Starting phenix.real_space_refine on Sun Jul 5 22:45:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ndd_12284/07_2026/7ndd_12284.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ndd_12284/07_2026/7ndd_12284.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ndd_12284/07_2026/7ndd_12284.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ndd_12284/07_2026/7ndd_12284.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ndd_12284/07_2026/7ndd_12284.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ndd_12284/07_2026/7ndd_12284.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ndd_12284/07_2026/7ndd_12284.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ndd_12284/07_2026/7ndd_12284.map" } resolution = 4.2 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= 0.002 sd= 0.022 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 135 5.16 5 C 19449 2.51 5 N 5079 2.21 5 O 5982 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30645 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 8314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8314 Classifications: {'peptide': 1063} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 53, 'TRANS': 1009} Chain breaks: 5 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 8314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8314 Classifications: {'peptide': 1063} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 53, 'TRANS': 1009} Chain breaks: 5 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 8314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8314 Classifications: {'peptide': 1063} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 53, 'TRANS': 1009} Chain breaks: 5 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 856 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 793 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 856 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "G" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 793 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 856 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "L" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 793 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 7.04, per 1000 atoms: 0.23 Number of scatterers: 30645 At special positions: 0 Unit cell: (168.92, 182.04, 193.52, 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 135 16.00 O 5982 8.00 N 5079 7.00 C 19449 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.05 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " 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=0, 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 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 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 W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C 165 " " NAG I 1 " - " ASN A 234 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 234 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN C 234 " " NAG U 1 " - " ASN C 717 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1098 " " NAG X 1 " - " ASN C1134 " Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 1.2 seconds 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7158 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 59 sheets defined 22.6% alpha, 32.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.798A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.381A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.612A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 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: 3.646A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.138A 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 removed outlier: 3.905A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) 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 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.633A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.979A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.805A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.405A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.632A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.632A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.080A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.850A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.622A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.949A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.843A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.385A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.620A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 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: 3.664A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.096A 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 removed outlier: 3.880A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) 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 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.611A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.955A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.607A pdb=" N LYS D 65 " --> pdb=" O ASP D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'E' and resid 29 through 32 removed outlier: 3.994A pdb=" N ASN E 32 " --> pdb=" O ILE E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 29 through 32' Processing helix chain 'E' and resid 80 through 84 Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 62 through 65 removed outlier: 3.605A pdb=" N LYS F 65 " --> pdb=" O ASP F 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 62 through 65' Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'G' and resid 29 through 32 removed outlier: 3.992A pdb=" N ASN G 32 " --> pdb=" O ILE G 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 29 through 32' Processing helix chain 'G' and resid 80 through 84 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.607A pdb=" N LYS H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 29 through 32 removed outlier: 3.988A pdb=" N ASN L 32 " --> pdb=" O ILE L 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 29 through 32' Processing helix chain 'L' and resid 80 through 84 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 7.708A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.183A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.591A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.181A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.741A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A 567 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.266A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.817A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.447A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.655A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.655A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.466A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.560A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.533A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.181A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.367A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG B 567 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.127A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.710A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.468A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.880A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.880A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.400A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.621A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 55 Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.700A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL C 126 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TYR C 170 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.802A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.181A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.981A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.802A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.802A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.424A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AE7, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.227A pdb=" N GLY D 10 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.227A pdb=" N GLY D 10 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL D 112 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AF1, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.429A pdb=" N LEU E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TYR E 50 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.505A pdb=" N THR E 97 " --> pdb=" O GLN E 91 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AF4, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.227A pdb=" N GLY F 10 " --> pdb=" O THR F 120 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.227A pdb=" N GLY F 10 " --> pdb=" O THR F 120 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL F 112 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AF7, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.445A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 10 through 13 Processing sheet with id=AF9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AG1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.218A pdb=" N GLY H 10 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.218A pdb=" N GLY H 10 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL H 112 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AG4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.393A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 10 through 13 1257 hydrogen bonds defined for protein. 3342 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: 7.87 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9806 1.35 - 1.47: 8061 1.47 - 1.59: 13291 1.59 - 1.72: 0 1.72 - 1.84: 174 Bond restraints: 31332 Sorted by residual: bond pdb=" C1 NAG C1308 " pdb=" O5 NAG C1308 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 4.97e+00 bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.80e+00 bond pdb=" C1 NAG U 2 " pdb=" O5 NAG U 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.43e+00 bond pdb=" C1 NAG A1308 " pdb=" O5 NAG A1308 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.40e+00 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.40e+00 ... (remaining 31327 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.44: 42576 5.44 - 10.88: 26 10.88 - 16.32: 2 16.32 - 21.76: 1 21.76 - 27.20: 1 Bond angle restraints: 42606 Sorted by residual: angle pdb=" C ASN B 334 " pdb=" N LEU B 335 " pdb=" CA LEU B 335 " ideal model delta sigma weight residual 121.98 110.72 11.26 1.35e+00 5.49e-01 6.95e+01 angle pdb=" C GLY B 526 " pdb=" N PRO B 527 " pdb=" CD PRO B 527 " ideal model delta sigma weight residual 125.00 97.80 27.20 4.10e+00 5.95e-02 4.40e+01 angle pdb=" N THR B 333 " pdb=" CA THR B 333 " pdb=" C THR B 333 " ideal model delta sigma weight residual 108.65 98.55 10.10 1.85e+00 2.92e-01 2.98e+01 angle pdb=" CA PRO B 527 " pdb=" N PRO B 527 " pdb=" CD PRO B 527 " ideal model delta sigma weight residual 112.00 104.73 7.27 1.40e+00 5.10e-01 2.70e+01 angle pdb=" CA PRO A 527 " pdb=" N PRO A 527 " pdb=" CD PRO A 527 " ideal model delta sigma weight residual 112.00 105.46 6.54 1.40e+00 5.10e-01 2.18e+01 ... (remaining 42601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 17117 17.43 - 34.87: 805 34.87 - 52.30: 187 52.30 - 69.73: 53 69.73 - 87.17: 27 Dihedral angle restraints: 18189 sinusoidal: 7023 harmonic: 11166 Sorted by residual: dihedral pdb=" CA PRO B 527 " pdb=" C PRO B 527 " pdb=" N LYS B 528 " pdb=" CA LYS B 528 " ideal model delta harmonic sigma weight residual -180.00 -118.08 -61.92 0 5.00e+00 4.00e-02 1.53e+02 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -166.41 80.41 1 1.00e+01 1.00e-02 8.00e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -165.51 79.51 1 1.00e+01 1.00e-02 7.85e+01 ... (remaining 18186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 4879 0.123 - 0.246: 51 0.246 - 0.369: 3 0.369 - 0.492: 1 0.492 - 0.615: 1 Chirality restraints: 4935 Sorted by residual: chirality pdb=" CA PRO B 527 " pdb=" N PRO B 527 " pdb=" C PRO B 527 " pdb=" CB PRO B 527 " both_signs ideal model delta sigma weight residual False 2.72 2.10 0.61 2.00e-01 2.50e+01 9.45e+00 chirality pdb=" CB ILE B 332 " pdb=" CA ILE B 332 " pdb=" CG1 ILE B 332 " pdb=" CG2 ILE B 332 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.85e+00 chirality pdb=" C1 NAG C1308 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG C1308 " pdb=" O5 NAG C1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 4932 not shown) Planarity restraints: 5490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 526 " 0.144 5.00e-02 4.00e+02 2.18e-01 7.57e+01 pdb=" N PRO B 527 " -0.375 5.00e-02 4.00e+02 pdb=" CA PRO B 527 " 0.137 5.00e-02 4.00e+02 pdb=" CD PRO B 527 " 0.094 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 526 " 0.117 5.00e-02 4.00e+02 1.74e-01 4.85e+01 pdb=" N PRO C 527 " -0.301 5.00e-02 4.00e+02 pdb=" CA PRO C 527 " 0.102 5.00e-02 4.00e+02 pdb=" CD PRO C 527 " 0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 321 " -0.094 5.00e-02 4.00e+02 1.48e-01 3.51e+01 pdb=" N PRO B 322 " 0.256 5.00e-02 4.00e+02 pdb=" CA PRO B 322 " -0.088 5.00e-02 4.00e+02 pdb=" CD PRO B 322 " -0.075 5.00e-02 4.00e+02 ... (remaining 5487 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 2076 2.74 - 3.28: 29458 3.28 - 3.82: 49997 3.82 - 4.36: 59901 4.36 - 4.90: 104914 Nonbonded interactions: 246346 Sorted by model distance: nonbonded pdb=" OG1 THR A 33 " pdb=" O GLY A 219 " model vdw 2.194 3.040 nonbonded pdb=" O THR B 333 " pdb=" O ASN B 334 " model vdw 2.223 3.040 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.229 3.040 nonbonded pdb=" OG1 THR B 33 " pdb=" O GLY B 219 " model vdw 2.239 3.040 nonbonded pdb=" OG1 THR A 109 " pdb=" OD1 ASP A 111 " model vdw 2.241 3.040 ... (remaining 246341 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.140 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: 0.040 Extract box with map and model: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 29.210 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 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 : 0.003 0.072 31434 Z= 0.162 Angle : 0.624 27.202 42864 Z= 0.318 Chirality : 0.046 0.615 4935 Planarity : 0.006 0.218 5451 Dihedral : 11.709 87.167 10887 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.11 % Favored : 95.66 % Rotamer: Outliers : 0.43 % Allowed : 4.02 % Favored : 95.55 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.13), residues: 3798 helix: 0.65 (0.19), residues: 725 sheet: 0.29 (0.15), residues: 979 loop : -0.86 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 24 TYR 0.014 0.001 TYR C 200 PHE 0.012 0.001 PHE B1109 TRP 0.010 0.001 TRP A 258 HIS 0.008 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (31332) covalent geometry : angle 0.61329 / 0.32 (42606) SS BOND : bond 0.00356 / 0.29 ( 48) SS BOND : angle 1.00826 / 0.67 ( 96) hydrogen bonds : bond 0.18912 / 12.59 ( 1221) hydrogen bonds : angle 7.73359 / 5.36 ( 3342) link_BETA1-4 : bond 0.00257 / 0.14 ( 15) link_BETA1-4 : angle 0.97567 / 0.65 ( 45) link_NAG-ASN : bond 0.00272 / 0.15 ( 39) link_NAG-ASN : angle 2.09650 / 1.40 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 437 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9453 (mt) cc_final: 0.9073 (tp) REVERT: A 191 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7641 (mp0) REVERT: A 229 LEU cc_start: 0.8856 (mt) cc_final: 0.8500 (tt) REVERT: A 238 PHE cc_start: 0.8724 (p90) cc_final: 0.8116 (p90) REVERT: A 299 THR cc_start: 0.9629 (m) cc_final: 0.9279 (p) REVERT: A 386 LYS cc_start: 0.9404 (mttt) cc_final: 0.8776 (ptmt) REVERT: A 518 LEU cc_start: 0.8083 (mt) cc_final: 0.7811 (mt) REVERT: A 759 PHE cc_start: 0.8342 (m-80) cc_final: 0.8016 (m-80) REVERT: A 819 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8069 (mt-10) REVERT: A 895 GLN cc_start: 0.8365 (pm20) cc_final: 0.7888 (pm20) REVERT: A 1119 ASN cc_start: 0.8390 (m-40) cc_final: 0.7578 (m110) REVERT: B 54 LEU cc_start: 0.9613 (mt) cc_final: 0.9220 (tp) REVERT: B 91 TYR cc_start: 0.8523 (t80) cc_final: 0.7590 (t80) REVERT: B 104 TRP cc_start: 0.8839 (m-90) cc_final: 0.8323 (m-90) REVERT: B 137 ASN cc_start: 0.9447 (m-40) cc_final: 0.9087 (p0) REVERT: B 192 PHE cc_start: 0.9293 (m-80) cc_final: 0.9060 (m-80) REVERT: B 238 PHE cc_start: 0.9432 (p90) cc_final: 0.9120 (p90) REVERT: B 270 LEU cc_start: 0.8973 (mt) cc_final: 0.8476 (mp) REVERT: B 611 LEU cc_start: 0.9046 (tp) cc_final: 0.8821 (tp) REVERT: B 727 LEU cc_start: 0.9565 (mt) cc_final: 0.9356 (mp) REVERT: B 731 MET cc_start: 0.8450 (ptm) cc_final: 0.7791 (ppp) REVERT: B 776 LYS cc_start: 0.9081 (tttt) cc_final: 0.8720 (tppt) REVERT: B 869 MET cc_start: 0.9319 (mtt) cc_final: 0.8970 (mtm) REVERT: B 901 GLN cc_start: 0.8458 (tt0) cc_final: 0.8258 (tm-30) REVERT: B 979 ASP cc_start: 0.8927 (m-30) cc_final: 0.8618 (m-30) REVERT: B 1010 GLN cc_start: 0.8529 (mm110) cc_final: 0.8042 (tp-100) REVERT: C 191 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8132 (pm20) REVERT: C 297 SER cc_start: 0.8462 (m) cc_final: 0.8148 (p) REVERT: C 398 ASP cc_start: 0.6894 (m-30) cc_final: 0.5476 (m-30) REVERT: C 552 LEU cc_start: 0.9225 (mt) cc_final: 0.8905 (pp) REVERT: C 707 TYR cc_start: 0.8937 (t80) cc_final: 0.8420 (t80) REVERT: C 805 ILE cc_start: 0.9175 (pt) cc_final: 0.8780 (mm) REVERT: C 869 MET cc_start: 0.8630 (mtt) cc_final: 0.7893 (mtm) REVERT: C 878 LEU cc_start: 0.8166 (tp) cc_final: 0.7840 (tp) REVERT: C 909 ILE cc_start: 0.9401 (pt) cc_final: 0.9026 (mt) REVERT: C 955 ASN cc_start: 0.8760 (m-40) cc_final: 0.8067 (p0) REVERT: C 978 ASN cc_start: 0.9101 (m-40) cc_final: 0.8698 (t0) REVERT: C 1029 MET cc_start: 0.8371 (tpp) cc_final: 0.8124 (tpp) REVERT: D 83 MET cc_start: -0.1351 (mtp) cc_final: -0.1797 (mmt) outliers start: 14 outliers final: 2 residues processed: 451 average time/residue: 0.1840 time to fit residues: 132.8585 Evaluate side-chains 224 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 222 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 197 optimal weight: 0.3980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 2.9990 overall best weight: 2.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 GLN A 613 GLN A 914 ASN A 953 ASN A 978 ASN B 901 GLN C 321 GLN C 703 ASN C 774 GLN C 901 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.139467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.113664 restraints weight = 147101.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.109719 restraints weight = 179939.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.107087 restraints weight = 166653.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.107582 restraints weight = 143904.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.107490 restraints weight = 130538.949| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.117 31434 Z= 0.296 Angle : 0.737 10.872 42864 Z= 0.378 Chirality : 0.047 0.258 4935 Planarity : 0.005 0.104 5451 Dihedral : 4.731 54.642 4155 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.84 % Favored : 97.08 % Rotamer: Outliers : 0.15 % Allowed : 2.16 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.13), residues: 3798 helix: 1.30 (0.20), residues: 704 sheet: 0.23 (0.15), residues: 1001 loop : -0.54 (0.13), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 577 TYR 0.026 0.002 TYR A1067 PHE 0.023 0.002 PHE C1062 TRP 0.009 0.001 TRP A 353 HIS 0.019 0.002 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00656 / 0.30 (31332) covalent geometry : angle 0.72392 / 0.38 (42606) SS BOND : bond 0.00443 / 0.32 ( 48) SS BOND : angle 1.20975 / 0.80 ( 96) hydrogen bonds : bond 0.05002 / 3.39 ( 1221) hydrogen bonds : angle 6.28434 / 4.33 ( 3342) link_BETA1-4 : bond 0.00445 / 0.30 ( 15) link_BETA1-4 : angle 1.15530 / 0.88 ( 45) link_NAG-ASN : bond 0.00814 / 0.52 ( 39) link_NAG-ASN : angle 2.48701 / 1.67 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 236 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 54 LEU cc_start: 0.9408 (mt) cc_final: 0.9195 (tp) REVERT: A 223 LEU cc_start: 0.8302 (mp) cc_final: 0.8050 (mp) REVERT: A 224 GLU cc_start: 0.9298 (mt-10) cc_final: 0.8788 (mp0) REVERT: A 299 THR cc_start: 0.9627 (m) cc_final: 0.9309 (p) REVERT: A 386 LYS cc_start: 0.9294 (mttt) cc_final: 0.8962 (ptpp) REVERT: A 388 ASN cc_start: 0.8351 (p0) cc_final: 0.8129 (p0) REVERT: A 869 MET cc_start: 0.8951 (mtt) cc_final: 0.8457 (mtt) REVERT: A 895 GLN cc_start: 0.8579 (pm20) cc_final: 0.8163 (pm20) REVERT: A 914 ASN cc_start: 0.9272 (OUTLIER) cc_final: 0.9065 (p0) REVERT: B 56 LEU cc_start: 0.8890 (tp) cc_final: 0.8367 (tp) REVERT: B 91 TYR cc_start: 0.8244 (t80) cc_final: 0.7770 (t80) REVERT: B 297 SER cc_start: 0.9217 (m) cc_final: 0.8923 (p) REVERT: B 731 MET cc_start: 0.8738 (ptm) cc_final: 0.7875 (ppp) REVERT: B 947 LYS cc_start: 0.8899 (mttt) cc_final: 0.8534 (mmmt) REVERT: C 95 THR cc_start: 0.8137 (p) cc_final: 0.7924 (p) REVERT: C 229 LEU cc_start: 0.8955 (tp) cc_final: 0.8501 (tp) REVERT: C 277 LEU cc_start: 0.9195 (mp) cc_final: 0.8862 (tp) REVERT: C 297 SER cc_start: 0.8731 (m) cc_final: 0.8349 (p) REVERT: C 365 TYR cc_start: 0.8708 (m-80) cc_final: 0.8506 (m-10) REVERT: C 552 LEU cc_start: 0.9111 (mt) cc_final: 0.8812 (pp) REVERT: C 707 TYR cc_start: 0.9189 (t80) cc_final: 0.8498 (t80) REVERT: C 740 MET cc_start: 0.8954 (ttp) cc_final: 0.8554 (tmm) REVERT: C 780 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7461 (mt-10) REVERT: C 869 MET cc_start: 0.8421 (mtt) cc_final: 0.7957 (mtp) REVERT: C 978 ASN cc_start: 0.9146 (m-40) cc_final: 0.8770 (t0) REVERT: C 984 LEU cc_start: 0.8416 (mt) cc_final: 0.8060 (tp) REVERT: C 1029 MET cc_start: 0.7908 (tpp) cc_final: 0.7273 (tpp) REVERT: H 110 MET cc_start: 0.5324 (mmp) cc_final: 0.4934 (mmp) outliers start: 5 outliers final: 1 residues processed: 241 average time/residue: 0.1693 time to fit residues: 66.9668 Evaluate side-chains 157 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 155 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 213 optimal weight: 0.6980 chunk 190 optimal weight: 0.5980 chunk 238 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 275 optimal weight: 5.9990 chunk 225 optimal weight: 9.9990 chunk 278 optimal weight: 0.8980 chunk 173 optimal weight: 0.9990 chunk 200 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 787 GLN A 901 GLN B 901 GLN B1005 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.131682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.084876 restraints weight = 112753.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.082817 restraints weight = 87055.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.082852 restraints weight = 64090.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.083144 restraints weight = 61001.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.083409 restraints weight = 51004.251| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31434 Z= 0.131 Angle : 0.557 9.152 42864 Z= 0.289 Chirality : 0.044 0.222 4935 Planarity : 0.004 0.078 5451 Dihedral : 4.354 40.968 4155 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.90 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.13), residues: 3798 helix: 1.61 (0.20), residues: 718 sheet: 0.29 (0.15), residues: 1002 loop : -0.43 (0.14), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1107 TYR 0.014 0.001 TYR A 904 PHE 0.026 0.001 PHE A 464 TRP 0.011 0.001 TRP A 64 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (31332) covalent geometry : angle 0.54684 / 0.29 (42606) SS BOND : bond 0.00262 / 0.19 ( 48) SS BOND : angle 1.02915 / 0.74 ( 96) hydrogen bonds : bond 0.04092 / 2.76 ( 1221) hydrogen bonds : angle 5.74531 / 3.96 ( 3342) link_BETA1-4 : bond 0.00337 / 0.21 ( 15) link_BETA1-4 : angle 0.95144 / 0.68 ( 45) link_NAG-ASN : bond 0.00346 / 0.20 ( 39) link_NAG-ASN : angle 1.87034 / 1.24 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 54 LEU cc_start: 0.9394 (mt) cc_final: 0.9090 (tp) REVERT: A 223 LEU cc_start: 0.8597 (mp) cc_final: 0.8050 (mp) REVERT: A 224 GLU cc_start: 0.9343 (mt-10) cc_final: 0.8923 (mp0) REVERT: A 238 PHE cc_start: 0.9007 (p90) cc_final: 0.8757 (p90) REVERT: A 299 THR cc_start: 0.9524 (m) cc_final: 0.9192 (p) REVERT: A 386 LYS cc_start: 0.9332 (mttt) cc_final: 0.9090 (mtmm) REVERT: A 388 ASN cc_start: 0.8898 (p0) cc_final: 0.7719 (m-40) REVERT: A 1002 GLN cc_start: 0.8858 (tt0) cc_final: 0.8596 (tm-30) REVERT: A 1045 LYS cc_start: 0.7760 (tttm) cc_final: 0.7453 (tttm) REVERT: B 56 LEU cc_start: 0.9123 (tp) cc_final: 0.8764 (tp) REVERT: B 91 TYR cc_start: 0.8256 (t80) cc_final: 0.7895 (t80) REVERT: B 175 PHE cc_start: 0.9638 (m-10) cc_final: 0.9416 (m-80) REVERT: B 238 PHE cc_start: 0.9406 (p90) cc_final: 0.8938 (p90) REVERT: B 297 SER cc_start: 0.9168 (m) cc_final: 0.8858 (p) REVERT: C 95 THR cc_start: 0.8387 (p) cc_final: 0.8183 (p) REVERT: C 229 LEU cc_start: 0.9125 (tp) cc_final: 0.8740 (tp) REVERT: C 277 LEU cc_start: 0.9177 (mp) cc_final: 0.8808 (tp) REVERT: C 297 SER cc_start: 0.8551 (m) cc_final: 0.8110 (p) REVERT: C 365 TYR cc_start: 0.8719 (m-80) cc_final: 0.8497 (m-10) REVERT: C 414 GLN cc_start: 0.9034 (mm-40) cc_final: 0.8506 (tp-100) REVERT: C 552 LEU cc_start: 0.9380 (mt) cc_final: 0.8947 (pp) REVERT: C 707 TYR cc_start: 0.9175 (t80) cc_final: 0.8528 (t80) REVERT: C 740 MET cc_start: 0.9028 (ttp) cc_final: 0.8330 (tmm) REVERT: C 869 MET cc_start: 0.8425 (mtt) cc_final: 0.7989 (mtp) REVERT: C 878 LEU cc_start: 0.8864 (tp) cc_final: 0.8605 (tp) REVERT: C 978 ASN cc_start: 0.9325 (m-40) cc_final: 0.8798 (t0) REVERT: C 1029 MET cc_start: 0.9054 (tpp) cc_final: 0.8532 (tpp) REVERT: C 1031 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8157 (mt-10) REVERT: F 29 PHE cc_start: 0.8030 (t80) cc_final: 0.7687 (t80) REVERT: H 110 MET cc_start: 0.5421 (mmp) cc_final: 0.4664 (mmp) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.1572 time to fit residues: 60.2149 Evaluate side-chains 150 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 370 optimal weight: 50.0000 chunk 252 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 chunk 316 optimal weight: 3.9990 chunk 106 optimal weight: 30.0000 chunk 101 optimal weight: 0.6980 chunk 29 optimal weight: 20.0000 chunk 21 optimal weight: 9.9990 chunk 300 optimal weight: 3.9990 chunk 253 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN A 493 GLN B 913 GLN B1011 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.138870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.113511 restraints weight = 145494.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.110090 restraints weight = 183897.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.108193 restraints weight = 161100.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.108508 restraints weight = 153817.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.108530 restraints weight = 129524.600| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 31434 Z= 0.216 Angle : 0.605 11.529 42864 Z= 0.311 Chirality : 0.044 0.267 4935 Planarity : 0.004 0.050 5451 Dihedral : 4.313 30.888 4155 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.40 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.13), residues: 3798 helix: 1.58 (0.20), residues: 704 sheet: 0.35 (0.16), residues: 965 loop : -0.38 (0.13), residues: 2129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C1107 TYR 0.017 0.001 TYR A1067 PHE 0.024 0.002 PHE C1062 TRP 0.015 0.001 TRP C 104 HIS 0.009 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.22 (31332) covalent geometry : angle 0.59334 / 0.31 (42606) SS BOND : bond 0.00319 / 0.23 ( 48) SS BOND : angle 1.06988 / 0.75 ( 96) hydrogen bonds : bond 0.04185 / 2.81 ( 1221) hydrogen bonds : angle 5.69667 / 3.93 ( 3342) link_BETA1-4 : bond 0.00321 / 0.20 ( 15) link_BETA1-4 : angle 1.08779 / 0.80 ( 45) link_NAG-ASN : bond 0.00467 / 0.27 ( 39) link_NAG-ASN : angle 2.06930 / 1.37 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9331 (mt) cc_final: 0.9127 (tp) REVERT: A 223 LEU cc_start: 0.8488 (mp) cc_final: 0.8198 (mp) REVERT: A 224 GLU cc_start: 0.9182 (mt-10) cc_final: 0.8847 (mp0) REVERT: A 229 LEU cc_start: 0.8896 (mm) cc_final: 0.8624 (tp) REVERT: A 299 THR cc_start: 0.9535 (m) cc_final: 0.9248 (p) REVERT: A 869 MET cc_start: 0.9175 (mtt) cc_final: 0.8835 (mtp) REVERT: A 985 ASP cc_start: 0.9083 (t0) cc_final: 0.8824 (t0) REVERT: A 990 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8710 (pt0) REVERT: B 56 LEU cc_start: 0.8857 (tp) cc_final: 0.8375 (tp) REVERT: B 91 TYR cc_start: 0.7861 (t80) cc_final: 0.7590 (t80) REVERT: B 238 PHE cc_start: 0.8894 (p90) cc_final: 0.8671 (p90) REVERT: B 297 SER cc_start: 0.9148 (m) cc_final: 0.8851 (p) REVERT: B 611 LEU cc_start: 0.8979 (tp) cc_final: 0.8684 (tp) REVERT: B 697 MET cc_start: 0.8526 (ptm) cc_final: 0.7964 (ptp) REVERT: B 731 MET cc_start: 0.8728 (ptm) cc_final: 0.7905 (ppp) REVERT: C 95 THR cc_start: 0.7813 (p) cc_final: 0.7591 (p) REVERT: C 229 LEU cc_start: 0.9031 (tp) cc_final: 0.8720 (tp) REVERT: C 297 SER cc_start: 0.8658 (m) cc_final: 0.8196 (p) REVERT: C 414 GLN cc_start: 0.8942 (mm-40) cc_final: 0.8618 (tp-100) REVERT: C 552 LEU cc_start: 0.9026 (mt) cc_final: 0.8766 (pp) REVERT: C 740 MET cc_start: 0.8948 (ttp) cc_final: 0.8528 (tmm) REVERT: C 869 MET cc_start: 0.8438 (mtt) cc_final: 0.8033 (mtp) REVERT: C 878 LEU cc_start: 0.8536 (tp) cc_final: 0.8301 (tp) REVERT: C 955 ASN cc_start: 0.8651 (m-40) cc_final: 0.8427 (p0) REVERT: C 978 ASN cc_start: 0.9205 (m-40) cc_final: 0.8885 (t0) REVERT: C 1029 MET cc_start: 0.8610 (tpp) cc_final: 0.7823 (tpp) REVERT: D 110 MET cc_start: 0.3745 (mmp) cc_final: 0.3307 (mmp) REVERT: F 29 PHE cc_start: 0.8120 (t80) cc_final: 0.7573 (t80) REVERT: H 110 MET cc_start: 0.5296 (mmp) cc_final: 0.4361 (mmp) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.1630 time to fit residues: 54.3531 Evaluate side-chains 141 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 326 optimal weight: 8.9990 chunk 155 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 chunk 209 optimal weight: 2.9990 chunk 367 optimal weight: 9.9990 chunk 317 optimal weight: 5.9990 chunk 362 optimal weight: 50.0000 chunk 244 optimal weight: 10.0000 chunk 130 optimal weight: 0.0570 chunk 69 optimal weight: 0.9990 chunk 176 optimal weight: 0.6980 overall best weight: 0.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN C 207 HIS ** C 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN D 35 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.132851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.090174 restraints weight = 134120.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.088127 restraints weight = 104409.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.088025 restraints weight = 95124.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.088309 restraints weight = 88125.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.088374 restraints weight = 82689.303| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 31434 Z= 0.124 Angle : 0.531 11.043 42864 Z= 0.274 Chirality : 0.043 0.238 4935 Planarity : 0.004 0.048 5451 Dihedral : 4.117 28.376 4155 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.08 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.14), residues: 3798 helix: 1.75 (0.20), residues: 696 sheet: 0.41 (0.16), residues: 976 loop : -0.33 (0.14), residues: 2126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1019 TYR 0.024 0.001 TYR C 365 PHE 0.027 0.001 PHE C 135 TRP 0.032 0.001 TRP C 104 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (31332) covalent geometry : angle 0.51785 / 0.27 (42606) SS BOND : bond 0.00314 / 0.22 ( 48) SS BOND : angle 0.95932 / 0.64 ( 96) hydrogen bonds : bond 0.03795 / 2.54 ( 1221) hydrogen bonds : angle 5.42958 / 3.75 ( 3342) link_BETA1-4 : bond 0.00304 / 0.18 ( 15) link_BETA1-4 : angle 0.95796 / 0.68 ( 45) link_NAG-ASN : bond 0.00420 / 0.23 ( 39) link_NAG-ASN : angle 2.13676 / 1.34 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9379 (mt) cc_final: 0.9008 (tp) REVERT: A 223 LEU cc_start: 0.8690 (mp) cc_final: 0.8029 (mp) REVERT: A 224 GLU cc_start: 0.9430 (mt-10) cc_final: 0.9004 (mp0) REVERT: A 238 PHE cc_start: 0.9206 (p90) cc_final: 0.8959 (p90) REVERT: A 299 THR cc_start: 0.9549 (m) cc_final: 0.9235 (p) REVERT: A 388 ASN cc_start: 0.9008 (p0) cc_final: 0.8671 (p0) REVERT: A 985 ASP cc_start: 0.9316 (t0) cc_final: 0.9071 (t0) REVERT: A 990 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8751 (pt0) REVERT: B 56 LEU cc_start: 0.9158 (tp) cc_final: 0.8930 (tp) REVERT: B 91 TYR cc_start: 0.8296 (t80) cc_final: 0.7965 (t80) REVERT: B 104 TRP cc_start: 0.9193 (m-90) cc_final: 0.8755 (m-90) REVERT: B 238 PHE cc_start: 0.9644 (p90) cc_final: 0.9111 (p90) REVERT: B 271 GLN cc_start: 0.9551 (mt0) cc_final: 0.9271 (mp10) REVERT: B 297 SER cc_start: 0.9193 (m) cc_final: 0.8884 (p) REVERT: B 611 LEU cc_start: 0.9102 (tp) cc_final: 0.8893 (tp) REVERT: B 697 MET cc_start: 0.8233 (ptm) cc_final: 0.7818 (ptp) REVERT: B 984 LEU cc_start: 0.9213 (mm) cc_final: 0.8878 (tp) REVERT: C 229 LEU cc_start: 0.9308 (tp) cc_final: 0.9055 (tp) REVERT: C 238 PHE cc_start: 0.9077 (p90) cc_final: 0.8790 (p90) REVERT: C 297 SER cc_start: 0.8782 (m) cc_final: 0.8237 (p) REVERT: C 414 GLN cc_start: 0.9074 (mm-40) cc_final: 0.8422 (tp-100) REVERT: C 552 LEU cc_start: 0.9655 (mt) cc_final: 0.9176 (pp) REVERT: C 740 MET cc_start: 0.8901 (ttp) cc_final: 0.8493 (tmm) REVERT: C 869 MET cc_start: 0.8435 (mtt) cc_final: 0.8018 (mtp) REVERT: C 950 ASP cc_start: 0.8890 (p0) cc_final: 0.8674 (p0) REVERT: C 978 ASN cc_start: 0.9364 (m-40) cc_final: 0.8866 (t0) REVERT: C 1029 MET cc_start: 0.9022 (tpp) cc_final: 0.8335 (tpp) REVERT: H 110 MET cc_start: 0.4944 (mmp) cc_final: 0.4251 (mmp) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.1635 time to fit residues: 56.3543 Evaluate side-chains 152 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 290 optimal weight: 2.9990 chunk 152 optimal weight: 50.0000 chunk 69 optimal weight: 3.9990 chunk 245 optimal weight: 7.9990 chunk 296 optimal weight: 1.9990 chunk 350 optimal weight: 10.0000 chunk 304 optimal weight: 0.3980 chunk 250 optimal weight: 6.9990 chunk 129 optimal weight: 20.0000 chunk 299 optimal weight: 3.9990 chunk 121 optimal weight: 8.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 394 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 954 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN C 321 GLN C 751 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN H 35 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.136919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.111013 restraints weight = 146145.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.107835 restraints weight = 188717.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.104941 restraints weight = 165488.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.105366 restraints weight = 155845.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.105352 restraints weight = 136611.398| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.115 31434 Z= 0.282 Angle : 0.664 11.660 42864 Z= 0.339 Chirality : 0.044 0.214 4935 Planarity : 0.004 0.046 5451 Dihedral : 4.378 26.617 4155 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.92 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.14), residues: 3798 helix: 1.20 (0.20), residues: 694 sheet: 0.29 (0.16), residues: 960 loop : -0.37 (0.14), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1014 TYR 0.024 0.002 TYR C 873 PHE 0.037 0.002 PHE C1062 TRP 0.036 0.002 TRP C 104 HIS 0.009 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00628 / 0.28 (31332) covalent geometry : angle 0.65317 / 0.34 (42606) SS BOND : bond 0.00459 / 0.35 ( 48) SS BOND : angle 1.00470 / 0.75 ( 96) hydrogen bonds : bond 0.04382 / 2.93 ( 1221) hydrogen bonds : angle 5.76819 / 3.97 ( 3342) link_BETA1-4 : bond 0.00229 / 0.13 ( 15) link_BETA1-4 : angle 1.18687 / 0.90 ( 45) link_NAG-ASN : bond 0.00599 / 0.35 ( 39) link_NAG-ASN : angle 2.22346 / 1.45 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.8684 (mp) cc_final: 0.8347 (mp) REVERT: A 224 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8860 (mp0) REVERT: A 299 THR cc_start: 0.9547 (m) cc_final: 0.9284 (p) REVERT: A 388 ASN cc_start: 0.8210 (p0) cc_final: 0.7405 (m-40) REVERT: A 869 MET cc_start: 0.9521 (mtp) cc_final: 0.9123 (mtp) REVERT: B 54 LEU cc_start: 0.9256 (tp) cc_final: 0.8956 (tp) REVERT: B 56 LEU cc_start: 0.8945 (tp) cc_final: 0.8564 (tp) REVERT: B 91 TYR cc_start: 0.7779 (t80) cc_final: 0.7490 (t80) REVERT: B 238 PHE cc_start: 0.9061 (p90) cc_final: 0.8750 (p90) REVERT: B 293 LEU cc_start: 0.8998 (tp) cc_final: 0.8765 (tt) REVERT: B 297 SER cc_start: 0.9153 (m) cc_final: 0.8840 (p) REVERT: B 697 MET cc_start: 0.8417 (ptm) cc_final: 0.7817 (ptp) REVERT: B 731 MET cc_start: 0.8832 (ptm) cc_final: 0.7883 (ppp) REVERT: B 979 ASP cc_start: 0.8554 (m-30) cc_final: 0.8349 (t0) REVERT: C 297 SER cc_start: 0.8822 (m) cc_final: 0.8320 (p) REVERT: C 414 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8652 (tp40) REVERT: C 740 MET cc_start: 0.8909 (ttp) cc_final: 0.8498 (tmm) REVERT: C 869 MET cc_start: 0.8451 (mtt) cc_final: 0.8091 (mtp) REVERT: C 955 ASN cc_start: 0.9103 (m-40) cc_final: 0.8446 (p0) REVERT: C 978 ASN cc_start: 0.9231 (m-40) cc_final: 0.8516 (t0) REVERT: C 1029 MET cc_start: 0.8862 (tpp) cc_final: 0.7747 (tpp) REVERT: D 110 MET cc_start: 0.3129 (mmp) cc_final: 0.2571 (mmp) REVERT: H 110 MET cc_start: 0.4872 (mmp) cc_final: 0.3991 (mmp) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1719 time to fit residues: 51.1423 Evaluate side-chains 132 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 18 optimal weight: 8.9990 chunk 162 optimal weight: 1.9990 chunk 292 optimal weight: 0.5980 chunk 194 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 336 optimal weight: 50.0000 chunk 131 optimal weight: 5.9990 chunk 95 optimal weight: 0.2980 chunk 48 optimal weight: 7.9990 chunk 179 optimal weight: 0.5980 chunk 337 optimal weight: 50.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN G 90 GLN L 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.137857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.090741 restraints weight = 111595.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.089916 restraints weight = 80121.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.089044 restraints weight = 61815.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.089525 restraints weight = 61350.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.089535 restraints weight = 50172.484| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 31434 Z= 0.130 Angle : 0.541 11.670 42864 Z= 0.279 Chirality : 0.043 0.249 4935 Planarity : 0.003 0.047 5451 Dihedral : 4.139 25.154 4155 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.11 % Favored : 96.87 % Rotamer: Outliers : 0.03 % Allowed : 1.13 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.14), residues: 3798 helix: 1.57 (0.20), residues: 694 sheet: 0.42 (0.16), residues: 947 loop : -0.32 (0.14), residues: 2157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1019 TYR 0.022 0.001 TYR C 365 PHE 0.030 0.001 PHE A 906 TRP 0.030 0.001 TRP C 104 HIS 0.017 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (31332) covalent geometry : angle 0.52928 / 0.28 (42606) SS BOND : bond 0.00439 / 0.30 ( 48) SS BOND : angle 1.16372 / 0.92 ( 96) hydrogen bonds : bond 0.03831 / 2.55 ( 1221) hydrogen bonds : angle 5.39981 / 3.73 ( 3342) link_BETA1-4 : bond 0.00290 / 0.16 ( 15) link_BETA1-4 : angle 0.98594 / 0.70 ( 45) link_NAG-ASN : bond 0.00369 / 0.20 ( 39) link_NAG-ASN : angle 1.89115 / 1.21 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.8642 (mp) cc_final: 0.8181 (mp) REVERT: A 224 GLU cc_start: 0.9306 (mt-10) cc_final: 0.8964 (mp0) REVERT: A 299 THR cc_start: 0.9499 (m) cc_final: 0.9177 (p) REVERT: A 388 ASN cc_start: 0.8939 (p0) cc_final: 0.8735 (p0) REVERT: A 740 MET cc_start: 0.8900 (ppp) cc_final: 0.8543 (ppp) REVERT: A 780 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8471 (mm-30) REVERT: A 869 MET cc_start: 0.9492 (mtp) cc_final: 0.9112 (mtp) REVERT: A 985 ASP cc_start: 0.9262 (t0) cc_final: 0.9014 (t0) REVERT: B 54 LEU cc_start: 0.9372 (tp) cc_final: 0.9107 (tp) REVERT: B 91 TYR cc_start: 0.7924 (t80) cc_final: 0.7509 (t80) REVERT: B 104 TRP cc_start: 0.8988 (m-90) cc_final: 0.8640 (m-90) REVERT: B 238 PHE cc_start: 0.9578 (p90) cc_final: 0.9043 (p90) REVERT: B 297 SER cc_start: 0.9174 (m) cc_final: 0.8846 (p) REVERT: B 613 GLN cc_start: 0.9260 (OUTLIER) cc_final: 0.9023 (pp30) REVERT: B 697 MET cc_start: 0.8124 (ptm) cc_final: 0.7820 (ptp) REVERT: B 979 ASP cc_start: 0.8704 (m-30) cc_final: 0.8479 (t0) REVERT: B 984 LEU cc_start: 0.8942 (tp) cc_final: 0.8734 (tp) REVERT: C 297 SER cc_start: 0.8842 (m) cc_final: 0.8274 (p) REVERT: C 414 GLN cc_start: 0.9258 (mm-40) cc_final: 0.8733 (tp-100) REVERT: C 552 LEU cc_start: 0.9312 (tt) cc_final: 0.9064 (pp) REVERT: C 740 MET cc_start: 0.8840 (ttp) cc_final: 0.8472 (tmm) REVERT: C 869 MET cc_start: 0.8340 (mtt) cc_final: 0.8026 (mtp) REVERT: C 955 ASN cc_start: 0.9070 (m-40) cc_final: 0.8421 (p0) REVERT: C 978 ASN cc_start: 0.9337 (m-40) cc_final: 0.8528 (t0) REVERT: D 110 MET cc_start: 0.4233 (mmp) cc_final: 0.3375 (mmp) REVERT: H 110 MET cc_start: 0.4417 (mmp) cc_final: 0.3777 (mmp) outliers start: 1 outliers final: 0 residues processed: 191 average time/residue: 0.1682 time to fit residues: 53.4711 Evaluate side-chains 150 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 59 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 0.0170 chunk 338 optimal weight: 0.6980 chunk 252 optimal weight: 2.9990 chunk 225 optimal weight: 6.9990 chunk 277 optimal weight: 0.7980 chunk 251 optimal weight: 2.9990 chunk 323 optimal weight: 20.0000 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 901 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.139466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.113658 restraints weight = 146541.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.108181 restraints weight = 179114.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.106191 restraints weight = 145012.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.105599 restraints weight = 133710.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.105645 restraints weight = 136413.402| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31434 Z= 0.117 Angle : 0.526 11.756 42864 Z= 0.272 Chirality : 0.043 0.250 4935 Planarity : 0.003 0.047 5451 Dihedral : 4.039 24.124 4155 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.34 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.14), residues: 3798 helix: 1.68 (0.20), residues: 688 sheet: 0.46 (0.16), residues: 1015 loop : -0.28 (0.14), residues: 2095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1019 TYR 0.017 0.001 TYR C 365 PHE 0.023 0.001 PHE A 464 TRP 0.035 0.001 TRP C 104 HIS 0.010 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (31332) covalent geometry : angle 0.51404 / 0.27 (42606) SS BOND : bond 0.00293 / 0.21 ( 48) SS BOND : angle 1.35535 / 0.92 ( 96) hydrogen bonds : bond 0.03658 / 2.45 ( 1221) hydrogen bonds : angle 5.26441 / 3.65 ( 3342) link_BETA1-4 : bond 0.00281 / 0.16 ( 15) link_BETA1-4 : angle 0.98968 / 0.70 ( 45) link_NAG-ASN : bond 0.00361 / 0.19 ( 39) link_NAG-ASN : angle 1.85504 / 1.19 ( 117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.8636 (mp) cc_final: 0.8164 (mp) REVERT: A 224 GLU cc_start: 0.9338 (mt-10) cc_final: 0.9001 (mp0) REVERT: A 299 THR cc_start: 0.9496 (m) cc_final: 0.9174 (p) REVERT: A 773 GLU cc_start: 0.9057 (tt0) cc_final: 0.8603 (tp30) REVERT: A 780 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8386 (mm-30) REVERT: A 869 MET cc_start: 0.9541 (mtp) cc_final: 0.9182 (mtp) REVERT: B 54 LEU cc_start: 0.9295 (tp) cc_final: 0.8979 (tp) REVERT: B 91 TYR cc_start: 0.7902 (t80) cc_final: 0.7511 (t80) REVERT: B 104 TRP cc_start: 0.8579 (m-90) cc_final: 0.8350 (m-90) REVERT: B 153 MET cc_start: 0.6510 (pmm) cc_final: 0.6247 (pmm) REVERT: B 238 PHE cc_start: 0.9338 (p90) cc_final: 0.8855 (p90) REVERT: B 297 SER cc_start: 0.9153 (m) cc_final: 0.8807 (p) REVERT: C 229 LEU cc_start: 0.8928 (tp) cc_final: 0.8645 (tp) REVERT: C 297 SER cc_start: 0.8854 (m) cc_final: 0.8294 (p) REVERT: C 414 GLN cc_start: 0.9259 (mm-40) cc_final: 0.8744 (tp-100) REVERT: C 740 MET cc_start: 0.8679 (ttp) cc_final: 0.8470 (tmm) REVERT: C 774 GLN cc_start: 0.9268 (mm-40) cc_final: 0.8586 (mm-40) REVERT: C 858 LEU cc_start: 0.8952 (mt) cc_final: 0.8637 (mp) REVERT: C 869 MET cc_start: 0.8359 (mtt) cc_final: 0.7956 (mtp) REVERT: C 955 ASN cc_start: 0.8789 (m-40) cc_final: 0.8404 (p0) REVERT: C 978 ASN cc_start: 0.9268 (m-40) cc_final: 0.8412 (t0) REVERT: D 110 MET cc_start: 0.3779 (mmp) cc_final: 0.2902 (mmp) REVERT: F 29 PHE cc_start: 0.8453 (t80) cc_final: 0.8192 (t80) REVERT: H 110 MET cc_start: 0.4931 (mmp) cc_final: 0.4351 (mmp) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.1683 time to fit residues: 53.5102 Evaluate side-chains 140 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 375 optimal weight: 0.9990 chunk 244 optimal weight: 9.9990 chunk 169 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 239 optimal weight: 5.9990 chunk 212 optimal weight: 40.0000 chunk 57 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1048 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 901 GLN ** C 901 GLN ** 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 = 0.4366 r_free = 0.4366 target = 0.138701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.112555 restraints weight = 146719.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.106973 restraints weight = 180643.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.105827 restraints weight = 148655.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.104402 restraints weight = 134525.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.104571 restraints weight = 138954.165| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 31434 Z= 0.143 Angle : 0.538 11.382 42864 Z= 0.277 Chirality : 0.043 0.241 4935 Planarity : 0.004 0.062 5451 Dihedral : 4.021 22.833 4155 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.40 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.14), residues: 3798 helix: 1.64 (0.20), residues: 688 sheet: 0.46 (0.16), residues: 1017 loop : -0.31 (0.14), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1019 TYR 0.021 0.001 TYR C 873 PHE 0.024 0.001 PHE C 906 TRP 0.054 0.001 TRP C 104 HIS 0.009 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (31332) covalent geometry : angle 0.52637 / 0.27 (42606) SS BOND : bond 0.00321 / 0.22 ( 48) SS BOND : angle 1.14031 / 0.77 ( 96) hydrogen bonds : bond 0.03790 / 2.52 ( 1221) hydrogen bonds : angle 5.22144 / 3.62 ( 3342) link_BETA1-4 : bond 0.00244 / 0.14 ( 15) link_BETA1-4 : angle 1.02198 / 0.74 ( 45) link_NAG-ASN : bond 0.00362 / 0.20 ( 39) link_NAG-ASN : angle 1.87901 / 1.21 ( 117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.8680 (mp) cc_final: 0.8180 (mp) REVERT: A 224 GLU cc_start: 0.9329 (mt-10) cc_final: 0.8995 (mp0) REVERT: A 299 THR cc_start: 0.9490 (m) cc_final: 0.9172 (p) REVERT: A 354 ASN cc_start: 0.9534 (t0) cc_final: 0.9260 (t0) REVERT: A 571 ASP cc_start: 0.8912 (m-30) cc_final: 0.8661 (m-30) REVERT: A 773 GLU cc_start: 0.8808 (tt0) cc_final: 0.8397 (tp30) REVERT: A 780 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8293 (mm-30) REVERT: A 869 MET cc_start: 0.9558 (mtp) cc_final: 0.9164 (mtp) REVERT: B 54 LEU cc_start: 0.9316 (tp) cc_final: 0.9034 (tp) REVERT: B 91 TYR cc_start: 0.7968 (t80) cc_final: 0.7505 (t80) REVERT: B 104 TRP cc_start: 0.8668 (m-90) cc_final: 0.8416 (m-90) REVERT: B 153 MET cc_start: 0.6236 (pmm) cc_final: 0.5980 (pmm) REVERT: B 175 PHE cc_start: 0.9594 (m-10) cc_final: 0.9385 (m-80) REVERT: B 238 PHE cc_start: 0.9390 (p90) cc_final: 0.8898 (p90) REVERT: B 297 SER cc_start: 0.9203 (m) cc_final: 0.8878 (p) REVERT: B 731 MET cc_start: 0.8809 (ptm) cc_final: 0.7995 (ppp) REVERT: B 979 ASP cc_start: 0.8498 (m-30) cc_final: 0.8288 (t0) REVERT: C 297 SER cc_start: 0.8876 (m) cc_final: 0.8307 (p) REVERT: C 414 GLN cc_start: 0.9282 (mm-40) cc_final: 0.8696 (tp-100) REVERT: C 858 LEU cc_start: 0.8949 (mt) cc_final: 0.8629 (mp) REVERT: C 869 MET cc_start: 0.8314 (mtt) cc_final: 0.7946 (mtp) REVERT: C 955 ASN cc_start: 0.8799 (m-40) cc_final: 0.8421 (p0) REVERT: C 978 ASN cc_start: 0.9295 (m-40) cc_final: 0.8565 (t0) REVERT: C 1029 MET cc_start: 0.8848 (tpp) cc_final: 0.7922 (tpp) REVERT: D 110 MET cc_start: 0.3863 (mmp) cc_final: 0.2912 (mmp) REVERT: F 29 PHE cc_start: 0.8446 (t80) cc_final: 0.8210 (t80) REVERT: H 110 MET cc_start: 0.4918 (mmp) cc_final: 0.4334 (mmp) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.1668 time to fit residues: 50.8752 Evaluate side-chains 138 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 141 optimal weight: 8.9990 chunk 96 optimal weight: 0.4980 chunk 95 optimal weight: 0.7980 chunk 363 optimal weight: 40.0000 chunk 298 optimal weight: 2.9990 chunk 314 optimal weight: 2.9990 chunk 288 optimal weight: 3.9990 chunk 266 optimal weight: 8.9990 chunk 216 optimal weight: 0.9980 chunk 320 optimal weight: 40.0000 chunk 79 optimal weight: 0.5980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN B 613 GLN B 703 ASN B 901 GLN B1005 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.138565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.113154 restraints weight = 145523.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.108898 restraints weight = 179923.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.106353 restraints weight = 167217.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.106750 restraints weight = 152471.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.107027 restraints weight = 124838.237| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31434 Z= 0.143 Angle : 0.532 11.546 42864 Z= 0.274 Chirality : 0.043 0.240 4935 Planarity : 0.004 0.056 5451 Dihedral : 3.996 21.241 4155 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.42 % Favored : 96.55 % Rotamer: Outliers : 0.03 % Allowed : 0.24 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.14), residues: 3798 helix: 1.51 (0.20), residues: 698 sheet: 0.45 (0.16), residues: 1041 loop : -0.32 (0.14), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1039 TYR 0.018 0.001 TYR C 873 PHE 0.028 0.001 PHE C 275 TRP 0.043 0.001 TRP C 104 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (31332) covalent geometry : angle 0.52116 / 0.27 (42606) SS BOND : bond 0.00302 / 0.21 ( 48) SS BOND : angle 1.09608 / 0.74 ( 96) hydrogen bonds : bond 0.03718 / 2.48 ( 1221) hydrogen bonds : angle 5.17569 / 3.59 ( 3342) link_BETA1-4 : bond 0.00250 / 0.14 ( 15) link_BETA1-4 : angle 1.03255 / 0.75 ( 45) link_NAG-ASN : bond 0.00378 / 0.20 ( 39) link_NAG-ASN : angle 1.84173 / 1.18 ( 117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 VAL cc_start: 0.8853 (m) cc_final: 0.8320 (t) REVERT: A 223 LEU cc_start: 0.8527 (mp) cc_final: 0.8212 (mp) REVERT: A 224 GLU cc_start: 0.9198 (mt-10) cc_final: 0.8818 (mp0) REVERT: A 299 THR cc_start: 0.9492 (m) cc_final: 0.9179 (p) REVERT: A 354 ASN cc_start: 0.9174 (t0) cc_final: 0.8962 (t0) REVERT: A 773 GLU cc_start: 0.9140 (tt0) cc_final: 0.8698 (tp30) REVERT: A 869 MET cc_start: 0.9582 (mtp) cc_final: 0.9159 (mtp) REVERT: A 979 ASP cc_start: 0.9085 (m-30) cc_final: 0.8754 (t0) REVERT: B 54 LEU cc_start: 0.9236 (tp) cc_final: 0.8931 (tp) REVERT: B 91 TYR cc_start: 0.7755 (t80) cc_final: 0.7271 (t80) REVERT: B 175 PHE cc_start: 0.9257 (m-10) cc_final: 0.9056 (m-80) REVERT: B 177 MET cc_start: 0.7151 (mmp) cc_final: 0.6590 (ppp) REVERT: B 238 PHE cc_start: 0.9031 (p90) cc_final: 0.8674 (p90) REVERT: B 297 SER cc_start: 0.9228 (m) cc_final: 0.8909 (p) REVERT: B 697 MET cc_start: 0.8446 (ptm) cc_final: 0.7395 (ttm) REVERT: B 979 ASP cc_start: 0.8468 (m-30) cc_final: 0.8267 (t0) REVERT: C 297 SER cc_start: 0.8847 (m) cc_final: 0.8298 (p) REVERT: C 414 GLN cc_start: 0.9177 (mm-40) cc_final: 0.8624 (tp-100) REVERT: C 858 LEU cc_start: 0.9010 (mt) cc_final: 0.8731 (mp) REVERT: C 869 MET cc_start: 0.8371 (mtt) cc_final: 0.7884 (mtp) REVERT: C 955 ASN cc_start: 0.8795 (m-40) cc_final: 0.8422 (p0) REVERT: C 1029 MET cc_start: 0.8828 (tpp) cc_final: 0.7886 (tpp) REVERT: D 110 MET cc_start: 0.3503 (mmp) cc_final: 0.2688 (mmp) REVERT: F 29 PHE cc_start: 0.8245 (t80) cc_final: 0.7854 (t80) REVERT: H 110 MET cc_start: 0.4775 (mmp) cc_final: 0.4305 (mmp) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.1823 time to fit residues: 56.8757 Evaluate side-chains 137 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 304 optimal weight: 0.6980 chunk 237 optimal weight: 5.9990 chunk 350 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 221 optimal weight: 8.9990 chunk 174 optimal weight: 0.7980 chunk 348 optimal weight: 20.0000 chunk 345 optimal weight: 50.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 613 GLN B 703 ASN B 901 GLN C 901 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.139231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.112712 restraints weight = 146806.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.108033 restraints weight = 178541.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.105654 restraints weight = 133101.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.104628 restraints weight = 133070.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.105057 restraints weight = 133960.083| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31434 Z= 0.120 Angle : 0.519 11.595 42864 Z= 0.268 Chirality : 0.043 0.259 4935 Planarity : 0.004 0.056 5451 Dihedral : 3.939 20.538 4155 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.42 % Favored : 96.55 % Rotamer: Outliers : 0.03 % Allowed : 0.21 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.14), residues: 3798 helix: 1.57 (0.20), residues: 698 sheet: 0.54 (0.16), residues: 1028 loop : -0.32 (0.14), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1107 TYR 0.040 0.001 TYR A 904 PHE 0.024 0.001 PHE C 906 TRP 0.040 0.001 TRP C 104 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (31332) covalent geometry : angle 0.50884 / 0.27 (42606) SS BOND : bond 0.00271 / 0.19 ( 48) SS BOND : angle 1.03525 / 0.71 ( 96) hydrogen bonds : bond 0.03642 / 2.41 ( 1221) hydrogen bonds : angle 5.09189 / 3.53 ( 3342) link_BETA1-4 : bond 0.00253 / 0.15 ( 15) link_BETA1-4 : angle 1.01043 / 0.72 ( 45) link_NAG-ASN : bond 0.00350 / 0.18 ( 39) link_NAG-ASN : angle 1.80845 / 1.16 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4578.45 seconds wall clock time: 80 minutes 18.98 seconds (4818.98 seconds total)