Starting phenix.real_space_refine on Wed Nov 19 23:46:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xcn_22128/11_2025/6xcn_22128.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xcn_22128/11_2025/6xcn_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 { model { file = "/net/cci-nas-00/data/ceres_data/6xcn_22128/11_2025/6xcn_22128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xcn_22128/11_2025/6xcn_22128.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xcn_22128/11_2025/6xcn_22128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xcn_22128/11_2025/6xcn_22128.map" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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 dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 12.10, per 1000 atoms: 0.42 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: 2.82 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: 1.42 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: 7.88 Time building geometry restraints manager: 3.67 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 - 19.76: 16489 19.76 - 39.52: 1280 39.52 - 59.28: 195 59.28 - 79.05: 50 79.05 - 98.81: 73 Dihedral angle restraints: 18087 sinusoidal: 7578 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 18084 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: 4.500 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: 0.030 Extract box with map and model: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 37.060 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.080 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 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 : 15.407 98.808 11229 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 covalent geometry : bond 0.01104 (29289) covalent geometry : angle 0.93098 (39864) SS BOND : bond 0.00477 ( 42) SS BOND : angle 2.22943 ( 84) hydrogen bonds : bond 0.17682 ( 991) hydrogen bonds : angle 8.74749 ( 2676) Misc. bond : bond 0.00033 ( 3) link_BETA1-4 : bond 0.00499 ( 18) link_BETA1-4 : angle 1.99039 ( 54) link_BETA1-6 : bond 0.00488 ( 3) link_BETA1-6 : angle 2.57559 ( 9) link_NAG-ASN : bond 0.00786 ( 39) link_NAG-ASN : angle 2.59007 ( 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 : 1.140 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: 0.7416 (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: 0.2104 time to fit residues: 80.3570 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 : 1.117 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 487 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** 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 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 = 0.3971 r_free = 0.3971 target = 0.122428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.080720 restraints weight = 103930.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.080309 restraints weight = 52655.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.080121 restraints weight = 43985.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.080797 restraints weight = 38539.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.081001 restraints weight = 31425.823| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 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 = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1603 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 : 0.673 9.890 40128 Z= 0.339 Chirality : 0.045 0.179 4710 Planarity : 0.005 0.053 5055 Dihedral : 9.599 119.655 5155 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.76 % Allowed : 10.26 % Favored : 88.99 % 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: -2.70 (0.13), residues: 3555 helix: 1.03 (0.20), residues: 663 sheet: -2.57 (0.16), residues: 789 loop : -2.53 (0.12), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 71 TYR 0.022 0.002 TYR A1067 PHE 0.016 0.002 PHE A 140 TRP 0.032 0.002 TRP G 35 HIS 0.002 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00353 (29289) covalent geometry : angle 0.65853 (39864) SS BOND : bond 0.00259 ( 42) SS BOND : angle 1.53772 ( 84) hydrogen bonds : bond 0.04543 ( 991) hydrogen bonds : angle 6.31334 ( 2676) Misc. bond : bond 0.00031 ( 3) link_BETA1-4 : bond 0.00462 ( 18) link_BETA1-4 : angle 1.72201 ( 54) link_BETA1-6 : bond 0.00038 ( 3) link_BETA1-6 : angle 1.43915 ( 9) link_NAG-ASN : bond 0.00368 ( 39) link_NAG-ASN : angle 2.04081 ( 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 208 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 185 time to evaluate : 1.105 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 390 LEU cc_start: 0.8060 (mm) cc_final: 0.7758 (mm) REVERT: A 779 GLN cc_start: 0.8446 (tp40) cc_final: 0.8198 (tp40) REVERT: C 210 ILE cc_start: 0.8694 (pt) cc_final: 0.8468 (tp) REVERT: C 390 LEU cc_start: 0.8047 (mm) cc_final: 0.7745 (mm) REVERT: E 390 LEU cc_start: 0.8019 (mm) cc_final: 0.7727 (mm) REVERT: E 427 ASP cc_start: 0.7610 (OUTLIER) cc_final: 0.7256 (p0) REVERT: E 449 TYR cc_start: 0.5876 (m-80) cc_final: 0.5559 (m-80) REVERT: E 902 MET cc_start: 0.9353 (mmm) cc_final: 0.8888 (tpt) REVERT: H 59 TYR cc_start: 0.4670 (m-80) cc_final: 0.4255 (m-80) REVERT: H 82 MET cc_start: 0.4162 (ptp) cc_final: 0.3746 (pmm) REVERT: D 95 PHE cc_start: 0.7707 (t80) cc_final: 0.7327 (t80) REVERT: L 35 TRP cc_start: 0.5381 (m100) cc_final: 0.4966 (m100) outliers start: 23 outliers final: 17 residues processed: 201 average time/residue: 0.2045 time to fit residues: 65.2923 Evaluate side-chains 155 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain C residue 351 TYR 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: 9.9990 chunk 270 optimal weight: 0.9980 chunk 116 optimal weight: 8.9990 chunk 259 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 340 optimal weight: 9.9990 chunk 134 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 320 optimal weight: 20.0000 chunk 327 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 overall best weight: 7.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 690 GLN A 901 GLN A1071 GLN C 690 GLN C 901 GLN C1071 GLN E 388 ASN ** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 690 GLN E 901 GLN E1071 GLN L 39 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.118797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.077717 restraints weight = 97754.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.075885 restraints weight = 55483.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.075766 restraints weight = 47689.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.076352 restraints weight = 42195.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.076408 restraints weight = 37119.739| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.089 29394 Z= 0.401 Angle : 0.822 16.226 40128 Z= 0.407 Chirality : 0.050 0.204 4710 Planarity : 0.005 0.055 5055 Dihedral : 8.227 58.049 5139 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 2.17 % Allowed : 12.69 % Favored : 85.14 % 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: -2.59 (0.13), residues: 3555 helix: 0.87 (0.19), residues: 663 sheet: -2.58 (0.17), residues: 798 loop : -2.32 (0.12), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1019 TYR 0.025 0.003 TYR E 423 PHE 0.022 0.003 PHE E 817 TRP 0.020 0.002 TRP F 98 HIS 0.008 0.002 HIS E1048 Details of bonding type rmsd covalent geometry : bond 0.00948 (29289) covalent geometry : angle 0.80562 (39864) SS BOND : bond 0.00580 ( 42) SS BOND : angle 1.87206 ( 84) hydrogen bonds : bond 0.05210 ( 991) hydrogen bonds : angle 6.43106 ( 2676) Misc. bond : bond 0.00027 ( 3) link_BETA1-4 : bond 0.00453 ( 18) link_BETA1-4 : angle 1.83262 ( 54) link_BETA1-6 : bond 0.00396 ( 3) link_BETA1-6 : angle 1.88616 ( 9) link_NAG-ASN : bond 0.00650 ( 39) link_NAG-ASN : angle 2.55388 ( 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 205 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 139 time to evaluate : 1.173 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: C 427 ASP cc_start: 0.7526 (OUTLIER) cc_final: 0.7282 (p0) REVERT: E 449 TYR cc_start: 0.5829 (m-80) cc_final: 0.5491 (m-80) REVERT: B 82 MET cc_start: 0.4693 (ptp) cc_final: 0.4399 (pmm) REVERT: H 82 MET cc_start: 0.4174 (ptp) cc_final: 0.3628 (pmm) REVERT: D 46 LEU cc_start: 0.4517 (pt) cc_final: 0.3619 (tp) REVERT: D 95 PHE cc_start: 0.7630 (t80) cc_final: 0.7313 (t80) outliers start: 66 outliers final: 45 residues processed: 189 average time/residue: 0.1936 time to fit residues: 59.1990 Evaluate side-chains 176 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 130 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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 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 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 723 THR 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 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 D residue 106 VAL Chi-restraints excluded: chain G residue 4 LEU 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 4 LEU Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 106 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: 3.9990 chunk 290 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 280 optimal weight: 0.9990 chunk 169 optimal weight: 0.8980 chunk 239 optimal weight: 0.9990 chunk 237 optimal weight: 20.0000 chunk 272 optimal weight: 0.8980 chunk 184 optimal weight: 0.9990 chunk 229 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN A1071 GLN C 901 GLN C1071 GLN E 498 GLN E 501 ASN E 935 GLN E1071 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.122940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.081323 restraints weight = 103952.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.081437 restraints weight = 52622.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.081303 restraints weight = 40832.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.081888 restraints weight = 36895.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.082050 restraints weight = 30634.368| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29394 Z= 0.121 Angle : 0.616 15.262 40128 Z= 0.305 Chirality : 0.043 0.170 4710 Planarity : 0.004 0.053 5055 Dihedral : 7.161 55.619 5136 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.15 % Allowed : 14.63 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.94 (0.14), residues: 3555 helix: 1.60 (0.20), residues: 663 sheet: -2.19 (0.17), residues: 798 loop : -1.94 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1019 TYR 0.024 0.001 TYR B 52 PHE 0.016 0.001 PHE E 347 TRP 0.020 0.001 TRP F 98 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00269 (29289) covalent geometry : angle 0.60122 (39864) SS BOND : bond 0.00247 ( 42) SS BOND : angle 1.36587 ( 84) hydrogen bonds : bond 0.03957 ( 991) hydrogen bonds : angle 5.76726 ( 2676) Misc. bond : bond 0.00003 ( 3) link_BETA1-4 : bond 0.00521 ( 18) link_BETA1-4 : angle 1.67056 ( 54) link_BETA1-6 : bond 0.00211 ( 3) link_BETA1-6 : angle 1.23864 ( 9) link_NAG-ASN : bond 0.00334 ( 39) link_NAG-ASN : angle 2.05044 ( 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 199 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 164 time to evaluate : 1.106 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 390 LEU cc_start: 0.8023 (mm) cc_final: 0.7669 (mm) REVERT: A 427 ASP cc_start: 0.7735 (m-30) cc_final: 0.7344 (p0) REVERT: A 902 MET cc_start: 0.9513 (tpt) cc_final: 0.9234 (tpt) REVERT: C 427 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.7387 (p0) REVERT: C 451 TYR cc_start: 0.7442 (m-80) cc_final: 0.6967 (m-80) REVERT: C 902 MET cc_start: 0.9524 (tpt) cc_final: 0.9258 (tpt) REVERT: E 390 LEU cc_start: 0.7992 (mm) cc_final: 0.7658 (mm) REVERT: E 449 TYR cc_start: 0.5865 (m-80) cc_final: 0.5520 (m-80) REVERT: E 451 TYR cc_start: 0.7139 (m-80) cc_final: 0.6664 (m-80) REVERT: E 902 MET cc_start: 0.9383 (tpt) cc_final: 0.9089 (tpt) REVERT: H 82 MET cc_start: 0.4102 (ptp) cc_final: 0.3597 (pmm) REVERT: D 46 LEU cc_start: 0.4701 (pt) cc_final: 0.3882 (tp) REVERT: D 95 PHE cc_start: 0.7737 (t80) cc_final: 0.7379 (t80) REVERT: G 46 LEU cc_start: 0.4507 (pt) cc_final: 0.3329 (tp) REVERT: L 46 LEU cc_start: 0.4169 (pt) cc_final: 0.3322 (tp) outliers start: 35 outliers final: 27 residues processed: 188 average time/residue: 0.1970 time to fit residues: 60.2031 Evaluate side-chains 164 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 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 1104 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 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 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 75 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain L residue 75 VAL 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: 3.9990 chunk 285 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 298 optimal weight: 40.0000 chunk 200 optimal weight: 0.8980 chunk 170 optimal weight: 3.9990 chunk 252 optimal weight: 9.9990 chunk 179 optimal weight: 7.9990 chunk 208 optimal weight: 5.9990 chunk 253 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN A1071 GLN C1106 GLN D 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.121363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.078037 restraints weight = 99179.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.078906 restraints weight = 60788.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.079128 restraints weight = 38540.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.079399 restraints weight = 36905.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.079587 restraints weight = 32441.289| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29394 Z= 0.190 Angle : 0.626 14.661 40128 Z= 0.309 Chirality : 0.044 0.193 4710 Planarity : 0.004 0.051 5055 Dihedral : 7.035 55.766 5136 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.78 % Allowed : 15.09 % Favored : 83.14 % 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: -1.75 (0.14), residues: 3555 helix: 1.67 (0.20), residues: 663 sheet: -2.09 (0.17), residues: 792 loop : -1.78 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1019 TYR 0.020 0.002 TYR C 904 PHE 0.015 0.002 PHE H 27 TRP 0.021 0.001 TRP F 98 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00446 (29289) covalent geometry : angle 0.61172 (39864) SS BOND : bond 0.00275 ( 42) SS BOND : angle 1.44246 ( 84) hydrogen bonds : bond 0.04070 ( 991) hydrogen bonds : angle 5.64988 ( 2676) Misc. bond : bond 0.00017 ( 3) link_BETA1-4 : bond 0.00412 ( 18) link_BETA1-4 : angle 1.56441 ( 54) link_BETA1-6 : bond 0.00027 ( 3) link_BETA1-6 : angle 1.45454 ( 9) link_NAG-ASN : bond 0.00376 ( 39) link_NAG-ASN : angle 2.03109 ( 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 192 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 138 time to evaluate : 1.263 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 427 ASP cc_start: 0.7687 (m-30) cc_final: 0.7278 (p0) REVERT: A 451 TYR cc_start: 0.7313 (m-80) cc_final: 0.6784 (m-80) REVERT: C 427 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.7365 (p0) REVERT: C 451 TYR cc_start: 0.7191 (m-80) cc_final: 0.6699 (m-80) REVERT: E 390 LEU cc_start: 0.7943 (mm) cc_final: 0.7580 (mm) REVERT: E 449 TYR cc_start: 0.5892 (m-80) cc_final: 0.5532 (m-80) REVERT: E 451 TYR cc_start: 0.7042 (m-80) cc_final: 0.6545 (m-80) REVERT: E 902 MET cc_start: 0.9518 (tpt) cc_final: 0.9133 (tpt) REVERT: B 82 MET cc_start: 0.4633 (ptp) cc_final: 0.4285 (pmm) REVERT: H 82 MET cc_start: 0.3938 (ptp) cc_final: 0.3394 (pmm) REVERT: D 46 LEU cc_start: 0.4697 (pt) cc_final: 0.3839 (tp) REVERT: D 95 PHE cc_start: 0.7630 (t80) cc_final: 0.7263 (t80) REVERT: G 46 LEU cc_start: 0.4613 (pt) cc_final: 0.3363 (tp) REVERT: L 46 LEU cc_start: 0.4222 (pt) cc_final: 0.3323 (tp) outliers start: 54 outliers final: 43 residues processed: 176 average time/residue: 0.1964 time to fit residues: 56.5891 Evaluate side-chains 173 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 129 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 449 TYR Chi-restraints excluded: chain A residue 1040 VAL 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 390 LEU Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 449 TYR 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 934 ILE Chi-restraints excluded: chain E residue 951 VAL 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 69 ILE Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain B residue 109 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 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 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 96 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 35 optimal weight: 7.9990 chunk 345 optimal weight: 50.0000 chunk 196 optimal weight: 10.0000 chunk 200 optimal weight: 5.9990 chunk 177 optimal weight: 7.9990 chunk 137 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 162 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 133 optimal weight: 7.9990 chunk 310 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 901 GLN ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.119211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.077544 restraints weight = 113956.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.076728 restraints weight = 55288.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.077720 restraints weight = 42978.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.077969 restraints weight = 34116.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.077956 restraints weight = 32294.984| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 29394 Z= 0.330 Angle : 0.740 15.933 40128 Z= 0.364 Chirality : 0.047 0.226 4710 Planarity : 0.005 0.052 5055 Dihedral : 7.401 57.249 5136 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 2.10 % Allowed : 15.75 % Favored : 82.15 % 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: -1.89 (0.14), residues: 3555 helix: 1.35 (0.20), residues: 666 sheet: -2.18 (0.17), residues: 786 loop : -1.81 (0.13), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1019 TYR 0.023 0.002 TYR C1067 PHE 0.019 0.002 PHE E1103 TRP 0.021 0.002 TRP F 98 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00776 (29289) covalent geometry : angle 0.72353 (39864) SS BOND : bond 0.00422 ( 42) SS BOND : angle 1.81081 ( 84) hydrogen bonds : bond 0.04667 ( 991) hydrogen bonds : angle 5.96410 ( 2676) Misc. bond : bond 0.00019 ( 3) link_BETA1-4 : bond 0.00396 ( 18) link_BETA1-4 : angle 1.55533 ( 54) link_BETA1-6 : bond 0.00248 ( 3) link_BETA1-6 : angle 1.74760 ( 9) link_NAG-ASN : bond 0.00565 ( 39) link_NAG-ASN : angle 2.39811 ( 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 196 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 132 time to evaluate : 1.113 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: 0.7692 (m-30) cc_final: 0.7269 (p0) REVERT: A 451 TYR cc_start: 0.7252 (m-80) cc_final: 0.6705 (m-80) REVERT: C 427 ASP cc_start: 0.7584 (m-30) cc_final: 0.7336 (p0) REVERT: C 451 TYR cc_start: 0.7134 (m-80) cc_final: 0.6608 (m-80) REVERT: E 449 TYR cc_start: 0.5865 (m-80) cc_final: 0.5480 (m-80) REVERT: E 1029 MET cc_start: 0.9229 (tpp) cc_final: 0.8488 (ttm) REVERT: B 82 MET cc_start: 0.4221 (ptp) cc_final: 0.3933 (pmm) REVERT: H 82 MET cc_start: 0.3754 (ptp) cc_final: 0.3333 (pmm) REVERT: D 46 LEU cc_start: 0.4792 (pt) cc_final: 0.3857 (tp) REVERT: D 95 PHE cc_start: 0.7512 (t80) cc_final: 0.7143 (t80) REVERT: G 46 LEU cc_start: 0.4809 (pt) cc_final: 0.3533 (tp) REVERT: L 46 LEU cc_start: 0.4459 (pt) cc_final: 0.3469 (tp) outliers start: 64 outliers final: 53 residues processed: 176 average time/residue: 0.1850 time to fit residues: 53.5284 Evaluate side-chains 175 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 122 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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 449 TYR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 951 VAL 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 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 390 LEU Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1081 ILE 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 934 ILE Chi-restraints excluded: chain E residue 951 VAL 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 B residue 108 LEU Chi-restraints excluded: chain B residue 109 VAL 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 H residue 87 THR 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: 0.9990 chunk 131 optimal weight: 10.0000 chunk 258 optimal weight: 0.9990 chunk 224 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 221 optimal weight: 5.9990 chunk 357 optimal weight: 0.0170 chunk 359 optimal weight: 10.0000 chunk 292 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1071 GLN C 901 GLN E1106 GLN D 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.121570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.080555 restraints weight = 108848.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.080240 restraints weight = 54701.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.079681 restraints weight = 42544.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.080084 restraints weight = 45176.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.080913 restraints weight = 35963.855| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29394 Z= 0.145 Angle : 0.611 15.338 40128 Z= 0.301 Chirality : 0.043 0.210 4710 Planarity : 0.004 0.049 5055 Dihedral : 6.967 55.634 5136 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.38 % Allowed : 16.96 % Favored : 81.66 % 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: -1.60 (0.14), residues: 3555 helix: 1.73 (0.20), residues: 675 sheet: -2.05 (0.17), residues: 804 loop : -1.65 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 54 TYR 0.034 0.001 TYR A 423 PHE 0.011 0.001 PHE H 27 TRP 0.027 0.001 TRP F 98 HIS 0.002 0.001 HIS G 39 Details of bonding type rmsd covalent geometry : bond 0.00339 (29289) covalent geometry : angle 0.59709 (39864) SS BOND : bond 0.00275 ( 42) SS BOND : angle 1.29387 ( 84) hydrogen bonds : bond 0.03953 ( 991) hydrogen bonds : angle 5.57419 ( 2676) Misc. bond : bond 0.00011 ( 3) link_BETA1-4 : bond 0.00461 ( 18) link_BETA1-4 : angle 1.44444 ( 54) link_BETA1-6 : bond 0.00155 ( 3) link_BETA1-6 : angle 1.31940 ( 9) link_NAG-ASN : bond 0.00355 ( 39) link_NAG-ASN : angle 2.09632 ( 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 181 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 139 time to evaluate : 1.108 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: 0.7836 (m-30) cc_final: 0.7351 (p0) REVERT: A 451 TYR cc_start: 0.7063 (m-80) cc_final: 0.6518 (m-80) REVERT: C 427 ASP cc_start: 0.7663 (m-30) cc_final: 0.7434 (p0) REVERT: E 427 ASP cc_start: 0.7672 (m-30) cc_final: 0.7380 (p0) REVERT: E 449 TYR cc_start: 0.6048 (m-80) cc_final: 0.5679 (m-80) REVERT: E 451 TYR cc_start: 0.6755 (m-80) cc_final: 0.6278 (m-80) REVERT: E 779 GLN cc_start: 0.8374 (tp40) cc_final: 0.8148 (tp40) REVERT: E 1029 MET cc_start: 0.9109 (tpp) cc_final: 0.8482 (ttm) REVERT: B 82 MET cc_start: 0.4552 (ptp) cc_final: 0.4054 (pmm) REVERT: H 82 MET cc_start: 0.4124 (ptp) cc_final: 0.3402 (pmm) REVERT: D 46 LEU cc_start: 0.4683 (pt) cc_final: 0.3873 (tp) REVERT: D 95 PHE cc_start: 0.7579 (t80) cc_final: 0.7214 (t80) REVERT: G 46 LEU cc_start: 0.4702 (pt) cc_final: 0.3651 (tp) REVERT: L 46 LEU cc_start: 0.4648 (pt) cc_final: 0.3825 (tp) outliers start: 42 outliers final: 39 residues processed: 168 average time/residue: 0.2127 time to fit residues: 57.1435 Evaluate side-chains 167 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 128 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 449 TYR 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 449 TYR 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 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 68 THR Chi-restraints excluded: chain B residue 79 TYR 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 4 LEU 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 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: 2.9990 chunk 230 optimal weight: 4.9990 chunk 324 optimal weight: 9.9990 chunk 131 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 chunk 43 optimal weight: 0.0970 chunk 76 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 209 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN A1071 GLN A1106 GLN C 901 GLN ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.120484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.081099 restraints weight = 130511.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.079192 restraints weight = 72318.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.080614 restraints weight = 54738.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.080740 restraints weight = 41467.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.080989 restraints weight = 40161.985| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 29394 Z= 0.207 Angle : 0.640 14.715 40128 Z= 0.313 Chirality : 0.044 0.240 4710 Planarity : 0.004 0.051 5055 Dihedral : 6.971 56.180 5136 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 1.74 % Allowed : 16.83 % Favored : 81.43 % 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: -1.56 (0.14), residues: 3555 helix: 1.70 (0.20), residues: 678 sheet: -2.00 (0.18), residues: 786 loop : -1.62 (0.13), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1019 TYR 0.026 0.002 TYR A 423 PHE 0.013 0.002 PHE A 133 TRP 0.026 0.001 TRP F 98 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00488 (29289) covalent geometry : angle 0.62525 (39864) SS BOND : bond 0.00343 ( 42) SS BOND : angle 1.42005 ( 84) hydrogen bonds : bond 0.04092 ( 991) hydrogen bonds : angle 5.57901 ( 2676) Misc. bond : bond 0.00015 ( 3) link_BETA1-4 : bond 0.00400 ( 18) link_BETA1-4 : angle 1.40936 ( 54) link_BETA1-6 : bond 0.00030 ( 3) link_BETA1-6 : angle 1.50443 ( 9) link_NAG-ASN : bond 0.00409 ( 39) link_NAG-ASN : angle 2.14086 ( 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 183 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 130 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.7858 (m-30) cc_final: 0.7368 (p0) REVERT: A 451 TYR cc_start: 0.7196 (m-80) cc_final: 0.6711 (m-80) REVERT: C 427 ASP cc_start: 0.7606 (m-30) cc_final: 0.7381 (p0) REVERT: E 427 ASP cc_start: 0.7576 (m-30) cc_final: 0.7293 (p0) REVERT: E 449 TYR cc_start: 0.5984 (m-80) cc_final: 0.5590 (m-80) REVERT: E 1029 MET cc_start: 0.9194 (tpp) cc_final: 0.8602 (ttm) REVERT: B 82 MET cc_start: 0.4423 (ptp) cc_final: 0.4001 (pmm) REVERT: H 82 MET cc_start: 0.3944 (ptp) cc_final: 0.3336 (pmm) REVERT: D 46 LEU cc_start: 0.4762 (pt) cc_final: 0.3885 (tp) REVERT: D 95 PHE cc_start: 0.7505 (t80) cc_final: 0.7105 (t80) REVERT: G 46 LEU cc_start: 0.4935 (pt) cc_final: 0.3776 (tp) REVERT: L 46 LEU cc_start: 0.4651 (pt) cc_final: 0.3721 (tp) outliers start: 53 outliers final: 45 residues processed: 167 average time/residue: 0.1869 time to fit residues: 51.2375 Evaluate side-chains 168 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 123 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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 449 TYR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 47 VAL 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 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 390 LEU 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 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 4 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 250 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 295 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 160 optimal weight: 6.9990 chunk 194 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 186 optimal weight: 0.5980 chunk 328 optimal weight: 0.0000 chunk 157 optimal weight: 4.9990 overall best weight: 1.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1071 GLN C 901 GLN E 437 ASN ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.122474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.079314 restraints weight = 91847.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.081282 restraints weight = 55348.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.080845 restraints weight = 32416.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.081162 restraints weight = 34996.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.081412 restraints weight = 30472.826| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29394 Z= 0.116 Angle : 0.583 13.855 40128 Z= 0.287 Chirality : 0.043 0.237 4710 Planarity : 0.004 0.049 5055 Dihedral : 6.690 56.167 5136 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.22 % Allowed : 17.52 % Favored : 81.26 % 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: -1.34 (0.14), residues: 3555 helix: 2.05 (0.20), residues: 675 sheet: -1.91 (0.18), residues: 801 loop : -1.50 (0.13), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1019 TYR 0.031 0.001 TYR A 423 PHE 0.012 0.001 PHE A 374 TRP 0.022 0.001 TRP F 98 HIS 0.002 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00266 (29289) covalent geometry : angle 0.57077 (39864) SS BOND : bond 0.00263 ( 42) SS BOND : angle 1.14868 ( 84) hydrogen bonds : bond 0.03679 ( 991) hydrogen bonds : angle 5.29997 ( 2676) Misc. bond : bond 0.00023 ( 3) link_BETA1-4 : bond 0.00463 ( 18) link_BETA1-4 : angle 1.39021 ( 54) link_BETA1-6 : bond 0.00227 ( 3) link_BETA1-6 : angle 1.26755 ( 9) link_NAG-ASN : bond 0.00324 ( 39) link_NAG-ASN : angle 1.92441 ( 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 184 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 1.156 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: 0.7789 (m-30) cc_final: 0.7209 (p0) REVERT: A 451 TYR cc_start: 0.7177 (m-80) cc_final: 0.5432 (m-80) REVERT: A 505 TYR cc_start: 0.6841 (t80) cc_final: 0.6249 (t80) REVERT: C 427 ASP cc_start: 0.7589 (m-30) cc_final: 0.7298 (p0) REVERT: C 451 TYR cc_start: 0.7141 (m-80) cc_final: 0.6698 (m-80) REVERT: C 505 TYR cc_start: 0.6352 (t80) cc_final: 0.6142 (t80) REVERT: E 427 ASP cc_start: 0.7628 (m-30) cc_final: 0.7332 (p0) REVERT: E 449 TYR cc_start: 0.5987 (m-80) cc_final: 0.5584 (m-80) REVERT: E 451 TYR cc_start: 0.6818 (m-80) cc_final: 0.6477 (m-80) REVERT: E 1029 MET cc_start: 0.9163 (tpp) cc_final: 0.8530 (ttm) REVERT: B 82 MET cc_start: 0.4308 (ptp) cc_final: 0.3920 (pmm) REVERT: H 82 MET cc_start: 0.4000 (ptp) cc_final: 0.3412 (pmm) REVERT: D 46 LEU cc_start: 0.4706 (pt) cc_final: 0.3895 (tp) REVERT: D 95 PHE cc_start: 0.7470 (t80) cc_final: 0.7074 (t80) REVERT: G 46 LEU cc_start: 0.4900 (pt) cc_final: 0.3776 (tp) REVERT: L 46 LEU cc_start: 0.4806 (pt) cc_final: 0.3927 (tp) outliers start: 37 outliers final: 36 residues processed: 173 average time/residue: 0.1916 time to fit residues: 54.1158 Evaluate side-chains 167 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 1.140 ------------------------------------------------------------------------------- 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 449 TYR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 47 VAL 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 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 22 CYS 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 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 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: 10.0000 chunk 248 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 157 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 249 optimal weight: 10.0000 chunk 82 optimal weight: 0.1980 chunk 277 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.121991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.081156 restraints weight = 104926.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.080789 restraints weight = 50983.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.081332 restraints weight = 40301.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.081575 restraints weight = 38269.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.081659 restraints weight = 31664.488| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29394 Z= 0.144 Angle : 0.592 13.300 40128 Z= 0.291 Chirality : 0.043 0.194 4710 Planarity : 0.004 0.050 5055 Dihedral : 6.642 56.620 5133 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.31 % Allowed : 17.59 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.14), residues: 3555 helix: 2.03 (0.20), residues: 678 sheet: -1.81 (0.18), residues: 816 loop : -1.44 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1019 TYR 0.032 0.001 TYR A 423 PHE 0.024 0.001 PHE A 168 TRP 0.018 0.001 TRP F 98 HIS 0.003 0.001 HIS E1058 Details of bonding type rmsd covalent geometry : bond 0.00339 (29289) covalent geometry : angle 0.57947 (39864) SS BOND : bond 0.00276 ( 42) SS BOND : angle 1.19795 ( 84) hydrogen bonds : bond 0.03739 ( 991) hydrogen bonds : angle 5.26222 ( 2676) Misc. bond : bond 0.00011 ( 3) link_BETA1-4 : bond 0.00420 ( 18) link_BETA1-4 : angle 1.35126 ( 54) link_BETA1-6 : bond 0.00115 ( 3) link_BETA1-6 : angle 1.36624 ( 9) link_NAG-ASN : bond 0.00323 ( 39) link_NAG-ASN : angle 1.89537 ( 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 169 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 129 time to evaluate : 1.162 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: 0.7807 (m-30) cc_final: 0.7283 (p0) REVERT: A 505 TYR cc_start: 0.6822 (t80) cc_final: 0.6238 (t80) REVERT: C 427 ASP cc_start: 0.7596 (m-30) cc_final: 0.7284 (p0) REVERT: C 451 TYR cc_start: 0.7102 (m-80) cc_final: 0.6642 (m-80) REVERT: C 505 TYR cc_start: 0.6405 (t80) cc_final: 0.6176 (t80) REVERT: E 427 ASP cc_start: 0.7597 (m-30) cc_final: 0.7318 (p0) REVERT: E 449 TYR cc_start: 0.5950 (m-80) cc_final: 0.5540 (m-80) REVERT: E 451 TYR cc_start: 0.6804 (m-80) cc_final: 0.6446 (m-80) REVERT: E 1029 MET cc_start: 0.9133 (tpp) cc_final: 0.8512 (ttm) REVERT: B 82 MET cc_start: 0.4285 (ptp) cc_final: 0.3883 (pmm) REVERT: H 82 MET cc_start: 0.4030 (ptp) cc_final: 0.3404 (pmm) REVERT: D 46 LEU cc_start: 0.4744 (pt) cc_final: 0.3939 (tp) REVERT: D 95 PHE cc_start: 0.7513 (t80) cc_final: 0.7093 (t80) REVERT: G 46 LEU cc_start: 0.4902 (pt) cc_final: 0.3837 (tp) REVERT: L 46 LEU cc_start: 0.4873 (pt) cc_final: 0.3961 (tp) outliers start: 40 outliers final: 40 residues processed: 157 average time/residue: 0.1988 time to fit residues: 51.1519 Evaluate side-chains 167 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 127 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 449 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 1040 VAL 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 E residue 33 THR Chi-restraints excluded: chain E residue 47 VAL 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 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 79 TYR Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 22 CYS 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 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 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: 30.0000 chunk 350 optimal weight: 8.9990 chunk 358 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 163 optimal weight: 4.9990 chunk 320 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 292 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 334 optimal weight: 6.9990 chunk 146 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.121928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.080834 restraints weight = 103293.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.080285 restraints weight = 52373.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.080362 restraints weight = 41187.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.080746 restraints weight = 42270.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.081205 restraints weight = 33649.086| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 29394 Z= 0.156 Angle : 0.597 13.042 40128 Z= 0.293 Chirality : 0.043 0.190 4710 Planarity : 0.004 0.050 5055 Dihedral : 6.639 56.628 5133 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.38 % Allowed : 17.52 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.14), residues: 3555 helix: 2.01 (0.20), residues: 678 sheet: -1.69 (0.18), residues: 807 loop : -1.43 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1019 TYR 0.032 0.001 TYR A 423 PHE 0.021 0.001 PHE A 168 TRP 0.018 0.001 TRP F 98 HIS 0.003 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00368 (29289) covalent geometry : angle 0.58430 (39864) SS BOND : bond 0.00287 ( 42) SS BOND : angle 1.25362 ( 84) hydrogen bonds : bond 0.03797 ( 991) hydrogen bonds : angle 5.25985 ( 2676) Misc. bond : bond 0.00013 ( 3) link_BETA1-4 : bond 0.00406 ( 18) link_BETA1-4 : angle 1.30806 ( 54) link_BETA1-6 : bond 0.00095 ( 3) link_BETA1-6 : angle 1.38179 ( 9) link_NAG-ASN : bond 0.00338 ( 39) link_NAG-ASN : angle 1.91014 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5777.98 seconds wall clock time: 100 minutes 30.64 seconds (6030.64 seconds total)