 removed outlier: 5.734A pdb=" N TRP L 35 " --> pdb=" O MET L 47 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 9 through 11 Processing sheet with id=AH6, first strand: chain 'L' and resid 19 through 24 1006 hydrogen bonds defined for protein. 2676 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: 8.12 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9050 1.34 - 1.46: 7505 1.46 - 1.58: 12575 1.58 - 1.70: 3 1.70 - 1.83: 156 Bond restraints: 29289 Sorted by residual: bond pdb=" CA LEU A 189 " pdb=" CB LEU A 189 " ideal model delta sigma weight residual 1.528 1.486 0.041 1.39e-02 5.18e+03 8.83e+00 bond pdb=" CA LEU C 189 " pdb=" CB LEU C 189 " ideal model delta sigma weight residual 1.528 1.486 0.041 1.39e-02 5.18e+03 8.71e+00 bond pdb=" CA LEU E 189 " pdb=" CB LEU E 189 " ideal model delta sigma weight residual 1.528 1.487 0.041 1.39e-02 5.18e+03 8.59e+00 bond pdb=" C PHE C 559 " pdb=" N LEU C 560 " ideal model delta sigma weight residual 1.329 1.243 0.086 3.03e-02 1.09e+03 8.08e+00 bond pdb=" C PHE E 559 " pdb=" N LEU E 560 " ideal model delta sigma weight residual 1.329 1.243 0.086 3.03e-02 1.09e+03 8.05e+00 ... (remaining 29284 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 39016 2.62 - 5.24: 773 5.24 - 7.86: 63 7.86 - 10.48: 3 10.48 - 13.10: 9 Bond angle restraints: 39864 Sorted by residual: angle pdb=" CA GLU F 85 " pdb=" CB GLU F 85 " pdb=" CG GLU F 85 " ideal model delta sigma weight residual 114.10 127.20 -13.10 2.00e+00 2.50e-01 4.29e+01 angle pdb=" CA GLU H 85 " pdb=" CB GLU H 85 " pdb=" CG GLU H 85 " ideal model delta sigma weight residual 114.10 127.18 -13.08 2.00e+00 2.50e-01 4.28e+01 angle pdb=" CA GLU B 85 " pdb=" CB GLU B 85 " pdb=" CG GLU B 85 " ideal model delta sigma weight residual 114.10 127.17 -13.07 2.00e+00 2.50e-01 4.27e+01 angle pdb=" N PHE A 133 " pdb=" CA PHE A 133 " pdb=" C PHE A 133 " ideal model delta sigma weight residual 110.33 115.75 -5.42 1.29e+00 6.01e-01 1.76e+01 angle pdb=" N PHE C 133 " pdb=" CA PHE C 133 " pdb=" C PHE C 133 " ideal model delta sigma weight residual 110.33 115.72 -5.39 1.29e+00 6.01e-01 1.75e+01 ... (remaining 39859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 15212 17.96 - 35.92: 1348 35.92 - 53.88: 204 53.88 - 71.84: 33 71.84 - 89.79: 48 Dihedral angle restraints: 16845 sinusoidal: 6336 harmonic: 10509 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 179.32 -86.32 1 1.00e+01 1.00e-02 8.98e+01 dihedral pdb=" CB CYS E1032 " pdb=" SG CYS E1032 " pdb=" SG CYS E1043 " pdb=" CB CYS E1043 " ideal model delta sinusoidal sigma weight residual 93.00 179.31 -86.31 1 1.00e+01 1.00e-02 8.98e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 179.31 -86.31 1 1.00e+01 1.00e-02 8.98e+01 ... (remaining 16842 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3252 0.052 - 0.103: 1237 0.103 - 0.155: 189 0.155 - 0.207: 20 0.207 - 0.258: 12 Chirality restraints: 4710 Sorted by residual: chirality pdb=" C5 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C6 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" C5 BMA V 3 " pdb=" C4 BMA V 3 " pdb=" C6 BMA V 3 " pdb=" O5 BMA V 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" C5 BMA Q 3 " pdb=" C4 BMA Q 3 " pdb=" C6 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 4707 not shown) Planarity restraints: 5094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL G 58 " 0.037 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO G 59 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO G 59 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO G 59 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 58 " -0.037 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO D 59 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO D 59 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 59 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 58 " 0.037 5.00e-02 4.00e+02 5.60e-02 5.01e+00 pdb=" N PRO L 59 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO L 59 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO L 59 " 0.031 5.00e-02 4.00e+02 ... (remaining 5091 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 1073 2.67 - 3.23: 29269 3.23 - 3.79: 44394 3.79 - 4.34: 57411 4.34 - 4.90: 96041 Nonbonded interactions: 228188 Sorted by model distance: nonbonded pdb=" OH TYR A 91 " pdb=" OE1 GLU A 191 " model vdw 2.117 3.040 nonbonded pdb=" OH TYR E 91 " pdb=" OE1 GLU E 191 " model vdw 2.118 3.040 nonbonded pdb=" OH TYR C 91 " pdb=" OE1 GLU C 191 " model vdw 2.118 3.040 nonbonded pdb=" O ARG E 457 " pdb=" OG SER F 53 " model vdw 2.136 3.040 nonbonded pdb=" O ARG A 457 " pdb=" OG SER B 53 " model vdw 2.138 3.040 ... (remaining 228183 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: 0.08 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 476 or resid 478 through 1312)) selection = (chain 'C' and (resid 27 through 476 or resid 478 through 1312)) selection = (chain 'E' and (resid 27 through 476 or resid 478 through 1312)) } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'W' } ncs_group { reference = (chain 'K' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) } 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=0.33 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 36.630 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.130 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:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 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 : 0.011 0.086 29394 Z= 0.488 Angle : 0.948 13.095 40128 Z= 0.510 Chirality : 0.053 0.258 4710 Planarity : 0.005 0.056 5055 Dihedral : 14.044 89.795 9987 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % Rotamer: Outliers : 1.08 % Allowed : 7.92 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -4.10 (0.12), residues: 3555 helix: -0.97 (0.18), residues: 669 sheet: -3.09 (0.15), residues: 825 loop : -3.30 (0.11), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 466 TYR 0.021 0.002 TYR A 91 PHE 0.022 0.003 PHE A 275 TRP 0.009 0.002 TRP H 103 HIS 0.010 0.002 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.01104 / 0.49 (29289) covalent geometry : angle 0.93098 / 0.51 (39864) SS BOND : bond 0.00477 / 0.30 ( 42) SS BOND : angle 2.22943 / 1.38 ( 84) hydrogen bonds : bond 0.17682 / 11.11 ( 991) hydrogen bonds : angle 8.74749 / 5.97 ( 2676) Misc. bond : bond 0.00033 / 0.02 ( 3) link_BETA1-4 : bond 0.00499 / 0.28 ( 18) link_BETA1-4 : angle 1.99039 / 1.23 ( 54) link_BETA1-6 : bond 0.00488 / 0.22 ( 3) link_BETA1-6 : angle 2.57559 / 1.45 ( 9) link_NAG-ASN : bond 0.00786 / 0.45 ( 39) link_NAG-ASN : angle 2.59007 / 1.70 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 210 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7960 (m-10) cc_final: 0.7741 (t80) REVERT: A 390 LEU cc_start: 0.8105 (mm) cc_final: 0.7745 (mm) REVERT: A 869 MET cc_start: 0.9086 (mtp) cc_final: 0.8285 (mtm) REVERT: C 390 LEU cc_start: 0.7963 (mm) cc_final: 0.7570 (mm) REVERT: C 451 TYR cc_start: 0.7417 (m-80) cc_final: 0.7048 (m-80) REVERT: E 133 PHE cc_start: 0.7950 (m-10) cc_final: 0.7660 (t80) REVERT: E 390 LEU cc_start: 0.8005 (mm) cc_final: 0.7657 (mm) REVERT: E 869 MET cc_start: 0.9051 (mtp) cc_final: 0.8783 (mtt) REVERT: E 902 MET cc_start: 0.9364 (mmm) cc_final: 0.9059 (tpt) REVERT: B 20 LEU cc_start: 0.5118 (mm) cc_final: 0.4872 (mm) REVERT: D 49 TYR cc_start: 0.6466 (p90) cc_final: 0.6246 (t80) REVERT: D 95 PHE cc_start: 0.7545 (t80) cc_final: 0.7264 (t80) REVERT: L 53 LYS cc_start: 0.7077 (ttpt) cc_final: 0.6699 (tttm) outliers start: 33 outliers final: 14 residues processed: 243 average time/residue: 0.2114 time to fit residues: 81.7428 Evaluate side-chains 150 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 27 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 7.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 487 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 GLN A1106 GLN C 487 ASN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 GLN C1106 GLN E 487 ASN ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1071 GLN E1106 GLN B 32 ASN F 32 ASN H 32 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.122284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.080603 restraints weight = 103922.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.080723 restraints weight = 50367.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.080124 restraints weight = 41170.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.080812 restraints weight = 38943.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.081668 restraints weight = 31817.877| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29394 Z= 0.157 Angle : 0.664 9.808 40128 Z= 0.338 Chirality : 0.045 0.183 4710 Planarity : 0.005 0.053 5055 Dihedral : 6.519 119.916 3913 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.72 % Allowed : 10.26 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.75 (0.13), residues: 3555 helix: 0.99 (0.20), residues: 663 sheet: -2.59 (0.16), residues: 789 loop : -2.56 (0.12), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E1019 TYR 0.022 0.002 TYR A1067 PHE 0.015 0.002 PHE A 140 TRP 0.034 0.002 TRP G 35 HIS 0.002 0.001 HIS C1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (29289) covalent geometry : angle 0.65160 / 0.33 (39864) SS BOND : bond 0.00313 / 0.22 ( 42) SS BOND : angle 1.59661 / 0.99 ( 84) hydrogen bonds : bond 0.04658 / 3.05 ( 991) hydrogen bonds : angle 6.36942 / 4.39 ( 2676) Misc. bond : bond 0.00038 / 0.02 ( 3) link_BETA1-4 : bond 0.00374 / 0.21 ( 18) link_BETA1-4 : angle 1.21485 / 0.77 ( 54) link_BETA1-6 : bond 0.00046 / 0.02 ( 3) link_BETA1-6 : angle 1.40650 / 0.79 ( 9) link_NAG-ASN : bond 0.00382 / 0.26 ( 39) link_NAG-ASN : angle 2.00854 / 1.36 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 LEU cc_start: 0.8061 (mm) cc_final: 0.7749 (mm) REVERT: A 779 GLN cc_start: 0.8450 (tp40) cc_final: 0.8221 (tp40) REVERT: C 210 ILE cc_start: 0.8663 (pt) cc_final: 0.8428 (tp) REVERT: C 390 LEU cc_start: 0.8050 (mm) cc_final: 0.7742 (mm) REVERT: E 390 LEU cc_start: 0.8003 (mm) cc_final: 0.7702 (mm) REVERT: E 427 ASP cc_start: 0.7604 (OUTLIER) cc_final: 0.7252 (p0) REVERT: H 59 TYR cc_start: 0.4675 (m-80) cc_final: 0.4261 (m-80) REVERT: H 82 MET cc_start: 0.4188 (ptp) cc_final: 0.3764 (pmm) REVERT: D 46 LEU cc_start: 0.3484 (pt) cc_final: 0.3277 (tp) REVERT: D 95 PHE cc_start: 0.7719 (t80) cc_final: 0.7335 (t80) REVERT: L 35 TRP cc_start: 0.5350 (m100) cc_final: 0.5075 (m100) outliers start: 22 outliers final: 16 residues processed: 197 average time/residue: 0.2064 time to fit residues: 64.9140 Evaluate side-chains 156 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 79 TYR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 331 optimal weight: 10.0000 chunk 270 optimal weight: 0.9980 chunk 116 optimal weight: 10.0000 chunk 259 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 340 optimal weight: 10.0000 chunk 134 optimal weight: 0.0870 chunk 4 optimal weight: 8.9990 chunk 320 optimal weight: 20.0000 chunk 327 optimal weight: 7.9990 chunk 104 optimal weight: 9.9990 overall best weight: 4.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 690 GLN A 901 GLN A1071 GLN C 901 GLN C1071 GLN E 388 ASN E 690 GLN E 901 GLN E1071 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.120294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.078305 restraints weight = 97806.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.077409 restraints weight = 55843.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.077067 restraints weight = 47719.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.077624 restraints weight = 43108.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.078231 restraints weight = 36101.071| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (4 function evaluations) r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 29394 Z= 0.286 Angle : 0.725 14.854 40128 Z= 0.358 Chirality : 0.046 0.187 4710 Planarity : 0.005 0.053 5055 Dihedral : 5.280 43.983 3897 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 1.87 % Allowed : 12.00 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.37 (0.13), residues: 3555 helix: 1.14 (0.20), residues: 663 sheet: -2.55 (0.17), residues: 765 loop : -2.17 (0.12), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E1107 TYR 0.029 0.002 TYR E 423 PHE 0.021 0.002 PHE A 133 TRP 0.024 0.002 TRP F 98 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00676 / 0.29 (29289) covalent geometry : angle 0.71209 / 0.35 (39864) SS BOND : bond 0.00439 / 0.30 ( 42) SS BOND : angle 1.58790 / 0.99 ( 84) hydrogen bonds : bond 0.04726 / 3.09 ( 991) hydrogen bonds : angle 6.15354 / 4.22 ( 2676) Misc. bond : bond 0.00010 / 0.00 ( 3) link_BETA1-4 : bond 0.00353 / 0.20 ( 18) link_BETA1-4 : angle 1.26339 / 0.76 ( 54) link_BETA1-6 : bond 0.00201 / 0.09 ( 3) link_BETA1-6 : angle 1.61172 / 0.91 ( 9) link_NAG-ASN : bond 0.00521 / 0.31 ( 39) link_NAG-ASN : angle 2.21691 / 1.48 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 145 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 LEU cc_start: 0.8111 (mm) cc_final: 0.7741 (mm) REVERT: A 427 ASP cc_start: 0.7553 (OUTLIER) cc_final: 0.7312 (p0) REVERT: A 449 TYR cc_start: 0.5763 (m-80) cc_final: 0.5469 (m-80) REVERT: C 427 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7263 (p0) REVERT: C 451 TYR cc_start: 0.7581 (m-80) cc_final: 0.7186 (m-80) REVERT: C 464 PHE cc_start: 0.6948 (m-80) cc_final: 0.6719 (m-80) REVERT: E 390 LEU cc_start: 0.8054 (mm) cc_final: 0.7689 (mm) REVERT: H 82 MET cc_start: 0.4221 (ptp) cc_final: 0.3690 (pmm) REVERT: D 46 LEU cc_start: 0.4374 (pt) cc_final: 0.3579 (tp) REVERT: D 95 PHE cc_start: 0.7683 (t80) cc_final: 0.7393 (t80) outliers start: 57 outliers final: 39 residues processed: 185 average time/residue: 0.1926 time to fit residues: 59.0325 Evaluate side-chains 172 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 351 TYR Chi-restraints excluded: chain E residue 731 MET Chi-restraints excluded: chain E residue 780 GLU Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 79 TYR Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 44 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 chunk 290 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 280 optimal weight: 0.9990 chunk 169 optimal weight: 0.7980 chunk 239 optimal weight: 0.3980 chunk 237 optimal weight: 10.0000 chunk 272 optimal weight: 0.9980 chunk 184 optimal weight: 0.6980 chunk 229 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 935 GLN A1071 GLN C1071 GLN E 437 ASN E 901 GLN E 935 GLN E1071 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.123979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.081785 restraints weight = 104084.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.082810 restraints weight = 58363.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.082247 restraints weight = 38400.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.082904 restraints weight = 37874.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.083078 restraints weight = 31862.423| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (4 function evaluations) r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 29394 Z= 0.111 Angle : 0.600 14.342 40128 Z= 0.296 Chirality : 0.043 0.206 4710 Planarity : 0.004 0.049 5055 Dihedral : 4.684 34.847 3894 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.31 % Allowed : 13.68 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.83 (0.14), residues: 3555 helix: 1.63 (0.20), residues: 675 sheet: -2.18 (0.17), residues: 798 loop : -1.85 (0.13), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1019 TYR 0.025 0.001 TYR F 52 PHE 0.013 0.001 PHE A 133 TRP 0.021 0.001 TRP F 98 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (29289) covalent geometry : angle 0.58852 / 0.29 (39864) SS BOND : bond 0.00149 / 0.10 ( 42) SS BOND : angle 1.31557 / 0.80 ( 84) hydrogen bonds : bond 0.03798 / 2.50 ( 991) hydrogen bonds : angle 5.57300 / 3.83 ( 2676) Misc. bond : bond 0.00013 / 0.01 ( 3) link_BETA1-4 : bond 0.00464 / 0.25 ( 18) link_BETA1-4 : angle 1.15115 / 0.76 ( 54) link_BETA1-6 : bond 0.00265 / 0.12 ( 3) link_BETA1-6 : angle 1.14601 / 0.63 ( 9) link_NAG-ASN : bond 0.00309 / 0.22 ( 39) link_NAG-ASN : angle 1.86293 / 1.27 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 173 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 LEU cc_start: 0.8024 (mm) cc_final: 0.7692 (mm) REVERT: A 427 ASP cc_start: 0.7689 (m-30) cc_final: 0.7388 (p0) REVERT: A 449 TYR cc_start: 0.5873 (m-80) cc_final: 0.5549 (m-80) REVERT: C 210 ILE cc_start: 0.8738 (pt) cc_final: 0.8511 (tp) REVERT: C 390 LEU cc_start: 0.7987 (mm) cc_final: 0.7652 (mm) REVERT: C 427 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7337 (p0) REVERT: C 451 TYR cc_start: 0.7130 (m-80) cc_final: 0.6699 (m-80) REVERT: C 902 MET cc_start: 0.9488 (tpt) cc_final: 0.9288 (tpt) REVERT: E 210 ILE cc_start: 0.8647 (pt) cc_final: 0.8322 (tp) REVERT: E 390 LEU cc_start: 0.7947 (mm) cc_final: 0.7628 (mm) REVERT: E 451 TYR cc_start: 0.7300 (m-80) cc_final: 0.6768 (m-80) REVERT: H 82 MET cc_start: 0.4154 (ptp) cc_final: 0.3645 (pmm) REVERT: D 46 LEU cc_start: 0.4594 (pt) cc_final: 0.3877 (tp) REVERT: D 95 PHE cc_start: 0.7713 (t80) cc_final: 0.7358 (t80) REVERT: G 46 LEU cc_start: 0.4535 (pt) cc_final: 0.3418 (tp) REVERT: L 46 LEU cc_start: 0.4071 (pt) cc_final: 0.3052 (tp) outliers start: 40 outliers final: 30 residues processed: 201 average time/residue: 0.1969 time to fit residues: 64.4690 Evaluate side-chains 175 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 351 TYR Chi-restraints excluded: chain E residue 449 TYR Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 79 TYR Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 304 optimal weight: 0.9990 chunk 285 optimal weight: 0.6980 chunk 183 optimal weight: 6.9990 chunk 87 optimal weight: 0.5980 chunk 298 optimal weight: 30.0000 chunk 200 optimal weight: 0.5980 chunk 170 optimal weight: 3.9990 chunk 252 optimal weight: 0.0470 chunk 179 optimal weight: 10.0000 chunk 208 optimal weight: 10.0000 chunk 253 optimal weight: 4.9990 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN C 901 GLN C1106 GLN E1106 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.124096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.081954 restraints weight = 99126.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.082986 restraints weight = 52287.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.082349 restraints weight = 39434.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.082749 restraints weight = 36959.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.082941 restraints weight = 32788.502| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (4 function evaluations) r_final: 0.3243 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 29394 Z= 0.103 Angle : 0.574 12.510 40128 Z= 0.284 Chirality : 0.043 0.207 4710 Planarity : 0.004 0.049 5055 Dihedral : 4.465 31.021 3894 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.15 % Allowed : 14.43 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.14), residues: 3555 helix: 1.96 (0.20), residues: 675 sheet: -1.99 (0.18), residues: 777 loop : -1.63 (0.13), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.000 ARG C 509 TYR 0.015 0.001 TYR C1067 PHE 0.015 0.001 PHE A 374 TRP 0.024 0.001 TRP F 98 HIS 0.002 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (29289) covalent geometry : angle 0.56471 / 0.28 (39864) SS BOND : bond 0.00211 / 0.14 ( 42) SS BOND : angle 1.12923 / 0.70 ( 84) hydrogen bonds : bond 0.03617 / 2.37 ( 991) hydrogen bonds : angle 5.30735 / 3.66 ( 2676) Misc. bond : bond 0.00001 / 0.00 ( 3) link_BETA1-4 : bond 0.00419 / 0.23 ( 18) link_BETA1-4 : angle 1.09639 / 0.69 ( 54) link_BETA1-6 : bond 0.00263 / 0.12 ( 3) link_BETA1-6 : angle 1.20041 / 0.67 ( 9) link_NAG-ASN : bond 0.00270 / 0.19 ( 39) link_NAG-ASN : angle 1.69058 / 1.16 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 LEU cc_start: 0.8003 (mm) cc_final: 0.7657 (mm) REVERT: A 427 ASP cc_start: 0.7666 (m-30) cc_final: 0.7343 (p0) REVERT: A 449 TYR cc_start: 0.5770 (m-80) cc_final: 0.5484 (m-80) REVERT: A 451 TYR cc_start: 0.7268 (m-80) cc_final: 0.6730 (m-80) REVERT: C 427 ASP cc_start: 0.7633 (OUTLIER) cc_final: 0.7320 (p0) REVERT: C 451 TYR cc_start: 0.7147 (m-80) cc_final: 0.6725 (m-80) REVERT: E 390 LEU cc_start: 0.7953 (mm) cc_final: 0.7619 (mm) REVERT: E 427 ASP cc_start: 0.7631 (m-30) cc_final: 0.7361 (p0) REVERT: E 451 TYR cc_start: 0.7295 (m-80) cc_final: 0.6748 (m-80) REVERT: E 779 GLN cc_start: 0.8409 (tp40) cc_final: 0.8162 (tp40) REVERT: H 82 MET cc_start: 0.4269 (ptp) cc_final: 0.3656 (pmm) REVERT: D 46 LEU cc_start: 0.4668 (pt) cc_final: 0.4010 (tp) REVERT: D 95 PHE cc_start: 0.7650 (t80) cc_final: 0.7313 (t80) REVERT: G 46 LEU cc_start: 0.4638 (pt) cc_final: 0.3414 (tp) REVERT: L 46 LEU cc_start: 0.4141 (pt) cc_final: 0.3170 (tp) outliers start: 35 outliers final: 29 residues processed: 175 average time/residue: 0.2053 time to fit residues: 57.8217 Evaluate side-chains 169 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 351 TYR Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 79 TYR Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 35 optimal weight: 8.9990 chunk 345 optimal weight: 50.0000 chunk 196 optimal weight: 10.0000 chunk 200 optimal weight: 6.9990 chunk 177 optimal weight: 8.9990 chunk 137 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 66.4248 > 50:) chunk 98 optimal weight: 10.0000 chunk 162 optimal weight: 0.1980 chunk 14 optimal weight: 8.9990 chunk 133 optimal weight: 20.0000 chunk 310 optimal weight: 20.0000 overall best weight: 6.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 ASN A 901 GLN A1071 GLN C 901 GLN C1071 GLN E 901 GLN E1071 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.119264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.077318 restraints weight = 113976.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.076726 restraints weight = 55313.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.077389 restraints weight = 44366.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.077699 restraints weight = 36712.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.077689 restraints weight = 33771.828| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.073 29394 Z= 0.380 Angle : 0.772 11.727 40128 Z= 0.382 Chirality : 0.049 0.227 4710 Planarity : 0.005 0.054 5055 Dihedral : 5.073 32.161 3894 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 1.91 % Allowed : 14.73 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.14), residues: 3555 helix: 1.36 (0.20), residues: 666 sheet: -2.05 (0.17), residues: 840 loop : -1.75 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1019 TYR 0.026 0.002 TYR A 91 PHE 0.024 0.003 PHE A 168 TRP 0.020 0.002 TRP F 98 HIS 0.007 0.002 HIS E1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00897 / 0.38 (29289) covalent geometry : angle 0.75771 / 0.38 (39864) SS BOND : bond 0.00438 / 0.29 ( 42) SS BOND : angle 1.92491 / 1.18 ( 84) hydrogen bonds : bond 0.04811 / 3.17 ( 991) hydrogen bonds : angle 5.93641 / 4.08 ( 2676) Misc. bond : bond 0.00004 / 0.00 ( 3) link_BETA1-4 : bond 0.00384 / 0.21 ( 18) link_BETA1-4 : angle 1.28081 / 0.76 ( 54) link_BETA1-6 : bond 0.00298 / 0.13 ( 3) link_BETA1-6 : angle 1.81089 / 1.03 ( 9) link_NAG-ASN : bond 0.00604 / 0.35 ( 39) link_NAG-ASN : angle 2.30401 / 1.52 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 129 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.7720 (m-30) cc_final: 0.7417 (p0) REVERT: A 449 TYR cc_start: 0.5915 (m-80) cc_final: 0.5526 (m-80) REVERT: A 451 TYR cc_start: 0.7297 (m-80) cc_final: 0.6478 (m-80) REVERT: C 427 ASP cc_start: 0.7609 (m-30) cc_final: 0.7364 (p0) REVERT: C 451 TYR cc_start: 0.7160 (m-80) cc_final: 0.6628 (m-80) REVERT: E 451 TYR cc_start: 0.7310 (m-80) cc_final: 0.6712 (m-80) REVERT: H 82 MET cc_start: 0.4035 (ptp) cc_final: 0.3464 (pmm) REVERT: D 46 LEU cc_start: 0.4682 (pt) cc_final: 0.3944 (tp) REVERT: D 95 PHE cc_start: 0.7572 (t80) cc_final: 0.7232 (t80) REVERT: L 46 LEU cc_start: 0.4369 (pt) cc_final: 0.3337 (tp) outliers start: 58 outliers final: 47 residues processed: 169 average time/residue: 0.1991 time to fit residues: 54.9765 Evaluate side-chains 165 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 118 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 351 TYR Chi-restraints excluded: chain E residue 449 TYR Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 275 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 131 optimal weight: 7.9990 chunk 258 optimal weight: 0.8980 chunk 224 optimal weight: 0.8980 chunk 8 optimal weight: 8.9990 chunk 221 optimal weight: 20.0000 chunk 357 optimal weight: 40.0000 chunk 359 optimal weight: 8.9990 chunk 292 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1071 GLN C 901 GLN C1071 GLN E1071 GLN E1135 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.121980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.080599 restraints weight = 108823.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.080540 restraints weight = 51944.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.080011 restraints weight = 45370.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.080599 restraints weight = 42705.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.082309 restraints weight = 35257.472| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (4 function evaluations) r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29394 Z= 0.138 Angle : 0.602 9.543 40128 Z= 0.298 Chirality : 0.043 0.201 4710 Planarity : 0.004 0.052 5055 Dihedral : 4.631 28.734 3894 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.28 % Allowed : 16.07 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.14), residues: 3555 helix: 1.80 (0.20), residues: 675 sheet: -1.91 (0.17), residues: 825 loop : -1.60 (0.13), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1019 TYR 0.040 0.001 TYR A 904 PHE 0.024 0.001 PHE A 168 TRP 0.015 0.001 TRP F 98 HIS 0.002 0.001 HIS E1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (29289) covalent geometry : angle 0.59027 / 0.30 (39864) SS BOND : bond 0.00267 / 0.18 ( 42) SS BOND : angle 1.27282 / 0.78 ( 84) hydrogen bonds : bond 0.03913 / 2.58 ( 991) hydrogen bonds : angle 5.46295 / 3.76 ( 2676) Misc. bond : bond 0.00003 / 0.00 ( 3) link_BETA1-4 : bond 0.00418 / 0.24 ( 18) link_BETA1-4 : angle 1.07433 / 0.69 ( 54) link_BETA1-6 : bond 0.00273 / 0.12 ( 3) link_BETA1-6 : angle 1.35311 / 0.75 ( 9) link_NAG-ASN : bond 0.00328 / 0.22 ( 39) link_NAG-ASN : angle 1.95355 / 1.32 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 132 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.7783 (m-30) cc_final: 0.7367 (p0) REVERT: A 449 TYR cc_start: 0.5812 (m-80) cc_final: 0.5488 (m-80) REVERT: A 451 TYR cc_start: 0.6878 (m-80) cc_final: 0.6407 (m-80) REVERT: A 505 TYR cc_start: 0.6896 (t80) cc_final: 0.6327 (t80) REVERT: A 1029 MET cc_start: 0.9099 (tpp) cc_final: 0.8163 (ttm) REVERT: C 427 ASP cc_start: 0.7574 (m-30) cc_final: 0.7373 (p0) REVERT: C 505 TYR cc_start: 0.6431 (t80) cc_final: 0.6213 (t80) REVERT: E 427 ASP cc_start: 0.7589 (m-30) cc_final: 0.7326 (p0) REVERT: E 451 TYR cc_start: 0.7180 (m-80) cc_final: 0.6611 (m-80) REVERT: E 505 TYR cc_start: 0.6796 (t80) cc_final: 0.6305 (t80) REVERT: E 779 GLN cc_start: 0.8460 (tp40) cc_final: 0.8185 (tp40) REVERT: H 82 MET cc_start: 0.4028 (ptp) cc_final: 0.3471 (pmm) REVERT: D 46 LEU cc_start: 0.4682 (pt) cc_final: 0.4025 (tp) REVERT: D 95 PHE cc_start: 0.7610 (t80) cc_final: 0.7238 (t80) REVERT: G 46 LEU cc_start: 0.4774 (pt) cc_final: 0.3565 (tp) REVERT: L 46 LEU cc_start: 0.4543 (pt) cc_final: 0.3477 (tp) outliers start: 39 outliers final: 38 residues processed: 161 average time/residue: 0.2109 time to fit residues: 54.3762 Evaluate side-chains 159 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 121 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 351 TYR Chi-restraints excluded: chain E residue 449 TYR Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 902 MET Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 79 TYR Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 269 optimal weight: 0.9980 chunk 230 optimal weight: 0.5980 chunk 324 optimal weight: 30.0000 chunk 131 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 36 optimal weight: 0.0030 chunk 209 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 437 ASN A1048 HIS E 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.123431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.082426 restraints weight = 130349.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.081868 restraints weight = 57656.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.083121 restraints weight = 42206.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.082949 restraints weight = 37766.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.083303 restraints weight = 32968.572| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (4 function evaluations) r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29394 Z= 0.110 Angle : 0.568 9.541 40128 Z= 0.281 Chirality : 0.043 0.208 4710 Planarity : 0.004 0.051 5055 Dihedral : 4.354 28.050 3894 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.05 % Allowed : 16.44 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.14), residues: 3555 helix: 2.21 (0.21), residues: 660 sheet: -1.81 (0.18), residues: 801 loop : -1.41 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1019 TYR 0.028 0.001 TYR A 423 PHE 0.021 0.001 PHE C 168 TRP 0.019 0.001 TRP E1102 HIS 0.002 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (29289) covalent geometry : angle 0.55846 / 0.28 (39864) SS BOND : bond 0.00253 / 0.17 ( 42) SS BOND : angle 1.09076 / 0.67 ( 84) hydrogen bonds : bond 0.03585 / 2.36 ( 991) hydrogen bonds : angle 5.19565 / 3.59 ( 2676) Misc. bond : bond 0.00003 / 0.00 ( 3) link_BETA1-4 : bond 0.00389 / 0.22 ( 18) link_BETA1-4 : angle 1.03508 / 0.65 ( 54) link_BETA1-6 : bond 0.00256 / 0.11 ( 3) link_BETA1-6 : angle 1.22538 / 0.68 ( 9) link_NAG-ASN : bond 0.00279 / 0.19 ( 39) link_NAG-ASN : angle 1.72466 / 1.18 ( 117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.7800 (m-30) cc_final: 0.7265 (p0) REVERT: A 449 TYR cc_start: 0.5797 (m-80) cc_final: 0.5461 (m-80) REVERT: A 451 TYR cc_start: 0.6841 (m-80) cc_final: 0.6363 (m-80) REVERT: A 505 TYR cc_start: 0.6780 (t80) cc_final: 0.6283 (t80) REVERT: A 1029 MET cc_start: 0.9161 (tpp) cc_final: 0.8483 (ttm) REVERT: C 427 ASP cc_start: 0.7621 (m-30) cc_final: 0.7318 (p0) REVERT: C 505 TYR cc_start: 0.6463 (t80) cc_final: 0.6198 (t80) REVERT: E 427 ASP cc_start: 0.7692 (m-30) cc_final: 0.7364 (p0) REVERT: E 451 TYR cc_start: 0.7023 (m-80) cc_final: 0.6456 (m-80) REVERT: E 505 TYR cc_start: 0.6752 (t80) cc_final: 0.6319 (t80) REVERT: E 779 GLN cc_start: 0.8381 (tp40) cc_final: 0.8129 (tp40) REVERT: H 82 MET cc_start: 0.4339 (ptp) cc_final: 0.3634 (pmm) REVERT: D 46 LEU cc_start: 0.4645 (pt) cc_final: 0.3977 (tp) REVERT: D 95 PHE cc_start: 0.7594 (t80) cc_final: 0.7229 (t80) REVERT: G 46 LEU cc_start: 0.5024 (pt) cc_final: 0.3843 (tp) REVERT: L 46 LEU cc_start: 0.4567 (pt) cc_final: 0.3617 (tp) outliers start: 32 outliers final: 30 residues processed: 164 average time/residue: 0.2090 time to fit residues: 54.8687 Evaluate side-chains 161 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 351 TYR Chi-restraints excluded: chain E residue 449 TYR Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 902 MET Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 250 optimal weight: 0.0370 chunk 107 optimal weight: 6.9990 chunk 295 optimal weight: 0.8980 chunk 174 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 160 optimal weight: 8.9990 chunk 194 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 186 optimal weight: 0.8980 chunk 328 optimal weight: 0.0170 chunk 157 optimal weight: 3.9990 overall best weight: 0.5696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN A1071 GLN A1135 ASN C 437 ASN C 935 GLN E1048 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.124925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.083245 restraints weight = 92250.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.084384 restraints weight = 52803.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.084272 restraints weight = 33330.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.084711 restraints weight = 34077.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.084853 restraints weight = 31092.080| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3280 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (4 function evaluations) r_final: 0.3280 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 29394 Z= 0.096 Angle : 0.550 9.214 40128 Z= 0.273 Chirality : 0.043 0.210 4710 Planarity : 0.004 0.049 5055 Dihedral : 4.096 27.872 3891 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.05 % Allowed : 16.57 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.14), residues: 3555 helix: 2.56 (0.21), residues: 642 sheet: -1.52 (0.18), residues: 816 loop : -1.22 (0.13), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E1019 TYR 0.031 0.001 TYR E 423 PHE 0.020 0.001 PHE C 168 TRP 0.012 0.001 TRP A 436 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (29289) covalent geometry : angle 0.54168 / 0.27 (39864) SS BOND : bond 0.00212 / 0.15 ( 42) SS BOND : angle 0.92084 / 0.58 ( 84) hydrogen bonds : bond 0.03353 / 2.20 ( 991) hydrogen bonds : angle 4.95491 / 3.43 ( 2676) Misc. bond : bond 0.00003 / 0.00 ( 3) link_BETA1-4 : bond 0.00422 / 0.23 ( 18) link_BETA1-4 : angle 1.04959 / 0.67 ( 54) link_BETA1-6 : bond 0.00357 / 0.16 ( 3) link_BETA1-6 : angle 1.16404 / 0.64 ( 9) link_NAG-ASN : bond 0.00281 / 0.20 ( 39) link_NAG-ASN : angle 1.57939 / 1.09 ( 117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.7734 (m-30) cc_final: 0.7158 (p0) REVERT: A 449 TYR cc_start: 0.5760 (m-80) cc_final: 0.5399 (m-80) REVERT: A 451 TYR cc_start: 0.6840 (m-80) cc_final: 0.6387 (m-80) REVERT: A 505 TYR cc_start: 0.6730 (t80) cc_final: 0.6375 (t80) REVERT: A 1029 MET cc_start: 0.9057 (tpp) cc_final: 0.8429 (ttm) REVERT: A 1135 ASN cc_start: 0.8856 (OUTLIER) cc_final: 0.8610 (t0) REVERT: C 427 ASP cc_start: 0.7567 (m-30) cc_final: 0.7271 (p0) REVERT: C 505 TYR cc_start: 0.6387 (t80) cc_final: 0.6138 (t80) REVERT: C 1019 ARG cc_start: 0.7917 (ttp80) cc_final: 0.7579 (ttp80) REVERT: C 1029 MET cc_start: 0.9047 (tpp) cc_final: 0.8475 (ttm) REVERT: E 427 ASP cc_start: 0.7696 (m-30) cc_final: 0.7348 (p0) REVERT: E 451 TYR cc_start: 0.7074 (m-80) cc_final: 0.6563 (m-80) REVERT: E 779 GLN cc_start: 0.8383 (tp40) cc_final: 0.8121 (tp40) REVERT: H 82 MET cc_start: 0.4169 (ptp) cc_final: 0.3571 (pmm) REVERT: D 46 LEU cc_start: 0.4610 (pt) cc_final: 0.3978 (tp) REVERT: D 95 PHE cc_start: 0.7532 (t80) cc_final: 0.7141 (t80) REVERT: G 46 LEU cc_start: 0.5011 (pt) cc_final: 0.3954 (tp) REVERT: L 46 LEU cc_start: 0.4643 (pt) cc_final: 0.3684 (tp) outliers start: 32 outliers final: 29 residues processed: 179 average time/residue: 0.2029 time to fit residues: 58.5297 Evaluate side-chains 168 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 351 TYR Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 449 TYR Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 79 TYR Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 157 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 249 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 chunk 277 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1071 GLN A1135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.124630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.083755 restraints weight = 105329.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.083702 restraints weight = 52519.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.083909 restraints weight = 39936.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.084488 restraints weight = 38034.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.084376 restraints weight = 30187.486| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3258 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (4 function evaluations) r_final: 0.3258 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.173 29394 Z= 0.158 Angle : 0.676 59.200 40128 Z= 0.366 Chirality : 0.047 1.175 4710 Planarity : 0.004 0.093 5055 Dihedral : 4.108 27.899 3891 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.83 % Favored : 96.14 % Rotamer: Outliers : 1.08 % Allowed : 17.03 % Favored : 81.89 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.14), residues: 3555 helix: 2.51 (0.21), residues: 645 sheet: -1.50 (0.18), residues: 816 loop : -1.21 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.000 ARG A1107 TYR 0.054 0.001 TYR C 904 PHE 0.019 0.001 PHE C 168 TRP 0.012 0.001 TRP A 436 HIS 0.005 0.001 HIS E1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (29289) covalent geometry : angle 0.66969 / 0.37 (39864) SS BOND : bond 0.00206 / 0.14 ( 42) SS BOND : angle 0.90382 / 0.57 ( 84) hydrogen bonds : bond 0.03387 / 2.22 ( 991) hydrogen bonds : angle 4.95652 / 3.43 ( 2676) Misc. bond : bond 0.00005 / 0.00 ( 3) link_BETA1-4 : bond 0.00407 / 0.22 ( 18) link_BETA1-4 : angle 1.07069 / 0.68 ( 54) link_BETA1-6 : bond 0.00359 / 0.16 ( 3) link_BETA1-6 : angle 1.15669 / 0.64 ( 9) link_NAG-ASN : bond 0.00304 / 0.21 ( 39) link_NAG-ASN : angle 1.57991 / 1.09 ( 117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.7796 (m-30) cc_final: 0.7258 (p0) REVERT: A 449 TYR cc_start: 0.5793 (m-80) cc_final: 0.5453 (m-80) REVERT: A 451 TYR cc_start: 0.6789 (m-80) cc_final: 0.6294 (m-80) REVERT: A 505 TYR cc_start: 0.6742 (t80) cc_final: 0.6334 (t80) REVERT: A 1029 MET cc_start: 0.9054 (tpp) cc_final: 0.8443 (ttm) REVERT: A 1107 ARG cc_start: 0.7698 (mpt180) cc_final: 0.7411 (mpt180) REVERT: C 427 ASP cc_start: 0.7633 (m-30) cc_final: 0.7298 (p0) REVERT: C 1019 ARG cc_start: 0.7913 (ttp80) cc_final: 0.7551 (ttp80) REVERT: C 1029 MET cc_start: 0.9056 (tpp) cc_final: 0.8509 (ttm) REVERT: E 427 ASP cc_start: 0.7767 (m-30) cc_final: 0.7395 (p0) REVERT: E 451 TYR cc_start: 0.7029 (m-80) cc_final: 0.6468 (m-80) REVERT: E 779 GLN cc_start: 0.8395 (tp40) cc_final: 0.8131 (tp40) REVERT: H 82 MET cc_start: 0.4320 (ptp) cc_final: 0.3604 (pmm) REVERT: D 46 LEU cc_start: 0.4567 (pt) cc_final: 0.3948 (tp) REVERT: D 95 PHE cc_start: 0.7582 (t80) cc_final: 0.7206 (t80) REVERT: G 46 LEU cc_start: 0.4956 (pt) cc_final: 0.3925 (tp) REVERT: L 46 LEU cc_start: 0.4617 (pt) cc_final: 0.3676 (tp) outliers start: 33 outliers final: 33 residues processed: 161 average time/residue: 0.1949 time to fit residues: 50.9669 Evaluate side-chains 169 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 351 TYR Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 449 TYR Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 79 TYR Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 349 optimal weight: 7.9990 chunk 350 optimal weight: 0.9980 chunk 358 optimal weight: 30.0000 chunk 19 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 chunk 320 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 292 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 334 optimal weight: 30.0000 chunk 146 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.124606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.083502 restraints weight = 103596.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.084079 restraints weight = 55371.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.084049 restraints weight = 40802.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.084651 restraints weight = 36810.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.084687 restraints weight = 30060.586| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (4 function evaluations) r_final: 0.3265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.173 29394 Z= 0.158 Angle : 0.676 59.200 40128 Z= 0.366 Chirality : 0.047 1.175 4710 Planarity : 0.004 0.093 5055 Dihedral : 4.108 27.899 3891 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.83 % Favored : 96.14 % Rotamer: Outliers : 1.08 % Allowed : 17.03 % Favored : 81.89 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.14), residues: 3555 helix: 2.51 (0.21), residues: 645 sheet: -1.50 (0.18), residues: 816 loop : -1.21 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.000 ARG A1107 TYR 0.054 0.001 TYR C 904 PHE 0.019 0.001 PHE C 168 TRP 0.012 0.001 TRP A 436 HIS 0.005 0.001 HIS E1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (29289) covalent geometry : angle 0.66969 / 0.37 (39864) SS BOND : bond 0.00206 / 0.14 ( 42) SS BOND : angle 0.90382 / 0.57 ( 84) hydrogen bonds : bond 0.03387 / 2.22 ( 991) hydrogen bonds : angle 4.95652 / 3.43 ( 2676) Misc. bond : bond 0.00005 / 0.00 ( 3) link_BETA1-4 : bond 0.00407 / 0.22 ( 18) link_BETA1-4 : angle 1.07069 / 0.68 ( 54) link_BETA1-6 : bond 0.00359 / 0.16 ( 3) link_BETA1-6 : angle 1.15669 / 0.64 ( 9) link_NAG-ASN : bond 0.00304 / 0.21 ( 39) link_NAG-ASN : angle 1.57991 / 1.09 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5604.83 seconds wall clock time: 97 minutes 43.77 seconds (5863.77 seconds total)