Starting phenix.real_space_refine on Fri Mar 6 02:21:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z9q_14575/03_2026/7z9q_14575.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z9q_14575/03_2026/7z9q_14575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z9q_14575/03_2026/7z9q_14575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z9q_14575/03_2026/7z9q_14575.map" model { file = "/net/cci-nas-00/data/ceres_data/7z9q_14575/03_2026/7z9q_14575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z9q_14575/03_2026/7z9q_14575.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 117 5.16 5 C 17225 2.51 5 N 4462 2.21 5 O 5261 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27065 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 7646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 7646 Classifications: {'peptide': 987} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 49, 'TRANS': 937} Chain breaks: 9 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 5, 'ASN:plan1': 4, 'GLU:plan': 4, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 7677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7677 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 49, 'TRANS': 942} Chain breaks: 8 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 55 Chain: "C" Number of atoms: 7659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7659 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 49, 'TRANS': 940} Chain breaks: 7 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 3, 'GLU:plan': 6, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 48 Chain: "D" Number of atoms: 1053 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 134, 1049 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 131} Conformer: "B" Number of residues, atoms: 134, 1049 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 131} bond proxies already assigned to first conformer: 1073 Chain: "E" Number of atoms: 1053 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 134, 1049 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 131} Conformer: "B" Number of residues, atoms: 134, 1049 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 131} bond proxies already assigned to first conformer: 1073 Chain: "F" Number of atoms: 1053 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 134, 1049 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 131} Conformer: "B" Number of residues, atoms: 134, 1049 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 131} bond proxies already assigned to first conformer: 1073 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.99, per 1000 atoms: 0.26 Number of scatterers: 27065 At special positions: 0 Unit cell: (131.44, 137.8, 227.9, 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 117 16.00 O 5261 8.00 N 4462 7.00 C 17225 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.05 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 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=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.05 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.07 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=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 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=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.06 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.00 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.00 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.00 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG 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 Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 603 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A 165 " " NAG A1308 " - " ASN A 343 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B 343 " " NAG C1401 " - " ASN C 343 " " NAG C1402 " - " ASN C 61 " " NAG C1403 " - " ASN C 234 " " NAG C1404 " - " ASN C 331 " " NAG C1405 " - " ASN C 603 " " NAG C1406 " - " ASN C 616 " " NAG C1407 " - " ASN C 657 " " NAG C1408 " - " ASN C 165 " " NAG G 1 " - " ASN A 122 " " NAG H 1 " - " ASN A 234 " " NAG I 1 " - " ASN A 282 " " NAG J 1 " - " ASN A 331 " " NAG K 1 " - " ASN A 717 " " NAG L 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B1098 " " NAG R 1 " - " ASN B1134 " " NAG S 1 " - " ASN C 122 " " NAG T 1 " - " ASN C 282 " " NAG U 1 " - " ASN C 709 " " NAG V 1 " - " ASN C 717 " " NAG W 1 " - " ASN C 801 " " NAG X 1 " - " ASN C1074 " " NAG Y 1 " - " ASN C1098 " " NAG Z 1 " - " ASN C1134 " Time building additional restraints: 2.46 Conformation dependent library (CDL) restraints added in 1.5 seconds 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6290 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 54 sheets defined 24.6% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.964A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.261A 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 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 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.646A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.098A 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: 3.674A 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 984 removed outlier: 3.668A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.407A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.093A 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 337 through 343 removed outlier: 4.028A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 384 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.262A 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 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: 3.675A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.644A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.112A 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: 3.695A 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 984 removed outlier: 3.637A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.411A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.091A 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 337 through 343 removed outlier: 4.022A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 384 through 389 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.280A 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 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 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.642A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.106A 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: 3.664A 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 984 removed outlier: 3.637A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.332A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.086A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 111 Processing helix chain 'E' and resid 105 through 111 Processing helix chain 'F' and resid 105 through 111 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.647A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.564A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.571A pdb=" N ASN A 125 " --> pdb=" O ASN A 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.555A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 327 removed outlier: 6.660A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.497A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (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: 6.561A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.863A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.969A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.195A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.705A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.376A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.654A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.571A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.588A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.130A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.482A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 653 through 655 removed outlier: 6.556A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.860A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.978A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.195A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 788 through 790 removed outlier: 5.788A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.378A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.652A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.876A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.583A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.133A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.493A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 653 through 655 removed outlier: 6.561A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.864A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.968A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.188A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.379A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AF2, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.198A pdb=" N GLY D 10 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N SER D 126 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N MET D 12 " --> pdb=" O SER D 126 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA D 33 " --> pdb=" O PHE D 99 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ARG D 38 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N PHE D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.198A pdb=" N GLY D 10 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N SER D 126 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N MET D 12 " --> pdb=" O SER D 126 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.198A pdb=" N GLY E 10 " --> pdb=" O THR E 124 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N SER E 126 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N MET E 12 " --> pdb=" O SER E 126 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA E 33 " --> pdb=" O PHE E 99 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ARG E 38 " --> pdb=" O PHE E 47 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N PHE E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.198A pdb=" N GLY E 10 " --> pdb=" O THR E 124 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N SER E 126 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N MET E 12 " --> pdb=" O SER E 126 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AF8, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.198A pdb=" N GLY F 10 " --> pdb=" O THR F 124 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N SER F 126 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N MET F 12 " --> pdb=" O SER F 126 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA F 33 " --> pdb=" O PHE F 99 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ARG F 38 " --> pdb=" O PHE F 47 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N PHE F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.198A pdb=" N GLY F 10 " --> pdb=" O THR F 124 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N SER F 126 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N MET F 12 " --> pdb=" O SER F 126 " (cutoff:3.500A) 1172 hydrogen bonds defined for protein. 3129 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.75 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: 1.19 - 1.32: 4489 1.32 - 1.44: 7761 1.44 - 1.57: 15271 1.57 - 1.69: 0 1.69 - 1.82: 150 Bond restraints: 27671 Sorted by residual: bond pdb=" C TRP F 117 " pdb=" O TRP F 117 " ideal model delta sigma weight residual 1.234 1.290 -0.056 1.22e-02 6.72e+03 2.13e+01 bond pdb=" C TRP D 117 " pdb=" O TRP D 117 " ideal model delta sigma weight residual 1.234 1.290 -0.056 1.22e-02 6.72e+03 2.11e+01 bond pdb=" C TRP E 117 " pdb=" O TRP E 117 " ideal model delta sigma weight residual 1.234 1.290 -0.056 1.22e-02 6.72e+03 2.09e+01 bond pdb=" C VAL D 125 " pdb=" O VAL D 125 " ideal model delta sigma weight residual 1.237 1.192 0.046 1.10e-02 8.26e+03 1.71e+01 bond pdb=" C VAL F 125 " pdb=" O VAL F 125 " ideal model delta sigma weight residual 1.237 1.192 0.045 1.10e-02 8.26e+03 1.70e+01 ... (remaining 27666 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 31220 2.03 - 4.06: 5781 4.06 - 6.08: 576 6.08 - 8.11: 59 8.11 - 10.14: 10 Bond angle restraints: 37646 Sorted by residual: angle pdb=" C LYS A 113 " pdb=" CA LYS A 113 " pdb=" CB LYS A 113 " ideal model delta sigma weight residual 109.83 116.61 -6.78 9.90e-01 1.02e+00 4.69e+01 angle pdb=" C PRO C 600 " pdb=" CA PRO C 600 " pdb=" CB PRO C 600 " ideal model delta sigma weight residual 111.44 102.60 8.84 1.51e+00 4.39e-01 3.42e+01 angle pdb=" CA ASP F 115 " pdb=" CB ASP F 115 " pdb=" CG ASP F 115 " ideal model delta sigma weight residual 112.60 118.40 -5.80 1.00e+00 1.00e+00 3.37e+01 angle pdb=" CA ASP D 115 " pdb=" CB ASP D 115 " pdb=" CG ASP D 115 " ideal model delta sigma weight residual 112.60 118.40 -5.80 1.00e+00 1.00e+00 3.36e+01 angle pdb=" CA ASP E 115 " pdb=" CB ASP E 115 " pdb=" CG ASP E 115 " ideal model delta sigma weight residual 112.60 118.38 -5.78 1.00e+00 1.00e+00 3.34e+01 ... (remaining 37641 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 15900 17.53 - 35.05: 1059 35.05 - 52.58: 218 52.58 - 70.10: 41 70.10 - 87.63: 26 Dihedral angle restraints: 17244 sinusoidal: 7451 harmonic: 9793 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 -179.37 -87.63 1 1.00e+01 1.00e-02 9.20e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 -179.68 -87.32 1 1.00e+01 1.00e-02 9.15e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 -179.76 -87.24 1 1.00e+01 1.00e-02 9.14e+01 ... (remaining 17241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 3869 0.126 - 0.252: 560 0.252 - 0.378: 23 0.378 - 0.504: 2 0.504 - 0.630: 1 Chirality restraints: 4455 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 1.93e+01 chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B 603 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 9.92e+00 chirality pdb=" C1 NAG Y 2 " pdb=" O4 NAG Y 1 " pdb=" C2 NAG Y 2 " pdb=" O5 NAG Y 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 9.92e+00 ... (remaining 4452 not shown) Planarity restraints: 4810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 80 " 0.044 2.00e-02 2.50e+03 4.00e-02 3.20e+01 pdb=" CG TYR D 80 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR D 80 " -0.075 2.00e-02 2.50e+03 pdb=" CD2 TYR D 80 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR D 80 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR D 80 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR D 80 " 0.053 2.00e-02 2.50e+03 pdb=" OH TYR D 80 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 80 " 0.045 2.00e-02 2.50e+03 3.99e-02 3.18e+01 pdb=" CG TYR F 80 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR F 80 " -0.075 2.00e-02 2.50e+03 pdb=" CD2 TYR F 80 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR F 80 " 0.039 2.00e-02 2.50e+03 pdb=" CE2 TYR F 80 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR F 80 " 0.052 2.00e-02 2.50e+03 pdb=" OH TYR F 80 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 80 " -0.044 2.00e-02 2.50e+03 3.99e-02 3.18e+01 pdb=" CG TYR E 80 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR E 80 " 0.075 2.00e-02 2.50e+03 pdb=" CD2 TYR E 80 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR E 80 " -0.039 2.00e-02 2.50e+03 pdb=" CE2 TYR E 80 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR E 80 " -0.052 2.00e-02 2.50e+03 pdb=" OH TYR E 80 " 0.014 2.00e-02 2.50e+03 ... (remaining 4807 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 80 2.56 - 3.14: 21144 3.14 - 3.73: 40222 3.73 - 4.31: 60934 4.31 - 4.90: 97995 Nonbonded interactions: 220375 Sorted by model distance: nonbonded pdb=" O ASN A 81 " pdb=" NE2 GLN A 239 " model vdw 1.974 3.120 nonbonded pdb=" NH1 ARG C 328 " pdb=" OD2 ASP C 578 " model vdw 2.204 3.120 nonbonded pdb=" OH TYR B 200 " pdb=" OE1 GLU C 516 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR B 200 " pdb=" OH TYR C 396 " model vdw 2.215 3.040 nonbonded pdb=" NE2 GLN C 804 " pdb=" OE1 GLN C 935 " model vdw 2.279 3.120 ... (remaining 220370 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 66 or resid 82 through 96 or (resi \ d 97 and (name N or name CA or name C or name O or name CB )) or resid 98 or (re \ sid 99 and (name N or name CA or name C or name O or name CB )) or resid 100 thr \ ough 110 or (resid 111 through 113 and (name N or name CA or name C or name O or \ name CB )) or resid 116 through 128 or (resid 129 and (name N or name CA or nam \ e C or name O or name CB )) or resid 130 through 134 or (resid 135 through 138 a \ nd (name N or name CA or name C or name O or name CB )) or resid 139 through 140 \ or resid 166 through 168 or (resid 169 and (name N or name CA or name C or name \ O or name CB )) or resid 170 through 172 or resid 187 or (resid 188 and (name N \ or name CA or name C or name O or name CB )) or resid 189 through 210 or (resid \ 211 through 215 and (name N or name CA or name C or name O or name CB )) or res \ id 216 through 241 or (resid 242 through 263 and (name N or name CA or name C or \ name O or name CB )) or resid 265 through 280 or (resid 281 and (name N or name \ CA or name C or name O or name CB )) or resid 282 through 567 or (resid 568 and \ (name N or name CA or name C or name O or name CB )) or resid 569 through 570 o \ r (resid 571 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 72 through 581 or (resid 582 through 583 and (name N or name CA or name C or nam \ e O or name CB )) or resid 584 through 585 or (resid 586 and (name N or name CA \ or name C or name O or name CB )) or resid 587 through 660 or (resid 661 and (na \ me N or name CA or name C or name O or name CB )) or resid 662 through 676 or re \ sid 690 through 747 or (resid 748 and (name N or name CA or name C or name O or \ name CB )) or resid 749 through 810 or (resid 811 and (name N or name CA or name \ C or name O or name CB )) or resid 812 through 827 or resid 856 through 939 or \ (resid 940 and (name N or name CA or name C or name O or name CB )) or resid 941 \ through 984 or (resid 985 and (name N or name CA or name C or name O or name CB \ )) or resid 986 through 1143 or (resid 1144 through 1146 and (name N or name CA \ or name C or name O or name CB )) or resid 1147 through 1308)) selection = (chain 'B' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 66 or resid 82 throug \ h 95 or (resid 96 through 97 and (name N or name CA or name C or name O or name \ CB )) or resid 98 through 111 or (resid 112 through 113 and (name N or name CA o \ r name C or name O or name CB )) or resid 116 through 124 or (resid 125 and (nam \ e N or name CA or name C or name O or name CB )) or resid 126 through 131 or (re \ sid 132 and (name N or name CA or name C or name O or name CB )) or resid 133 or \ (resid 134 through 138 and (name N or name CA or name C or name O or name CB )) \ or resid 139 through 140 or resid 166 through 168 or (resid 169 and (name N or \ name CA or name C or name O or name CB )) or resid 170 through 171 or (resid 172 \ and (name N or name CA or name C or name O or name CB )) or resid 187 through 1 \ 96 or resid 200 through 210 or (resid 211 and (name N or name CA or name C or na \ me O or name CB )) or (resid 215 and (name N or name CA or name C or name O or n \ ame CB )) or resid 216 through 263 or resid 265 through 528 or (resid 529 and (n \ ame N or name CA or name C or name O or name CB )) or resid 530 through 660 or ( \ resid 661 and (name N or name CA or name C or name O or name CB )) or resid 662 \ through 747 or (resid 748 and (name N or name CA or name C or name O or name CB \ )) or resid 749 through 810 or (resid 811 and (name N or name CA or name C or na \ me O or name CB )) or resid 812 through 827 or resid 856 through 939 or (resid 9 \ 40 and (name N or name CA or name C or name O or name CB )) or resid 941 through \ 984 or (resid 985 and (name N or name CA or name C or name O or name CB )) or r \ esid 986 through 1141 or (resid 1142 and (name N or name CA or name C or name O \ or name CB )) or resid 1143 through 1144 or (resid 1145 through 1146 and (name N \ or name CA or name C or name O or name CB )) or resid 1147 through 1308)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 110 or (resid 111 through 113 and (name N or name CA or name C o \ r name O or name CB )) or resid 116 through 124 or (resid 125 and (name N or nam \ e CA or name C or name O or name CB )) or resid 126 through 128 or (resid 129 an \ d (name N or name CA or name C or name O or name CB )) or resid 130 through 133 \ or (resid 134 through 138 and (name N or name CA or name C or name O or name CB \ )) or resid 139 through 140 or resid 166 through 187 or (resid 188 and (name N o \ r name CA or name C or name O or name CB )) or resid 189 through 196 or resid 20 \ 0 through 211 or (resid 215 and (name N or name CA or name C or name O or name C \ B )) or resid 216 through 528 or (resid 529 and (name N or name CA or name C or \ name O or name CB )) or resid 530 through 567 or (resid 568 and (name N or name \ CA or name C or name O or name CB )) or resid 569 through 570 or (resid 571 and \ (name N or name CA or name C or name O or name CB )) or resid 572 through 581 or \ (resid 582 through 583 and (name N or name CA or name C or name O or name CB )) \ or resid 584 through 585 or (resid 586 and (name N or name CA or name C or name \ O or name CB )) or resid 587 through 1141 or (resid 1142 and (name N or name CA \ or name C or name O or name CB )) or resid 1143 or (resid 1144 through 1146 and \ (name N or name CA or name C or name O or name CB )) or resid 1147 through 1408 \ )) } ncs_group { reference = (chain 'D' and (resid 1 through 4 or resid 6 through 134)) selection = (chain 'E' and (resid 1 through 4 or resid 6 through 134)) selection = (chain 'F' and (resid 1 through 4 or resid 6 through 134)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' 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' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 30.880 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4577 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 : 0.010 0.056 27779 Z= 0.688 Angle : 1.560 12.064 37928 Z= 1.048 Chirality : 0.087 0.630 4455 Planarity : 0.007 0.053 4764 Dihedral : 12.573 85.484 10828 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.44 % Favored : 96.25 % Rotamer: Outliers : 0.88 % Allowed : 5.15 % Favored : 93.98 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.13), residues: 3314 helix: -0.61 (0.18), residues: 671 sheet: 0.11 (0.17), residues: 799 loop : -1.11 (0.13), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.003 ARG B 328 TYR 0.075 0.008 TYR E 80 PHE 0.036 0.006 PHE B 565 TRP 0.054 0.007 TRP F 112 HIS 0.062 0.003 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.01024 (27671) covalent geometry : angle 1.54249 (37646) SS BOND : bond 0.01450 ( 42) SS BOND : angle 3.18534 ( 84) hydrogen bonds : bond 0.13091 ( 1160) hydrogen bonds : angle 7.25311 ( 3129) link_BETA1-4 : bond 0.00524 ( 20) link_BETA1-4 : angle 3.23685 ( 60) link_NAG-ASN : bond 0.00926 ( 46) link_NAG-ASN : angle 2.94367 ( 138) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 625 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.5015 (t70) cc_final: 0.4799 (t-170) REVERT: A 64 TRP cc_start: 0.5818 (t60) cc_final: 0.5548 (t60) REVERT: A 218 GLN cc_start: 0.7287 (tt0) cc_final: 0.6901 (tm-30) REVERT: A 307 THR cc_start: 0.7977 (m) cc_final: 0.7653 (t) REVERT: A 316 SER cc_start: 0.4937 (t) cc_final: 0.4424 (p) REVERT: A 369 TYR cc_start: 0.6862 (p90) cc_final: 0.6219 (p90) REVERT: A 554 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7983 (mp0) REVERT: A 568 ASP cc_start: 0.6020 (t0) cc_final: 0.5685 (m-30) REVERT: A 591 SER cc_start: 0.6413 (t) cc_final: 0.6170 (p) REVERT: A 666 ILE cc_start: 0.7531 (mt) cc_final: 0.7188 (mp) REVERT: A 693 ILE cc_start: 0.6297 (pt) cc_final: 0.5857 (pt) REVERT: A 702 GLU cc_start: 0.7713 (pt0) cc_final: 0.7306 (mp0) REVERT: A 758 SER cc_start: 0.5122 (m) cc_final: 0.4845 (t) REVERT: A 804 GLN cc_start: 0.6830 (mm-40) cc_final: 0.6506 (mt0) REVERT: A 968 SER cc_start: 0.7296 (m) cc_final: 0.6792 (t) REVERT: B 54 LEU cc_start: 0.7836 (mt) cc_final: 0.7610 (mt) REVERT: B 290 ASP cc_start: 0.5856 (t0) cc_final: 0.5651 (t0) REVERT: B 320 VAL cc_start: 0.5679 (t) cc_final: 0.4743 (m) REVERT: B 358 ILE cc_start: 0.6547 (mm) cc_final: 0.6239 (mp) REVERT: B 359 SER cc_start: 0.6548 (p) cc_final: 0.6291 (t) REVERT: B 389 ASP cc_start: 0.8250 (m-30) cc_final: 0.7515 (t70) REVERT: B 400 PHE cc_start: 0.5291 (p90) cc_final: 0.4962 (p90) REVERT: B 409 GLN cc_start: 0.4909 (mt0) cc_final: 0.4680 (mt0) REVERT: B 465 GLU cc_start: 0.4787 (tt0) cc_final: 0.4399 (tt0) REVERT: B 468 ILE cc_start: 0.5543 (pp) cc_final: 0.5153 (mp) REVERT: B 492 LEU cc_start: 0.3638 (mt) cc_final: 0.3327 (mt) REVERT: B 497 PHE cc_start: 0.3858 (m-80) cc_final: 0.3638 (m-80) REVERT: B 508 TYR cc_start: 0.6093 (m-80) cc_final: 0.5485 (m-80) REVERT: B 534 VAL cc_start: 0.6403 (t) cc_final: 0.6102 (p) REVERT: B 574 ASP cc_start: 0.6189 (OUTLIER) cc_final: 0.5980 (p0) REVERT: B 646 ARG cc_start: 0.6710 (tpp80) cc_final: 0.5906 (tpt90) REVERT: B 671 CYS cc_start: 0.6008 (m) cc_final: 0.5640 (m) REVERT: B 912 THR cc_start: 0.7500 (OUTLIER) cc_final: 0.7171 (p) REVERT: B 973 ILE cc_start: 0.6821 (pt) cc_final: 0.6506 (pt) REVERT: B 977 LEU cc_start: 0.5435 (tp) cc_final: 0.5233 (tp) REVERT: B 990 GLU cc_start: 0.5034 (mt-10) cc_final: 0.4829 (tt0) REVERT: C 48 LEU cc_start: 0.6680 (mt) cc_final: 0.6082 (mt) REVERT: C 65 PHE cc_start: 0.5665 (m-80) cc_final: 0.5125 (m-80) REVERT: C 189 LEU cc_start: 0.5832 (tp) cc_final: 0.5132 (tp) REVERT: C 191 GLU cc_start: 0.5942 (mt-10) cc_final: 0.5610 (mp0) REVERT: C 306 PHE cc_start: 0.3737 (m-80) cc_final: 0.2833 (m-80) REVERT: C 314 GLN cc_start: 0.7042 (tt0) cc_final: 0.6835 (tm-30) REVERT: C 317 ASN cc_start: 0.6428 (m-40) cc_final: 0.6006 (t0) REVERT: C 319 ARG cc_start: 0.5623 (mtp85) cc_final: 0.5366 (mtp85) REVERT: C 385 THR cc_start: 0.6944 (p) cc_final: 0.6705 (p) REVERT: C 605 SER cc_start: 0.6048 (t) cc_final: 0.5565 (p) REVERT: C 607 GLN cc_start: 0.6725 (tt0) cc_final: 0.6206 (pt0) REVERT: C 740 MET cc_start: 0.6916 (ttt) cc_final: 0.6515 (ttm) REVERT: C 751 ASN cc_start: 0.7638 (m-40) cc_final: 0.7426 (m110) REVERT: C 791 THR cc_start: 0.7730 (OUTLIER) cc_final: 0.7522 (t) REVERT: C 973 ILE cc_start: 0.7384 (tt) cc_final: 0.6968 (pt) REVERT: C 1017 GLU cc_start: 0.6721 (tt0) cc_final: 0.6472 (tm-30) REVERT: C 1045 LYS cc_start: 0.7222 (tttt) cc_final: 0.6838 (tttt) REVERT: C 1125 ASN cc_start: 0.6483 (p0) cc_final: 0.6263 (p0) REVERT: C 1144 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6572 (mp0) REVERT: F 51 ILE cc_start: 0.3968 (tt) cc_final: 0.1185 (tt) REVERT: F 71 SER cc_start: 0.5285 (p) cc_final: 0.5052 (t) REVERT: F 78 THR cc_start: 0.4483 (m) cc_final: 0.4113 (m) REVERT: F 83 MET cc_start: 0.2778 (mtp) cc_final: 0.1958 (ptp) outliers start: 25 outliers final: 3 residues processed: 645 average time/residue: 0.1869 time to fit residues: 189.8790 Evaluate side-chains 311 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 305 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain E residue 2 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 4.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 784 GLN A 804 GLN A 935 GLN A 955 ASN A 957 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN B 607 GLN B 978 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 506 GLN C 607 GLN C 784 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN C1023 ASN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.177432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.125720 restraints weight = 53613.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.125573 restraints weight = 29860.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.125763 restraints weight = 20482.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.126214 restraints weight = 20798.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.126335 restraints weight = 18042.941| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3534 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27779 Z= 0.153 Angle : 0.666 11.433 37928 Z= 0.338 Chirality : 0.046 0.268 4455 Planarity : 0.004 0.030 4764 Dihedral : 6.227 62.507 5018 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.10 % Allowed : 10.40 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.14), residues: 3314 helix: 0.98 (0.20), residues: 685 sheet: 0.31 (0.17), residues: 806 loop : -0.52 (0.14), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 319 TYR 0.028 0.002 TYR D 116 PHE 0.026 0.002 PHE B 541 TRP 0.020 0.001 TRP B 436 HIS 0.006 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00336 (27671) covalent geometry : angle 0.64521 (37646) SS BOND : bond 0.00331 ( 42) SS BOND : angle 1.52204 ( 84) hydrogen bonds : bond 0.04761 ( 1160) hydrogen bonds : angle 5.77870 ( 3129) link_BETA1-4 : bond 0.00398 ( 20) link_BETA1-4 : angle 1.63994 ( 60) link_NAG-ASN : bond 0.00283 ( 46) link_NAG-ASN : angle 2.38755 ( 138) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 362 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7907 (pttt) cc_final: 0.7336 (ptpp) REVERT: A 551 VAL cc_start: 0.9149 (OUTLIER) cc_final: 0.8935 (m) REVERT: A 567 ARG cc_start: 0.6971 (OUTLIER) cc_final: 0.6532 (mmt180) REVERT: A 568 ASP cc_start: 0.6703 (t0) cc_final: 0.6267 (m-30) REVERT: A 574 ASP cc_start: 0.7180 (p0) cc_final: 0.6569 (p0) REVERT: A 1107 ARG cc_start: 0.7711 (mtm180) cc_final: 0.7323 (mtm-85) REVERT: B 54 LEU cc_start: 0.8402 (mt) cc_final: 0.8042 (mt) REVERT: B 241 LEU cc_start: 0.7798 (mt) cc_final: 0.7525 (pp) REVERT: B 389 ASP cc_start: 0.7706 (m-30) cc_final: 0.7386 (t70) REVERT: B 409 GLN cc_start: 0.6008 (mt0) cc_final: 0.5284 (mt0) REVERT: B 535 LYS cc_start: 0.7942 (ttpt) cc_final: 0.6975 (mtmt) REVERT: B 977 LEU cc_start: 0.8868 (tp) cc_final: 0.8648 (tp) REVERT: C 61 ASN cc_start: 0.5236 (m-40) cc_final: 0.4758 (m110) REVERT: C 165 ASN cc_start: 0.1952 (OUTLIER) cc_final: 0.1637 (p0) REVERT: C 189 LEU cc_start: 0.6720 (tp) cc_final: 0.6343 (tp) REVERT: C 278 LYS cc_start: 0.8419 (tttt) cc_final: 0.8072 (tttp) REVERT: C 540 ASN cc_start: 0.8031 (OUTLIER) cc_final: 0.7640 (t0) REVERT: C 740 MET cc_start: 0.7846 (ttt) cc_final: 0.7512 (ttm) REVERT: C 856 ASN cc_start: 0.6966 (OUTLIER) cc_final: 0.6526 (m110) REVERT: C 938 LEU cc_start: 0.7075 (mt) cc_final: 0.6688 (mp) REVERT: C 1144 GLU cc_start: 0.6917 (mm-30) cc_final: 0.6527 (mp0) REVERT: F 34 MET cc_start: 0.2618 (OUTLIER) cc_final: 0.2274 (ptp) REVERT: F 47 PHE cc_start: 0.4022 (t80) cc_final: 0.3387 (t80) REVERT: F 83 MET cc_start: 0.2160 (mtp) cc_final: 0.1047 (ptp) outliers start: 60 outliers final: 27 residues processed: 407 average time/residue: 0.1737 time to fit residues: 115.1147 Evaluate side-chains 291 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 258 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain F residue 34 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 303 optimal weight: 20.0000 chunk 205 optimal weight: 9.9990 chunk 156 optimal weight: 0.5980 chunk 120 optimal weight: 0.9980 chunk 164 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 281 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 49 HIS A 207 HIS A 450 ASN A 644 GLN A 901 GLN A1048 HIS ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS B 675 GLN B 901 GLN B1048 HIS C 125 ASN C 450 ASN C 751 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN C1048 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.177402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.123827 restraints weight = 65990.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.124458 restraints weight = 38586.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.124363 restraints weight = 27993.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.125496 restraints weight = 25655.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.125512 restraints weight = 20303.066| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3421 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3421 r_free = 0.3421 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3421 r_free = 0.3421 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3421 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 27779 Z= 0.240 Angle : 0.706 11.828 37928 Z= 0.358 Chirality : 0.048 0.346 4455 Planarity : 0.004 0.062 4764 Dihedral : 6.010 59.137 5013 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.01 % Allowed : 11.94 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.14), residues: 3314 helix: 1.10 (0.20), residues: 682 sheet: 0.29 (0.17), residues: 834 loop : -0.64 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1107 TYR 0.031 0.002 TYR A 369 PHE 0.038 0.002 PHE C 135 TRP 0.022 0.002 TRP A 64 HIS 0.014 0.002 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00553 (27671) covalent geometry : angle 0.68332 (37646) SS BOND : bond 0.00809 ( 42) SS BOND : angle 1.90897 ( 84) hydrogen bonds : bond 0.04935 ( 1160) hydrogen bonds : angle 5.80420 ( 3129) link_BETA1-4 : bond 0.00412 ( 20) link_BETA1-4 : angle 1.53082 ( 60) link_NAG-ASN : bond 0.00454 ( 46) link_NAG-ASN : angle 2.55037 ( 138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 286 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.8970 (t) cc_final: 0.8527 (m) REVERT: A 129 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7519 (pttp) REVERT: A 567 ARG cc_start: 0.6925 (OUTLIER) cc_final: 0.6620 (mmt180) REVERT: A 572 THR cc_start: 0.7383 (OUTLIER) cc_final: 0.6894 (t) REVERT: A 773 GLU cc_start: 0.7453 (tt0) cc_final: 0.6984 (tt0) REVERT: A 855 PHE cc_start: 0.7200 (m-10) cc_final: 0.6972 (m-10) REVERT: A 957 GLN cc_start: 0.8217 (tm-30) cc_final: 0.8015 (tt0) REVERT: B 241 LEU cc_start: 0.7932 (mt) cc_final: 0.7724 (pp) REVERT: B 278 LYS cc_start: 0.8033 (tttt) cc_final: 0.7770 (ptmt) REVERT: B 347 PHE cc_start: 0.6744 (m-10) cc_final: 0.6311 (m-80) REVERT: B 389 ASP cc_start: 0.7977 (m-30) cc_final: 0.7622 (t70) REVERT: B 400 PHE cc_start: 0.6705 (p90) cc_final: 0.6476 (p90) REVERT: B 409 GLN cc_start: 0.6213 (mt0) cc_final: 0.5499 (mt0) REVERT: B 523 THR cc_start: 0.7758 (p) cc_final: 0.7378 (t) REVERT: B 817 PHE cc_start: 0.7878 (t80) cc_final: 0.7551 (t80) REVERT: C 61 ASN cc_start: 0.5464 (m-40) cc_final: 0.4886 (m-40) REVERT: C 237 ARG cc_start: 0.7113 (OUTLIER) cc_final: 0.6677 (ttp80) REVERT: C 388 ASN cc_start: 0.7737 (m110) cc_final: 0.7448 (m110) REVERT: C 453 TYR cc_start: 0.4913 (p90) cc_final: 0.4134 (p90) REVERT: C 938 LEU cc_start: 0.7054 (mt) cc_final: 0.6777 (mp) REVERT: C 1144 GLU cc_start: 0.7099 (mm-30) cc_final: 0.6555 (mp0) REVERT: F 12 MET cc_start: 0.1422 (mtm) cc_final: 0.0973 (mtm) REVERT: F 34 MET cc_start: 0.3288 (ptt) cc_final: 0.2760 (ptp) outliers start: 83 outliers final: 57 residues processed: 359 average time/residue: 0.1730 time to fit residues: 101.8516 Evaluate side-chains 299 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 238 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 644 GLN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 107 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 54 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 274 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 331 optimal weight: 7.9990 chunk 179 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 312 optimal weight: 8.9990 chunk 264 optimal weight: 3.9990 chunk 258 optimal weight: 0.8980 chunk 326 optimal weight: 30.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 207 HIS A1071 GLN B 30 ASN B 196 ASN B 414 GLN B 439 ASN B 474 GLN B 675 GLN C 99 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C1005 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.170833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.112607 restraints weight = 66986.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.115421 restraints weight = 36380.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.115888 restraints weight = 24570.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.116200 restraints weight = 19443.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.116360 restraints weight = 17997.006| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3393 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3393 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 27779 Z= 0.183 Angle : 0.630 13.120 37928 Z= 0.320 Chirality : 0.046 0.314 4455 Planarity : 0.004 0.046 4764 Dihedral : 5.628 58.487 5012 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.40 % Allowed : 12.99 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.14), residues: 3314 helix: 1.39 (0.20), residues: 678 sheet: 0.23 (0.17), residues: 812 loop : -0.63 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1107 TYR 0.032 0.002 TYR C 904 PHE 0.025 0.002 PHE B 541 TRP 0.018 0.001 TRP C 104 HIS 0.008 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00424 (27671) covalent geometry : angle 0.61045 (37646) SS BOND : bond 0.00399 ( 42) SS BOND : angle 1.84249 ( 84) hydrogen bonds : bond 0.04454 ( 1160) hydrogen bonds : angle 5.59236 ( 3129) link_BETA1-4 : bond 0.00241 ( 20) link_BETA1-4 : angle 1.34384 ( 60) link_NAG-ASN : bond 0.00289 ( 46) link_NAG-ASN : angle 2.17283 ( 138) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 276 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6511 (mmt-90) cc_final: 0.6235 (mmp80) REVERT: A 129 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7507 (pttp) REVERT: A 567 ARG cc_start: 0.6929 (OUTLIER) cc_final: 0.6689 (mmt180) REVERT: A 572 THR cc_start: 0.7389 (OUTLIER) cc_final: 0.6893 (t) REVERT: A 773 GLU cc_start: 0.7194 (tt0) cc_final: 0.6826 (tt0) REVERT: B 278 LYS cc_start: 0.8116 (tttt) cc_final: 0.7791 (ptmt) REVERT: B 347 PHE cc_start: 0.6975 (m-10) cc_final: 0.6417 (m-80) REVERT: B 389 ASP cc_start: 0.7820 (m-30) cc_final: 0.7438 (t70) REVERT: B 400 PHE cc_start: 0.6768 (p90) cc_final: 0.6490 (p90) REVERT: B 409 GLN cc_start: 0.6262 (mt0) cc_final: 0.5779 (mt0) REVERT: B 643 PHE cc_start: 0.7594 (t80) cc_final: 0.7381 (t80) REVERT: B 983 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7224 (ttp-170) REVERT: C 61 ASN cc_start: 0.5620 (m-40) cc_final: 0.5140 (m-40) REVERT: C 237 ARG cc_start: 0.7078 (OUTLIER) cc_final: 0.6603 (ttp80) REVERT: C 388 ASN cc_start: 0.7764 (m110) cc_final: 0.7476 (m110) REVERT: C 396 TYR cc_start: 0.7494 (m-80) cc_final: 0.7210 (m-10) REVERT: C 468 ILE cc_start: 0.2739 (OUTLIER) cc_final: 0.2419 (pp) REVERT: C 564 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7380 (tt0) REVERT: C 791 THR cc_start: 0.8498 (OUTLIER) cc_final: 0.8277 (m) REVERT: C 938 LEU cc_start: 0.7048 (mt) cc_final: 0.6727 (mp) REVERT: C 983 ARG cc_start: 0.6526 (OUTLIER) cc_final: 0.6308 (ttp80) REVERT: C 1144 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6594 (mp0) REVERT: F 34 MET cc_start: 0.2922 (ptt) cc_final: 0.2407 (ptp) outliers start: 94 outliers final: 59 residues processed: 352 average time/residue: 0.1606 time to fit residues: 93.1497 Evaluate side-chains 301 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 233 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 107 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 78 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 293 optimal weight: 1.9990 chunk 32 optimal weight: 0.0980 chunk 334 optimal weight: 6.9990 chunk 83 optimal weight: 0.4980 chunk 243 optimal weight: 0.9990 chunk 196 optimal weight: 0.0370 chunk 178 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 overall best weight: 0.5060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 207 HIS A 901 GLN A 913 GLN B 564 GLN C 519 HIS ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.173172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.116674 restraints weight = 69577.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.119762 restraints weight = 35016.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.119996 restraints weight = 20062.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.120644 restraints weight = 19608.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.120932 restraints weight = 17590.541| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3458 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3458 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 27779 Z= 0.112 Angle : 0.567 12.367 37928 Z= 0.288 Chirality : 0.044 0.225 4455 Planarity : 0.003 0.048 4764 Dihedral : 5.064 57.305 5012 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.52 % Allowed : 14.12 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.14), residues: 3314 helix: 1.76 (0.20), residues: 676 sheet: 0.34 (0.17), residues: 823 loop : -0.50 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 995 TYR 0.023 0.001 TYR A 369 PHE 0.034 0.001 PHE B 140 TRP 0.013 0.001 TRP A 64 HIS 0.008 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00248 (27671) covalent geometry : angle 0.54980 (37646) SS BOND : bond 0.00550 ( 42) SS BOND : angle 1.78687 ( 84) hydrogen bonds : bond 0.03869 ( 1160) hydrogen bonds : angle 5.33746 ( 3129) link_BETA1-4 : bond 0.00442 ( 20) link_BETA1-4 : angle 1.30936 ( 60) link_NAG-ASN : bond 0.00216 ( 46) link_NAG-ASN : angle 1.80393 ( 138) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 285 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: A 49 HIS cc_start: 0.7717 (t70) cc_final: 0.7514 (t-90) REVERT: A 64 TRP cc_start: 0.6981 (t60) cc_final: 0.6712 (t60) REVERT: A 102 ARG cc_start: 0.6575 (mmt-90) cc_final: 0.4088 (mtp180) REVERT: A 129 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7423 (pttp) REVERT: A 567 ARG cc_start: 0.6902 (OUTLIER) cc_final: 0.6698 (mmt180) REVERT: B 278 LYS cc_start: 0.8109 (tttt) cc_final: 0.7812 (ptmt) REVERT: B 347 PHE cc_start: 0.6722 (m-10) cc_final: 0.6352 (m-80) REVERT: B 374 PHE cc_start: 0.6590 (m-80) cc_final: 0.6357 (m-80) REVERT: B 389 ASP cc_start: 0.7891 (m-30) cc_final: 0.7415 (t70) REVERT: B 400 PHE cc_start: 0.6678 (p90) cc_final: 0.6370 (p90) REVERT: B 409 GLN cc_start: 0.6247 (mt0) cc_final: 0.5726 (mt0) REVERT: B 505 TYR cc_start: 0.6457 (m-80) cc_final: 0.6229 (m-80) REVERT: B 564 GLN cc_start: 0.6345 (mt0) cc_final: 0.5791 (mm-40) REVERT: B 643 PHE cc_start: 0.7511 (t80) cc_final: 0.7283 (t80) REVERT: B 983 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.7189 (ttp-170) REVERT: B 1050 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8632 (ptp) REVERT: C 52 GLN cc_start: 0.7526 (tm-30) cc_final: 0.7167 (tm-30) REVERT: C 61 ASN cc_start: 0.5677 (m-40) cc_final: 0.5246 (m-40) REVERT: C 237 ARG cc_start: 0.6895 (OUTLIER) cc_final: 0.6442 (ttp80) REVERT: C 388 ASN cc_start: 0.7830 (m110) cc_final: 0.7496 (m110) REVERT: C 468 ILE cc_start: 0.2745 (OUTLIER) cc_final: 0.2433 (pp) REVERT: C 564 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.7091 (tt0) REVERT: C 938 LEU cc_start: 0.7147 (mt) cc_final: 0.6829 (mp) REVERT: C 1144 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6527 (mp0) REVERT: E 34 MET cc_start: -0.1364 (mmt) cc_final: -0.1715 (ptp) REVERT: F 34 MET cc_start: 0.2724 (OUTLIER) cc_final: 0.1744 (mtm) outliers start: 69 outliers final: 37 residues processed: 332 average time/residue: 0.1583 time to fit residues: 86.6177 Evaluate side-chains 296 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 251 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 107 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 258 optimal weight: 0.9990 chunk 139 optimal weight: 0.5980 chunk 212 optimal weight: 0.0370 chunk 39 optimal weight: 9.9990 chunk 156 optimal weight: 0.6980 chunk 11 optimal weight: 6.9990 chunk 263 optimal weight: 0.1980 chunk 267 optimal weight: 2.9990 chunk 38 optimal weight: 20.0000 chunk 93 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 overall best weight: 0.5060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS B 30 ASN B 675 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.173000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.117623 restraints weight = 61460.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.120409 restraints weight = 33436.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.121285 restraints weight = 19708.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.121738 restraints weight = 18264.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.121946 restraints weight = 16978.277| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3474 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3474 r_free = 0.3474 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3474 r_free = 0.3474 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3474 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 27779 Z= 0.107 Angle : 0.552 9.848 37928 Z= 0.281 Chirality : 0.044 0.222 4455 Planarity : 0.004 0.048 4764 Dihedral : 4.807 56.524 5012 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.63 % Allowed : 14.61 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.14), residues: 3314 helix: 1.95 (0.21), residues: 669 sheet: 0.39 (0.17), residues: 820 loop : -0.45 (0.14), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 273 TYR 0.022 0.001 TYR A 369 PHE 0.030 0.001 PHE B 541 TRP 0.010 0.001 TRP D 53 HIS 0.005 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00238 (27671) covalent geometry : angle 0.53609 (37646) SS BOND : bond 0.00276 ( 42) SS BOND : angle 1.67756 ( 84) hydrogen bonds : bond 0.03740 ( 1160) hydrogen bonds : angle 5.22215 ( 3129) link_BETA1-4 : bond 0.00311 ( 20) link_BETA1-4 : angle 1.22815 ( 60) link_NAG-ASN : bond 0.00190 ( 46) link_NAG-ASN : angle 1.72850 ( 138) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 275 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7019 (t60) cc_final: 0.6667 (t60) REVERT: A 129 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7423 (pttp) REVERT: A 567 ARG cc_start: 0.6964 (OUTLIER) cc_final: 0.6743 (mmt180) REVERT: A 654 GLU cc_start: 0.6983 (mt-10) cc_final: 0.6773 (mp0) REVERT: A 1110 TYR cc_start: 0.8867 (t80) cc_final: 0.8570 (t80) REVERT: B 106 PHE cc_start: 0.6437 (m-80) cc_final: 0.6151 (m-80) REVERT: B 278 LYS cc_start: 0.8095 (tttt) cc_final: 0.7832 (ptmt) REVERT: B 347 PHE cc_start: 0.6791 (m-10) cc_final: 0.6447 (m-80) REVERT: B 374 PHE cc_start: 0.6596 (m-80) cc_final: 0.6392 (m-80) REVERT: B 389 ASP cc_start: 0.7813 (m-30) cc_final: 0.7379 (t70) REVERT: B 400 PHE cc_start: 0.6615 (p90) cc_final: 0.6313 (p90) REVERT: B 409 GLN cc_start: 0.6193 (mt0) cc_final: 0.5720 (mt0) REVERT: B 421 TYR cc_start: 0.7870 (m-80) cc_final: 0.7523 (m-80) REVERT: B 505 TYR cc_start: 0.6401 (m-80) cc_final: 0.6196 (m-80) REVERT: B 817 PHE cc_start: 0.7329 (t80) cc_final: 0.6975 (t80) REVERT: B 983 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.7347 (ttm170) REVERT: C 52 GLN cc_start: 0.7554 (tm-30) cc_final: 0.7229 (tm-30) REVERT: C 61 ASN cc_start: 0.5636 (m-40) cc_final: 0.5277 (m-40) REVERT: C 237 ARG cc_start: 0.7006 (OUTLIER) cc_final: 0.6657 (ttp80) REVERT: C 388 ASN cc_start: 0.7840 (m110) cc_final: 0.7442 (m110) REVERT: C 468 ILE cc_start: 0.2808 (OUTLIER) cc_final: 0.2490 (pp) REVERT: C 734 THR cc_start: 0.8931 (m) cc_final: 0.8660 (p) REVERT: C 1141 LEU cc_start: 0.7777 (tp) cc_final: 0.7497 (mt) REVERT: C 1144 GLU cc_start: 0.7025 (mm-30) cc_final: 0.6450 (mp0) REVERT: F 34 MET cc_start: 0.2774 (OUTLIER) cc_final: 0.1606 (mtm) outliers start: 72 outliers final: 47 residues processed: 327 average time/residue: 0.1702 time to fit residues: 90.9556 Evaluate side-chains 300 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 247 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 107 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 224 optimal weight: 10.0000 chunk 167 optimal weight: 4.9990 chunk 231 optimal weight: 10.0000 chunk 156 optimal weight: 0.6980 chunk 268 optimal weight: 2.9990 chunk 289 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 228 optimal weight: 0.5980 chunk 29 optimal weight: 20.0000 chunk 171 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS B 564 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C 935 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 = 0.4142 r_free = 0.4142 target = 0.170583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.114619 restraints weight = 72243.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.117533 restraints weight = 35115.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.117469 restraints weight = 20092.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.118089 restraints weight = 20169.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.118214 restraints weight = 18526.748| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3413 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3413 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 27779 Z= 0.148 Angle : 0.574 10.941 37928 Z= 0.290 Chirality : 0.044 0.215 4455 Planarity : 0.004 0.051 4764 Dihedral : 4.900 58.612 5012 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.73 % Allowed : 14.96 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.14), residues: 3314 helix: 1.78 (0.21), residues: 675 sheet: 0.43 (0.17), residues: 819 loop : -0.46 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 103 TYR 0.024 0.001 TYR C 170 PHE 0.028 0.001 PHE B 541 TRP 0.011 0.001 TRP A 64 HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00343 (27671) covalent geometry : angle 0.55827 (37646) SS BOND : bond 0.00276 ( 42) SS BOND : angle 1.57855 ( 84) hydrogen bonds : bond 0.04002 ( 1160) hydrogen bonds : angle 5.25923 ( 3129) link_BETA1-4 : bond 0.00307 ( 20) link_BETA1-4 : angle 1.20475 ( 60) link_NAG-ASN : bond 0.00237 ( 46) link_NAG-ASN : angle 1.80564 ( 138) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 255 time to evaluate : 0.990 Fit side-chains REVERT: A 90 VAL cc_start: 0.8948 (OUTLIER) cc_final: 0.8456 (m) REVERT: A 102 ARG cc_start: 0.6340 (mmp80) cc_final: 0.4139 (mtp180) REVERT: A 129 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7314 (pttp) REVERT: A 567 ARG cc_start: 0.7026 (OUTLIER) cc_final: 0.6812 (mmt180) REVERT: A 654 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6834 (mp0) REVERT: A 902 MET cc_start: 0.9248 (mmm) cc_final: 0.8895 (tpt) REVERT: B 278 LYS cc_start: 0.8161 (tttt) cc_final: 0.7793 (ptmt) REVERT: B 347 PHE cc_start: 0.7000 (m-10) cc_final: 0.6697 (m-80) REVERT: B 389 ASP cc_start: 0.7812 (m-30) cc_final: 0.7399 (t70) REVERT: B 400 PHE cc_start: 0.6773 (p90) cc_final: 0.6441 (p90) REVERT: B 409 GLN cc_start: 0.6281 (mt0) cc_final: 0.5880 (mt0) REVERT: B 505 TYR cc_start: 0.6565 (m-80) cc_final: 0.6284 (m-80) REVERT: B 983 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.7326 (ttm170) REVERT: B 988 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6919 (pt0) REVERT: C 52 GLN cc_start: 0.7738 (tm-30) cc_final: 0.7368 (tm-30) REVERT: C 61 ASN cc_start: 0.5741 (m-40) cc_final: 0.5386 (m-40) REVERT: C 237 ARG cc_start: 0.6920 (OUTLIER) cc_final: 0.6438 (ttp80) REVERT: C 388 ASN cc_start: 0.7964 (m110) cc_final: 0.6924 (t0) REVERT: C 468 ILE cc_start: 0.2930 (OUTLIER) cc_final: 0.2597 (pp) REVERT: C 564 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7302 (tt0) REVERT: C 734 THR cc_start: 0.8970 (m) cc_final: 0.8712 (p) REVERT: C 791 THR cc_start: 0.8471 (OUTLIER) cc_final: 0.8238 (m) REVERT: C 938 LEU cc_start: 0.7328 (mt) cc_final: 0.7038 (mp) REVERT: D 34 MET cc_start: 0.2660 (pmm) cc_final: 0.1948 (ptt) REVERT: F 34 MET cc_start: 0.2718 (OUTLIER) cc_final: 0.1718 (mtm) outliers start: 75 outliers final: 52 residues processed: 310 average time/residue: 0.1671 time to fit residues: 85.4031 Evaluate side-chains 304 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 242 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 107 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 259 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 161 optimal weight: 0.7980 chunk 266 optimal weight: 4.9990 chunk 192 optimal weight: 0.9990 chunk 218 optimal weight: 0.4980 chunk 96 optimal weight: 0.7980 chunk 243 optimal weight: 5.9990 chunk 264 optimal weight: 2.9990 chunk 247 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS B 564 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.170964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.115646 restraints weight = 58531.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.118123 restraints weight = 38433.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.118762 restraints weight = 22406.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.119028 restraints weight = 19753.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.119395 restraints weight = 18384.178| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3439 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3439 r_free = 0.3439 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3439 r_free = 0.3439 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3439 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 27779 Z= 0.131 Angle : 0.562 11.442 37928 Z= 0.283 Chirality : 0.044 0.217 4455 Planarity : 0.004 0.054 4764 Dihedral : 4.822 56.779 5012 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.59 % Allowed : 15.55 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.14), residues: 3314 helix: 1.85 (0.21), residues: 669 sheet: 0.42 (0.17), residues: 809 loop : -0.45 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 103 TYR 0.024 0.001 TYR A 369 PHE 0.028 0.001 PHE C 65 TRP 0.012 0.001 TRP A 64 HIS 0.002 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00303 (27671) covalent geometry : angle 0.54563 (37646) SS BOND : bond 0.00317 ( 42) SS BOND : angle 1.74883 ( 84) hydrogen bonds : bond 0.03839 ( 1160) hydrogen bonds : angle 5.22951 ( 3129) link_BETA1-4 : bond 0.00320 ( 20) link_BETA1-4 : angle 1.18158 ( 60) link_NAG-ASN : bond 0.00207 ( 46) link_NAG-ASN : angle 1.73306 ( 138) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 254 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7012 (t60) cc_final: 0.6586 (t60) REVERT: A 90 VAL cc_start: 0.8923 (OUTLIER) cc_final: 0.8451 (m) REVERT: A 102 ARG cc_start: 0.6333 (mmp80) cc_final: 0.3990 (mtp180) REVERT: A 129 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7287 (pttp) REVERT: A 567 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.6819 (mmt180) REVERT: A 654 GLU cc_start: 0.6956 (mt-10) cc_final: 0.6746 (mp0) REVERT: B 278 LYS cc_start: 0.8124 (tttt) cc_final: 0.7778 (ptmt) REVERT: B 389 ASP cc_start: 0.7789 (m-30) cc_final: 0.7386 (t70) REVERT: B 400 PHE cc_start: 0.6772 (p90) cc_final: 0.6552 (p90) REVERT: B 409 GLN cc_start: 0.6216 (mt0) cc_final: 0.5857 (mt0) REVERT: B 505 TYR cc_start: 0.6516 (m-80) cc_final: 0.6254 (m-80) REVERT: B 817 PHE cc_start: 0.7367 (t80) cc_final: 0.7059 (t80) REVERT: C 52 GLN cc_start: 0.7803 (tm-30) cc_final: 0.7425 (tm-30) REVERT: C 237 ARG cc_start: 0.6956 (OUTLIER) cc_final: 0.6505 (ttp80) REVERT: C 388 ASN cc_start: 0.7968 (m110) cc_final: 0.6993 (t0) REVERT: C 436 TRP cc_start: 0.6348 (p90) cc_final: 0.6088 (p90) REVERT: C 468 ILE cc_start: 0.2963 (OUTLIER) cc_final: 0.2628 (pp) REVERT: C 564 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7193 (tt0) REVERT: C 734 THR cc_start: 0.9020 (m) cc_final: 0.8752 (p) REVERT: C 791 THR cc_start: 0.8462 (OUTLIER) cc_final: 0.8233 (m) REVERT: D 34 MET cc_start: 0.3210 (pmm) cc_final: 0.2835 (ppp) REVERT: F 34 MET cc_start: 0.2654 (OUTLIER) cc_final: 0.2246 (ptp) outliers start: 71 outliers final: 51 residues processed: 302 average time/residue: 0.1576 time to fit residues: 78.6308 Evaluate side-chains 298 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 239 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 107 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 261 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 3 optimal weight: 0.0370 chunk 266 optimal weight: 4.9990 chunk 181 optimal weight: 0.7980 chunk 240 optimal weight: 0.0370 chunk 157 optimal weight: 0.5980 chunk 257 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 chunk 226 optimal weight: 0.7980 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS B 564 GLN B 675 GLN B 955 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 935 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.172598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.116471 restraints weight = 63829.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.120241 restraints weight = 33090.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.121453 restraints weight = 18019.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.121659 restraints weight = 17925.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.122026 restraints weight = 15298.580| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3476 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3476 r_free = 0.3476 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3476 r_free = 0.3476 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3476 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.4794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 27779 Z= 0.105 Angle : 0.544 10.419 37928 Z= 0.276 Chirality : 0.043 0.222 4455 Planarity : 0.004 0.056 4764 Dihedral : 4.543 55.691 5012 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.35 % Allowed : 15.73 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.15), residues: 3314 helix: 2.03 (0.21), residues: 672 sheet: 0.50 (0.18), residues: 797 loop : -0.37 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 103 TYR 0.026 0.001 TYR A 369 PHE 0.026 0.001 PHE B 541 TRP 0.013 0.001 TRP C 436 HIS 0.009 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00237 (27671) covalent geometry : angle 0.52935 (37646) SS BOND : bond 0.00260 ( 42) SS BOND : angle 1.66591 ( 84) hydrogen bonds : bond 0.03604 ( 1160) hydrogen bonds : angle 5.11393 ( 3129) link_BETA1-4 : bond 0.00338 ( 20) link_BETA1-4 : angle 1.14724 ( 60) link_NAG-ASN : bond 0.00187 ( 46) link_NAG-ASN : angle 1.58801 ( 138) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 277 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.8889 (OUTLIER) cc_final: 0.8403 (m) REVERT: A 102 ARG cc_start: 0.6253 (mmp80) cc_final: 0.3962 (ttp-170) REVERT: A 129 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.7131 (pttp) REVERT: A 546 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.5979 (mp) REVERT: A 870 ILE cc_start: 0.9225 (mm) cc_final: 0.9003 (mt) REVERT: B 237 ARG cc_start: 0.7180 (mtp85) cc_final: 0.6613 (mtm110) REVERT: B 278 LYS cc_start: 0.8165 (tttt) cc_final: 0.7769 (ptmt) REVERT: B 389 ASP cc_start: 0.7683 (m-30) cc_final: 0.7321 (t70) REVERT: B 400 PHE cc_start: 0.6741 (p90) cc_final: 0.6525 (p90) REVERT: B 409 GLN cc_start: 0.6156 (mt0) cc_final: 0.5899 (mt0) REVERT: B 817 PHE cc_start: 0.7339 (t80) cc_final: 0.7021 (t80) REVERT: B 988 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6900 (pt0) REVERT: C 45 SER cc_start: 0.7845 (p) cc_final: 0.7629 (p) REVERT: C 52 GLN cc_start: 0.7615 (tm-30) cc_final: 0.7225 (tm-30) REVERT: C 237 ARG cc_start: 0.6971 (OUTLIER) cc_final: 0.6602 (ttp80) REVERT: C 351 TYR cc_start: 0.5270 (p90) cc_final: 0.5039 (p90) REVERT: C 388 ASN cc_start: 0.7896 (m110) cc_final: 0.7052 (t0) REVERT: C 436 TRP cc_start: 0.6339 (p90) cc_final: 0.6128 (p90) REVERT: C 468 ILE cc_start: 0.3090 (OUTLIER) cc_final: 0.2756 (pp) REVERT: C 564 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7137 (tt0) REVERT: C 734 THR cc_start: 0.8941 (m) cc_final: 0.8662 (p) REVERT: C 825 LYS cc_start: 0.7818 (mmmm) cc_final: 0.7436 (tptp) REVERT: C 904 TYR cc_start: 0.7276 (m-80) cc_final: 0.6974 (m-80) REVERT: D 34 MET cc_start: 0.3196 (pmm) cc_final: 0.2116 (mtp) REVERT: F 34 MET cc_start: 0.2676 (OUTLIER) cc_final: 0.2253 (ptp) outliers start: 64 outliers final: 46 residues processed: 322 average time/residue: 0.1642 time to fit residues: 87.0432 Evaluate side-chains 317 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 263 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 107 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 151 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 216 optimal weight: 0.9980 chunk 130 optimal weight: 0.3980 chunk 121 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 51 optimal weight: 0.0040 chunk 278 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 184 optimal weight: 1.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS B 564 GLN C 774 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 935 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.172291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.118340 restraints weight = 76228.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.120384 restraints weight = 37253.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.120234 restraints weight = 22397.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.120926 restraints weight = 22870.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.121033 restraints weight = 20228.060| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3463 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3463 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27779 Z= 0.110 Angle : 0.548 10.620 37928 Z= 0.278 Chirality : 0.043 0.223 4455 Planarity : 0.004 0.054 4764 Dihedral : 4.463 56.783 5012 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.00 % Allowed : 16.36 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.15), residues: 3314 helix: 2.03 (0.21), residues: 671 sheet: 0.54 (0.18), residues: 790 loop : -0.35 (0.14), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 237 TYR 0.027 0.001 TYR A 369 PHE 0.026 0.001 PHE B 541 TRP 0.012 0.001 TRP C 436 HIS 0.007 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00252 (27671) covalent geometry : angle 0.53463 (37646) SS BOND : bond 0.00255 ( 42) SS BOND : angle 1.55849 ( 84) hydrogen bonds : bond 0.03616 ( 1160) hydrogen bonds : angle 5.08037 ( 3129) link_BETA1-4 : bond 0.00314 ( 20) link_BETA1-4 : angle 1.14211 ( 60) link_NAG-ASN : bond 0.00177 ( 46) link_NAG-ASN : angle 1.58991 ( 138) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 269 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.8876 (OUTLIER) cc_final: 0.8425 (m) REVERT: A 102 ARG cc_start: 0.6220 (mmp80) cc_final: 0.4023 (mtp180) REVERT: A 129 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7169 (pttp) REVERT: B 237 ARG cc_start: 0.7168 (mtp85) cc_final: 0.6621 (mtm110) REVERT: B 278 LYS cc_start: 0.8183 (tttt) cc_final: 0.7822 (ptmt) REVERT: B 374 PHE cc_start: 0.6318 (m-80) cc_final: 0.6112 (m-80) REVERT: B 389 ASP cc_start: 0.7594 (m-30) cc_final: 0.7290 (t70) REVERT: B 409 GLN cc_start: 0.6225 (mt0) cc_final: 0.5926 (mt0) REVERT: B 817 PHE cc_start: 0.7309 (t80) cc_final: 0.6996 (t80) REVERT: B 988 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6933 (pt0) REVERT: C 52 GLN cc_start: 0.7672 (tm-30) cc_final: 0.7289 (tm-30) REVERT: C 237 ARG cc_start: 0.7061 (ttp-170) cc_final: 0.6736 (ttp80) REVERT: C 351 TYR cc_start: 0.5301 (p90) cc_final: 0.5086 (p90) REVERT: C 388 ASN cc_start: 0.7929 (m110) cc_final: 0.7064 (t0) REVERT: C 436 TRP cc_start: 0.6420 (p90) cc_final: 0.6167 (p90) REVERT: C 468 ILE cc_start: 0.3214 (OUTLIER) cc_final: 0.2864 (pp) REVERT: C 564 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.7141 (tt0) REVERT: C 734 THR cc_start: 0.8926 (m) cc_final: 0.8671 (p) REVERT: D 34 MET cc_start: 0.2909 (pmm) cc_final: 0.1918 (mtp) REVERT: F 34 MET cc_start: 0.2611 (OUTLIER) cc_final: 0.1589 (mtm) outliers start: 54 outliers final: 44 residues processed: 308 average time/residue: 0.1694 time to fit residues: 85.9324 Evaluate side-chains 298 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 248 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 107 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 104 optimal weight: 9.9990 chunk 92 optimal weight: 0.5980 chunk 166 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 270 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 221 optimal weight: 1.9990 chunk 202 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 311 optimal weight: 10.0000 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 655 HIS A 913 GLN B 564 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 935 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.173337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.120217 restraints weight = 58216.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.121348 restraints weight = 32425.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.120661 restraints weight = 22782.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.121364 restraints weight = 23410.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.121541 restraints weight = 20326.478| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3414 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3414 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 27779 Z= 0.168 Angle : 0.600 10.347 37928 Z= 0.303 Chirality : 0.044 0.214 4455 Planarity : 0.004 0.056 4764 Dihedral : 4.854 59.197 5012 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.24 % Allowed : 16.43 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.14), residues: 3314 helix: 1.80 (0.21), residues: 679 sheet: 0.44 (0.17), residues: 833 loop : -0.43 (0.14), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 103 TYR 0.025 0.001 TYR A 369 PHE 0.025 0.002 PHE C 65 TRP 0.031 0.001 TRP F 53 HIS 0.007 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00394 (27671) covalent geometry : angle 0.58326 (37646) SS BOND : bond 0.00308 ( 42) SS BOND : angle 1.84138 ( 84) hydrogen bonds : bond 0.04071 ( 1160) hydrogen bonds : angle 5.28613 ( 3129) link_BETA1-4 : bond 0.00290 ( 20) link_BETA1-4 : angle 1.18365 ( 60) link_NAG-ASN : bond 0.00256 ( 46) link_NAG-ASN : angle 1.82099 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5403.37 seconds wall clock time: 93 minutes 53.24 seconds (5633.24 seconds total)