Starting phenix.real_space_refine on Fri Mar 6 14:03:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uap_26429/03_2026/7uap_26429.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uap_26429/03_2026/7uap_26429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7uap_26429/03_2026/7uap_26429.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uap_26429/03_2026/7uap_26429.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uap_26429/03_2026/7uap_26429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uap_26429/03_2026/7uap_26429.map" } resolution = 2.8 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= 0.106 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 138 5.16 5 C 20083 2.51 5 N 5243 2.21 5 O 6193 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 107 residue(s): 0.02s 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: 31657 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 8447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1081, 8447 Classifications: {'peptide': 1081} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 58, 'TRANS': 1022} Chain breaks: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 8447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1081, 8447 Classifications: {'peptide': 1081} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 58, 'TRANS': 1022} Chain breaks: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 8447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1081, 8447 Classifications: {'peptide': 1081} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 58, 'TRANS': 1022} Chain breaks: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 997 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "L" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 833 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 997 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "N" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 833 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 997 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "P" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 833 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 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: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 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 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.59, per 1000 atoms: 0.24 Number of scatterers: 31657 At special positions: 0 Unit cell: (182.31, 168.92, 168.92, 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 138 16.00 O 6193 8.00 N 5243 7.00 C 20083 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.09 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=2.04 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=2.01 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.05 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.07 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.05 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.01 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.06 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.04 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A 717 " " NAG A1309 " - " ASN A 801 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B 717 " " NAG B1309 " - " ASN B 801 " " NAG B1310 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C 717 " " NAG C1309 " - " ASN C 801 " " NAG C1310 " - " ASN C1074 " " NAG C1311 " - " ASN C1134 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 149 " " NAG F 1 " - " ASN A 234 " " NAG G 1 " - " ASN A1098 " " NAG I 1 " - " ASN B 122 " " NAG J 1 " - " ASN B 149 " " NAG K 1 " - " ASN B 234 " " NAG L 301 " - " ASN L 20 " " NAG N 301 " - " ASN N 20 " " NAG P 301 " - " ASN P 20 " " NAG Q 1 " - " ASN B1098 " " NAG R 1 " - " ASN C 122 " " NAG S 1 " - " ASN C 149 " " NAG T 1 " - " ASN C 234 " " NAG U 1 " - " ASN C1098 " Time building additional restraints: 2.83 Conformation dependent library (CDL) restraints added in 1.3 seconds 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7350 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 73 sheets defined 21.0% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 369 removed outlier: 4.191A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 364 through 369' Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.535A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.402A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.524A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 618 No H-bonds generated for 'chain 'A' and resid 616 through 618' Processing helix chain 'A' and resid 619 through 625 Processing helix chain 'A' and resid 626 through 629 Processing helix chain 'A' and resid 630 through 638 removed outlier: 4.165A pdb=" N TYR A 636 " --> pdb=" O THR A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 748 through 754 Processing helix chain 'A' and resid 756 through 783 removed outlier: 4.168A pdb=" N CYS A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.251A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 938 Processing helix chain 'A' and resid 945 through 967 removed outlier: 3.942A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 removed outlier: 3.807A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 5.248A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.948A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 366 No H-bonds generated for 'chain 'B' and resid 364 through 366' Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.235A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.534A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 403 through 407 removed outlier: 3.737A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.532A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 625 Processing helix chain 'B' and resid 626 through 629 Processing helix chain 'B' and resid 630 through 638 removed outlier: 3.899A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 748 through 783 removed outlier: 6.221A pdb=" N SER B 758 " --> pdb=" O LEU B 754 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N PHE B 759 " --> pdb=" O GLN B 755 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 883 Processing helix chain 'B' and resid 897 through 907 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 912 through 919 removed outlier: 4.404A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 938 Processing helix chain 'B' and resid 945 through 967 removed outlier: 3.970A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 981 removed outlier: 3.757A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 5.318A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 364 through 369 removed outlier: 4.241A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 364 through 369' Processing helix chain 'C' and resid 384 through 388 removed outlier: 3.737A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 388' Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.752A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.830A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 625 Processing helix chain 'C' and resid 626 through 629 Processing helix chain 'C' and resid 630 through 638 removed outlier: 3.621A pdb=" N VAL C 635 " --> pdb=" O PRO C 631 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 748 through 783 removed outlier: 4.111A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N SER C 758 " --> pdb=" O LEU C 754 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N PHE C 759 " --> pdb=" O GLN C 755 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.517A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.562A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 886 through 891' Processing helix chain 'C' and resid 897 through 907 Processing helix chain 'C' and resid 908 through 910 No H-bonds generated for 'chain 'C' and resid 908 through 910' Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.500A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 938 Processing helix chain 'C' and resid 945 through 967 removed outlier: 4.148A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 981 removed outlier: 3.701A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1029 removed outlier: 5.222A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.859A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.652A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 29 removed outlier: 3.714A pdb=" N ASN L 29 " --> pdb=" O SER L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.613A pdb=" N ASP L 82 " --> pdb=" O GLN L 79 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 83' Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.788A pdb=" N THR M 87 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 26 through 29 removed outlier: 3.755A pdb=" N ASN N 29 " --> pdb=" O SER N 27 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.579A pdb=" N ASP N 82 " --> pdb=" O GLN N 79 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU N 83 " --> pdb=" O SER N 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 79 through 83' Processing helix chain 'O' and resid 28 through 32 removed outlier: 3.938A pdb=" N ILE O 31 " --> pdb=" O THR O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 87 removed outlier: 3.648A pdb=" N THR O 87 " --> pdb=" O ALA O 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 29 removed outlier: 3.503A pdb=" N HIS P 28 " --> pdb=" O SER P 26 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN P 29 " --> pdb=" O SER P 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 26 through 29' Processing helix chain 'P' and resid 79 through 83 removed outlier: 4.196A pdb=" N ASP P 82 " --> pdb=" O GLN P 79 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU P 83 " --> pdb=" O SER P 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 79 through 83' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.307A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TRP A 64 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 removed outlier: 4.281A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 104 removed outlier: 6.343A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 117 Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 117 Processing sheet with id=AA6, first strand: chain 'A' and resid 144 through 145 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.549A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.496A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.413A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.822A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 539 through 543 removed outlier: 3.522A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP A 586 " --> pdb=" O THR A 553 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 565 through 566 removed outlier: 3.520A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 653 through 659 removed outlier: 6.052A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 727 removed outlier: 6.593A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 711 through 727 removed outlier: 6.593A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AC1, first strand: chain 'A' and resid 787 through 789 removed outlier: 6.656A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 1081 through 1083 Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.866A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.540A pdb=" N GLN B 271 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 224 through 229 removed outlier: 5.730A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 101 through 104 removed outlier: 6.451A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR B 144 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N MET B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 116 through 117 removed outlier: 3.555A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 116 through 117 Processing sheet with id=AC9, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AD1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.515A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.685A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD5, first strand: chain 'B' and resid 538 through 543 removed outlier: 3.578A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP B 586 " --> pdb=" O THR B 553 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.151A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA B 672 " --> pdb=" O ILE B 664 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 712 through 727 removed outlier: 6.371A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 712 through 727 removed outlier: 6.371A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AE1, first strand: chain 'B' and resid 787 through 789 Processing sheet with id=AE2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.718A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.674A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.560A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS C 278 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 101 through 104 removed outlier: 6.554A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 116 through 117 Processing sheet with id=AE7, first strand: chain 'C' and resid 120 through 121 removed outlier: 3.530A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 144 through 145 removed outlier: 4.051A pdb=" N TYR C 144 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'C' and resid 311 through 313 removed outlier: 3.577A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 327 through 328 removed outlier: 7.984A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS C 537 " --> pdb=" O LEU C 552 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C 552 " --> pdb=" O LYS C 537 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.637A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 361 through 362 removed outlier: 5.991A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF5, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.764A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 565 through 566 Processing sheet with id=AF7, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.959A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA C 672 " --> pdb=" O ILE C 664 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 712 through 727 removed outlier: 6.503A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 712 through 727 removed outlier: 6.503A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AG2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.463A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.768A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU H 20 " --> pdb=" O LEU H 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU H 80 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 56 through 57 removed outlier: 7.064A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN H 35 " --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA H 93 " --> pdb=" O ASN H 35 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE H 112 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 88 through 89 removed outlier: 3.514A pdb=" N ALA H 88 " --> pdb=" O VAL H 119 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AG7, first strand: chain 'L' and resid 44 through 50 removed outlier: 6.803A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N SER L 49 " --> pdb=" O ILE L 33 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.871A pdb=" N GLN M 3 " --> pdb=" O SER M 25 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER M 25 " --> pdb=" O GLN M 3 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL M 5 " --> pdb=" O VAL M 23 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER M 7 " --> pdb=" O ALA M 21 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA M 21 " --> pdb=" O SER M 7 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU M 20 " --> pdb=" O LEU M 80 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'M' and resid 16 through 17 removed outlier: 5.000A pdb=" N GLY M 16 " --> pdb=" O SER M 82B" (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'M' and resid 46 through 51 removed outlier: 5.682A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN M 35 " --> pdb=" O ALA M 93 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA M 93 " --> pdb=" O ASN M 35 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE M 112 " --> pdb=" O ARG M 94 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AH3, first strand: chain 'N' and resid 44 through 46 Processing sheet with id=AH4, first strand: chain 'O' and resid 3 through 7 removed outlier: 3.701A pdb=" N GLN O 3 " --> pdb=" O SER O 25 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER O 25 " --> pdb=" O GLN O 3 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU O 20 " --> pdb=" O LEU O 80 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'O' and resid 34 through 35 removed outlier: 3.578A pdb=" N ILE O 51 " --> pdb=" O MET O 34 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'O' and resid 88 through 89 Processing sheet with id=AH7, first strand: chain 'O' and resid 93 through 95 removed outlier: 4.451A pdb=" N ILE O 112 " --> pdb=" O ARG O 94 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'P' and resid 5 through 6 Processing sheet with id=AH9, first strand: chain 'P' and resid 33 through 38 removed outlier: 6.440A pdb=" N ILE P 33 " --> pdb=" O SER P 49 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N SER P 49 " --> pdb=" O ILE P 33 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU P 47 " --> pdb=" O TRP P 35 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'P' and resid 62 through 64 1003 hydrogen bonds defined for protein. 2718 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.85 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.06 - 1.24: 4367 1.24 - 1.42: 9374 1.42 - 1.60: 18473 1.60 - 1.78: 21 1.78 - 1.96: 160 Bond restraints: 32395 Sorted by residual: bond pdb=" C PRO B 897 " pdb=" O PRO B 897 " ideal model delta sigma weight residual 1.233 1.061 0.172 1.24e-02 6.50e+03 1.92e+02 bond pdb=" C PRO A 897 " pdb=" O PRO A 897 " ideal model delta sigma weight residual 1.233 1.085 0.148 1.23e-02 6.61e+03 1.44e+02 bond pdb=" C MET A 902 " pdb=" O MET A 902 " ideal model delta sigma weight residual 1.237 1.116 0.121 1.19e-02 7.06e+03 1.03e+02 bond pdb=" C PRO C 899 " pdb=" O PRO C 899 " ideal model delta sigma weight residual 1.237 1.104 0.133 1.32e-02 5.74e+03 1.02e+02 bond pdb=" C PRO C 897 " pdb=" O PRO C 897 " ideal model delta sigma weight residual 1.233 1.110 0.122 1.24e-02 6.50e+03 9.75e+01 ... (remaining 32390 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.48: 44059 10.48 - 20.97: 27 20.97 - 31.45: 3 31.45 - 41.93: 2 41.93 - 52.42: 2 Bond angle restraints: 44093 Sorted by residual: angle pdb=" CA CYS A 391 " pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " ideal model delta sigma weight residual 114.40 151.12 -36.72 2.30e+00 1.89e-01 2.55e+02 angle pdb=" N PRO A 897 " pdb=" CA PRO A 897 " pdb=" CB PRO A 897 " ideal model delta sigma weight residual 103.32 90.00 13.32 8.40e-01 1.42e+00 2.51e+02 angle pdb=" CA CYS A 525 " pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " ideal model delta sigma weight residual 114.40 149.56 -35.16 2.30e+00 1.89e-01 2.34e+02 angle pdb=" C THR C 941 " pdb=" N PRO C 942 " pdb=" CD PRO C 942 " ideal model delta sigma weight residual 125.00 72.58 52.42 4.10e+00 5.95e-02 1.63e+02 angle pdb=" C THR B 941 " pdb=" N PRO B 942 " pdb=" CD PRO B 942 " ideal model delta sigma weight residual 125.00 75.15 49.85 4.10e+00 5.95e-02 1.48e+02 ... (remaining 44088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.94: 18890 24.94 - 49.88: 887 49.88 - 74.82: 149 74.82 - 99.76: 41 99.76 - 124.70: 10 Dihedral angle restraints: 19977 sinusoidal: 8502 harmonic: 11475 Sorted by residual: dihedral pdb=" CA ASN P 20 " pdb=" C ASN P 20 " pdb=" N LEU P 21 " pdb=" CA LEU P 21 " ideal model delta harmonic sigma weight residual -180.00 -124.13 -55.87 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA VAL P 19 " pdb=" C VAL P 19 " pdb=" N ASN P 20 " pdb=" CA ASN P 20 " ideal model delta harmonic sigma weight residual 180.00 125.38 54.62 0 5.00e+00 4.00e-02 1.19e+02 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual -86.00 -8.53 -77.47 1 1.00e+01 1.00e-02 7.52e+01 ... (remaining 19974 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.315: 5084 0.315 - 0.630: 19 0.630 - 0.945: 5 0.945 - 1.260: 1 1.260 - 1.576: 1 Chirality restraints: 5110 Sorted by residual: 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 -0.82 -1.58 2.00e-01 2.50e+01 6.21e+01 chirality pdb=" C1 NAG A1311 " pdb=" ND2 ASN A1134 " pdb=" C2 NAG A1311 " pdb=" O5 NAG A1311 " both_signs ideal model delta sigma weight residual False -2.40 -1.39 -1.01 2.00e-01 2.50e+01 2.57e+01 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.46 -0.94 2.00e-01 2.50e+01 2.21e+01 ... (remaining 5107 not shown) Planarity restraints: 5683 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 941 " 0.171 5.00e-02 4.00e+02 2.48e-01 9.84e+01 pdb=" N PRO B 942 " -0.423 5.00e-02 4.00e+02 pdb=" CA PRO B 942 " 0.183 5.00e-02 4.00e+02 pdb=" CD PRO B 942 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 941 " 0.168 5.00e-02 4.00e+02 2.43e-01 9.45e+01 pdb=" N PRO C 942 " -0.413 5.00e-02 4.00e+02 pdb=" CA PRO C 942 " 0.182 5.00e-02 4.00e+02 pdb=" CD PRO C 942 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 891 " 0.121 5.00e-02 4.00e+02 1.85e-01 5.46e+01 pdb=" N PRO A 892 " -0.319 5.00e-02 4.00e+02 pdb=" CA PRO A 892 " 0.114 5.00e-02 4.00e+02 pdb=" CD PRO A 892 " 0.084 5.00e-02 4.00e+02 ... (remaining 5680 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 477 2.61 - 3.18: 27924 3.18 - 3.76: 48118 3.76 - 4.33: 68124 4.33 - 4.90: 109729 Nonbonded interactions: 254372 Sorted by model distance: nonbonded pdb=" NE2 GLN A 804 " pdb=" OE1 GLN A 935 " model vdw 2.041 3.120 nonbonded pdb=" OG1 THR C 393 " pdb=" O PRO C 521 " model vdw 2.072 3.040 nonbonded pdb=" OG SER A 383 " pdb=" OE2 GLU C 988 " model vdw 2.105 3.040 nonbonded pdb=" O LYS C 97 " pdb=" OH TYR O 105 " model vdw 2.105 3.040 nonbonded pdb=" O SER B 967 " pdb=" OG SER B 975 " model vdw 2.112 3.040 ... (remaining 254367 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 14 through 1310) selection = chain 'B' selection = (chain 'C' and resid 14 through 1310) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.450 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 31.460 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6281 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 : 0.007 0.172 32502 Z= 0.383 Angle : 1.363 52.416 44366 Z= 0.711 Chirality : 0.075 1.576 5110 Planarity : 0.009 0.248 5636 Dihedral : 14.621 124.697 12483 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 19.84 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.08 % Favored : 92.36 % Rotamer: Outliers : 0.29 % Allowed : 1.20 % Favored : 98.51 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.12), residues: 3915 helix: -0.94 (0.18), residues: 723 sheet: -0.68 (0.19), residues: 738 loop : -2.07 (0.11), residues: 2454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 577 TYR 0.055 0.003 TYR A 873 PHE 0.035 0.003 PHE C 194 TRP 0.102 0.003 TRP C 64 HIS 0.012 0.002 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00699 (32395) covalent geometry : angle 1.26657 (44093) SS BOND : bond 0.01317 ( 48) SS BOND : angle 4.69637 ( 96) hydrogen bonds : bond 0.23113 ( 965) hydrogen bonds : angle 9.56091 ( 2718) link_BETA1-4 : bond 0.00787 ( 12) link_BETA1-4 : angle 3.74672 ( 36) link_NAG-ASN : bond 0.01337 ( 47) link_NAG-ASN : angle 8.03959 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 471 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 82 MET cc_start: 0.2574 (tpp) cc_final: 0.2346 (mmm) outliers start: 10 outliers final: 5 residues processed: 477 average time/residue: 0.5357 time to fit residues: 311.8683 Evaluate side-chains 296 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 291 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 897 PRO Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 900 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 0.0970 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 207 HIS A 655 HIS A1010 GLN B 580 GLN B 784 GLN B 804 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1074 ASN B1101 HIS B1135 ASN C 69 HIS ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 856 ASN C 907 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN H 35 ASN H 55 HIS L 28 HIS L 54BHIS M 96 GLN O 81 GLN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 54BHIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.237606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.186882 restraints weight = 40941.994| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 2.32 r_work: 0.3782 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 32502 Z= 0.169 Angle : 0.868 19.073 44366 Z= 0.417 Chirality : 0.055 0.708 5110 Planarity : 0.006 0.167 5636 Dihedral : 10.821 109.518 5525 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.16 % Favored : 93.56 % Rotamer: Outliers : 2.28 % Allowed : 10.30 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.13), residues: 3915 helix: 0.01 (0.19), residues: 716 sheet: -0.50 (0.18), residues: 791 loop : -1.91 (0.11), residues: 2408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 995 TYR 0.025 0.002 TYR A1067 PHE 0.029 0.002 PHE C 168 TRP 0.046 0.002 TRP C 64 HIS 0.007 0.002 HIS O 106 Details of bonding type rmsd covalent geometry : bond 0.00388 (32395) covalent geometry : angle 0.79330 (44093) SS BOND : bond 0.00682 ( 48) SS BOND : angle 2.52836 ( 96) hydrogen bonds : bond 0.04845 ( 965) hydrogen bonds : angle 6.71582 ( 2718) link_BETA1-4 : bond 0.00772 ( 12) link_BETA1-4 : angle 2.86272 ( 36) link_NAG-ASN : bond 0.00950 ( 47) link_NAG-ASN : angle 5.80852 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 347 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8208 (p) cc_final: 0.8002 (p) REVERT: A 515 PHE cc_start: 0.8091 (m-80) cc_final: 0.7874 (m-80) REVERT: A 573 THR cc_start: 0.7641 (m) cc_final: 0.7428 (p) REVERT: A 725 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7804 (tt0) REVERT: B 177 MET cc_start: 0.6453 (mpp) cc_final: 0.6222 (mmm) REVERT: B 493 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.7278 (mm-40) REVERT: B 818 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7732 (mt) REVERT: C 48 LEU cc_start: 0.8085 (mm) cc_final: 0.7690 (mm) REVERT: C 64 TRP cc_start: 0.6203 (t-100) cc_final: 0.5925 (t-100) REVERT: C 595 VAL cc_start: 0.7874 (p) cc_final: 0.7631 (t) REVERT: C 790 LYS cc_start: 0.6976 (mmmt) cc_final: 0.6678 (pttm) REVERT: H 96 GLN cc_start: 0.7257 (tp40) cc_final: 0.6780 (tp40) REVERT: O 118 MET cc_start: 0.5210 (tpt) cc_final: 0.4762 (tpp) REVERT: P 48 MET cc_start: 0.2179 (mpt) cc_final: 0.0330 (tpp) outliers start: 78 outliers final: 25 residues processed: 394 average time/residue: 0.4809 time to fit residues: 237.0299 Evaluate side-chains 300 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 272 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 34 MET Chi-restraints excluded: chain P residue 62 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 78 optimal weight: 3.9990 chunk 38 optimal weight: 0.0000 chunk 285 optimal weight: 0.7980 chunk 214 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 138 optimal weight: 20.0000 chunk 255 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 261 optimal weight: 0.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A1010 GLN B 271 GLN B 901 GLN ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN C1135 ASN H 35 ASN O 82AASN P 6 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.234325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.182925 restraints weight = 40292.961| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 2.38 r_work: 0.3701 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 32502 Z= 0.164 Angle : 0.805 16.307 44366 Z= 0.383 Chirality : 0.054 0.682 5110 Planarity : 0.005 0.151 5636 Dihedral : 9.469 96.168 5514 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.33 % Favored : 93.38 % Rotamer: Outliers : 2.87 % Allowed : 13.58 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.13), residues: 3915 helix: 0.51 (0.20), residues: 693 sheet: -0.56 (0.18), residues: 788 loop : -1.78 (0.12), residues: 2434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 995 TYR 0.025 0.002 TYR C 351 PHE 0.019 0.002 PHE B 59 TRP 0.034 0.002 TRP C 64 HIS 0.016 0.002 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00382 (32395) covalent geometry : angle 0.73505 (44093) SS BOND : bond 0.00620 ( 48) SS BOND : angle 2.21198 ( 96) hydrogen bonds : bond 0.04660 ( 965) hydrogen bonds : angle 6.21339 ( 2718) link_BETA1-4 : bond 0.00578 ( 12) link_BETA1-4 : angle 2.93384 ( 36) link_NAG-ASN : bond 0.00933 ( 47) link_NAG-ASN : angle 5.44398 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 295 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASN cc_start: 0.7027 (t0) cc_final: 0.6780 (p0) REVERT: A 377 PHE cc_start: 0.7948 (t80) cc_final: 0.7726 (t80) REVERT: A 573 THR cc_start: 0.7762 (m) cc_final: 0.7493 (p) REVERT: A 725 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7906 (tt0) REVERT: A 934 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.7435 (tp) REVERT: B 126 VAL cc_start: 0.5054 (OUTLIER) cc_final: 0.4787 (t) REVERT: B 271 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.7002 (pm20) REVERT: B 458 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7909 (mttp) REVERT: B 493 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.7377 (mm-40) REVERT: B 1045 LYS cc_start: 0.8434 (tppp) cc_final: 0.8212 (tmmt) REVERT: C 18 LEU cc_start: 0.3456 (OUTLIER) cc_final: 0.3082 (pp) REVERT: C 64 TRP cc_start: 0.6437 (t-100) cc_final: 0.6053 (t-100) REVERT: C 129 LYS cc_start: 0.7383 (mptt) cc_final: 0.6941 (mppt) REVERT: C 740 MET cc_start: 0.7524 (mtt) cc_final: 0.7294 (mmm) REVERT: C 947 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8068 (tttp) REVERT: H 38 ARG cc_start: 0.5033 (OUTLIER) cc_final: 0.3464 (mtm-85) REVERT: H 96 GLN cc_start: 0.7197 (tp40) cc_final: 0.6778 (tp40) REVERT: M 82 MET cc_start: -0.0499 (tpt) cc_final: -0.1192 (tpt) REVERT: O 30 SER cc_start: 0.5315 (OUTLIER) cc_final: 0.4553 (t) REVERT: O 118 MET cc_start: 0.4987 (tpt) cc_final: 0.4529 (tpp) outliers start: 98 outliers final: 33 residues processed: 360 average time/residue: 0.4807 time to fit residues: 216.3237 Evaluate side-chains 294 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 251 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 78 PHE Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain O residue 30 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.6980 chunk 159 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 234 optimal weight: 0.9980 chunk 371 optimal weight: 8.9990 chunk 363 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 221 optimal weight: 9.9990 chunk 330 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN A 644 GLN A 655 HIS A1010 GLN B 146 HIS B 148 ASN B 544 ASN B 804 GLN ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 GLN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 ASN H 55 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.233472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.183784 restraints weight = 40036.606| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 2.48 r_work: 0.3671 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 32502 Z= 0.153 Angle : 0.773 15.948 44366 Z= 0.368 Chirality : 0.052 0.651 5110 Planarity : 0.005 0.064 5636 Dihedral : 8.690 92.438 5514 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.13 % Favored : 93.59 % Rotamer: Outliers : 3.19 % Allowed : 15.22 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.13), residues: 3915 helix: 0.62 (0.20), residues: 704 sheet: -0.49 (0.18), residues: 779 loop : -1.72 (0.12), residues: 2432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1014 TYR 0.024 0.002 TYR C 351 PHE 0.022 0.001 PHE A 133 TRP 0.026 0.001 TRP C 64 HIS 0.006 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00355 (32395) covalent geometry : angle 0.70540 (44093) SS BOND : bond 0.00635 ( 48) SS BOND : angle 2.47307 ( 96) hydrogen bonds : bond 0.04364 ( 965) hydrogen bonds : angle 5.94399 ( 2718) link_BETA1-4 : bond 0.00800 ( 12) link_BETA1-4 : angle 2.80483 ( 36) link_NAG-ASN : bond 0.00940 ( 47) link_NAG-ASN : angle 5.10745 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 291 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 GLU cc_start: 0.1892 (OUTLIER) cc_final: 0.1399 (tm-30) REVERT: A 357 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7550 (mmm-85) REVERT: A 573 THR cc_start: 0.7838 (m) cc_final: 0.7595 (p) REVERT: A 934 ILE cc_start: 0.7529 (OUTLIER) cc_final: 0.7326 (tp) REVERT: B 126 VAL cc_start: 0.5263 (OUTLIER) cc_final: 0.5048 (t) REVERT: B 312 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7822 (mm) REVERT: C 64 TRP cc_start: 0.6279 (t-100) cc_final: 0.5969 (t-100) REVERT: C 129 LYS cc_start: 0.7409 (mptt) cc_final: 0.6944 (mppt) REVERT: C 351 TYR cc_start: 0.6732 (p90) cc_final: 0.6113 (p90) REVERT: C 508 TYR cc_start: 0.8337 (m-80) cc_final: 0.8079 (m-80) REVERT: C 598 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8138 (pt) REVERT: C 947 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7942 (tttp) REVERT: H 96 GLN cc_start: 0.6929 (tp40) cc_final: 0.6564 (tp40) REVERT: M 82 MET cc_start: -0.0522 (tpt) cc_final: -0.1285 (tpt) REVERT: O 30 SER cc_start: 0.5239 (OUTLIER) cc_final: 0.4537 (t) REVERT: O 118 MET cc_start: 0.4676 (tpt) cc_final: 0.4248 (tpp) outliers start: 109 outliers final: 43 residues processed: 367 average time/residue: 0.4842 time to fit residues: 222.6521 Evaluate side-chains 316 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 265 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 78 PHE Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain P residue 62 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 71 optimal weight: 0.0470 chunk 10 optimal weight: 0.9980 chunk 269 optimal weight: 0.2980 chunk 64 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 284 optimal weight: 0.9990 chunk 291 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 314 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 231 optimal weight: 10.0000 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 655 HIS A1010 GLN ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN H 35 ASN H 55 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.233178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.178830 restraints weight = 40179.101| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 2.29 r_work: 0.3683 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3553 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 32502 Z= 0.136 Angle : 0.742 15.604 44366 Z= 0.352 Chirality : 0.051 0.628 5110 Planarity : 0.004 0.059 5636 Dihedral : 8.342 89.205 5511 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.03 % Favored : 93.72 % Rotamer: Outliers : 3.28 % Allowed : 16.13 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.13), residues: 3915 helix: 0.80 (0.20), residues: 704 sheet: -0.40 (0.18), residues: 771 loop : -1.67 (0.12), residues: 2440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 995 TYR 0.021 0.001 TYR A1067 PHE 0.025 0.001 PHE M 78 TRP 0.022 0.001 TRP C 64 HIS 0.005 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00312 (32395) covalent geometry : angle 0.67496 (44093) SS BOND : bond 0.00691 ( 48) SS BOND : angle 2.44697 ( 96) hydrogen bonds : bond 0.04101 ( 965) hydrogen bonds : angle 5.71388 ( 2718) link_BETA1-4 : bond 0.00707 ( 12) link_BETA1-4 : angle 2.77890 ( 36) link_NAG-ASN : bond 0.00926 ( 47) link_NAG-ASN : angle 4.97538 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 287 time to evaluate : 0.844 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 122 ASN cc_start: 0.7227 (t0) cc_final: 0.6943 (p0) REVERT: A 156 GLU cc_start: 0.1996 (OUTLIER) cc_final: 0.1442 (tm-30) REVERT: A 347 PHE cc_start: 0.7069 (OUTLIER) cc_final: 0.5034 (t80) REVERT: A 441 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8023 (tt) REVERT: A 573 THR cc_start: 0.7833 (m) cc_final: 0.7560 (p) REVERT: A 819 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7693 (mt-10) REVERT: B 126 VAL cc_start: 0.5528 (OUTLIER) cc_final: 0.5238 (t) REVERT: B 153 MET cc_start: 0.4848 (ppp) cc_final: 0.4568 (ppp) REVERT: B 357 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7809 (tpt170) REVERT: B 455 LEU cc_start: 0.8781 (tm) cc_final: 0.8489 (tm) REVERT: C 18 LEU cc_start: 0.3390 (OUTLIER) cc_final: 0.3115 (pp) REVERT: C 129 LYS cc_start: 0.7377 (mptt) cc_final: 0.6833 (mppt) REVERT: C 281 GLU cc_start: 0.5905 (tp30) cc_final: 0.5599 (mm-30) REVERT: C 351 TYR cc_start: 0.6758 (p90) cc_final: 0.6130 (p90) REVERT: C 508 TYR cc_start: 0.8445 (m-80) cc_final: 0.8162 (m-80) REVERT: C 577 ARG cc_start: 0.4072 (OUTLIER) cc_final: 0.3012 (tpp-160) REVERT: C 598 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.8072 (pt) REVERT: C 778 THR cc_start: 0.9206 (t) cc_final: 0.8621 (m) REVERT: C 947 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.8046 (tttp) REVERT: C 1031 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7300 (pt0) REVERT: H 96 GLN cc_start: 0.6829 (tp40) cc_final: 0.6406 (tp40) REVERT: M 82 MET cc_start: -0.0484 (tpt) cc_final: -0.1191 (tpt) REVERT: O 30 SER cc_start: 0.5452 (OUTLIER) cc_final: 0.5213 (t) REVERT: O 118 MET cc_start: 0.4956 (tpt) cc_final: 0.4509 (tpp) outliers start: 112 outliers final: 44 residues processed: 363 average time/residue: 0.4648 time to fit residues: 212.4797 Evaluate side-chains 311 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 255 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain H residue 78 PHE Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 30 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 326 optimal weight: 10.0000 chunk 296 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 165 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 199 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 390 optimal weight: 40.0000 chunk 281 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN A 314 GLN A 655 HIS A1010 GLN B 30 ASN B 69 HIS B 271 GLN B 703 ASN B 965 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 ASN H 55 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.227818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.171570 restraints weight = 39376.123| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 2.35 r_work: 0.3568 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.115 32502 Z= 0.241 Angle : 0.842 15.519 44366 Z= 0.405 Chirality : 0.055 0.623 5110 Planarity : 0.005 0.059 5636 Dihedral : 8.337 86.095 5511 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.59 % Favored : 93.13 % Rotamer: Outliers : 3.66 % Allowed : 17.03 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.13), residues: 3915 helix: 0.57 (0.20), residues: 699 sheet: -0.56 (0.18), residues: 781 loop : -1.67 (0.12), residues: 2435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 995 TYR 0.026 0.002 TYR C1067 PHE 0.019 0.002 PHE C 718 TRP 0.043 0.002 TRP C 64 HIS 0.008 0.002 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00585 (32395) covalent geometry : angle 0.78070 (44093) SS BOND : bond 0.00886 ( 48) SS BOND : angle 3.20377 ( 96) hydrogen bonds : bond 0.05429 ( 965) hydrogen bonds : angle 5.99462 ( 2718) link_BETA1-4 : bond 0.00701 ( 12) link_BETA1-4 : angle 2.86426 ( 36) link_NAG-ASN : bond 0.00942 ( 47) link_NAG-ASN : angle 4.85466 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 275 time to evaluate : 1.119 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 141 LEU cc_start: 0.8308 (mp) cc_final: 0.7385 (tp) REVERT: A 347 PHE cc_start: 0.7535 (OUTLIER) cc_final: 0.5370 (t80) REVERT: A 441 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7905 (tt) REVERT: A 725 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7942 (tt0) REVERT: A 819 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8119 (mt-10) REVERT: A 934 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7828 (tp) REVERT: B 126 VAL cc_start: 0.5850 (OUTLIER) cc_final: 0.5620 (t) REVERT: B 153 MET cc_start: 0.5086 (ppp) cc_final: 0.4822 (ppp) REVERT: B 177 MET cc_start: 0.6743 (ptp) cc_final: 0.6109 (mpp) REVERT: B 455 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8418 (tm) REVERT: B 554 GLU cc_start: 0.7267 (tp30) cc_final: 0.6813 (pm20) REVERT: C 50 SER cc_start: 0.7318 (OUTLIER) cc_final: 0.7005 (p) REVERT: C 129 LYS cc_start: 0.7580 (mptt) cc_final: 0.7175 (mptt) REVERT: C 351 TYR cc_start: 0.6939 (p90) cc_final: 0.6452 (p90) REVERT: C 378 LYS cc_start: 0.7750 (pttt) cc_final: 0.6949 (pmtt) REVERT: C 508 TYR cc_start: 0.8541 (m-80) cc_final: 0.8305 (m-80) REVERT: C 577 ARG cc_start: 0.4345 (OUTLIER) cc_final: 0.3745 (tpp-160) REVERT: C 1031 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7652 (pt0) REVERT: H 96 GLN cc_start: 0.6945 (tp40) cc_final: 0.6623 (tp40) REVERT: H 110 PHE cc_start: 0.6218 (m-80) cc_final: 0.5985 (m-10) REVERT: M 82 MET cc_start: -0.0699 (tpt) cc_final: -0.1361 (tpt) REVERT: O 118 MET cc_start: 0.5084 (tpt) cc_final: 0.4515 (tpp) outliers start: 125 outliers final: 61 residues processed: 365 average time/residue: 0.4632 time to fit residues: 213.3752 Evaluate side-chains 326 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 255 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 78 PHE Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 63 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 200 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 257 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 302 optimal weight: 0.6980 chunk 300 optimal weight: 0.9990 chunk 209 optimal weight: 0.7980 chunk 94 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B1002 GLN C 99 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 710 ASN C 856 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 ASN H 55 HIS ** P 54BHIS ** 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 = 0.4611 r_free = 0.4611 target = 0.230310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.176221 restraints weight = 40065.966| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 2.27 r_work: 0.3640 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 32502 Z= 0.146 Angle : 0.753 15.232 44366 Z= 0.358 Chirality : 0.051 0.605 5110 Planarity : 0.004 0.058 5636 Dihedral : 8.148 84.056 5511 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.80 % Favored : 94.00 % Rotamer: Outliers : 3.13 % Allowed : 18.58 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.13), residues: 3915 helix: 0.77 (0.20), residues: 697 sheet: -0.44 (0.18), residues: 760 loop : -1.58 (0.12), residues: 2458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 995 TYR 0.020 0.001 TYR A1067 PHE 0.021 0.001 PHE M 78 TRP 0.013 0.001 TRP L 35 HIS 0.005 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00341 (32395) covalent geometry : angle 0.69206 (44093) SS BOND : bond 0.00698 ( 48) SS BOND : angle 2.56918 ( 96) hydrogen bonds : bond 0.04332 ( 965) hydrogen bonds : angle 5.68415 ( 2718) link_BETA1-4 : bond 0.00731 ( 12) link_BETA1-4 : angle 2.79325 ( 36) link_NAG-ASN : bond 0.00874 ( 47) link_NAG-ASN : angle 4.70623 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 267 time to evaluate : 1.085 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 293 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.6797 (pt) REVERT: A 347 PHE cc_start: 0.7504 (OUTLIER) cc_final: 0.5577 (t80) REVERT: A 441 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.8036 (tt) REVERT: A 573 THR cc_start: 0.7957 (m) cc_final: 0.7545 (p) REVERT: A 725 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7800 (tt0) REVERT: A 819 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.7764 (mt-10) REVERT: A 985 ASP cc_start: 0.7348 (OUTLIER) cc_final: 0.7105 (t70) REVERT: B 126 VAL cc_start: 0.5857 (OUTLIER) cc_final: 0.5599 (t) REVERT: B 153 MET cc_start: 0.5173 (OUTLIER) cc_final: 0.4820 (ppp) REVERT: B 455 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8440 (tm) REVERT: B 554 GLU cc_start: 0.7243 (tp30) cc_final: 0.6951 (pm20) REVERT: B 606 ASN cc_start: 0.7683 (t0) cc_final: 0.7397 (m-40) REVERT: B 661 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6603 (pm20) REVERT: B 722 VAL cc_start: 0.8604 (m) cc_final: 0.8400 (t) REVERT: B 902 MET cc_start: 0.8624 (tpp) cc_final: 0.8355 (mmm) REVERT: C 50 SER cc_start: 0.7348 (OUTLIER) cc_final: 0.7049 (p) REVERT: C 64 TRP cc_start: 0.6959 (OUTLIER) cc_final: 0.6450 (t60) REVERT: C 129 LYS cc_start: 0.7508 (mptt) cc_final: 0.7101 (mptt) REVERT: C 239 GLN cc_start: 0.7353 (tm-30) cc_final: 0.7072 (tm-30) REVERT: C 351 TYR cc_start: 0.6980 (p90) cc_final: 0.6514 (p90) REVERT: C 378 LYS cc_start: 0.7698 (pttt) cc_final: 0.7231 (pttm) REVERT: C 508 TYR cc_start: 0.8460 (m-80) cc_final: 0.8179 (m-80) REVERT: C 577 ARG cc_start: 0.4279 (OUTLIER) cc_final: 0.3695 (tpp-160) REVERT: C 598 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8128 (pt) REVERT: C 778 THR cc_start: 0.9298 (t) cc_final: 0.8856 (m) REVERT: C 923 ILE cc_start: 0.8428 (mm) cc_final: 0.8057 (mm) REVERT: C 1031 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7624 (pt0) REVERT: H 96 GLN cc_start: 0.6846 (tp40) cc_final: 0.6443 (tp40) REVERT: H 110 PHE cc_start: 0.6171 (m-80) cc_final: 0.5898 (m-10) REVERT: O 82 MET cc_start: 0.1321 (mmm) cc_final: 0.1029 (mtp) REVERT: O 118 MET cc_start: 0.5003 (tpt) cc_final: 0.4507 (tpp) outliers start: 107 outliers final: 52 residues processed: 342 average time/residue: 0.4460 time to fit residues: 193.3866 Evaluate side-chains 319 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 252 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain H residue 78 PHE Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 98 HIS Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 100 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 383 optimal weight: 10.0000 chunk 152 optimal weight: 9.9990 chunk 285 optimal weight: 0.7980 chunk 363 optimal weight: 30.0000 chunk 114 optimal weight: 0.9980 chunk 308 optimal weight: 1.9990 chunk 262 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 252 optimal weight: 7.9990 chunk 107 optimal weight: 0.0370 chunk 373 optimal weight: 30.0000 overall best weight: 1.5662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A1010 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B1002 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN C 856 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN H 35 ASN H 55 HIS H 81 GLN ** P 54BHIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.227697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.172691 restraints weight = 39738.095| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 2.40 r_work: 0.3570 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 32502 Z= 0.199 Angle : 0.792 16.739 44366 Z= 0.379 Chirality : 0.053 0.601 5110 Planarity : 0.005 0.057 5636 Dihedral : 8.060 78.907 5511 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.62 % Favored : 93.18 % Rotamer: Outliers : 3.39 % Allowed : 18.85 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.13), residues: 3915 helix: 0.67 (0.20), residues: 694 sheet: -0.47 (0.18), residues: 773 loop : -1.57 (0.12), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 34 TYR 0.021 0.002 TYR A1067 PHE 0.017 0.002 PHE C 718 TRP 0.014 0.001 TRP L 35 HIS 0.008 0.001 HIS H 98 Details of bonding type rmsd covalent geometry : bond 0.00483 (32395) covalent geometry : angle 0.73356 (44093) SS BOND : bond 0.00782 ( 48) SS BOND : angle 2.74667 ( 96) hydrogen bonds : bond 0.04991 ( 965) hydrogen bonds : angle 5.80568 ( 2718) link_BETA1-4 : bond 0.00842 ( 12) link_BETA1-4 : angle 2.78375 ( 36) link_NAG-ASN : bond 0.00755 ( 47) link_NAG-ASN : angle 4.68243 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 271 time to evaluate : 1.206 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 293 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.6836 (pt) REVERT: A 347 PHE cc_start: 0.7548 (OUTLIER) cc_final: 0.5621 (t80) REVERT: A 441 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7991 (tt) REVERT: A 725 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7933 (tt0) REVERT: A 819 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8071 (mt-10) REVERT: A 934 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7820 (tp) REVERT: A 950 ASP cc_start: 0.8078 (m-30) cc_final: 0.7830 (m-30) REVERT: A 985 ASP cc_start: 0.7306 (OUTLIER) cc_final: 0.6967 (t70) REVERT: A 1084 ASP cc_start: 0.7863 (m-30) cc_final: 0.7630 (t0) REVERT: B 126 VAL cc_start: 0.5960 (OUTLIER) cc_final: 0.5756 (t) REVERT: B 153 MET cc_start: 0.5219 (OUTLIER) cc_final: 0.4867 (ppp) REVERT: B 455 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8400 (tm) REVERT: B 606 ASN cc_start: 0.7835 (t0) cc_final: 0.7582 (m-40) REVERT: B 661 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6840 (pm20) REVERT: B 722 VAL cc_start: 0.8666 (m) cc_final: 0.8332 (t) REVERT: C 34 ARG cc_start: 0.6078 (mmm160) cc_final: 0.5169 (mmt-90) REVERT: C 50 SER cc_start: 0.7417 (OUTLIER) cc_final: 0.7078 (p) REVERT: C 64 TRP cc_start: 0.7042 (OUTLIER) cc_final: 0.6552 (t60) REVERT: C 129 LYS cc_start: 0.7543 (mptt) cc_final: 0.7079 (mppt) REVERT: C 153 MET cc_start: 0.6321 (mmt) cc_final: 0.6107 (mmm) REVERT: C 239 GLN cc_start: 0.7368 (tm-30) cc_final: 0.7093 (tm-30) REVERT: C 265 TYR cc_start: 0.7042 (p90) cc_final: 0.6821 (p90) REVERT: C 314 GLN cc_start: 0.7271 (OUTLIER) cc_final: 0.6786 (mm110) REVERT: C 378 LYS cc_start: 0.7717 (pttt) cc_final: 0.7246 (pttm) REVERT: C 441 LEU cc_start: 0.7313 (mt) cc_final: 0.7037 (mt) REVERT: C 508 TYR cc_start: 0.8499 (m-80) cc_final: 0.8199 (m-80) REVERT: C 577 ARG cc_start: 0.4481 (OUTLIER) cc_final: 0.3829 (tpp-160) REVERT: C 646 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7995 (mmt180) REVERT: C 1031 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7653 (pt0) REVERT: H 96 GLN cc_start: 0.6868 (tp40) cc_final: 0.6454 (tp40) REVERT: M 82 MET cc_start: -0.0479 (tpt) cc_final: -0.1168 (tpt) REVERT: M 91 TYR cc_start: 0.3759 (m-10) cc_final: 0.2151 (p90) REVERT: O 118 MET cc_start: 0.5025 (tpt) cc_final: 0.4508 (tpp) outliers start: 116 outliers final: 65 residues processed: 354 average time/residue: 0.4551 time to fit residues: 205.0560 Evaluate side-chains 329 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 247 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 78 PHE Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 98 HIS Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 100 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 134 optimal weight: 4.9990 chunk 298 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 279 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 285 optimal weight: 0.6980 chunk 154 optimal weight: 0.9980 chunk 290 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 309 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A1010 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B1002 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN C 856 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 ASN H 55 HIS ** M 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 54BHIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.227943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.174998 restraints weight = 39640.095| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 2.40 r_work: 0.3583 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 32502 Z= 0.165 Angle : 0.903 59.199 44366 Z= 0.438 Chirality : 0.053 0.884 5110 Planarity : 0.005 0.057 5636 Dihedral : 8.080 78.469 5511 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.28 % Favored : 93.51 % Rotamer: Outliers : 2.90 % Allowed : 19.46 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.13), residues: 3915 helix: 0.74 (0.20), residues: 694 sheet: -0.44 (0.18), residues: 772 loop : -1.56 (0.12), residues: 2449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 34 TYR 0.025 0.002 TYR C 351 PHE 0.017 0.002 PHE A 898 TRP 0.011 0.001 TRP L 35 HIS 0.006 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00385 (32395) covalent geometry : angle 0.82987 (44093) SS BOND : bond 0.00696 ( 48) SS BOND : angle 2.87971 ( 96) hydrogen bonds : bond 0.04716 ( 965) hydrogen bonds : angle 5.78255 ( 2718) link_BETA1-4 : bond 0.00798 ( 12) link_BETA1-4 : angle 2.72054 ( 36) link_NAG-ASN : bond 0.00818 ( 47) link_NAG-ASN : angle 5.80890 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 257 time to evaluate : 1.184 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 144 TYR cc_start: 0.6619 (m-80) cc_final: 0.5700 (m-80) REVERT: A 293 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6663 (pt) REVERT: A 347 PHE cc_start: 0.7444 (OUTLIER) cc_final: 0.5519 (t80) REVERT: A 441 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8057 (tt) REVERT: A 725 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7592 (tt0) REVERT: A 819 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.7893 (mt-10) REVERT: A 934 ILE cc_start: 0.7971 (OUTLIER) cc_final: 0.7738 (tp) REVERT: A 985 ASP cc_start: 0.7198 (OUTLIER) cc_final: 0.6855 (t70) REVERT: B 153 MET cc_start: 0.5039 (OUTLIER) cc_final: 0.4716 (ppp) REVERT: B 455 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8408 (tm) REVERT: B 606 ASN cc_start: 0.7731 (t0) cc_final: 0.7451 (m-40) REVERT: B 661 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6807 (pm20) REVERT: B 722 VAL cc_start: 0.8562 (m) cc_final: 0.8273 (t) REVERT: C 34 ARG cc_start: 0.6027 (mmm160) cc_final: 0.5324 (mmt180) REVERT: C 50 SER cc_start: 0.7307 (OUTLIER) cc_final: 0.6979 (p) REVERT: C 64 TRP cc_start: 0.6902 (OUTLIER) cc_final: 0.6446 (t60) REVERT: C 129 LYS cc_start: 0.7436 (mptt) cc_final: 0.7050 (mppt) REVERT: C 239 GLN cc_start: 0.7178 (tm-30) cc_final: 0.6887 (tm-30) REVERT: C 265 TYR cc_start: 0.7034 (p90) cc_final: 0.6830 (p90) REVERT: C 378 LYS cc_start: 0.7591 (pttt) cc_final: 0.7089 (pttm) REVERT: C 441 LEU cc_start: 0.7329 (mt) cc_final: 0.7059 (mt) REVERT: C 508 TYR cc_start: 0.8314 (m-80) cc_final: 0.8004 (m-80) REVERT: C 577 ARG cc_start: 0.4343 (OUTLIER) cc_final: 0.3751 (tpp-160) REVERT: C 646 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7795 (mmt180) REVERT: C 1031 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7569 (pt0) REVERT: H 96 GLN cc_start: 0.6878 (tp40) cc_final: 0.6468 (tp40) REVERT: M 82 MET cc_start: -0.0078 (tpt) cc_final: -0.0976 (tpt) REVERT: M 91 TYR cc_start: 0.3711 (m-10) cc_final: 0.2138 (p90) REVERT: O 82 MET cc_start: 0.1112 (mtp) cc_final: 0.0882 (mmm) REVERT: O 118 MET cc_start: 0.4750 (tpt) cc_final: 0.4279 (tpp) outliers start: 99 outliers final: 67 residues processed: 326 average time/residue: 0.4721 time to fit residues: 193.9780 Evaluate side-chains 329 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 247 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 774 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 100 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 336 optimal weight: 1.9990 chunk 243 optimal weight: 0.9980 chunk 184 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 159 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 310 optimal weight: 0.8980 chunk 185 optimal weight: 0.4980 chunk 124 optimal weight: 0.0040 chunk 247 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B1002 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN C 856 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN H 35 ASN H 55 HIS ** M 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 54BHIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.228097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.171939 restraints weight = 39755.441| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 2.36 r_work: 0.3586 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.482 32502 Z= 0.196 Angle : 0.934 59.199 44366 Z= 0.455 Chirality : 0.053 0.821 5110 Planarity : 0.005 0.057 5636 Dihedral : 8.063 78.433 5511 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.44 % Favored : 93.38 % Rotamer: Outliers : 2.90 % Allowed : 19.43 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.13), residues: 3915 helix: 0.75 (0.20), residues: 694 sheet: -0.44 (0.18), residues: 772 loop : -1.56 (0.12), residues: 2449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 34 TYR 0.023 0.002 TYR C 351 PHE 0.017 0.001 PHE A 898 TRP 0.010 0.001 TRP L 35 HIS 0.005 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00517 (32395) covalent geometry : angle 0.83377 (44093) SS BOND : bond 0.00788 ( 48) SS BOND : angle 5.76742 ( 96) hydrogen bonds : bond 0.04688 ( 965) hydrogen bonds : angle 5.78136 ( 2718) link_BETA1-4 : bond 0.00607 ( 12) link_BETA1-4 : angle 2.74903 ( 36) link_NAG-ASN : bond 0.00940 ( 47) link_NAG-ASN : angle 5.70149 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 250 time to evaluate : 1.184 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 144 TYR cc_start: 0.6597 (m-80) cc_final: 0.5704 (m-80) REVERT: A 293 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.6801 (pt) REVERT: A 347 PHE cc_start: 0.7528 (OUTLIER) cc_final: 0.5589 (t80) REVERT: A 441 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.8004 (tt) REVERT: A 725 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7952 (tt0) REVERT: A 819 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.7911 (mt-10) REVERT: A 934 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7847 (tp) REVERT: A 985 ASP cc_start: 0.7254 (OUTLIER) cc_final: 0.6915 (t70) REVERT: B 153 MET cc_start: 0.5296 (OUTLIER) cc_final: 0.4936 (ppp) REVERT: B 455 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8426 (tm) REVERT: B 606 ASN cc_start: 0.7837 (t0) cc_final: 0.7561 (m-40) REVERT: B 661 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6901 (pm20) REVERT: B 722 VAL cc_start: 0.8644 (m) cc_final: 0.8339 (t) REVERT: C 34 ARG cc_start: 0.6007 (mmm160) cc_final: 0.5246 (mmt180) REVERT: C 50 SER cc_start: 0.7371 (OUTLIER) cc_final: 0.7031 (p) REVERT: C 64 TRP cc_start: 0.7037 (OUTLIER) cc_final: 0.6543 (t60) REVERT: C 129 LYS cc_start: 0.7470 (mptt) cc_final: 0.7023 (mppt) REVERT: C 239 GLN cc_start: 0.7309 (tm-30) cc_final: 0.7026 (tm-30) REVERT: C 265 TYR cc_start: 0.7010 (p90) cc_final: 0.6797 (p90) REVERT: C 378 LYS cc_start: 0.7658 (pttt) cc_final: 0.7164 (pttm) REVERT: C 441 LEU cc_start: 0.7296 (mt) cc_final: 0.7019 (mt) REVERT: C 455 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7412 (mp) REVERT: C 508 TYR cc_start: 0.8461 (m-80) cc_final: 0.8161 (m-80) REVERT: C 577 ARG cc_start: 0.4444 (OUTLIER) cc_final: 0.3845 (tpp-160) REVERT: C 646 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7924 (mmt180) REVERT: C 1031 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7752 (pt0) REVERT: H 96 GLN cc_start: 0.6854 (tp40) cc_final: 0.6516 (tp40) REVERT: M 82 MET cc_start: -0.0310 (tpt) cc_final: -0.1126 (tpt) REVERT: M 91 TYR cc_start: 0.3740 (m-10) cc_final: 0.2168 (p90) REVERT: O 50 TYR cc_start: 0.4938 (OUTLIER) cc_final: 0.3803 (m-80) REVERT: O 82 MET cc_start: 0.1200 (mtp) cc_final: 0.0858 (mmm) REVERT: O 118 MET cc_start: 0.5075 (tpt) cc_final: 0.4552 (tpp) outliers start: 99 outliers final: 73 residues processed: 317 average time/residue: 0.4746 time to fit residues: 189.3838 Evaluate side-chains 339 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 249 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 774 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain O residue 100 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 274 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 340 optimal weight: 2.9990 chunk 317 optimal weight: 1.9990 chunk 195 optimal weight: 0.0000 chunk 303 optimal weight: 5.9990 chunk 192 optimal weight: 0.2980 chunk 290 optimal weight: 0.6980 chunk 382 optimal weight: 20.0000 chunk 206 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN C 856 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 ASN H 55 HIS ** M 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 54BHIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.228036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.171553 restraints weight = 39968.809| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.33 r_work: 0.3590 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.487 32502 Z= 0.239 Angle : 0.938 59.199 44366 Z= 0.457 Chirality : 0.053 0.821 5110 Planarity : 0.005 0.057 5636 Dihedral : 8.063 78.433 5511 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.44 % Favored : 93.38 % Rotamer: Outliers : 2.75 % Allowed : 19.52 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.13), residues: 3915 helix: 0.75 (0.20), residues: 694 sheet: -0.44 (0.18), residues: 772 loop : -1.56 (0.12), residues: 2449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 34 TYR 0.023 0.002 TYR C 351 PHE 0.017 0.001 PHE A 898 TRP 0.010 0.001 TRP L 35 HIS 0.005 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00517 (32395) covalent geometry : angle 0.83377 (44093) SS BOND : bond 0.07105 ( 48) SS BOND : angle 6.08945 ( 96) hydrogen bonds : bond 0.04688 ( 965) hydrogen bonds : angle 5.78136 ( 2718) link_BETA1-4 : bond 0.00607 ( 12) link_BETA1-4 : angle 2.74903 ( 36) link_NAG-ASN : bond 0.00940 ( 47) link_NAG-ASN : angle 5.70149 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12323.82 seconds wall clock time: 210 minutes 7.04 seconds (12607.04 seconds total)