Starting phenix.real_space_refine on Fri Mar 6 00:34:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k8w_22733/03_2026/7k8w_22733_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k8w_22733/03_2026/7k8w_22733.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 { model { file = "/net/cci-nas-00/data/ceres_data/7k8w_22733/03_2026/7k8w_22733_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k8w_22733/03_2026/7k8w_22733_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k8w_22733/03_2026/7k8w_22733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k8w_22733/03_2026/7k8w_22733.map" } 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= 0.002 sd= 0.019 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 122 5.16 5 C 16817 2.51 5 N 4356 2.21 5 O 5204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 166 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: 26499 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 7612 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 990, 7606 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'CIS': 1, 'PTRANS': 48, 'TRANS': 940} Chain breaks: 10 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 4, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 7, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 88 Conformer: "B" Number of residues, atoms: 990, 7606 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'CIS': 1, 'PTRANS': 48, 'TRANS': 940} Chain breaks: 10 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 4, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 7, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 88 bond proxies already assigned to first conformer: 7766 Chain: "B" Number of atoms: 6865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 6865 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 46, 'TRANS': 902} Chain breaks: 13 Unresolved non-hydrogen bonds: 576 Unresolved non-hydrogen angles: 742 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'ASP:plan': 13, 'ASN:plan1': 17, 'GLU:plan': 12, 'GLN:plan1': 9, 'ARG:plan': 9, 'PHE:plan': 9, 'TYR:plan': 13, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 382 Chain: "G" Number of atoms: 7604 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 990, 7598 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 48, 'TRANS': 941} Chain breaks: 8 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 4, 'ASP:plan': 9, 'GLN:plan1': 2, 'GLU:plan': 10, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 94 Conformer: "B" Number of residues, atoms: 990, 7598 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 48, 'TRANS': 941} Chain breaks: 8 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 4, 'ASP:plan': 9, 'GLN:plan1': 2, 'GLU:plan': 10, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 94 bond proxies already assigned to first conformer: 7761 Chain: "H" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 988 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "L" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 801 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 105} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "N" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 988 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "S" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 801 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 105} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" 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: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "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: "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: "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: "A" 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: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "G" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ASER A 459 " occ=0.60 ... (10 atoms not shown) pdb=" OG BSER A 459 " occ=0.40 residue: pdb=" N ASER G 459 " occ=0.60 ... (10 atoms not shown) pdb=" OG BSER G 459 " occ=0.40 Time building chain proxies: 8.79, per 1000 atoms: 0.33 Number of scatterers: 26499 At special positions: 0 Unit cell: (134.596, 134.596, 203.984, 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 122 16.00 O 5204 8.00 N 4356 7.00 C 16817 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=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.01 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 166 " distance=2.02 Simple disulfide: pdb=" SG CYS G 291 " - pdb=" SG CYS G 301 " distance=2.03 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=2.01 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 391 " - pdb=" SG CYS G 525 " distance=2.04 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 488 " distance=2.03 Simple disulfide: pdb=" SG CYS G 538 " - pdb=" SG CYS G 590 " distance=2.03 Simple disulfide: pdb=" SG CYS G 617 " - pdb=" SG CYS G 649 " distance=2.03 Simple disulfide: pdb=" SG CYS G 662 " - pdb=" SG CYS G 671 " distance=2.03 Simple disulfide: pdb=" SG CYS G 738 " - pdb=" SG CYS G 760 " distance=2.03 Simple disulfide: pdb=" SG CYS G 743 " - pdb=" SG CYS G 749 " distance=2.02 Simple disulfide: pdb=" SG CYS G1032 " - pdb=" SG CYS G1043 " distance=2.03 Simple disulfide: pdb=" SG CYS G1082 " - pdb=" SG CYS G1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 87 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A 343 " " NAG A1310 " - " ASN A 331 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 603 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B 717 " " NAG B1312 " - " ASN B1074 " " NAG B1313 " - " ASN B 165 " " NAG C 1 " - " ASN A 234 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1098 " " NAG G1301 " - " ASN G 61 " " NAG G1302 " - " ASN G 122 " " NAG G1303 " - " ASN G 234 " " NAG G1304 " - " ASN G 282 " " NAG G1305 " - " ASN G 603 " " NAG G1306 " - " ASN G 616 " " NAG G1307 " - " ASN G 657 " " NAG G1308 " - " ASN G 709 " " NAG G1309 " - " ASN G1074 " " NAG G1310 " - " ASN G 165 " " NAG G1311 " - " ASN G 331 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG O 1 " - " ASN G 717 " " NAG P 1 " - " ASN G 801 " " NAG Q 1 " - " ASN G1098 " " NAG R 1 " - " ASN G1134 " " NAG T 1 " - " ASN G 343 " Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 2.0 seconds 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6346 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 55 sheets defined 23.4% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 403 through 410 removed outlier: 4.086A 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 737 through 744 removed outlier: 3.615A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 4.086A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.977A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.783A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.845A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.754A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (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: 3.608A pdb=" N GLN A 965 " --> pdb=" O THR A 961 " (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 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.551A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.030A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.901A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.649A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.645A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.780A pdb=" N THR B 881 " --> pdb=" O LEU B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.031A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 907 removed outlier: 3.512A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 910 No H-bonds generated for 'chain 'B' and resid 908 through 910' Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.791A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.585A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) 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: 4.314A 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 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.823A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.970A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 304 removed outlier: 3.573A pdb=" N THR G 302 " --> pdb=" O GLU G 298 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 343 Processing helix chain 'G' and resid 365 through 370 Processing helix chain 'G' and resid 386 through 390 removed outlier: 3.882A pdb=" N LEU G 390 " --> pdb=" O LEU G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 410 Processing helix chain 'G' and resid 416 through 422 Processing helix chain 'G' and resid 616 through 620 Processing helix chain 'G' and resid 737 through 744 Processing helix chain 'G' and resid 746 through 755 removed outlier: 4.038A pdb=" N LEU G 752 " --> pdb=" O GLU G 748 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN G 755 " --> pdb=" O ASN G 751 " (cutoff:3.500A) Processing helix chain 'G' and resid 758 through 783 Processing helix chain 'G' and resid 816 through 825 removed outlier: 3.518A pdb=" N LEU G 822 " --> pdb=" O ILE G 818 " (cutoff:3.500A) Processing helix chain 'G' and resid 866 through 885 removed outlier: 3.511A pdb=" N THR G 881 " --> pdb=" O LEU G 877 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY G 885 " --> pdb=" O THR G 881 " (cutoff:3.500A) Processing helix chain 'G' and resid 886 through 891 removed outlier: 4.140A pdb=" N ALA G 890 " --> pdb=" O TRP G 886 " (cutoff:3.500A) Processing helix chain 'G' and resid 897 through 908 removed outlier: 3.614A pdb=" N ALA G 903 " --> pdb=" O ALA G 899 " (cutoff:3.500A) Processing helix chain 'G' and resid 913 through 918 removed outlier: 3.609A pdb=" N TYR G 917 " --> pdb=" O GLN G 913 " (cutoff:3.500A) Processing helix chain 'G' and resid 919 through 941 removed outlier: 3.679A pdb=" N ILE G 934 " --> pdb=" O ALA G 930 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN G 935 " --> pdb=" O ILE G 931 " (cutoff:3.500A) Processing helix chain 'G' and resid 942 through 944 No H-bonds generated for 'chain 'G' and resid 942 through 944' Processing helix chain 'G' and resid 945 through 965 removed outlier: 3.610A pdb=" N ASN G 955 " --> pdb=" O VAL G 951 " (cutoff:3.500A) Processing helix chain 'G' and resid 966 through 968 No H-bonds generated for 'chain 'G' and resid 966 through 968' Processing helix chain 'G' and resid 976 through 984 removed outlier: 3.549A pdb=" N ILE G 980 " --> pdb=" O VAL G 976 " (cutoff:3.500A) Processing helix chain 'G' and resid 985 through 1033 removed outlier: 4.476A pdb=" N VAL G 991 " --> pdb=" O PRO G 987 " (cutoff:3.500A) Processing helix chain 'G' and resid 1140 through 1147 removed outlier: 3.949A pdb=" N GLU G1144 " --> pdb=" O PRO G1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 78 through 82 Processing helix chain 'N' and resid 61 through 64 Processing helix chain 'N' and resid 83 through 87 Processing helix chain 'S' and resid 78 through 82 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.633A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.440A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.513A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.060A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.354A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 448 through 454 removed outlier: 3.559A pdb=" N GLY A 496 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ASN A 450 " --> pdb=" O SER A 494 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N SER A 494 " --> pdb=" O ASN A 450 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N LEU A 452 " --> pdb=" O LEU A 492 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N LEU A 492 " --> pdb=" O LEU A 452 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 538 through 543 removed outlier: 5.787A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.921A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.504A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.504A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 789 through 790 removed outlier: 3.596A pdb=" N LYS A 790 " --> pdb=" O ASN G 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 3.950A pdb=" N SER A1123 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 31 removed outlier: 4.084A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.645A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.174A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.642A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.545A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.725A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL B 595 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.562A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.307A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC6, first strand: chain 'B' and resid 538 through 541 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 656 removed outlier: 6.076A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.138A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.138A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 5.748A pdb=" N VAL B1122 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N PHE B1089 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLY B1124 " --> pdb=" O ALA B1087 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD4, first strand: chain 'G' and resid 28 through 31 removed outlier: 4.094A pdb=" N SER G 60 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ASN G 61 " --> pdb=" O TYR G 269 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N TYR G 269 " --> pdb=" O ASN G 61 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR G 265 " --> pdb=" O PHE G 65 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN G 188 " --> pdb=" O GLU G 96 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL G 227 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N SER G 205 " --> pdb=" O PRO G 225 " (cutoff:3.500A) removed outlier: 9.395A pdb=" N HIS G 207 " --> pdb=" O LEU G 223 " (cutoff:3.500A) removed outlier: 9.640A pdb=" N LEU G 223 " --> pdb=" O HIS G 207 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N VAL G 36 " --> pdb=" O LEU G 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 48 through 55 removed outlier: 4.167A pdb=" N ASP G 287 " --> pdb=" O LYS G 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 83 through 85 Processing sheet with id=AD7, first strand: chain 'G' and resid 311 through 319 removed outlier: 6.079A pdb=" N ILE G 312 " --> pdb=" O THR G 599 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N THR G 599 " --> pdb=" O ILE G 312 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLN G 314 " --> pdb=" O VAL G 597 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL G 597 " --> pdb=" O GLN G 314 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER G 316 " --> pdb=" O VAL G 595 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLY G 594 " --> pdb=" O GLN G 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 324 through 325 removed outlier: 7.225A pdb=" N GLU G 324 " --> pdb=" O ASN G 540 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N ASN G 542 " --> pdb=" O GLU G 324 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ASP G 574 " --> pdb=" O ILE G 587 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA G 575 " --> pdb=" O GLY G 566 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 354 through 358 removed outlier: 4.391A pdb=" N ASN G 354 " --> pdb=" O SER G 399 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER G 399 " --> pdb=" O ASN G 354 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY G 431 " --> pdb=" O TYR G 380 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 448 through 454 removed outlier: 7.837A pdb=" N TYR G 451 " --> pdb=" O TYR G 495 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 473 through 474 Processing sheet with id=AE3, first strand: chain 'G' and resid 654 through 660 removed outlier: 4.277A pdb=" N THR G 696 " --> pdb=" O VAL G 656 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASN G 658 " --> pdb=" O THR G 696 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE G 670 " --> pdb=" O ILE G 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 711 through 728 removed outlier: 3.546A pdb=" N LYS G1073 " --> pdb=" O ILE G 714 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLN G1071 " --> pdb=" O THR G 716 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N PHE G 718 " --> pdb=" O PRO G1069 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ILE G 720 " --> pdb=" O TYR G1067 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N TYR G1067 " --> pdb=" O ILE G 720 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL G 722 " --> pdb=" O VAL G1065 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL G1065 " --> pdb=" O VAL G 722 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR G 724 " --> pdb=" O LEU G1063 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU G1063 " --> pdb=" O THR G 724 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE G 726 " --> pdb=" O VAL G1061 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL G1061 " --> pdb=" O ILE G 726 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N GLY G1059 " --> pdb=" O PRO G 728 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE G1052 " --> pdb=" O LEU G1063 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N TYR G1067 " --> pdb=" O HIS G1048 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N HIS G1048 " --> pdb=" O TYR G1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 711 through 728 removed outlier: 3.546A pdb=" N LYS G1073 " --> pdb=" O ILE G 714 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLN G1071 " --> pdb=" O THR G 716 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N PHE G 718 " --> pdb=" O PRO G1069 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ILE G 720 " --> pdb=" O TYR G1067 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N TYR G1067 " --> pdb=" O ILE G 720 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL G 722 " --> pdb=" O VAL G1065 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL G1065 " --> pdb=" O VAL G 722 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR G 724 " --> pdb=" O LEU G1063 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU G1063 " --> pdb=" O THR G 724 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE G 726 " --> pdb=" O VAL G1061 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL G1061 " --> pdb=" O ILE G 726 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N GLY G1059 " --> pdb=" O PRO G 728 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR G1076 " --> pdb=" O SER G1097 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 734 through 736 Processing sheet with id=AE7, first strand: chain 'G' and resid 1120 through 1125 removed outlier: 5.696A pdb=" N VAL G1122 " --> pdb=" O PHE G1089 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N PHE G1089 " --> pdb=" O VAL G1122 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLY G1124 " --> pdb=" O ALA G1087 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.573A pdb=" N LEU H 82 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU H 81 " --> pdb=" O THR H 68 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR H 68 " --> pdb=" O GLU H 81 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AF1, first strand: chain 'H' and resid 57 through 59 removed outlier: 3.501A pdb=" N SER H 58 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ILE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N MET H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.644A pdb=" N GLY L 12 " --> pdb=" O THR L 104 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N GLN L 36 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU L 45 " --> pdb=" O GLN L 36 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.644A pdb=" N GLY L 12 " --> pdb=" O THR L 104 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AF5, first strand: chain 'N' and resid 10 through 12 Processing sheet with id=AF6, first strand: chain 'N' and resid 17 through 23 removed outlier: 3.573A pdb=" N LEU N 82 " --> pdb=" O VAL N 18 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU N 81 " --> pdb=" O THR N 68 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR N 68 " --> pdb=" O GLU N 81 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 57 through 59 removed outlier: 3.501A pdb=" N SER N 58 " --> pdb=" O ILE N 50 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N TRP N 36 " --> pdb=" O MET N 48 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ILE N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N MET N 34 " --> pdb=" O ILE N 50 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL N 102 " --> pdb=" O ARG N 94 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'S' and resid 9 through 12 removed outlier: 3.643A pdb=" N GLY S 12 " --> pdb=" O THR S 104 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'S' and resid 9 through 12 removed outlier: 3.643A pdb=" N GLY S 12 " --> pdb=" O THR S 104 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'S' and resid 18 through 23 1036 hydrogen bonds defined for protein. 2796 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.66 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.08 - 1.23: 782 1.23 - 1.38: 9848 1.38 - 1.54: 15867 1.54 - 1.69: 393 1.69 - 1.84: 161 Bond restraints: 27051 Sorted by residual: bond pdb=" N PRO A 330 " pdb=" CA PRO A 330 " ideal model delta sigma weight residual 1.466 1.689 -0.223 1.24e-02 6.50e+03 3.23e+02 bond pdb=" CG PRO G1079 " pdb=" CD PRO G1079 " ideal model delta sigma weight residual 1.503 1.167 0.336 3.40e-02 8.65e+02 9.76e+01 bond pdb=" C PHE A 329 " pdb=" N PRO A 330 " ideal model delta sigma weight residual 1.332 1.448 -0.117 1.34e-02 5.57e+03 7.57e+01 bond pdb=" CB PRO G1079 " pdb=" CG PRO G1079 " ideal model delta sigma weight residual 1.492 1.079 0.413 5.00e-02 4.00e+02 6.82e+01 bond pdb=" CG PRO A 479 " pdb=" CD PRO A 479 " ideal model delta sigma weight residual 1.503 1.243 0.260 3.40e-02 8.65e+02 5.83e+01 ... (remaining 27046 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.98: 36837 10.98 - 21.95: 14 21.95 - 32.93: 2 32.93 - 43.91: 0 43.91 - 54.88: 1 Bond angle restraints: 36854 Sorted by residual: angle pdb=" C PHE A 329 " pdb=" N PRO A 330 " pdb=" CA PRO A 330 " ideal model delta sigma weight residual 119.78 139.63 -19.85 1.03e+00 9.43e-01 3.72e+02 angle pdb=" N PRO G1079 " pdb=" CD PRO G1079 " pdb=" CG PRO G1079 " ideal model delta sigma weight residual 103.20 76.11 27.09 1.50e+00 4.44e-01 3.26e+02 angle pdb=" CB PRO G1079 " pdb=" CG PRO G1079 " pdb=" CD PRO G1079 " ideal model delta sigma weight residual 106.10 160.98 -54.88 3.20e+00 9.77e-02 2.94e+02 angle pdb=" CA PRO A 479 " pdb=" N PRO A 479 " pdb=" CD PRO A 479 " ideal model delta sigma weight residual 112.00 93.36 18.64 1.40e+00 5.10e-01 1.77e+02 angle pdb=" C VAL A 382 " pdb=" N SER A 383 " pdb=" CA SER A 383 " ideal model delta sigma weight residual 120.68 100.82 19.86 1.52e+00 4.33e-01 1.71e+02 ... (remaining 36849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.11: 15631 18.11 - 36.23: 920 36.23 - 54.34: 184 54.34 - 72.46: 51 72.46 - 90.57: 34 Dihedral angle restraints: 16820 sinusoidal: 6953 harmonic: 9867 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -3.64 -82.36 1 1.00e+01 1.00e-02 8.32e+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 93.00 170.49 -77.49 1 1.00e+01 1.00e-02 7.52e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 169.44 -76.44 1 1.00e+01 1.00e-02 7.35e+01 ... (remaining 16817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.276: 4434 0.276 - 0.552: 5 0.552 - 0.827: 2 0.827 - 1.103: 1 1.103 - 1.379: 1 Chirality restraints: 4443 Sorted by residual: chirality pdb=" C1 NAG A1310 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1310 " pdb=" O5 NAG A1310 " both_signs ideal model delta sigma weight residual False -2.40 -1.02 -1.38 2.00e-01 2.50e+01 4.76e+01 chirality pdb=" C1 NAG G1308 " pdb=" ND2 ASN G 709 " pdb=" C2 NAG G1308 " pdb=" O5 NAG G1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.37 -1.03 2.00e-01 2.50e+01 2.64e+01 chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 282 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.64 -0.76 2.00e-01 2.50e+01 1.43e+01 ... (remaining 4440 not shown) Planarity restraints: 4715 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 478 " 0.091 5.00e-02 4.00e+02 1.22e-01 2.36e+01 pdb=" N PRO A 479 " -0.209 5.00e-02 4.00e+02 pdb=" CA PRO A 479 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 479 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 449 " 0.031 2.00e-02 2.50e+03 3.18e-02 2.02e+01 pdb=" CG TYR G 449 " -0.077 2.00e-02 2.50e+03 pdb=" CD1 TYR G 449 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR G 449 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR G 449 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR G 449 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR G 449 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR G 449 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 329 " 0.068 5.00e-02 4.00e+02 1.02e-01 1.65e+01 pdb=" N PRO B 330 " -0.176 5.00e-02 4.00e+02 pdb=" CA PRO B 330 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO B 330 " 0.056 5.00e-02 4.00e+02 ... (remaining 4712 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.17: 18 2.17 - 2.85: 9592 2.85 - 3.53: 36977 3.53 - 4.22: 61511 4.22 - 4.90: 103228 Nonbonded interactions: 211326 Sorted by model distance: nonbonded pdb=" NH2 ARG G 403 " pdb=" OD1 ASP N 100B" model vdw 1.483 3.120 nonbonded pdb=" OH TYR N 100I" pdb=" OD1 ASP S 49 " model vdw 1.566 3.040 nonbonded pdb=" OD1 ASN A 331 " pdb=" OE1 GLN A 580 " model vdw 1.891 3.040 nonbonded pdb=" OG SER A 816 " pdb=" OE1 GLU A 819 " model vdw 2.017 3.040 nonbonded pdb=" OD1 ASN G 450 " pdb=" OG SER S 92 " model vdw 2.043 3.040 ... (remaining 211321 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 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 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) or re \ sid 89 through 95 or (resid 96 through 97 and (name N or name CA or name C or na \ me O or name CB )) or resid 98 through 109 or (resid 110 through 113 and (name N \ or name CA or name C or name O or name CB )) or resid 116 through 124 or (resid \ 125 and (name N or name CA or name C or name O or name CB )) or resid 126 throu \ gh 131 or (resid 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 an \ d (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 \ 186 through 190 or (resid 191 and (name N or name CA or name C or name O or name \ CB )) or resid 192 through 196 or resid 200 through 210 or (resid 211 and (name \ N or name CA or name C or name O or name CB )) or (resid 215 and (name N or nam \ e CA or name C or name O or name CB )) or resid 216 through 217 or (resid 218 an \ d (name N or name CA or name C or name O or name CB )) or resid 219 through 223 \ or (resid 224 and (name N or name CA or name C or name O or name CB )) or resid \ 225 through 238 or (resid 239 and (name N or name CA or name C or name O or name \ CB )) or resid 240 through 263 or resid 265 through 308 or (resid 309 and (name \ N or name CA or name C or name O or name CB )) or resid 310 through 323 or (res \ id 324 and (name N or name CA or name C or name O or name CB )) or resid 325 thr \ ough 332 or (resid 333 through 334 and (name N or name CA or name C or name O or \ name CB )) or resid 335 through 339 or (resid 340 and (name N or name CA or nam \ e C or name O or name CB )) or resid 341 through 344 or (resid 345 through 360 a \ nd (name N or name CA or name C or name O or name CB )) or resid 361 or (resid 3 \ 62 through 378 and (name N or name CA or name C or name O or name CB )) or resid \ 379 or (resid 380 and (name N or name CA or name C or name O or name CB )) or r \ esid 381 or (resid 382 through 383 and (name N or name CA or name C or name O or \ name CB )) or resid 384 or (resid 385 through 390 and (name N or name CA or nam \ e C or name O or name CB )) or resid 391 or (resid 392 through 403 and (name N o \ r name CA or name C or name O or name CB )) or resid 404 or (resid 405 through 4 \ 11 and (name N or name CA or name C or name O or name CB )) or resid 412 through \ 413 or (resid 414 through 415 and (name N or name CA or name C or name O or nam \ e CB )) or resid 416 or (resid 417 through 425 and (name N or name CA or name C \ or name O or name CB )) or resid 426 or (resid 427 through 430 and (name N or na \ me CA or name C or name O or name CB )) or resid 431 through 432 or (resid 433 t \ hrough 445 and (name N or name CA or name C or name O or name CB )) or resid 446 \ through 447 or (resid 448 through 454 and (name N or name CA or name C or name \ O or name CB )) or (resid 462 and (name N or name CA or name C or name O or name \ CB )) or resid 463 or (resid 464 through 466 and (name N or name CA or name C o \ r name O or name CB )) or resid 491 or (resid 492 through 495 and (name N or nam \ e CA or name C or name O or name CB )) or resid 496 or (resid 497 through 498 an \ d (name N or name CA or name C or name O or name CB )) or resid 499 or (resid 50 \ 0 through 501 and (name N or name CA or name C or name O or name CB )) or resid \ 502 or (resid 503 and (name N or name CA or name C or name O or name CB )) or (r \ esid 504 through 506 and (name N or name CA or name C or name O or name CB )) or \ resid 507 or (resid 508 through 515 and (name N or name CA or name C or name O \ or name CB )) or (resid 522 through 524 and (name N or name CA or name C or name \ O or name CB )) or resid 525 through 527 or (resid 528 through 529 and (name N \ or name CA or name C or name O or name CB )) or resid 530 through 553 or (resid \ 554 and (name N or name CA or name C or name O or name CB )) or resid 555 throug \ h 793 or (resid 794 and (name N or name CA or name C or name O or name CB )) or \ resid 795 or (resid 796 and (name N or name CA or name C or name O or name CB )) \ or resid 797 through 810 or (resid 811 and (name N or name CA or name C or name \ O or name CB )) or resid 813 through 827 or resid 856 through 866 or (resid 867 \ through 868 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 69 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 987 or (resid 988 through 989 and (na \ me N or name CA or name C or name O or name CB )) or resid 990 through 1141 or ( \ resid 1142 and (name N or name CA or name C or name O or name CB )) or resid 114 \ 3 through 1144 or (resid 1145 through 1146 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1147 through 1310)) 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 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) or re \ sid 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 through 109 or (resid 110 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 n \ ame CA or name C or name O or name CB )) or resid 130 through 134 or (resid 135 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 140 or resid 166 through 168 or (resid 169 and (name N or name CA or n \ ame C or name O or name CB )) or resid 170 through 187 or (resid 188 and (name N \ or name CA or name C or name O or name CB )) or resid 189 through 190 or (resid \ 191 and (name N or name CA or name C or name O or name CB )) or resid 192 throu \ gh 195 or (resid 196 and (name N or name CA or name C or name O or name CB )) or \ resid 200 through 210 or (resid 211 through 215 and (name N or name CA or name \ C or name O or name CB )) or resid 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 o \ r (resid 281 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 82 through 323 or (resid 324 and (name N or name CA or name C or name O or name \ CB )) or resid 325 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 thr \ ough 583 and (name N or name CA or name C or name O or name CB )) or resid 584 t \ hrough 585 or (resid 586 and (name N or name CA or name C or name O or name CB ) \ ) or resid 587 through 613 or (resid 614 and (name N or name CA or name C or nam \ e O or name CB )) or resid 615 through 618 or (resid 619 and (name N or name CA \ or name C or name O or name CB )) or resid 620 through 676 or resid 690 through \ 744 or (resid 745 and (name N or name CA or name C or name O or name CB )) or re \ sid 746 through 810 or (resid 811 and (name N or name CA or name C or name O or \ name CB )) or resid 813 through 827 or resid 856 through 866 or (resid 867 throu \ gh 868 and (name N or name CA or name C or name O or name CB )) or resid 869 thr \ ough 920 or (resid 921 and (name N or name CA or name C or name O or name CB )) \ or resid 922 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 987 or (resid 988 through 9 \ 89 and (name N or name CA or name C or name O or name CB )) or resid 990 through \ 1072 or (resid 1073 and (name N or name CA or name C or name O or name CB )) or \ resid 1074 through 1117 or (resid 1118 and (name N or name CA or name C or name \ O or name CB )) or resid 1119 through 1143 or (resid 1144 through 1146 and (nam \ e N or name CA or name C or name O or name CB )) or resid 1147 through 1310)) selection = (chain 'G' 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 134 or (resid 135 through 138 and (n \ ame N or name CA or name C or name O or name CB )) or resid 139 through 140 or r \ esid 166 through 187 or (resid 188 and (name N or name CA or name C or name O or \ name CB )) or resid 189 through 195 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB )) or resid 200 through 211 or resid 215 through 217 or \ (resid 218 and (name N or name CA or name C or name O or name CB )) or resid 21 \ 9 through 223 or (resid 224 and (name N or name CA or name C or name O or name C \ B )) or resid 225 through 238 or (resid 239 and (name N or name CA or name C or \ name O or name CB )) or resid 240 through 308 or (resid 309 and (name N or name \ CA or name C or name O or name CB )) or resid 310 through 332 or (resid 333 thro \ ugh 334 and (name N or name CA or name C or name O or name CB )) or resid 335 th \ rough 339 or (resid 340 and (name N or name CA or name C or name O or name CB )) \ or resid 341 through 344 or (resid 345 through 360 and (name N or name CA or na \ me C or name O or name CB )) or resid 361 or (resid 362 through 378 and (name N \ or name CA or name C or name O or name CB )) or resid 379 or (resid 380 and (nam \ e N or name CA or name C or name O or name CB )) or resid 381 or (resid 382 thro \ ugh 383 and (name N or name CA or name C or name O or name CB )) or resid 384 or \ (resid 385 through 390 and (name N or name CA or name C or name O or name CB )) \ or resid 391 or (resid 392 through 403 and (name N or name CA or name C or name \ O or name CB )) or resid 404 or (resid 405 through 411 and (name N or name CA o \ r name C or name O or name CB )) or resid 412 through 413 or (resid 414 through \ 415 and (name N or name CA or name C or name O or name CB )) or resid 416 or (re \ sid 417 through 425 and (name N or name CA or name C or name O or name CB )) or \ resid 426 or (resid 427 through 430 and (name N or name CA or name C or name O o \ r name CB )) or resid 431 through 432 or (resid 433 through 445 and (name N or n \ ame CA or name C or name O or name CB )) or resid 446 through 447 or (resid 448 \ through 454 and (name N or name CA or name C or name O or name CB )) or (resid 4 \ 62 and (name N or name CA or name C or name O or name CB )) or resid 463 or (res \ id 464 through 466 and (name N or name CA or name C or name O or name CB )) or r \ esid 491 or (resid 492 through 495 and (name N or name CA or name C or name O or \ name CB )) or resid 496 or (resid 497 through 498 and (name N or name CA or nam \ e C or name O or name CB )) or resid 499 or (resid 500 through 501 and (name N o \ r name CA or name C or name O or name CB )) or resid 502 or (resid 503 and (name \ N or name CA or name C or name O or name CB )) or (resid 504 through 506 and (n \ ame N or name CA or name C or name O or name CB )) or resid 507 or (resid 508 th \ rough 515 and (name N or name CA or name C or name O or name CB )) or (resid 522 \ through 524 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 25 through 527 or (resid 528 through 529 and (name N or name CA or name C or nam \ e O or name CB )) or resid 530 through 553 or (resid 554 and (name N or name CA \ or name C or name O or name CB )) or resid 555 through 567 or (resid 568 and (na \ me N or name CA or name C or name O or name CB )) or resid 569 through 570 or (r \ esid 571 and (name N or name CA or name C or name O or name CB )) or resid 572 t \ hrough 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 n \ ame C or name O or name CB )) or resid 587 through 618 or (resid 619 and (name N \ or name CA or name C or name O or name CB )) or resid 620 through 645 or (resid \ 646 through 647 and (name N or name CA or name C or name O or name CB )) or res \ id 648 through 793 or (resid 794 and (name N or name CA or name C or name O or n \ ame CB )) or resid 795 or (resid 796 and (name N or name CA or name C or name O \ or name CB )) or resid 797 through 920 or (resid 921 and (name N or name CA or n \ ame C or name O or name CB )) or resid 922 through 1072 or (resid 1073 and (name \ N or name CA or name C or name O or name CB )) or resid 1074 through 1117 or (r \ esid 1118 and (name N or name CA or name C or name O or name CB )) or resid 1119 \ 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 1310)) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' } ncs_group { reference = chain 'H' selection = chain 'N' } ncs_group { reference = chain 'L' selection = chain 'S' } 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=0.40 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: 3.450 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: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 30.470 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.413 27153 Z= 0.373 Angle : 1.093 54.885 37118 Z= 0.593 Chirality : 0.061 1.379 4443 Planarity : 0.006 0.122 4668 Dihedral : 12.579 90.574 10348 Min Nonbonded Distance : 1.483 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.13 % Favored : 93.81 % Rotamer: Outliers : 0.26 % Allowed : 0.95 % Favored : 98.79 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -1.54 (0.14), residues: 3333 helix: -0.51 (0.19), residues: 647 sheet: -0.68 (0.18), residues: 798 loop : -1.36 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 66 TYR 0.077 0.003 TYR G 449 PHE 0.043 0.003 PHE A1121 TRP 0.053 0.003 TRP H 103 HIS 0.015 0.002 HIS S 38 Details of bonding type rmsd covalent geometry : bond 0.00819 (27051) covalent geometry : angle 1.05099 (36854) SS BOND : bond 0.00702 ( 42) SS BOND : angle 2.82831 ( 84) hydrogen bonds : bond 0.26654 ( 1011) hydrogen bonds : angle 10.16128 ( 2796) link_BETA1-4 : bond 0.00353 ( 13) link_BETA1-4 : angle 2.00478 ( 39) link_NAG-ASN : bond 0.00761 ( 47) link_NAG-ASN : angle 4.45228 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 384 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 698 SER cc_start: 0.8764 (t) cc_final: 0.8236 (p) REVERT: A 739 THR cc_start: 0.7581 (m) cc_final: 0.7353 (m) REVERT: A 1107 ARG cc_start: 0.7237 (mtt90) cc_final: 0.7028 (mpt180) REVERT: B 64 TRP cc_start: 0.8065 (t60) cc_final: 0.7568 (t60) REVERT: B 773 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8104 (mt-10) REVERT: B 878 LEU cc_start: 0.8475 (tp) cc_final: 0.7753 (mp) REVERT: B 1111 GLU cc_start: 0.7630 (mp0) cc_final: 0.7400 (mp0) REVERT: G 287 ASP cc_start: 0.8274 (m-30) cc_final: 0.7828 (m-30) REVERT: G 290 ASP cc_start: 0.6999 (t0) cc_final: 0.6416 (t0) REVERT: H 34 MET cc_start: 0.8861 (mmp) cc_final: 0.8274 (mmm) REVERT: H 82 LEU cc_start: 0.7145 (mt) cc_final: 0.6816 (tp) REVERT: L 20 ILE cc_start: 0.8251 (mt) cc_final: 0.8005 (tt) REVERT: L 34 TRP cc_start: 0.4188 (m100) cc_final: 0.3840 (m100) REVERT: L 85 TYR cc_start: 0.5541 (m-80) cc_final: 0.5164 (m-80) REVERT: L 86 TYR cc_start: 0.7144 (m-80) cc_final: 0.6876 (m-80) REVERT: N 36 TRP cc_start: 0.7206 (m100) cc_final: 0.6794 (m100) REVERT: N 48 MET cc_start: 0.8375 (mmt) cc_final: 0.7965 (mmt) REVERT: S 46 MET cc_start: 0.6997 (mtp) cc_final: 0.6515 (ptp) REVERT: S 103 LEU cc_start: 0.8021 (tp) cc_final: 0.7804 (mt) outliers start: 7 outliers final: 2 residues processed: 389 average time/residue: 0.1525 time to fit residues: 98.2655 Evaluate side-chains 255 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 253 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain G residue 517 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.0770 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 804 GLN A 895 GLN A 955 ASN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN B 196 ASN B 207 HIS B 895 GLN B 935 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS G 388 ASN ** G 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 901 GLN G1023 ASN ** G1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1106 GLN N 96 ASN N 97 HIS S 36 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.145545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.104824 restraints weight = 87993.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.110078 restraints weight = 42267.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.111178 restraints weight = 21408.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.112085 restraints weight = 15947.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.112336 restraints weight = 14423.198| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3733 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3733 r_free = 0.3733 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3733 r_free = 0.3733 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3733 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 27153 Z= 0.180 Angle : 0.781 13.495 37118 Z= 0.399 Chirality : 0.049 0.702 4443 Planarity : 0.005 0.062 4668 Dihedral : 7.434 59.979 4885 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.02 % Favored : 94.92 % Rotamer: Outliers : 1.10 % Allowed : 7.97 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.14), residues: 3333 helix: 0.40 (0.20), residues: 658 sheet: -0.51 (0.17), residues: 798 loop : -1.22 (0.14), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 357 TYR 0.040 0.002 TYR G 449 PHE 0.031 0.002 PHE G 400 TRP 0.044 0.003 TRP H 103 HIS 0.010 0.002 HIS G1048 Details of bonding type rmsd covalent geometry : bond 0.00407 (27051) covalent geometry : angle 0.74534 (36854) SS BOND : bond 0.00523 ( 42) SS BOND : angle 2.24578 ( 84) hydrogen bonds : bond 0.05681 ( 1011) hydrogen bonds : angle 7.23379 ( 2796) link_BETA1-4 : bond 0.00559 ( 13) link_BETA1-4 : angle 1.58032 ( 39) link_NAG-ASN : bond 0.00525 ( 47) link_NAG-ASN : angle 3.41849 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 316 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6758 (pt0) REVERT: A 297 SER cc_start: 0.8353 (m) cc_final: 0.7686 (t) REVERT: A 698 SER cc_start: 0.8593 (t) cc_final: 0.8210 (p) REVERT: A 759 PHE cc_start: 0.8735 (m-80) cc_final: 0.8191 (m-80) REVERT: A 915 VAL cc_start: 0.6913 (p) cc_final: 0.6622 (t) REVERT: B 229 LEU cc_start: 0.9162 (mt) cc_final: 0.8885 (mp) REVERT: B 319 ARG cc_start: 0.7601 (ttm-80) cc_final: 0.7280 (ttm-80) REVERT: B 773 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8118 (mt-10) REVERT: B 858 LEU cc_start: 0.9142 (tt) cc_final: 0.8894 (mp) REVERT: G 135 PHE cc_start: 0.5007 (m-80) cc_final: 0.4765 (m-80) REVERT: G 265 TYR cc_start: 0.5762 (p90) cc_final: 0.5470 (p90) REVERT: G 287 ASP cc_start: 0.8227 (m-30) cc_final: 0.7517 (m-30) REVERT: G 1002 GLN cc_start: 0.8839 (tm-30) cc_final: 0.8461 (tm-30) REVERT: G 1005 GLN cc_start: 0.8789 (tp40) cc_final: 0.8572 (mm-40) REVERT: H 34 MET cc_start: 0.8797 (mmp) cc_final: 0.8205 (mmm) REVERT: H 52 ASN cc_start: 0.7430 (t0) cc_final: 0.7090 (t0) REVERT: H 63 LEU cc_start: 0.8497 (tp) cc_final: 0.7551 (mt) REVERT: H 69 MET cc_start: 0.4879 (pmm) cc_final: 0.3926 (pmm) REVERT: H 80 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8088 (mmm) REVERT: H 81 GLU cc_start: 0.6944 (mp0) cc_final: 0.5804 (mp0) REVERT: L 20 ILE cc_start: 0.8209 (mt) cc_final: 0.7867 (tt) REVERT: N 36 TRP cc_start: 0.6064 (m100) cc_final: 0.5256 (m100) REVERT: N 48 MET cc_start: 0.8448 (mmt) cc_final: 0.7923 (mmt) REVERT: N 80 MET cc_start: 0.7576 (tmm) cc_final: 0.6946 (tmm) REVERT: S 30 LYS cc_start: 0.5872 (pttt) cc_final: 0.5276 (ptpp) REVERT: S 46 MET cc_start: 0.7391 (mtp) cc_final: 0.6623 (ptt) outliers start: 30 outliers final: 14 residues processed: 336 average time/residue: 0.1552 time to fit residues: 86.4213 Evaluate side-chains 269 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 254 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain G residue 574 ASP Chi-restraints excluded: chain G residue 969 ASN Chi-restraints excluded: chain G residue 1077 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 92 optimal weight: 0.6980 chunk 68 optimal weight: 0.0670 chunk 75 optimal weight: 2.9990 chunk 259 optimal weight: 6.9990 chunk 221 optimal weight: 0.3980 chunk 88 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 220 optimal weight: 7.9990 chunk 329 optimal weight: 40.0000 chunk 197 optimal weight: 0.0470 chunk 181 optimal weight: 3.9990 overall best weight: 0.8418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN A 895 GLN A 935 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 895 GLN B 955 ASN B1010 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS G 895 GLN G 901 GLN ** G 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 97 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.145876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.104577 restraints weight = 126347.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.110238 restraints weight = 52567.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.111929 restraints weight = 25092.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.112064 restraints weight = 19611.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.112468 restraints weight = 17583.921| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3742 r_free = 0.3742 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3742 r_free = 0.3742 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27153 Z= 0.139 Angle : 0.686 12.735 37118 Z= 0.347 Chirality : 0.047 0.579 4443 Planarity : 0.004 0.052 4668 Dihedral : 6.488 55.759 4881 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.69 % Favored : 95.25 % Rotamer: Outliers : 1.57 % Allowed : 9.28 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.14), residues: 3333 helix: 0.70 (0.20), residues: 657 sheet: -0.32 (0.17), residues: 792 loop : -1.12 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 60 TYR 0.030 0.002 TYR G 449 PHE 0.025 0.002 PHE A 497 TRP 0.031 0.002 TRP S 34 HIS 0.009 0.002 HIS G1101 Details of bonding type rmsd covalent geometry : bond 0.00309 (27051) covalent geometry : angle 0.65352 (36854) SS BOND : bond 0.00563 ( 42) SS BOND : angle 1.94104 ( 84) hydrogen bonds : bond 0.04445 ( 1011) hydrogen bonds : angle 6.57289 ( 2796) link_BETA1-4 : bond 0.00448 ( 13) link_BETA1-4 : angle 1.43273 ( 39) link_NAG-ASN : bond 0.00480 ( 47) link_NAG-ASN : angle 3.05271 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 306 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6689 (pt0) REVERT: A 414 GLN cc_start: 0.8294 (tp-100) cc_final: 0.7991 (mm-40) REVERT: A 501 ASN cc_start: 0.8729 (m-40) cc_final: 0.8346 (m110) REVERT: A 698 SER cc_start: 0.8636 (t) cc_final: 0.8156 (p) REVERT: A 759 PHE cc_start: 0.8664 (m-80) cc_final: 0.8112 (m-80) REVERT: A 1107 ARG cc_start: 0.7324 (mpt180) cc_final: 0.6957 (mpt180) REVERT: B 317 ASN cc_start: 0.8648 (t0) cc_final: 0.7604 (p0) REVERT: B 773 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8077 (mt-10) REVERT: B 800 PHE cc_start: 0.7212 (m-80) cc_final: 0.6515 (m-80) REVERT: B 858 LEU cc_start: 0.9129 (tt) cc_final: 0.8906 (mp) REVERT: B 902 MET cc_start: 0.7897 (mmt) cc_final: 0.7531 (mmt) REVERT: B 1107 ARG cc_start: 0.6872 (mpt180) cc_final: 0.6127 (mpt180) REVERT: G 265 TYR cc_start: 0.5829 (p90) cc_final: 0.5539 (p90) REVERT: G 287 ASP cc_start: 0.8240 (m-30) cc_final: 0.7471 (m-30) REVERT: G 584 ILE cc_start: 0.9376 (mm) cc_final: 0.9122 (mm) REVERT: G 1002 GLN cc_start: 0.8844 (tm-30) cc_final: 0.8349 (tm-30) REVERT: G 1107 ARG cc_start: 0.6913 (mmm160) cc_final: 0.6046 (ttm170) REVERT: H 34 MET cc_start: 0.8737 (mmp) cc_final: 0.8255 (mmm) REVERT: H 48 MET cc_start: 0.7354 (mmt) cc_final: 0.7141 (mpp) REVERT: H 52 ASN cc_start: 0.7502 (t0) cc_final: 0.7218 (t0) REVERT: H 63 LEU cc_start: 0.8348 (tp) cc_final: 0.7513 (mt) REVERT: H 69 MET cc_start: 0.5179 (pmm) cc_final: 0.4344 (pmm) REVERT: H 82 LEU cc_start: 0.5138 (mt) cc_final: 0.4680 (mm) REVERT: L 34 TRP cc_start: 0.6730 (m100) cc_final: 0.6147 (m100) REVERT: L 36 GLN cc_start: 0.5113 (OUTLIER) cc_final: 0.4209 (pm20) REVERT: N 35 HIS cc_start: 0.8770 (m90) cc_final: 0.8095 (m-70) REVERT: N 36 TRP cc_start: 0.5658 (m100) cc_final: 0.5162 (m100) REVERT: N 80 MET cc_start: 0.7644 (tmm) cc_final: 0.6878 (tmm) REVERT: N 98 GLU cc_start: 0.7762 (mp0) cc_final: 0.7544 (mp0) REVERT: N 100 TYR cc_start: 0.5141 (m-10) cc_final: 0.4900 (m-10) REVERT: S 30 LYS cc_start: 0.5513 (pttt) cc_final: 0.4884 (ptpp) REVERT: S 46 MET cc_start: 0.7334 (mtp) cc_final: 0.6550 (ptt) outliers start: 43 outliers final: 24 residues processed: 330 average time/residue: 0.1480 time to fit residues: 79.6361 Evaluate side-chains 276 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 251 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 716 THR Chi-restraints excluded: chain G residue 772 VAL Chi-restraints excluded: chain G residue 969 ASN Chi-restraints excluded: chain G residue 1077 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 36 GLN Chi-restraints excluded: chain N residue 92 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 101 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 chunk 240 optimal weight: 0.0570 chunk 125 optimal weight: 50.0000 chunk 31 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 330 optimal weight: 20.0000 chunk 193 optimal weight: 10.0000 overall best weight: 3.1304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 895 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS G 895 GLN G 901 GLN G 969 ASN ** G1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1119 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.144949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.102271 restraints weight = 123376.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.107588 restraints weight = 51306.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.109519 restraints weight = 25932.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.110832 restraints weight = 16910.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.110985 restraints weight = 15353.340| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3677 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3677 r_free = 0.3677 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3677 r_free = 0.3677 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3677 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 27153 Z= 0.231 Angle : 0.736 12.505 37118 Z= 0.374 Chirality : 0.048 0.589 4443 Planarity : 0.005 0.054 4668 Dihedral : 6.383 55.743 4881 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.16 % Favored : 93.81 % Rotamer: Outliers : 2.16 % Allowed : 11.29 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.96 (0.14), residues: 3333 helix: 0.59 (0.20), residues: 651 sheet: -0.52 (0.17), residues: 841 loop : -1.14 (0.14), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 60 TYR 0.034 0.002 TYR N 100G PHE 0.038 0.002 PHE G1089 TRP 0.039 0.002 TRP S 34 HIS 0.010 0.002 HIS G1048 Details of bonding type rmsd covalent geometry : bond 0.00532 (27051) covalent geometry : angle 0.70563 (36854) SS BOND : bond 0.00704 ( 42) SS BOND : angle 2.15942 ( 84) hydrogen bonds : bond 0.04522 ( 1011) hydrogen bonds : angle 6.48821 ( 2796) link_BETA1-4 : bond 0.00584 ( 13) link_BETA1-4 : angle 1.47826 ( 39) link_NAG-ASN : bond 0.00531 ( 47) link_NAG-ASN : angle 3.03057 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 261 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.7169 (t80) cc_final: 0.6887 (t80) REVERT: A 414 GLN cc_start: 0.8389 (tp-100) cc_final: 0.8131 (mm-40) REVERT: A 501 ASN cc_start: 0.8737 (m-40) cc_final: 0.8435 (m110) REVERT: A 698 SER cc_start: 0.8701 (t) cc_final: 0.8320 (p) REVERT: A 856 ASN cc_start: 0.7533 (m-40) cc_final: 0.7206 (t0) REVERT: B 317 ASN cc_start: 0.8634 (t0) cc_final: 0.7783 (p0) REVERT: B 773 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8187 (mt-10) REVERT: B 1029 MET cc_start: 0.6428 (tpp) cc_final: 0.6204 (mtt) REVERT: B 1107 ARG cc_start: 0.7080 (mpt180) cc_final: 0.6373 (mpt180) REVERT: G 135 PHE cc_start: 0.4917 (m-80) cc_final: 0.4009 (m-80) REVERT: G 287 ASP cc_start: 0.8247 (m-30) cc_final: 0.7436 (m-30) REVERT: G 584 ILE cc_start: 0.9352 (mm) cc_final: 0.9080 (mm) REVERT: G 1002 GLN cc_start: 0.8912 (tm-30) cc_final: 0.8484 (tp-100) REVERT: G 1006 THR cc_start: 0.8461 (m) cc_final: 0.7872 (m) REVERT: G 1107 ARG cc_start: 0.7063 (mmm160) cc_final: 0.6080 (ttm170) REVERT: H 34 MET cc_start: 0.8790 (mmp) cc_final: 0.8294 (mmm) REVERT: H 47 TRP cc_start: 0.6871 (t60) cc_final: 0.6185 (t60) REVERT: H 48 MET cc_start: 0.7490 (mmt) cc_final: 0.7060 (mpp) REVERT: H 69 MET cc_start: 0.4810 (pmm) cc_final: 0.3904 (pmm) REVERT: H 80 MET cc_start: 0.8609 (tpp) cc_final: 0.8264 (mmm) REVERT: H 100 TYR cc_start: 0.5746 (p90) cc_final: 0.5256 (p90) REVERT: L 34 TRP cc_start: 0.6742 (m100) cc_final: 0.6028 (m100) REVERT: L 36 GLN cc_start: 0.5366 (OUTLIER) cc_final: 0.4448 (pm20) REVERT: L 82 GLU cc_start: 0.6864 (tt0) cc_final: 0.6646 (pt0) REVERT: N 34 MET cc_start: 0.7849 (mmm) cc_final: 0.7525 (mmm) REVERT: N 35 HIS cc_start: 0.8701 (m90) cc_final: 0.7989 (m-70) REVERT: N 80 MET cc_start: 0.7637 (tmm) cc_final: 0.6997 (tmm) REVERT: N 100 TYR cc_start: 0.5501 (m-10) cc_final: 0.5237 (m-10) REVERT: S 46 MET cc_start: 0.7498 (mtp) cc_final: 0.6699 (ptt) outliers start: 59 outliers final: 44 residues processed: 300 average time/residue: 0.1455 time to fit residues: 72.9729 Evaluate side-chains 278 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 233 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 716 THR Chi-restraints excluded: chain G residue 738 CYS Chi-restraints excluded: chain G residue 772 VAL Chi-restraints excluded: chain G residue 902 MET Chi-restraints excluded: chain G residue 969 ASN Chi-restraints excluded: chain G residue 1077 THR Chi-restraints excluded: chain G residue 1117 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 36 GLN Chi-restraints excluded: chain L residue 38 HIS Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain N residue 92 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 291 optimal weight: 6.9990 chunk 295 optimal weight: 40.0000 chunk 172 optimal weight: 6.9990 chunk 281 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 218 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 267 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 311 optimal weight: 30.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 895 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS G 394 ASN G 493 GLN G 804 GLN G 895 GLN ** G1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.148414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.106518 restraints weight = 122996.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.112169 restraints weight = 51170.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.114243 restraints weight = 24218.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.116036 restraints weight = 15631.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.115972 restraints weight = 13673.397| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3680 r_free = 0.3680 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3680 r_free = 0.3680 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 27153 Z= 0.198 Angle : 0.708 11.951 37118 Z= 0.359 Chirality : 0.047 0.548 4443 Planarity : 0.005 0.055 4668 Dihedral : 6.259 55.458 4881 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.83 % Favored : 94.14 % Rotamer: Outliers : 2.78 % Allowed : 12.24 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.94 (0.14), residues: 3333 helix: 0.64 (0.20), residues: 655 sheet: -0.54 (0.17), residues: 856 loop : -1.13 (0.14), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 60 TYR 0.026 0.002 TYR A 200 PHE 0.028 0.002 PHE G1089 TRP 0.023 0.002 TRP B1102 HIS 0.010 0.001 HIS G1048 Details of bonding type rmsd covalent geometry : bond 0.00451 (27051) covalent geometry : angle 0.67448 (36854) SS BOND : bond 0.00569 ( 42) SS BOND : angle 2.36570 ( 84) hydrogen bonds : bond 0.04222 ( 1011) hydrogen bonds : angle 6.33097 ( 2796) link_BETA1-4 : bond 0.00534 ( 13) link_BETA1-4 : angle 1.38973 ( 39) link_NAG-ASN : bond 0.00546 ( 47) link_NAG-ASN : angle 3.00630 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 249 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.7177 (t80) cc_final: 0.6874 (t80) REVERT: A 501 ASN cc_start: 0.8677 (m-40) cc_final: 0.8416 (m110) REVERT: A 698 SER cc_start: 0.8691 (t) cc_final: 0.8272 (p) REVERT: A 856 ASN cc_start: 0.7686 (m-40) cc_final: 0.7307 (t0) REVERT: B 317 ASN cc_start: 0.8625 (t0) cc_final: 0.7890 (p0) REVERT: B 773 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8175 (mt-10) REVERT: B 878 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.7820 (mp) REVERT: B 1107 ARG cc_start: 0.7159 (mpt180) cc_final: 0.6477 (mpt180) REVERT: G 287 ASP cc_start: 0.8275 (m-30) cc_final: 0.7560 (m-30) REVERT: G 584 ILE cc_start: 0.9344 (mm) cc_final: 0.9039 (mm) REVERT: G 1002 GLN cc_start: 0.8929 (tm-30) cc_final: 0.8661 (tp-100) REVERT: G 1006 THR cc_start: 0.8590 (m) cc_final: 0.8313 (m) REVERT: G 1107 ARG cc_start: 0.7033 (mmm160) cc_final: 0.6187 (ttm170) REVERT: H 34 MET cc_start: 0.8764 (mmp) cc_final: 0.8295 (mmm) REVERT: H 47 TRP cc_start: 0.6892 (t60) cc_final: 0.6399 (t60) REVERT: H 48 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.7139 (mpp) REVERT: H 63 LEU cc_start: 0.8341 (tp) cc_final: 0.7530 (mt) REVERT: H 69 MET cc_start: 0.5346 (pmm) cc_final: 0.4573 (pmm) REVERT: H 100 TYR cc_start: 0.5554 (p90) cc_final: 0.5128 (p90) REVERT: L 34 TRP cc_start: 0.6505 (m100) cc_final: 0.5869 (m100) REVERT: L 35 TYR cc_start: 0.7220 (m-80) cc_final: 0.6574 (m-80) REVERT: L 36 GLN cc_start: 0.5284 (OUTLIER) cc_final: 0.4812 (pm20) REVERT: L 60 ARG cc_start: 0.6428 (mtm110) cc_final: 0.6213 (mtm110) REVERT: L 82 GLU cc_start: 0.6918 (tt0) cc_final: 0.6714 (pt0) REVERT: N 34 MET cc_start: 0.7809 (mmm) cc_final: 0.7577 (mmm) REVERT: N 35 HIS cc_start: 0.8603 (m90) cc_final: 0.8062 (m-70) REVERT: S 30 LYS cc_start: 0.5207 (OUTLIER) cc_final: 0.4932 (pptt) REVERT: S 46 MET cc_start: 0.7306 (mtp) cc_final: 0.6403 (ptt) outliers start: 76 outliers final: 59 residues processed: 300 average time/residue: 0.1406 time to fit residues: 71.2167 Evaluate side-chains 291 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 228 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 312 ILE Chi-restraints excluded: chain G residue 326 ILE Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 716 THR Chi-restraints excluded: chain G residue 738 CYS Chi-restraints excluded: chain G residue 772 VAL Chi-restraints excluded: chain G residue 858 LEU Chi-restraints excluded: chain G residue 902 MET Chi-restraints excluded: chain G residue 915 VAL Chi-restraints excluded: chain G residue 969 ASN Chi-restraints excluded: chain G residue 990 GLU Chi-restraints excluded: chain G residue 1077 THR Chi-restraints excluded: chain G residue 1117 THR Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 36 GLN Chi-restraints excluded: chain L residue 38 HIS Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain N residue 92 CYS Chi-restraints excluded: chain S residue 30 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 180 optimal weight: 0.8980 chunk 296 optimal weight: 30.0000 chunk 195 optimal weight: 9.9990 chunk 324 optimal weight: 50.0000 chunk 45 optimal weight: 5.9990 chunk 325 optimal weight: 6.9990 chunk 270 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 145 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 895 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS B1108 ASN G 360 ASN ** G 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 895 GLN G 969 ASN ** G1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.141408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.099512 restraints weight = 114577.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.104986 restraints weight = 50798.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.106159 restraints weight = 23375.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.106528 restraints weight = 17776.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.106865 restraints weight = 17321.341| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 27153 Z= 0.287 Angle : 0.774 11.815 37118 Z= 0.393 Chirality : 0.049 0.586 4443 Planarity : 0.005 0.058 4668 Dihedral : 6.564 59.107 4881 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.76 % Favored : 93.21 % Rotamer: Outliers : 3.33 % Allowed : 12.79 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.14), residues: 3333 helix: 0.40 (0.20), residues: 657 sheet: -0.55 (0.17), residues: 839 loop : -1.30 (0.14), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 60 TYR 0.027 0.002 TYR G1047 PHE 0.040 0.003 PHE G1089 TRP 0.021 0.002 TRP G1102 HIS 0.010 0.002 HIS G1048 Details of bonding type rmsd covalent geometry : bond 0.00657 (27051) covalent geometry : angle 0.74185 (36854) SS BOND : bond 0.00646 ( 42) SS BOND : angle 2.45675 ( 84) hydrogen bonds : bond 0.04503 ( 1011) hydrogen bonds : angle 6.46437 ( 2796) link_BETA1-4 : bond 0.00492 ( 13) link_BETA1-4 : angle 1.51657 ( 39) link_NAG-ASN : bond 0.00579 ( 47) link_NAG-ASN : angle 3.11499 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 252 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.7573 (t80) cc_final: 0.7222 (t80) REVERT: A 501 ASN cc_start: 0.8682 (m-40) cc_final: 0.8413 (m110) REVERT: A 528 LYS cc_start: 0.8131 (mmmt) cc_final: 0.7740 (pttp) REVERT: A 698 SER cc_start: 0.8830 (t) cc_final: 0.8426 (p) REVERT: A 856 ASN cc_start: 0.7775 (m-40) cc_final: 0.7437 (t0) REVERT: B 42 VAL cc_start: 0.9316 (t) cc_final: 0.9098 (p) REVERT: B 290 ASP cc_start: 0.8332 (t0) cc_final: 0.7980 (t0) REVERT: B 317 ASN cc_start: 0.8664 (t0) cc_final: 0.8023 (p0) REVERT: B 758 SER cc_start: 0.9012 (m) cc_final: 0.8660 (p) REVERT: B 773 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8223 (mt-10) REVERT: B 787 GLN cc_start: 0.6825 (mm-40) cc_final: 0.6502 (mm-40) REVERT: B 1107 ARG cc_start: 0.7236 (mpt180) cc_final: 0.6681 (mpt180) REVERT: G 118 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7236 (pp) REVERT: G 287 ASP cc_start: 0.8355 (m-30) cc_final: 0.7557 (m-30) REVERT: G 584 ILE cc_start: 0.9347 (mm) cc_final: 0.9035 (mm) REVERT: G 1002 GLN cc_start: 0.8959 (tm-30) cc_final: 0.8672 (tp-100) REVERT: G 1006 THR cc_start: 0.8831 (m) cc_final: 0.8578 (m) REVERT: G 1107 ARG cc_start: 0.7235 (mmm160) cc_final: 0.6099 (ttm170) REVERT: H 34 MET cc_start: 0.8757 (mmp) cc_final: 0.8304 (mmm) REVERT: H 47 TRP cc_start: 0.7028 (t60) cc_final: 0.6733 (t60) REVERT: H 48 MET cc_start: 0.7461 (OUTLIER) cc_final: 0.7100 (mpp) REVERT: H 63 LEU cc_start: 0.8392 (tp) cc_final: 0.7616 (mt) REVERT: H 69 MET cc_start: 0.5633 (pmm) cc_final: 0.4753 (pmm) REVERT: H 80 MET cc_start: 0.8205 (tpp) cc_final: 0.7914 (mmm) REVERT: H 100 MET cc_start: 0.7378 (ppp) cc_final: 0.7167 (tmm) REVERT: L 34 TRP cc_start: 0.6534 (m100) cc_final: 0.5822 (m100) REVERT: L 35 TYR cc_start: 0.7004 (m-80) cc_final: 0.6558 (m-80) REVERT: L 36 GLN cc_start: 0.5513 (OUTLIER) cc_final: 0.4867 (pm20) REVERT: L 60 ARG cc_start: 0.6604 (mtm110) cc_final: 0.6184 (mtm110) REVERT: N 34 MET cc_start: 0.7778 (mmm) cc_final: 0.7530 (mmm) REVERT: N 35 HIS cc_start: 0.8472 (m90) cc_final: 0.7904 (m90) REVERT: S 30 LYS cc_start: 0.5272 (OUTLIER) cc_final: 0.5005 (pptt) REVERT: S 46 MET cc_start: 0.7296 (mtp) cc_final: 0.6362 (ptt) outliers start: 91 outliers final: 73 residues processed: 314 average time/residue: 0.1424 time to fit residues: 75.0138 Evaluate side-chains 304 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 227 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 312 ILE Chi-restraints excluded: chain G residue 326 ILE Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 461 LEU Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 525 CYS Chi-restraints excluded: chain G residue 697 MET Chi-restraints excluded: chain G residue 716 THR Chi-restraints excluded: chain G residue 738 CYS Chi-restraints excluded: chain G residue 772 VAL Chi-restraints excluded: chain G residue 858 LEU Chi-restraints excluded: chain G residue 915 VAL Chi-restraints excluded: chain G residue 969 ASN Chi-restraints excluded: chain G residue 990 GLU Chi-restraints excluded: chain G residue 1029 MET Chi-restraints excluded: chain G residue 1077 THR Chi-restraints excluded: chain G residue 1117 THR Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 36 GLN Chi-restraints excluded: chain L residue 38 HIS Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain N residue 92 CYS Chi-restraints excluded: chain S residue 30 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 122 optimal weight: 3.9990 chunk 326 optimal weight: 6.9990 chunk 28 optimal weight: 0.2980 chunk 273 optimal weight: 0.7980 chunk 154 optimal weight: 0.3980 chunk 266 optimal weight: 6.9990 chunk 286 optimal weight: 6.9990 chunk 297 optimal weight: 7.9990 chunk 216 optimal weight: 3.9990 chunk 211 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 787 GLN B 895 GLN B 949 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS G 314 GLN G 394 ASN G 895 GLN ** G1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.143017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.100867 restraints weight = 118359.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.106454 restraints weight = 47507.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.108297 restraints weight = 22634.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.110283 restraints weight = 15187.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.110089 restraints weight = 13417.618| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27153 Z= 0.139 Angle : 0.675 11.355 37118 Z= 0.338 Chirality : 0.046 0.482 4443 Planarity : 0.004 0.055 4668 Dihedral : 6.106 57.954 4881 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.99 % Favored : 94.98 % Rotamer: Outliers : 2.30 % Allowed : 14.66 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.14), residues: 3333 helix: 0.68 (0.20), residues: 655 sheet: -0.44 (0.17), residues: 839 loop : -1.11 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 357 TYR 0.024 0.002 TYR A 451 PHE 0.025 0.002 PHE G 497 TRP 0.022 0.002 TRP B1102 HIS 0.009 0.001 HIS G1048 Details of bonding type rmsd covalent geometry : bond 0.00313 (27051) covalent geometry : angle 0.64050 (36854) SS BOND : bond 0.00452 ( 42) SS BOND : angle 2.26785 ( 84) hydrogen bonds : bond 0.03891 ( 1011) hydrogen bonds : angle 6.12020 ( 2796) link_BETA1-4 : bond 0.00363 ( 13) link_BETA1-4 : angle 1.28813 ( 39) link_NAG-ASN : bond 0.00454 ( 47) link_NAG-ASN : angle 3.03366 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 270 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ASN cc_start: 0.8349 (t0) cc_final: 0.7326 (p0) REVERT: A 501 ASN cc_start: 0.8661 (m-40) cc_final: 0.8421 (m110) REVERT: A 698 SER cc_start: 0.8708 (t) cc_final: 0.8234 (p) REVERT: A 856 ASN cc_start: 0.7672 (m-40) cc_final: 0.7324 (t0) REVERT: A 869 MET cc_start: 0.7393 (mtp) cc_final: 0.7153 (mtp) REVERT: A 1050 MET cc_start: 0.6847 (ptm) cc_final: 0.6605 (ptt) REVERT: A 1109 PHE cc_start: 0.7211 (OUTLIER) cc_final: 0.6522 (m-80) REVERT: B 42 VAL cc_start: 0.9306 (t) cc_final: 0.9106 (p) REVERT: B 290 ASP cc_start: 0.8004 (t0) cc_final: 0.7668 (t70) REVERT: B 317 ASN cc_start: 0.8632 (t0) cc_final: 0.8011 (p0) REVERT: B 773 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8098 (mt-10) REVERT: B 787 GLN cc_start: 0.6445 (mm110) cc_final: 0.6150 (mm-40) REVERT: B 1107 ARG cc_start: 0.7246 (mpt180) cc_final: 0.7025 (mpt180) REVERT: G 118 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7234 (pp) REVERT: G 287 ASP cc_start: 0.8339 (m-30) cc_final: 0.7523 (m-30) REVERT: G 584 ILE cc_start: 0.9333 (mm) cc_final: 0.9017 (mm) REVERT: G 1002 GLN cc_start: 0.8894 (tm-30) cc_final: 0.8575 (tp-100) REVERT: G 1006 THR cc_start: 0.8707 (m) cc_final: 0.8414 (m) REVERT: G 1107 ARG cc_start: 0.7068 (mmm160) cc_final: 0.6228 (ttm170) REVERT: H 34 MET cc_start: 0.8620 (mmp) cc_final: 0.8219 (mmm) REVERT: H 47 TRP cc_start: 0.7112 (t60) cc_final: 0.6768 (t60) REVERT: H 48 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.7261 (mpp) REVERT: H 69 MET cc_start: 0.6125 (pmm) cc_final: 0.5258 (pmm) REVERT: L 34 TRP cc_start: 0.6409 (m100) cc_final: 0.5360 (m100) REVERT: L 35 TYR cc_start: 0.7006 (m-80) cc_final: 0.6508 (m-80) REVERT: L 36 GLN cc_start: 0.5463 (OUTLIER) cc_final: 0.4966 (pm20) REVERT: N 34 MET cc_start: 0.7894 (mmm) cc_final: 0.7635 (mmm) REVERT: N 35 HIS cc_start: 0.8565 (m90) cc_final: 0.8013 (m90) REVERT: N 83 ARG cc_start: 0.8420 (ptm160) cc_final: 0.8189 (ptp90) REVERT: S 30 LYS cc_start: 0.5538 (pptt) cc_final: 0.4925 (pptt) REVERT: S 46 MET cc_start: 0.7169 (mtp) cc_final: 0.6252 (ptt) outliers start: 63 outliers final: 52 residues processed: 314 average time/residue: 0.1387 time to fit residues: 73.3157 Evaluate side-chains 283 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 227 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 1109 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 326 ILE Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 525 CYS Chi-restraints excluded: chain G residue 697 MET Chi-restraints excluded: chain G residue 738 CYS Chi-restraints excluded: chain G residue 902 MET Chi-restraints excluded: chain G residue 1029 MET Chi-restraints excluded: chain G residue 1077 THR Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 36 GLN Chi-restraints excluded: chain L residue 38 HIS Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 92 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 141 optimal weight: 10.0000 chunk 49 optimal weight: 20.0000 chunk 123 optimal weight: 40.0000 chunk 192 optimal weight: 0.8980 chunk 291 optimal weight: 3.9990 chunk 176 optimal weight: 7.9990 chunk 283 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 185 optimal weight: 0.6980 chunk 180 optimal weight: 2.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN A 895 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 895 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS G 895 GLN G 969 ASN ** G1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.139833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.097448 restraints weight = 104459.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.101218 restraints weight = 43603.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.103747 restraints weight = 25417.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.105375 restraints weight = 17861.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.106292 restraints weight = 14245.288| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3639 r_free = 0.3639 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3639 r_free = 0.3639 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 27153 Z= 0.225 Angle : 0.743 11.519 37118 Z= 0.372 Chirality : 0.048 0.473 4443 Planarity : 0.005 0.062 4668 Dihedral : 6.140 55.592 4881 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.88 % Favored : 93.09 % Rotamer: Outliers : 3.18 % Allowed : 14.66 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.14), residues: 3333 helix: 0.54 (0.20), residues: 653 sheet: -0.45 (0.18), residues: 828 loop : -1.19 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 60 TYR 0.024 0.002 TYR A 451 PHE 0.031 0.002 PHE G1089 TRP 0.018 0.002 TRP G1102 HIS 0.010 0.001 HIS G1048 Details of bonding type rmsd covalent geometry : bond 0.00519 (27051) covalent geometry : angle 0.70740 (36854) SS BOND : bond 0.00564 ( 42) SS BOND : angle 2.38752 ( 84) hydrogen bonds : bond 0.04226 ( 1011) hydrogen bonds : angle 6.21558 ( 2796) link_BETA1-4 : bond 0.00388 ( 13) link_BETA1-4 : angle 1.41899 ( 39) link_NAG-ASN : bond 0.00527 ( 47) link_NAG-ASN : angle 3.23189 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 232 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 TYR cc_start: 0.7715 (m-80) cc_final: 0.7041 (m-80) REVERT: A 354 ASN cc_start: 0.8423 (t0) cc_final: 0.7499 (p0) REVERT: A 501 ASN cc_start: 0.8655 (m-40) cc_final: 0.8449 (m110) REVERT: A 698 SER cc_start: 0.8774 (t) cc_final: 0.8404 (p) REVERT: A 699 LEU cc_start: 0.8021 (tt) cc_final: 0.7804 (tp) REVERT: A 856 ASN cc_start: 0.7781 (m-40) cc_final: 0.7554 (t0) REVERT: A 957 GLN cc_start: 0.8591 (mt0) cc_final: 0.8343 (mt0) REVERT: A 1109 PHE cc_start: 0.7436 (OUTLIER) cc_final: 0.7090 (m-80) REVERT: B 116 SER cc_start: 0.7355 (OUTLIER) cc_final: 0.6606 (p) REVERT: B 290 ASP cc_start: 0.8117 (t0) cc_final: 0.7866 (t70) REVERT: B 317 ASN cc_start: 0.8564 (t0) cc_final: 0.8095 (p0) REVERT: B 773 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8123 (mt-10) REVERT: G 118 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7319 (pp) REVERT: G 287 ASP cc_start: 0.8430 (m-30) cc_final: 0.7609 (m-30) REVERT: G 584 ILE cc_start: 0.9309 (mm) cc_final: 0.8996 (mm) REVERT: G 1002 GLN cc_start: 0.8861 (tm-30) cc_final: 0.8559 (tp-100) REVERT: G 1006 THR cc_start: 0.8917 (m) cc_final: 0.8679 (m) REVERT: G 1094 VAL cc_start: 0.4726 (OUTLIER) cc_final: 0.4411 (p) REVERT: G 1107 ARG cc_start: 0.7222 (mmm160) cc_final: 0.6349 (ttm170) REVERT: H 34 MET cc_start: 0.8653 (mmp) cc_final: 0.8297 (mmm) REVERT: H 47 TRP cc_start: 0.7235 (t60) cc_final: 0.6978 (t60) REVERT: H 48 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.7256 (mpp) REVERT: H 69 MET cc_start: 0.5807 (pmm) cc_final: 0.4935 (pmm) REVERT: H 80 MET cc_start: 0.8219 (tpp) cc_final: 0.7968 (mmm) REVERT: H 100 MET cc_start: 0.7631 (tmm) cc_final: 0.7366 (ppp) REVERT: L 34 TRP cc_start: 0.6453 (m100) cc_final: 0.5711 (m100) REVERT: L 35 TYR cc_start: 0.7086 (m-80) cc_final: 0.6597 (m-80) REVERT: L 36 GLN cc_start: 0.5606 (OUTLIER) cc_final: 0.5049 (pm20) REVERT: L 60 ARG cc_start: 0.6766 (mtm110) cc_final: 0.6147 (ttp-110) REVERT: N 34 MET cc_start: 0.7871 (mmm) cc_final: 0.7639 (mmm) REVERT: N 35 HIS cc_start: 0.8491 (m90) cc_final: 0.7948 (m90) REVERT: N 83 ARG cc_start: 0.8373 (ptm160) cc_final: 0.8155 (ptp90) REVERT: S 4 LEU cc_start: 0.7299 (mm) cc_final: 0.6561 (mt) REVERT: S 30 LYS cc_start: 0.5629 (OUTLIER) cc_final: 0.5134 (pptt) REVERT: S 46 MET cc_start: 0.7142 (mtp) cc_final: 0.6228 (ptt) outliers start: 87 outliers final: 64 residues processed: 295 average time/residue: 0.1401 time to fit residues: 69.1120 Evaluate side-chains 291 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 220 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1109 PHE Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 312 ILE Chi-restraints excluded: chain G residue 326 ILE Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 525 CYS Chi-restraints excluded: chain G residue 697 MET Chi-restraints excluded: chain G residue 712 ILE Chi-restraints excluded: chain G residue 716 THR Chi-restraints excluded: chain G residue 738 CYS Chi-restraints excluded: chain G residue 969 ASN Chi-restraints excluded: chain G residue 1077 THR Chi-restraints excluded: chain G residue 1094 VAL Chi-restraints excluded: chain G residue 1117 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 36 GLN Chi-restraints excluded: chain L residue 38 HIS Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 92 CYS Chi-restraints excluded: chain S residue 30 LYS Chi-restraints excluded: chain S residue 38 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 298 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 294 optimal weight: 8.9990 chunk 196 optimal weight: 1.9990 chunk 168 optimal weight: 0.7980 chunk 243 optimal weight: 0.9980 chunk 98 optimal weight: 20.0000 chunk 187 optimal weight: 2.9990 chunk 233 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN A 895 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 895 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS G 895 GLN G 913 GLN G 969 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.144372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.103025 restraints weight = 110697.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.108747 restraints weight = 50142.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.109464 restraints weight = 22501.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.109880 restraints weight = 18661.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.110211 restraints weight = 16659.785| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3661 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3661 r_free = 0.3661 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3661 r_free = 0.3661 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 27153 Z= 0.153 Angle : 0.685 11.589 37118 Z= 0.340 Chirality : 0.047 0.442 4443 Planarity : 0.004 0.054 4668 Dihedral : 5.872 55.445 4881 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.89 % Allowed : 15.31 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.14), residues: 3333 helix: 0.76 (0.20), residues: 659 sheet: -0.36 (0.18), residues: 820 loop : -1.09 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 60 TYR 0.019 0.002 TYR A 451 PHE 0.026 0.002 PHE G 497 TRP 0.019 0.002 TRP G 886 HIS 0.009 0.001 HIS G1048 Details of bonding type rmsd covalent geometry : bond 0.00352 (27051) covalent geometry : angle 0.65089 (36854) SS BOND : bond 0.00421 ( 42) SS BOND : angle 2.07064 ( 84) hydrogen bonds : bond 0.03879 ( 1011) hydrogen bonds : angle 6.06621 ( 2796) link_BETA1-4 : bond 0.00391 ( 13) link_BETA1-4 : angle 1.27083 ( 39) link_NAG-ASN : bond 0.00461 ( 47) link_NAG-ASN : angle 3.12900 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 242 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 TYR cc_start: 0.7621 (m-80) cc_final: 0.6986 (m-80) REVERT: A 354 ASN cc_start: 0.8414 (t0) cc_final: 0.7455 (p0) REVERT: A 501 ASN cc_start: 0.8727 (m-40) cc_final: 0.8510 (m110) REVERT: A 699 LEU cc_start: 0.7799 (tt) cc_final: 0.7477 (tp) REVERT: A 856 ASN cc_start: 0.7761 (m-40) cc_final: 0.7518 (t0) REVERT: A 869 MET cc_start: 0.7302 (mtp) cc_final: 0.7049 (mtp) REVERT: A 957 GLN cc_start: 0.8436 (mt0) cc_final: 0.8176 (mt0) REVERT: A 1109 PHE cc_start: 0.7462 (OUTLIER) cc_final: 0.7049 (m-80) REVERT: B 290 ASP cc_start: 0.8046 (t0) cc_final: 0.7833 (t70) REVERT: B 317 ASN cc_start: 0.8520 (t0) cc_final: 0.8072 (p0) REVERT: B 773 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8095 (mt-10) REVERT: B 1086 LYS cc_start: 0.8450 (tmmt) cc_final: 0.8157 (ttpp) REVERT: G 118 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7299 (pp) REVERT: G 287 ASP cc_start: 0.8428 (m-30) cc_final: 0.7607 (m-30) REVERT: G 584 ILE cc_start: 0.9286 (mm) cc_final: 0.8985 (mm) REVERT: G 1002 GLN cc_start: 0.8851 (tm-30) cc_final: 0.8530 (tp-100) REVERT: G 1006 THR cc_start: 0.8889 (m) cc_final: 0.8641 (m) REVERT: G 1094 VAL cc_start: 0.4550 (OUTLIER) cc_final: 0.4309 (p) REVERT: G 1107 ARG cc_start: 0.7091 (mmm160) cc_final: 0.6437 (ttm170) REVERT: H 34 MET cc_start: 0.8658 (mmp) cc_final: 0.8242 (mmm) REVERT: H 47 TRP cc_start: 0.7132 (t60) cc_final: 0.6869 (t60) REVERT: H 48 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.7247 (mpp) REVERT: H 50 ILE cc_start: 0.6289 (pt) cc_final: 0.5910 (pt) REVERT: H 69 MET cc_start: 0.5779 (pmm) cc_final: 0.4880 (pmm) REVERT: H 80 MET cc_start: 0.8231 (tpp) cc_final: 0.7857 (mmm) REVERT: H 100 TYR cc_start: 0.5039 (p90) cc_final: 0.4710 (p90) REVERT: L 34 TRP cc_start: 0.6510 (m100) cc_final: 0.5725 (m100) REVERT: L 35 TYR cc_start: 0.7003 (m-80) cc_final: 0.6527 (m-80) REVERT: L 36 GLN cc_start: 0.5568 (OUTLIER) cc_final: 0.4953 (pm20) REVERT: L 60 ARG cc_start: 0.6782 (mtm110) cc_final: 0.6249 (mtm110) REVERT: N 35 HIS cc_start: 0.8428 (m90) cc_final: 0.7897 (m90) REVERT: N 83 ARG cc_start: 0.8365 (ptm160) cc_final: 0.8155 (ptp90) REVERT: S 4 LEU cc_start: 0.7360 (mm) cc_final: 0.6656 (mt) REVERT: S 30 LYS cc_start: 0.5674 (OUTLIER) cc_final: 0.5041 (pptt) REVERT: S 46 MET cc_start: 0.6695 (mtp) cc_final: 0.5774 (ptt) outliers start: 79 outliers final: 65 residues processed: 294 average time/residue: 0.1499 time to fit residues: 73.3357 Evaluate side-chains 292 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 221 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 1109 PHE Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 312 ILE Chi-restraints excluded: chain G residue 326 ILE Chi-restraints excluded: chain G residue 336 CYS Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 525 CYS Chi-restraints excluded: chain G residue 697 MET Chi-restraints excluded: chain G residue 716 THR Chi-restraints excluded: chain G residue 738 CYS Chi-restraints excluded: chain G residue 902 MET Chi-restraints excluded: chain G residue 1077 THR Chi-restraints excluded: chain G residue 1094 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 36 GLN Chi-restraints excluded: chain L residue 38 HIS Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 92 CYS Chi-restraints excluded: chain S residue 30 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 58 optimal weight: 0.8980 chunk 95 optimal weight: 0.0020 chunk 57 optimal weight: 0.9980 chunk 177 optimal weight: 0.8980 chunk 225 optimal weight: 3.9990 chunk 284 optimal weight: 2.9990 chunk 174 optimal weight: 6.9990 chunk 202 optimal weight: 0.0010 chunk 36 optimal weight: 0.0270 chunk 111 optimal weight: 10.0000 chunk 256 optimal weight: 0.9980 overall best weight: 0.3652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 901 GLN B1002 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1108 ASN G 895 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.149765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.109593 restraints weight = 114638.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.115044 restraints weight = 48853.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.117181 restraints weight = 20909.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.117444 restraints weight = 17023.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.117716 restraints weight = 14596.161| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 27153 Z= 0.123 Angle : 0.666 12.760 37118 Z= 0.328 Chirality : 0.046 0.448 4443 Planarity : 0.004 0.078 4668 Dihedral : 5.492 54.801 4881 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.27 % Allowed : 16.23 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.59 (0.14), residues: 3333 helix: 0.89 (0.20), residues: 663 sheet: -0.18 (0.18), residues: 813 loop : -0.94 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 60 TYR 0.021 0.001 TYR B 707 PHE 0.025 0.002 PHE G 823 TRP 0.022 0.002 TRP B1102 HIS 0.008 0.001 HIS G1048 Details of bonding type rmsd covalent geometry : bond 0.00276 (27051) covalent geometry : angle 0.63501 (36854) SS BOND : bond 0.00347 ( 42) SS BOND : angle 1.73471 ( 84) hydrogen bonds : bond 0.03653 ( 1011) hydrogen bonds : angle 5.84416 ( 2796) link_BETA1-4 : bond 0.00470 ( 13) link_BETA1-4 : angle 1.22061 ( 39) link_NAG-ASN : bond 0.00448 ( 47) link_NAG-ASN : angle 3.01450 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 256 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 TYR cc_start: 0.7420 (m-80) cc_final: 0.6924 (m-80) REVERT: A 354 ASN cc_start: 0.8387 (t0) cc_final: 0.7427 (p0) REVERT: A 712 ILE cc_start: 0.4338 (tp) cc_final: 0.4067 (tp) REVERT: A 856 ASN cc_start: 0.7751 (m-40) cc_final: 0.7493 (t0) REVERT: A 869 MET cc_start: 0.7220 (mtp) cc_final: 0.6953 (mtp) REVERT: A 957 GLN cc_start: 0.8614 (mt0) cc_final: 0.8342 (mt0) REVERT: A 1109 PHE cc_start: 0.7112 (OUTLIER) cc_final: 0.6413 (m-80) REVERT: B 317 ASN cc_start: 0.8530 (t0) cc_final: 0.8072 (p0) REVERT: B 773 GLU cc_start: 0.8356 (mt-10) cc_final: 0.7825 (tm-30) REVERT: B 878 LEU cc_start: 0.8234 (tp) cc_final: 0.7836 (mp) REVERT: B 1050 MET cc_start: 0.5439 (ptp) cc_final: 0.5143 (ptp) REVERT: B 1086 LYS cc_start: 0.8302 (tmmt) cc_final: 0.8045 (ttpp) REVERT: B 1107 ARG cc_start: 0.7153 (mpt180) cc_final: 0.6357 (ttm170) REVERT: G 118 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7206 (pp) REVERT: G 287 ASP cc_start: 0.8356 (m-30) cc_final: 0.7535 (m-30) REVERT: G 584 ILE cc_start: 0.9260 (mm) cc_final: 0.8939 (mm) REVERT: G 1002 GLN cc_start: 0.8835 (tm-30) cc_final: 0.8493 (tp-100) REVERT: G 1006 THR cc_start: 0.8797 (m) cc_final: 0.8533 (m) REVERT: G 1107 ARG cc_start: 0.6884 (mmm160) cc_final: 0.6280 (ttm170) REVERT: H 34 MET cc_start: 0.8622 (mmp) cc_final: 0.8224 (mmm) REVERT: H 47 TRP cc_start: 0.7216 (t60) cc_final: 0.6812 (t60) REVERT: H 48 MET cc_start: 0.7605 (OUTLIER) cc_final: 0.7112 (mpp) REVERT: H 50 ILE cc_start: 0.6272 (pt) cc_final: 0.5912 (pt) REVERT: H 63 LEU cc_start: 0.8280 (tp) cc_final: 0.7706 (pp) REVERT: H 69 MET cc_start: 0.5681 (pmm) cc_final: 0.4942 (pmm) REVERT: H 80 MET cc_start: 0.8239 (tpp) cc_final: 0.7863 (mmm) REVERT: H 100 TYR cc_start: 0.5062 (p90) cc_final: 0.4788 (p90) REVERT: L 34 TRP cc_start: 0.6472 (m100) cc_final: 0.5562 (m100) REVERT: L 35 TYR cc_start: 0.7206 (m-80) cc_final: 0.6696 (m-80) REVERT: L 36 GLN cc_start: 0.5500 (OUTLIER) cc_final: 0.4997 (pm20) REVERT: L 60 ARG cc_start: 0.6711 (mtm110) cc_final: 0.6080 (ttp-110) REVERT: N 35 HIS cc_start: 0.8512 (m90) cc_final: 0.8017 (m90) REVERT: N 83 ARG cc_start: 0.8364 (ptm160) cc_final: 0.8161 (ptp90) REVERT: S 4 LEU cc_start: 0.7338 (mm) cc_final: 0.6630 (mt) REVERT: S 30 LYS cc_start: 0.5565 (OUTLIER) cc_final: 0.4920 (pptt) REVERT: S 46 MET cc_start: 0.6377 (mtp) cc_final: 0.5444 (ptt) outliers start: 62 outliers final: 49 residues processed: 294 average time/residue: 0.1495 time to fit residues: 72.5858 Evaluate side-chains 287 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 233 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 1109 PHE Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 326 ILE Chi-restraints excluded: chain G residue 336 CYS Chi-restraints excluded: chain G residue 347 PHE Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 525 CYS Chi-restraints excluded: chain G residue 697 MET Chi-restraints excluded: chain G residue 738 CYS Chi-restraints excluded: chain G residue 902 MET Chi-restraints excluded: chain G residue 911 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 36 GLN Chi-restraints excluded: chain L residue 38 HIS Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain S residue 30 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 262 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 311 optimal weight: 40.0000 chunk 233 optimal weight: 7.9990 chunk 174 optimal weight: 3.9990 chunk 273 optimal weight: 0.8980 chunk 150 optimal weight: 6.9990 chunk 156 optimal weight: 0.7980 chunk 235 optimal weight: 4.9990 chunk 315 optimal weight: 9.9990 chunk 177 optimal weight: 4.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN A 895 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 895 GLN B1064 HIS G 895 GLN G1071 GLN ** G1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.146375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.104772 restraints weight = 109783.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.109720 restraints weight = 47287.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.111478 restraints weight = 24392.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.112866 restraints weight = 16216.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.112840 restraints weight = 14566.003| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3681 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3681 r_free = 0.3681 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3681 r_free = 0.3681 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3681 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 27153 Z= 0.231 Angle : 0.730 14.963 37118 Z= 0.366 Chirality : 0.051 1.057 4443 Planarity : 0.005 0.076 4668 Dihedral : 5.540 54.936 4881 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.52 % Allowed : 16.56 % Favored : 80.92 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.61 (0.14), residues: 3333 helix: 0.88 (0.20), residues: 664 sheet: -0.14 (0.18), residues: 807 loop : -0.99 (0.14), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 60 TYR 0.044 0.002 TYR G 423 PHE 0.052 0.002 PHE G 392 TRP 0.017 0.002 TRP G 886 HIS 0.013 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00525 (27051) covalent geometry : angle 0.69877 (36854) SS BOND : bond 0.00548 ( 42) SS BOND : angle 1.87575 ( 84) hydrogen bonds : bond 0.03901 ( 1011) hydrogen bonds : angle 5.90723 ( 2796) link_BETA1-4 : bond 0.00438 ( 13) link_BETA1-4 : angle 1.36075 ( 39) link_NAG-ASN : bond 0.00575 ( 47) link_NAG-ASN : angle 3.16299 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5589.95 seconds wall clock time: 96 minutes 54.03 seconds (5814.03 seconds total)