Starting phenix.real_space_refine on Fri Mar 6 01:10:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6z43_11068/03_2026/6z43_11068.cif Found real_map, /net/cci-nas-00/data/ceres_data/6z43_11068/03_2026/6z43_11068.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6z43_11068/03_2026/6z43_11068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6z43_11068/03_2026/6z43_11068.map" model { file = "/net/cci-nas-00/data/ceres_data/6z43_11068/03_2026/6z43_11068.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6z43_11068/03_2026/6z43_11068.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 117 5.16 5 C 17016 2.51 5 N 4391 2.21 5 O 5201 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26725 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 7595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 7595 Classifications: {'peptide': 987} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 49, 'TRANS': 937} Chain breaks: 9 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 5, 'ASN:plan1': 4, 'GLU:plan': 9, 'GLN:plan1': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 84 Chain: "B" Number of atoms: 7630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7630 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 49, 'TRANS': 942} Chain breaks: 8 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 4, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 81 Chain: "C" Number of atoms: 7612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 991, 7612 Classifications: {'peptide': 991} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 49, 'TRANS': 941} Chain breaks: 7 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 4, 'ASP:plan': 9, 'GLN:plan1': 2, 'GLU:plan': 10} Unresolved non-hydrogen planarities: 87 Chain: "X" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 988 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 2, 'TRANS': 124} Chain: "Y" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 988 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 2, 'TRANS': 124} Chain: "Z" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 988 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 2, 'TRANS': 124} 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.13, per 1000 atoms: 0.23 Number of scatterers: 26725 At special positions: 0 Unit cell: (126.16, 137.78, 215.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 117 16.00 O 5201 8.00 N 4391 7.00 C 17016 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 22 " - pdb=" SG CYS Z 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1310 " - " ASN A 603 " " NAG A1311 " - " ASN A 616 " " NAG A1312 " - " ASN A 657 " " NAG A1313 " - " ASN A 709 " " NAG A1318 " - " ASN A1074 " " NAG A1323 " - " ASN A 165 " " NAG A1324 " - " ASN A 343 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1313 " - " ASN B1074 " " NAG B1318 " - " ASN B 343 " " NAG C1401 " - " ASN C 343 " " NAG C1402 " - " ASN C 61 " " NAG C1405 " - " ASN C 234 " " NAG C1408 " - " ASN C 331 " " NAG C1409 " - " ASN C 603 " " NAG C1410 " - " ASN C 616 " " NAG C1411 " - " ASN C 657 " " NAG C1424 " - " ASN C 165 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 234 " " NAG F 1 " - " ASN A 282 " " NAG G 1 " - " ASN A 331 " " NAG H 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 122 " " NAG Q 1 " - " ASN C 282 " " NAG R 1 " - " ASN C 709 " " NAG S 1 " - " ASN C 717 " " NAG T 1 " - " ASN C 801 " " NAG U 1 " - " ASN C1074 " " NAG V 1 " - " ASN C1098 " " NAG W 1 " - " ASN C1134 " Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 1.2 seconds 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6250 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 55 sheets defined 24.8% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.967A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.238A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.213A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.548A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.550A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.208A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.968A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 982 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.746A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.888A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.471A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.114A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.866A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.273A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.650A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.562A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.913A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.982A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 388 removed outlier: 4.053A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.013A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.698A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.657A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.238A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.552A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.521A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.083A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.148A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'X' and resid 87 through 91 Processing helix chain 'X' and resid 105 through 111 Processing helix chain 'Y' and resid 87 through 91 Processing helix chain 'Y' and resid 105 through 111 Processing helix chain 'Z' and resid 87 through 91 Processing helix chain 'Z' and resid 105 through 111 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.638A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.348A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.573A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.580A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.819A pdb=" N ASN A 125 " --> pdb=" O ASN A 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.650A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 327 removed outlier: 6.819A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.560A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.417A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.169A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.887A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.642A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.919A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.212A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.754A pdb=" N LYS A 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.487A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.164A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.763A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.719A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.408A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.618A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.911A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.974A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 719 through 728 removed outlier: 6.097A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.257A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.401A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.673A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.344A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.256A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.980A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.700A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.511A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 324 through 328 removed outlier: 3.967A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.181A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.054A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.973A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 719 through 728 removed outlier: 6.902A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.088A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.614A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'X' and resid 3 through 7 Processing sheet with id=AF3, first strand: chain 'X' and resid 11 through 12 removed outlier: 6.741A pdb=" N MET X 34 " --> pdb=" O ALA X 50 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ALA X 50 " --> pdb=" O MET X 34 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TRP X 36 " --> pdb=" O VAL X 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'X' and resid 11 through 12 Processing sheet with id=AF5, first strand: chain 'Y' and resid 3 through 7 Processing sheet with id=AF6, first strand: chain 'Y' and resid 11 through 12 removed outlier: 6.741A pdb=" N MET Y 34 " --> pdb=" O ALA Y 50 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ALA Y 50 " --> pdb=" O MET Y 34 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TRP Y 36 " --> pdb=" O VAL Y 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Y' and resid 11 through 12 Processing sheet with id=AF8, first strand: chain 'Z' and resid 3 through 7 Processing sheet with id=AF9, first strand: chain 'Z' and resid 11 through 12 removed outlier: 6.741A pdb=" N MET Z 34 " --> pdb=" O ALA Z 50 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ALA Z 50 " --> pdb=" O MET Z 34 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TRP Z 36 " --> pdb=" O VAL Z 48 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Z' and resid 11 through 12 1169 hydrogen bonds defined for protein. 3090 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: 6.90 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8414 1.34 - 1.46: 6079 1.46 - 1.58: 12665 1.58 - 1.70: 0 1.70 - 1.81: 150 Bond restraints: 27308 Sorted by residual: bond pdb=" CA LYS A 97 " pdb=" C LYS A 97 " ideal model delta sigma weight residual 1.521 1.565 -0.045 1.27e-02 6.20e+03 1.24e+01 bond pdb=" N LYS C 386 " pdb=" CA LYS C 386 " ideal model delta sigma weight residual 1.459 1.418 0.041 1.25e-02 6.40e+03 1.05e+01 bond pdb=" N GLN B 607 " pdb=" CA GLN B 607 " ideal model delta sigma weight residual 1.458 1.497 -0.040 1.24e-02 6.50e+03 1.02e+01 bond pdb=" N GLN C 607 " pdb=" CA GLN C 607 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.24e-02 6.50e+03 8.74e+00 bond pdb=" C ARG B 403 " pdb=" N GLY B 404 " ideal model delta sigma weight residual 1.334 1.369 -0.035 1.23e-02 6.61e+03 8.09e+00 ... (remaining 27303 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 36728 2.32 - 4.64: 423 4.64 - 6.96: 18 6.96 - 9.28: 4 9.28 - 11.60: 1 Bond angle restraints: 37174 Sorted by residual: angle pdb=" C ARG B 403 " pdb=" N GLY B 404 " pdb=" CA GLY B 404 " ideal model delta sigma weight residual 119.94 127.17 -7.23 1.11e+00 8.12e-01 4.24e+01 angle pdb=" N LYS C 386 " pdb=" CA LYS C 386 " pdb=" CB LYS C 386 " ideal model delta sigma weight residual 110.22 102.38 7.84 1.54e+00 4.22e-01 2.59e+01 angle pdb=" CB LYS A 41 " pdb=" CG LYS A 41 " pdb=" CD LYS A 41 " ideal model delta sigma weight residual 111.30 122.90 -11.60 2.30e+00 1.89e-01 2.55e+01 angle pdb=" O ILE B 402 " pdb=" C ILE B 402 " pdb=" N ARG B 403 " ideal model delta sigma weight residual 122.75 117.87 4.88 1.06e+00 8.90e-01 2.12e+01 angle pdb=" CA GLY A 89 " pdb=" C GLY A 89 " pdb=" N VAL A 90 " ideal model delta sigma weight residual 114.58 118.42 -3.84 8.60e-01 1.35e+00 1.99e+01 ... (remaining 37169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 16136 17.91 - 35.81: 686 35.81 - 53.72: 127 53.72 - 71.63: 51 71.63 - 89.53: 23 Dihedral angle restraints: 17023 sinusoidal: 7296 harmonic: 9727 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 168.64 -75.64 1 1.00e+01 1.00e-02 7.22e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 168.27 -75.27 1 1.00e+01 1.00e-02 7.16e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -157.91 71.91 1 1.00e+01 1.00e-02 6.62e+01 ... (remaining 17020 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.163: 4410 0.163 - 0.326: 14 0.326 - 0.489: 2 0.489 - 0.652: 5 0.652 - 0.815: 1 Chirality restraints: 4432 Sorted by residual: chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B 657 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -3.22 0.82 2.00e-01 2.50e+01 1.66e+01 chirality pdb=" C1 NAG A1311 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG A1311 " pdb=" O5 NAG A1311 " both_signs ideal model delta sigma weight residual False -2.40 -3.05 0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" C1 NAG A1310 " pdb=" ND2 ASN A 603 " pdb=" C2 NAG A1310 " pdb=" O5 NAG A1310 " both_signs ideal model delta sigma weight residual False -2.40 -3.02 0.62 2.00e-01 2.50e+01 9.53e+00 ... (remaining 4429 not shown) Planarity restraints: 4747 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 402 " -0.017 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C ILE B 402 " 0.057 2.00e-02 2.50e+03 pdb=" O ILE B 402 " -0.021 2.00e-02 2.50e+03 pdb=" N ARG B 403 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 122 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.90e+00 pdb=" C ASN C 122 " -0.045 2.00e-02 2.50e+03 pdb=" O ASN C 122 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA C 123 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1074 " -0.022 2.00e-02 2.50e+03 2.06e-02 5.31e+00 pdb=" CG ASN C1074 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN C1074 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN C1074 " 0.028 2.00e-02 2.50e+03 pdb=" C1 NAG U 1 " -0.025 2.00e-02 2.50e+03 ... (remaining 4744 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 426 2.65 - 3.22: 25277 3.22 - 3.78: 40404 3.78 - 4.34: 58138 4.34 - 4.90: 95439 Nonbonded interactions: 219684 Sorted by model distance: nonbonded pdb=" O3 NAG F 1 " pdb=" O7 NAG F 1 " model vdw 2.094 3.040 nonbonded pdb=" O3 NAG A1311 " pdb=" O7 NAG A1311 " model vdw 2.097 3.040 nonbonded pdb=" O3 NAG N 2 " pdb=" O7 NAG N 2 " model vdw 2.102 3.040 nonbonded pdb=" O SER Y 126 " pdb=" OG SER Y 127 " model vdw 2.113 3.040 nonbonded pdb=" O SER Z 126 " pdb=" OG SER Z 127 " model vdw 2.113 3.040 ... (remaining 219679 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) or re \ sid 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 through 109 or (resid 110 through 113 and (name N or name CA or name C \ or name O or name CB )) or resid 116 through 128 or (resid 129 and (name N or n \ ame CA or name C or name O or name CB )) or resid 130 through 134 or (resid 135 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 140 or resid 166 through 168 or (resid 169 and (name N or name CA or n \ ame C or name O or name CB )) or resid 170 through 187 or (resid 188 and (name N \ or name CA or name C or name O or name CB )) or resid 189 through 190 or (resid \ 191 and (name N or name CA or name C or name O or name CB )) or resid 192 throu \ gh 195 or (resid 196 and (name N or name CA or name C or name O or name CB )) or \ resid 200 through 210 or (resid 211 through 215 and (name N or name CA or name \ C or name O or name CB )) or resid 216 through 241 or (resid 242 through 263 and \ (name N or name CA or name C or name O or name CB )) or resid 265 through 280 o \ r (resid 281 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 82 through 323 or (resid 324 and (name N or name CA or name C or name O or name \ CB )) or resid 325 through 567 or (resid 568 and (name N or name CA or name C or \ name O or name CB )) or resid 569 through 570 or (resid 571 and (name N or name \ CA or name C or name O or name CB )) or resid 572 through 581 or (resid 582 thr \ ough 583 and (name N or name CA or name C or name O or name CB )) or resid 584 t \ hrough 585 or (resid 586 and (name N or name CA or name C or name O or name CB ) \ ) or resid 587 through 613 or (resid 614 and (name N or name CA or name C or nam \ e O or name CB )) or resid 615 through 618 or (resid 619 and (name N or name CA \ or name C or name O or name CB )) or resid 620 through 676 or resid 690 through \ 744 or (resid 745 and (name N or name CA or name C or name O or name CB )) or re \ sid 746 through 810 or (resid 811 and (name N or name CA or name C or name O or \ name CB )) or resid 812 through 827 or resid 856 through 866 or (resid 867 throu \ gh 868 and (name N or name CA or name C or name O or name CB )) or resid 869 thr \ ough 920 or (resid 921 and (name N or name CA or name C or name O or name CB )) \ or resid 922 through 939 or (resid 940 and (name N or name CA or name C or name \ O or name CB )) or resid 941 through 984 or (resid 985 and (name N or name CA or \ name C or name O or name CB )) or resid 986 through 987 or (resid 988 through 9 \ 89 and (name N or name CA or name C or name O or name CB )) or resid 990 through \ 1072 or (resid 1073 and (name N or name CA or name C or name O or name CB )) or \ resid 1074 through 1117 or (resid 1118 and (name N or name CA or name C or name \ O or name CB )) or resid 1119 through 1143 or (resid 1144 through 1146 and (nam \ e N or name CA or name C or name O or name CB )) or resid 1147 through 1324)) selection = (chain 'B' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 66 or resid 82 throug \ h 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) or re \ sid 89 through 95 or (resid 96 through 97 and (name N or name CA or name C or na \ me O or name CB )) or resid 98 through 109 or (resid 110 through 113 and (name N \ or name CA or name C or name O or name CB )) or resid 116 through 124 or (resid \ 125 and (name N or name CA or name C or name O or name CB )) or resid 126 throu \ gh 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) or \ resid 133 or (resid 134 through 138 and (name N or name CA or name C or name O \ or name CB )) or resid 139 through 140 or resid 166 through 168 or (resid 169 an \ d (name N or name CA or name C or name O or name CB )) or resid 170 through 171 \ or (resid 172 and (name N or name CA or name C or name O or name CB )) or resid \ 186 through 190 or (resid 191 and (name N or name CA or name C or name O or name \ CB )) or resid 192 through 196 or resid 200 through 210 or (resid 211 and (name \ N or name CA or name C or name O or name CB )) or (resid 215 and (name N or nam \ e CA or name C or name O or name CB )) or resid 216 through 217 or (resid 218 an \ d (name N or name CA or name C or name O or name CB )) or resid 219 through 223 \ or (resid 224 and (name N or name CA or name C or name O or name CB )) or resid \ 225 through 238 or (resid 239 and (name N or name CA or name C or name O or name \ CB )) or resid 240 through 263 or resid 265 through 308 or (resid 309 and (name \ N or name CA or name C or name O or name CB )) or resid 310 through 323 or (res \ id 324 and (name N or name CA or name C or name O or name CB )) or resid 325 thr \ ough 332 or (resid 333 and (name N or name CA or name C or name O or name CB )) \ or resid 334 through 528 or (resid 529 and (name N or name CA or name C or name \ O or name CB )) or resid 530 through 553 or (resid 554 and (name N or name CA or \ name C or name O or name CB )) or resid 555 through 793 or (resid 794 and (name \ N or name CA or name C or name O or name CB )) or resid 795 or (resid 796 and ( \ name N or name CA or name C or name O or name CB )) or resid 797 through 810 or \ (resid 811 and (name N or name CA or name C or name O or name CB )) or resid 812 \ through 827 or resid 856 through 866 or (resid 867 through 868 and (name N or n \ ame CA or name C or name O or name CB )) or resid 869 through 939 or (resid 940 \ and (name N or name CA or name C or name O or name CB )) or resid 941 through 98 \ 4 or (resid 985 and (name N or name CA or name C or name O or name CB )) or resi \ d 986 through 987 or (resid 988 through 989 and (name N or name CA or name C or \ name O or name CB )) or resid 990 through 1141 or (resid 1142 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1143 through 1144 or (resid 1145 \ through 1146 and (name N or name CA or name C or name O or name CB )) or resid \ 1147 through 1308)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 110 or (resid 111 through 113 and (name N or name CA or name C o \ r name O or name CB )) or resid 116 through 134 or (resid 135 through 138 and (n \ ame N or name CA or name C or name O or name CB )) or resid 139 through 140 or r \ esid 166 through 187 or (resid 188 and (name N or name CA or name C or name O or \ name CB )) or resid 189 through 195 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB )) or resid 200 through 211 or resid 215 through 217 or \ (resid 218 and (name N or name CA or name C or name O or name CB )) or resid 21 \ 9 through 223 or (resid 224 and (name N or name CA or name C or name O or name C \ B )) or resid 225 through 238 or (resid 239 and (name N or name CA or name C or \ name O or name CB )) or resid 240 through 308 or (resid 309 and (name N or name \ CA or name C or name O or name CB )) or resid 310 through 332 or (resid 333 and \ (name N or name CA or name C or name O or name CB )) or resid 334 through 528 or \ (resid 529 and (name N or name CA or name C or name O or name CB )) or resid 53 \ 0 through 553 or (resid 554 and (name N or name CA or name C or name O or name C \ B )) or resid 555 through 567 or (resid 568 and (name N or name CA or name C or \ name O or name CB )) or resid 569 through 570 or (resid 571 and (name N or name \ CA or name C or name O or name CB )) or resid 572 through 581 or (resid 582 thro \ ugh 583 and (name N or name CA or name C or name O or name CB )) or resid 584 th \ rough 585 or (resid 586 and (name N or name CA or name C or name O or name CB )) \ or resid 587 through 618 or (resid 619 and (name N or name CA or name C or name \ O or name CB )) or resid 620 through 645 or (resid 646 through 647 and (name N \ or name CA or name C or name O or name CB )) or resid 648 through 793 or (resid \ 794 and (name N or name CA or name C or name O or name CB )) or resid 795 or (re \ sid 796 and (name N or name CA or name C or name O or name CB )) or resid 797 th \ rough 920 or (resid 921 and (name N or name CA or name C or name O or name CB )) \ or resid 922 through 1072 or (resid 1073 and (name N or name CA or name C or na \ me O or name CB )) or resid 1074 through 1117 or (resid 1118 and (name N or name \ CA or name C or name O or name CB )) or resid 1119 through 1141 or (resid 1142 \ and (name N or name CA or name C or name O or name CB )) or resid 1143 or (resid \ 1144 through 1146 and (name N or name CA or name C or name O or name CB )) or r \ esid 1147 through 1424)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } ncs_group { reference = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 10.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 26.510 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.100 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: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 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 : 0.006 0.222 27416 Z= 0.273 Angle : 0.670 18.322 37456 Z= 0.345 Chirality : 0.052 0.815 4432 Planarity : 0.003 0.043 4701 Dihedral : 10.967 89.535 10647 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.68 % Allowed : 3.50 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.14), residues: 3291 helix: 0.30 (0.21), residues: 667 sheet: -0.32 (0.17), residues: 853 loop : -0.89 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 765 TYR 0.018 0.001 TYR B 200 PHE 0.016 0.001 PHE B 565 TRP 0.006 0.001 TRP C 886 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00552 (27308) covalent geometry : angle 0.60963 (37174) SS BOND : bond 0.00294 ( 42) SS BOND : angle 0.74499 ( 84) hydrogen bonds : bond 0.11829 ( 1154) hydrogen bonds : angle 7.04857 ( 3090) link_BETA1-4 : bond 0.00551 ( 20) link_BETA1-4 : angle 3.05340 ( 60) link_NAG-ASN : bond 0.04757 ( 46) link_NAG-ASN : angle 4.15437 ( 138) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 424 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 452 LEU cc_start: 0.8971 (mt) cc_final: 0.8765 (mm) REVERT: B 472 ILE cc_start: 0.9050 (mm) cc_final: 0.8515 (mt) REVERT: B 506 GLN cc_start: 0.7921 (mt0) cc_final: 0.7526 (mt0) REVERT: B 508 TYR cc_start: 0.7399 (m-80) cc_final: 0.6636 (m-80) REVERT: B 528 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8253 (ttmm) REVERT: B 643 PHE cc_start: 0.8089 (t80) cc_final: 0.7761 (t80) REVERT: B 823 PHE cc_start: 0.7695 (m-80) cc_final: 0.7477 (m-80) REVERT: C 117 LEU cc_start: 0.8075 (mp) cc_final: 0.7677 (tt) REVERT: C 241 LEU cc_start: 0.8203 (mt) cc_final: 0.7859 (pp) REVERT: C 424 LYS cc_start: 0.8607 (tptt) cc_final: 0.8222 (tttp) REVERT: C 643 PHE cc_start: 0.7872 (t80) cc_final: 0.7605 (t80) REVERT: C 758 SER cc_start: 0.8149 (m) cc_final: 0.7769 (p) outliers start: 19 outliers final: 5 residues processed: 441 average time/residue: 0.1895 time to fit residues: 131.0721 Evaluate side-chains 226 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 220 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 607 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 50.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 935 GLN A1048 HIS B 87 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 370 ASN B 607 GLN B 613 GLN B 675 GLN B 935 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN C1048 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.183394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.110951 restraints weight = 39814.521| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 3.05 r_work: 0.2987 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 27416 Z= 0.172 Angle : 0.613 11.205 37456 Z= 0.312 Chirality : 0.046 0.215 4432 Planarity : 0.004 0.044 4701 Dihedral : 6.168 54.139 4995 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.25 % Allowed : 6.86 % Favored : 91.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.14), residues: 3291 helix: 1.03 (0.20), residues: 691 sheet: -0.00 (0.17), residues: 844 loop : -0.57 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 357 TYR 0.024 0.001 TYR B 200 PHE 0.017 0.002 PHE A 135 TRP 0.007 0.001 TRP C 886 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00403 (27308) covalent geometry : angle 0.59067 (37174) SS BOND : bond 0.00399 ( 42) SS BOND : angle 1.83509 ( 84) hydrogen bonds : bond 0.04343 ( 1154) hydrogen bonds : angle 5.87605 ( 3090) link_BETA1-4 : bond 0.00289 ( 20) link_BETA1-4 : angle 1.65191 ( 60) link_NAG-ASN : bond 0.00298 ( 46) link_NAG-ASN : angle 2.22089 ( 138) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 261 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 SER cc_start: 0.8979 (t) cc_final: 0.8773 (p) REVERT: B 102 ARG cc_start: 0.7696 (mmm-85) cc_final: 0.7419 (mmm-85) REVERT: B 205 SER cc_start: 0.8862 (p) cc_final: 0.8626 (t) REVERT: B 239 GLN cc_start: 0.7758 (tt0) cc_final: 0.7153 (tm-30) REVERT: B 369 TYR cc_start: 0.7852 (p90) cc_final: 0.7426 (p90) REVERT: B 452 LEU cc_start: 0.9018 (mt) cc_final: 0.8797 (mm) REVERT: B 471 GLU cc_start: 0.8354 (tp30) cc_final: 0.8135 (tp30) REVERT: B 472 ILE cc_start: 0.9127 (mm) cc_final: 0.8782 (mt) REVERT: B 508 TYR cc_start: 0.7673 (m-80) cc_final: 0.6732 (m-80) REVERT: B 528 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.7976 (ttmm) REVERT: B 643 PHE cc_start: 0.8520 (t80) cc_final: 0.8187 (t80) REVERT: B 675 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.6821 (pp30) REVERT: B 776 LYS cc_start: 0.8915 (tttt) cc_final: 0.8364 (tttm) REVERT: B 780 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8554 (mm-30) REVERT: B 823 PHE cc_start: 0.8289 (m-80) cc_final: 0.8010 (m-80) REVERT: B 994 ASP cc_start: 0.8214 (t70) cc_final: 0.7736 (t0) REVERT: C 86 PHE cc_start: 0.7227 (t80) cc_final: 0.6790 (t80) REVERT: C 117 LEU cc_start: 0.7997 (mp) cc_final: 0.7493 (tt) REVERT: C 239 GLN cc_start: 0.8132 (pp30) cc_final: 0.7797 (tm-30) REVERT: C 241 LEU cc_start: 0.8408 (mt) cc_final: 0.8049 (pp) REVERT: C 424 LYS cc_start: 0.8294 (tptt) cc_final: 0.7902 (tttp) REVERT: C 509 ARG cc_start: 0.7587 (mtt-85) cc_final: 0.6992 (mtt90) REVERT: C 643 PHE cc_start: 0.8272 (t80) cc_final: 0.7876 (t80) REVERT: C 758 SER cc_start: 0.8595 (m) cc_final: 0.8024 (p) REVERT: C 921 LYS cc_start: 0.8944 (mttt) cc_final: 0.8741 (mtpp) REVERT: X 34 MET cc_start: -0.5269 (ptt) cc_final: -0.5481 (ptt) REVERT: Y 12 MET cc_start: 0.5604 (pmm) cc_final: 0.5106 (pmm) REVERT: Y 108 ASP cc_start: 0.8528 (m-30) cc_final: 0.8228 (m-30) outliers start: 35 outliers final: 24 residues processed: 290 average time/residue: 0.1549 time to fit residues: 73.9137 Evaluate side-chains 239 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 213 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain X residue 30 SER Chi-restraints excluded: chain Z residue 34 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 330 optimal weight: 30.0000 chunk 79 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 319 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 232 optimal weight: 20.0000 chunk 161 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 144 optimal weight: 0.6980 chunk 210 optimal weight: 1.9990 chunk 243 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN B 207 HIS B 354 ASN B 519 HIS B1048 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 13 GLN Z 13 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.182227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.109132 restraints weight = 40187.145| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.03 r_work: 0.2946 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 27416 Z= 0.166 Angle : 0.572 9.406 37456 Z= 0.290 Chirality : 0.045 0.233 4432 Planarity : 0.004 0.044 4701 Dihedral : 5.788 57.383 4989 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.68 % Allowed : 8.01 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.14), residues: 3291 helix: 1.39 (0.20), residues: 689 sheet: 0.21 (0.17), residues: 835 loop : -0.44 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Y 52 TYR 0.021 0.001 TYR C 351 PHE 0.024 0.001 PHE B 565 TRP 0.008 0.001 TRP C 886 HIS 0.002 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00389 (27308) covalent geometry : angle 0.55414 (37174) SS BOND : bond 0.00297 ( 42) SS BOND : angle 1.32171 ( 84) hydrogen bonds : bond 0.04066 ( 1154) hydrogen bonds : angle 5.63223 ( 3090) link_BETA1-4 : bond 0.00357 ( 20) link_BETA1-4 : angle 1.55544 ( 60) link_NAG-ASN : bond 0.00246 ( 46) link_NAG-ASN : angle 2.00711 ( 138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 236 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 THR cc_start: 0.9104 (OUTLIER) cc_final: 0.8760 (p) REVERT: A 305 SER cc_start: 0.9016 (t) cc_final: 0.8793 (p) REVERT: B 102 ARG cc_start: 0.7688 (mmm-85) cc_final: 0.7400 (mmm-85) REVERT: B 239 GLN cc_start: 0.7756 (tt0) cc_final: 0.7126 (tm-30) REVERT: B 369 TYR cc_start: 0.8132 (p90) cc_final: 0.7902 (p90) REVERT: B 452 LEU cc_start: 0.9135 (mt) cc_final: 0.8899 (mm) REVERT: B 508 TYR cc_start: 0.7622 (m-80) cc_final: 0.6693 (m-80) REVERT: B 528 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8117 (ttmm) REVERT: B 643 PHE cc_start: 0.8521 (t80) cc_final: 0.8252 (t80) REVERT: B 776 LYS cc_start: 0.8983 (tttt) cc_final: 0.8367 (tttm) REVERT: B 780 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8499 (mm-30) REVERT: B 994 ASP cc_start: 0.8253 (t70) cc_final: 0.7854 (t0) REVERT: C 117 LEU cc_start: 0.7913 (mp) cc_final: 0.7392 (tt) REVERT: C 424 LYS cc_start: 0.8289 (tptt) cc_final: 0.7736 (tttp) REVERT: C 462 LYS cc_start: 0.8891 (tmmt) cc_final: 0.8672 (tmmt) REVERT: C 643 PHE cc_start: 0.8270 (t80) cc_final: 0.7804 (t80) REVERT: C 758 SER cc_start: 0.8626 (m) cc_final: 0.8038 (p) REVERT: C 995 ARG cc_start: 0.8273 (mtt-85) cc_final: 0.7955 (mtp85) REVERT: X 34 MET cc_start: -0.5235 (OUTLIER) cc_final: -0.5525 (ptt) REVERT: Y 12 MET cc_start: 0.5658 (pmm) cc_final: 0.5168 (pmm) REVERT: Y 100 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7159 (mt-10) REVERT: Y 108 ASP cc_start: 0.8463 (m-30) cc_final: 0.8156 (m-30) REVERT: Z 34 MET cc_start: 0.6175 (OUTLIER) cc_final: 0.1651 (pmm) outliers start: 47 outliers final: 33 residues processed: 272 average time/residue: 0.1680 time to fit residues: 75.1826 Evaluate side-chains 253 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 216 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain X residue 34 MET Chi-restraints excluded: chain Z residue 34 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 242 optimal weight: 0.6980 chunk 241 optimal weight: 2.9990 chunk 171 optimal weight: 0.5980 chunk 306 optimal weight: 30.0000 chunk 199 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 208 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 136 optimal weight: 7.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.180652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.105447 restraints weight = 39898.705| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 3.15 r_work: 0.2887 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27416 Z= 0.190 Angle : 0.564 9.462 37456 Z= 0.286 Chirality : 0.045 0.236 4432 Planarity : 0.004 0.044 4701 Dihedral : 5.468 55.614 4989 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.79 % Allowed : 8.44 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.14), residues: 3291 helix: 1.42 (0.20), residues: 688 sheet: 0.35 (0.17), residues: 837 loop : -0.38 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Y 52 TYR 0.019 0.001 TYR B 200 PHE 0.019 0.001 PHE B 565 TRP 0.009 0.001 TRP C 886 HIS 0.011 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00449 (27308) covalent geometry : angle 0.54854 (37174) SS BOND : bond 0.00341 ( 42) SS BOND : angle 1.14704 ( 84) hydrogen bonds : bond 0.04085 ( 1154) hydrogen bonds : angle 5.54870 ( 3090) link_BETA1-4 : bond 0.00248 ( 20) link_BETA1-4 : angle 1.47767 ( 60) link_NAG-ASN : bond 0.00237 ( 46) link_NAG-ASN : angle 1.89178 ( 138) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 233 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 THR cc_start: 0.9159 (OUTLIER) cc_final: 0.8925 (p) REVERT: A 305 SER cc_start: 0.9054 (t) cc_final: 0.8833 (p) REVERT: B 102 ARG cc_start: 0.7752 (mmm-85) cc_final: 0.7517 (mmm-85) REVERT: B 239 GLN cc_start: 0.7820 (tt0) cc_final: 0.7220 (tm-30) REVERT: B 452 LEU cc_start: 0.9216 (mt) cc_final: 0.8982 (mm) REVERT: B 471 GLU cc_start: 0.8506 (tp30) cc_final: 0.8269 (tp30) REVERT: B 472 ILE cc_start: 0.8821 (mt) cc_final: 0.8440 (tt) REVERT: B 508 TYR cc_start: 0.7606 (m-80) cc_final: 0.6709 (m-80) REVERT: B 528 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8093 (ttmm) REVERT: B 643 PHE cc_start: 0.8600 (t80) cc_final: 0.8352 (t80) REVERT: B 759 PHE cc_start: 0.8603 (OUTLIER) cc_final: 0.8289 (m-10) REVERT: B 776 LYS cc_start: 0.9054 (tttt) cc_final: 0.8512 (tttm) REVERT: B 780 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8535 (mm-30) REVERT: B 950 ASP cc_start: 0.8698 (m-30) cc_final: 0.8483 (m-30) REVERT: B 994 ASP cc_start: 0.8343 (t70) cc_final: 0.7847 (t0) REVERT: C 117 LEU cc_start: 0.7911 (mp) cc_final: 0.7372 (tt) REVERT: C 424 LYS cc_start: 0.8333 (tptt) cc_final: 0.7943 (tttp) REVERT: C 462 LYS cc_start: 0.8986 (tmmt) cc_final: 0.8704 (tmmt) REVERT: C 643 PHE cc_start: 0.8351 (t80) cc_final: 0.7813 (t80) REVERT: C 758 SER cc_start: 0.8643 (m) cc_final: 0.8078 (p) REVERT: C 950 ASP cc_start: 0.8670 (t70) cc_final: 0.8414 (t0) REVERT: X 34 MET cc_start: -0.5173 (OUTLIER) cc_final: -0.5445 (ptt) REVERT: Y 12 MET cc_start: 0.5855 (pmm) cc_final: 0.5317 (pmm) REVERT: Y 52 ARG cc_start: 0.8315 (mtp-110) cc_final: 0.8033 (mtp-110) REVERT: Y 108 ASP cc_start: 0.8540 (m-30) cc_final: 0.8241 (m-30) REVERT: Z 34 MET cc_start: 0.6299 (OUTLIER) cc_final: 0.1929 (pmm) outliers start: 50 outliers final: 38 residues processed: 277 average time/residue: 0.1623 time to fit residues: 74.8318 Evaluate side-chains 258 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 215 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain X residue 34 MET Chi-restraints excluded: chain Z residue 34 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 299 optimal weight: 50.0000 chunk 245 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 195 optimal weight: 0.9990 chunk 39 optimal weight: 20.0000 chunk 289 optimal weight: 0.7980 chunk 133 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 238 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 GLN C 239 GLN C1010 GLN C1088 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.178361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.102418 restraints weight = 40025.256| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.99 r_work: 0.2893 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 27416 Z= 0.208 Angle : 0.570 9.464 37456 Z= 0.289 Chirality : 0.045 0.238 4432 Planarity : 0.004 0.045 4701 Dihedral : 5.289 55.733 4989 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.32 % Allowed : 9.12 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.14), residues: 3291 helix: 1.45 (0.20), residues: 678 sheet: 0.44 (0.17), residues: 845 loop : -0.38 (0.15), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Y 52 TYR 0.033 0.001 TYR B 369 PHE 0.024 0.001 PHE A 192 TRP 0.010 0.001 TRP C 886 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00493 (27308) covalent geometry : angle 0.55572 (37174) SS BOND : bond 0.00377 ( 42) SS BOND : angle 1.12260 ( 84) hydrogen bonds : bond 0.04163 ( 1154) hydrogen bonds : angle 5.50424 ( 3090) link_BETA1-4 : bond 0.00241 ( 20) link_BETA1-4 : angle 1.41975 ( 60) link_NAG-ASN : bond 0.00249 ( 46) link_NAG-ASN : angle 1.80569 ( 138) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 228 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 THR cc_start: 0.9170 (OUTLIER) cc_final: 0.8941 (p) REVERT: A 305 SER cc_start: 0.9102 (t) cc_final: 0.8875 (p) REVERT: B 239 GLN cc_start: 0.7872 (tt0) cc_final: 0.7296 (tm-30) REVERT: B 452 LEU cc_start: 0.9370 (mt) cc_final: 0.9147 (mm) REVERT: B 471 GLU cc_start: 0.8545 (tp30) cc_final: 0.8284 (tp30) REVERT: B 472 ILE cc_start: 0.8840 (mt) cc_final: 0.8384 (tt) REVERT: B 508 TYR cc_start: 0.7545 (m-80) cc_final: 0.6572 (m-80) REVERT: B 512 VAL cc_start: 0.8401 (t) cc_final: 0.8153 (m) REVERT: B 643 PHE cc_start: 0.8715 (t80) cc_final: 0.8484 (t80) REVERT: B 776 LYS cc_start: 0.9113 (tttt) cc_final: 0.8547 (tttm) REVERT: B 780 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8642 (mm-30) REVERT: B 994 ASP cc_start: 0.8645 (t70) cc_final: 0.8266 (t0) REVERT: C 102 ARG cc_start: 0.8319 (mmt180) cc_final: 0.8114 (mmt-90) REVERT: C 121 ASN cc_start: 0.7581 (t0) cc_final: 0.6957 (t0) REVERT: C 400 PHE cc_start: 0.8721 (p90) cc_final: 0.8352 (p90) REVERT: C 424 LYS cc_start: 0.8388 (tptt) cc_final: 0.7998 (tttp) REVERT: C 462 LYS cc_start: 0.9023 (tmmt) cc_final: 0.8701 (tmmt) REVERT: C 509 ARG cc_start: 0.7673 (mtt-85) cc_final: 0.7120 (mtp85) REVERT: C 758 SER cc_start: 0.8719 (m) cc_final: 0.8152 (p) REVERT: C 878 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8993 (mt) REVERT: C 995 ARG cc_start: 0.8546 (mtt-85) cc_final: 0.8318 (mtp85) REVERT: X 34 MET cc_start: -0.4800 (OUTLIER) cc_final: -0.5230 (ptt) REVERT: Y 12 MET cc_start: 0.6033 (pmm) cc_final: 0.5488 (pmm) REVERT: Y 52 ARG cc_start: 0.8283 (mtp-110) cc_final: 0.7904 (mtp-110) REVERT: Y 108 ASP cc_start: 0.8606 (m-30) cc_final: 0.8299 (m-30) REVERT: Z 34 MET cc_start: 0.6355 (OUTLIER) cc_final: 0.2052 (pmm) outliers start: 65 outliers final: 51 residues processed: 279 average time/residue: 0.1602 time to fit residues: 73.6172 Evaluate side-chains 268 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 213 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain X residue 34 MET Chi-restraints excluded: chain Y residue 78 THR Chi-restraints excluded: chain Z residue 34 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 175 optimal weight: 0.5980 chunk 205 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 67 optimal weight: 0.4980 chunk 207 optimal weight: 4.9990 chunk 167 optimal weight: 0.7980 chunk 180 optimal weight: 0.6980 chunk 197 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 ASN B 388 ASN C 239 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.179386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.105267 restraints weight = 39971.311| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 3.06 r_work: 0.2895 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27416 Z= 0.144 Angle : 0.535 9.458 37456 Z= 0.271 Chirality : 0.043 0.234 4432 Planarity : 0.004 0.043 4701 Dihedral : 5.068 55.734 4989 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.97 % Allowed : 10.26 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.14), residues: 3291 helix: 1.59 (0.20), residues: 677 sheet: 0.52 (0.17), residues: 804 loop : -0.31 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Y 103 TYR 0.029 0.001 TYR A 369 PHE 0.025 0.001 PHE C 140 TRP 0.011 0.001 TRP Y 112 HIS 0.003 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00335 (27308) covalent geometry : angle 0.52229 (37174) SS BOND : bond 0.00253 ( 42) SS BOND : angle 0.97857 ( 84) hydrogen bonds : bond 0.03869 ( 1154) hydrogen bonds : angle 5.38850 ( 3090) link_BETA1-4 : bond 0.00265 ( 20) link_BETA1-4 : angle 1.35925 ( 60) link_NAG-ASN : bond 0.00184 ( 46) link_NAG-ASN : angle 1.68517 ( 138) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 223 time to evaluate : 1.033 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 284 THR cc_start: 0.9149 (OUTLIER) cc_final: 0.8928 (p) REVERT: A 305 SER cc_start: 0.9040 (t) cc_final: 0.8806 (p) REVERT: B 239 GLN cc_start: 0.7780 (tt0) cc_final: 0.7420 (tm-30) REVERT: B 324 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7872 (tt0) REVERT: B 452 LEU cc_start: 0.9350 (mt) cc_final: 0.9130 (mm) REVERT: B 471 GLU cc_start: 0.8481 (tp30) cc_final: 0.8193 (tp30) REVERT: B 472 ILE cc_start: 0.8835 (mt) cc_final: 0.8330 (tt) REVERT: B 508 TYR cc_start: 0.7540 (m-80) cc_final: 0.6567 (m-80) REVERT: B 643 PHE cc_start: 0.8586 (t80) cc_final: 0.8311 (t80) REVERT: B 776 LYS cc_start: 0.9003 (tttt) cc_final: 0.8508 (tttm) REVERT: B 994 ASP cc_start: 0.8334 (t70) cc_final: 0.7955 (t0) REVERT: C 121 ASN cc_start: 0.7352 (t0) cc_final: 0.6609 (t0) REVERT: C 190 ARG cc_start: 0.6160 (mmt180) cc_final: 0.5793 (mmt180) REVERT: C 239 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.7861 (tm-30) REVERT: C 400 PHE cc_start: 0.8637 (p90) cc_final: 0.8302 (p90) REVERT: C 424 LYS cc_start: 0.8347 (tptt) cc_final: 0.7962 (tttp) REVERT: C 462 LYS cc_start: 0.9006 (tmmt) cc_final: 0.8674 (tmmt) REVERT: C 509 ARG cc_start: 0.7683 (mtt-85) cc_final: 0.7159 (mtp85) REVERT: C 643 PHE cc_start: 0.8449 (t80) cc_final: 0.8139 (t80) REVERT: C 758 SER cc_start: 0.8541 (m) cc_final: 0.7972 (p) REVERT: C 878 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8895 (mt) REVERT: C 995 ARG cc_start: 0.8343 (mtt-85) cc_final: 0.8131 (mtp85) REVERT: X 34 MET cc_start: -0.4947 (OUTLIER) cc_final: -0.5369 (ptt) REVERT: Y 12 MET cc_start: 0.6049 (pmm) cc_final: 0.5496 (pmm) REVERT: Y 34 MET cc_start: 0.7055 (mmm) cc_final: 0.6654 (mmm) REVERT: Y 52 ARG cc_start: 0.8206 (mtp-110) cc_final: 0.7867 (mtp-110) REVERT: Y 103 ARG cc_start: 0.8407 (tpp-160) cc_final: 0.8188 (tpp-160) REVERT: Y 108 ASP cc_start: 0.8569 (m-30) cc_final: 0.8277 (m-30) REVERT: Z 34 MET cc_start: 0.6413 (OUTLIER) cc_final: 0.2246 (pmm) outliers start: 55 outliers final: 41 residues processed: 263 average time/residue: 0.1674 time to fit residues: 72.5655 Evaluate side-chains 261 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 214 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain X residue 34 MET Chi-restraints excluded: chain Y residue 78 THR Chi-restraints excluded: chain Z residue 34 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 188 optimal weight: 0.7980 chunk 98 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 165 optimal weight: 0.0770 chunk 100 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 chunk 37 optimal weight: 30.0000 chunk 267 optimal weight: 0.9980 chunk 309 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 29 optimal weight: 20.0000 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 872 GLN B 30 ASN Y 101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.179373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.104508 restraints weight = 39938.038| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.98 r_work: 0.2892 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 27416 Z= 0.179 Angle : 0.549 9.453 37456 Z= 0.277 Chirality : 0.044 0.237 4432 Planarity : 0.004 0.043 4701 Dihedral : 4.983 55.632 4988 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.18 % Allowed : 10.51 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.14), residues: 3291 helix: 1.58 (0.20), residues: 675 sheet: 0.47 (0.17), residues: 811 loop : -0.33 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Y 103 TYR 0.020 0.001 TYR C 351 PHE 0.022 0.001 PHE B 32 TRP 0.011 0.001 TRP Y 112 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00423 (27308) covalent geometry : angle 0.53610 (37174) SS BOND : bond 0.00298 ( 42) SS BOND : angle 1.01081 ( 84) hydrogen bonds : bond 0.03958 ( 1154) hydrogen bonds : angle 5.37234 ( 3090) link_BETA1-4 : bond 0.00220 ( 20) link_BETA1-4 : angle 1.36426 ( 60) link_NAG-ASN : bond 0.00202 ( 46) link_NAG-ASN : angle 1.67726 ( 138) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 222 time to evaluate : 0.977 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 284 THR cc_start: 0.9206 (OUTLIER) cc_final: 0.9005 (p) REVERT: A 305 SER cc_start: 0.9096 (t) cc_final: 0.8853 (p) REVERT: B 239 GLN cc_start: 0.7881 (tt0) cc_final: 0.7336 (tm-30) REVERT: B 324 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7913 (tt0) REVERT: B 369 TYR cc_start: 0.7849 (p90) cc_final: 0.7548 (p90) REVERT: B 452 LEU cc_start: 0.9428 (mt) cc_final: 0.9224 (mm) REVERT: B 471 GLU cc_start: 0.8535 (tp30) cc_final: 0.8265 (tp30) REVERT: B 472 ILE cc_start: 0.8884 (mt) cc_final: 0.8357 (tt) REVERT: B 508 TYR cc_start: 0.7511 (m-80) cc_final: 0.6517 (m-80) REVERT: B 643 PHE cc_start: 0.8714 (t80) cc_final: 0.8483 (t80) REVERT: B 776 LYS cc_start: 0.9095 (tttt) cc_final: 0.8702 (tttm) REVERT: B 994 ASP cc_start: 0.8620 (t70) cc_final: 0.8265 (t0) REVERT: C 190 ARG cc_start: 0.6348 (mmt180) cc_final: 0.5938 (mmt180) REVERT: C 400 PHE cc_start: 0.8748 (p90) cc_final: 0.8380 (p90) REVERT: C 424 LYS cc_start: 0.8409 (tptt) cc_final: 0.8008 (tttp) REVERT: C 462 LYS cc_start: 0.9011 (tmmt) cc_final: 0.8672 (tmmt) REVERT: C 509 ARG cc_start: 0.7707 (mtt-85) cc_final: 0.7173 (mtp85) REVERT: C 643 PHE cc_start: 0.8598 (t80) cc_final: 0.8372 (t80) REVERT: C 758 SER cc_start: 0.8675 (m) cc_final: 0.8107 (p) REVERT: C 878 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.8977 (mt) REVERT: X 34 MET cc_start: -0.4567 (OUTLIER) cc_final: -0.5093 (ptt) REVERT: Y 52 ARG cc_start: 0.8255 (mtp-110) cc_final: 0.7885 (mtp-110) REVERT: Y 103 ARG cc_start: 0.8495 (tpp-160) cc_final: 0.8158 (tpp-160) REVERT: Y 108 ASP cc_start: 0.8548 (m-30) cc_final: 0.8217 (m-30) REVERT: Z 34 MET cc_start: 0.6538 (OUTLIER) cc_final: 0.2455 (pmm) outliers start: 61 outliers final: 45 residues processed: 269 average time/residue: 0.1591 time to fit residues: 70.9328 Evaluate side-chains 260 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 210 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain X residue 34 MET Chi-restraints excluded: chain Y residue 78 THR Chi-restraints excluded: chain Y residue 101 ASN Chi-restraints excluded: chain Z residue 34 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 24 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 175 optimal weight: 1.9990 chunk 271 optimal weight: 0.2980 chunk 211 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 314 optimal weight: 6.9990 chunk 64 optimal weight: 0.0970 chunk 259 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 288 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 913 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.178269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.103954 restraints weight = 39605.059| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.96 r_work: 0.2899 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 27416 Z= 0.163 Angle : 0.543 9.453 37456 Z= 0.273 Chirality : 0.044 0.235 4432 Planarity : 0.004 0.044 4701 Dihedral : 4.887 55.681 4988 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.89 % Allowed : 10.94 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.14), residues: 3291 helix: 1.72 (0.21), residues: 663 sheet: 0.44 (0.17), residues: 815 loop : -0.30 (0.15), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Y 98 TYR 0.030 0.001 TYR A 369 PHE 0.019 0.001 PHE A 168 TRP 0.016 0.001 TRP Y 112 HIS 0.003 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00385 (27308) covalent geometry : angle 0.53080 (37174) SS BOND : bond 0.00268 ( 42) SS BOND : angle 0.97710 ( 84) hydrogen bonds : bond 0.03887 ( 1154) hydrogen bonds : angle 5.31851 ( 3090) link_BETA1-4 : bond 0.00231 ( 20) link_BETA1-4 : angle 1.33502 ( 60) link_NAG-ASN : bond 0.00185 ( 46) link_NAG-ASN : angle 1.62453 ( 138) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 215 time to evaluate : 0.761 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 305 SER cc_start: 0.9083 (t) cc_final: 0.8841 (p) REVERT: B 239 GLN cc_start: 0.7888 (tt0) cc_final: 0.7358 (tm-30) REVERT: B 369 TYR cc_start: 0.7873 (p90) cc_final: 0.7478 (p90) REVERT: B 471 GLU cc_start: 0.8511 (tp30) cc_final: 0.8224 (tp30) REVERT: B 472 ILE cc_start: 0.8908 (mt) cc_final: 0.8364 (tt) REVERT: B 508 TYR cc_start: 0.7509 (m-80) cc_final: 0.6481 (m-80) REVERT: B 643 PHE cc_start: 0.8732 (t80) cc_final: 0.8461 (t80) REVERT: B 776 LYS cc_start: 0.9094 (tttt) cc_final: 0.8707 (tttm) REVERT: B 994 ASP cc_start: 0.8625 (t70) cc_final: 0.8222 (t0) REVERT: C 190 ARG cc_start: 0.6400 (mmt180) cc_final: 0.5990 (mmt180) REVERT: C 239 GLN cc_start: 0.8627 (tt0) cc_final: 0.7976 (tm-30) REVERT: C 400 PHE cc_start: 0.8766 (p90) cc_final: 0.8362 (p90) REVERT: C 424 LYS cc_start: 0.8393 (tptt) cc_final: 0.8019 (tttp) REVERT: C 462 LYS cc_start: 0.9054 (tmmt) cc_final: 0.8690 (tmmt) REVERT: C 643 PHE cc_start: 0.8616 (t80) cc_final: 0.8376 (t80) REVERT: C 758 SER cc_start: 0.8649 (m) cc_final: 0.8075 (p) REVERT: C 878 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8971 (mt) REVERT: X 34 MET cc_start: -0.4525 (OUTLIER) cc_final: -0.5128 (ptt) REVERT: Y 52 ARG cc_start: 0.8210 (mtp-110) cc_final: 0.7822 (mtp-110) REVERT: Y 103 ARG cc_start: 0.8475 (tpp-160) cc_final: 0.7970 (tpp-160) REVERT: Y 108 ASP cc_start: 0.8520 (m-30) cc_final: 0.8297 (m-30) REVERT: Z 34 MET cc_start: 0.6544 (OUTLIER) cc_final: 0.2575 (pmm) outliers start: 53 outliers final: 45 residues processed: 257 average time/residue: 0.1579 time to fit residues: 67.5858 Evaluate side-chains 256 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 208 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain X residue 34 MET Chi-restraints excluded: chain Y residue 78 THR Chi-restraints excluded: chain Z residue 34 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 176 optimal weight: 2.9990 chunk 296 optimal weight: 40.0000 chunk 100 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 212 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 303 optimal weight: 10.0000 chunk 174 optimal weight: 0.6980 chunk 286 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.177859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.102863 restraints weight = 39615.584| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.89 r_work: 0.2901 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27416 Z= 0.169 Angle : 0.548 9.650 37456 Z= 0.275 Chirality : 0.044 0.237 4432 Planarity : 0.004 0.049 4701 Dihedral : 4.822 56.176 4988 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.89 % Allowed : 11.19 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.15), residues: 3291 helix: 1.70 (0.20), residues: 670 sheet: 0.47 (0.17), residues: 804 loop : -0.30 (0.15), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 995 TYR 0.019 0.001 TYR C 351 PHE 0.020 0.001 PHE A 192 TRP 0.013 0.001 TRP B 436 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00400 (27308) covalent geometry : angle 0.53638 (37174) SS BOND : bond 0.00277 ( 42) SS BOND : angle 0.97948 ( 84) hydrogen bonds : bond 0.03909 ( 1154) hydrogen bonds : angle 5.30342 ( 3090) link_BETA1-4 : bond 0.00247 ( 20) link_BETA1-4 : angle 1.32251 ( 60) link_NAG-ASN : bond 0.00178 ( 46) link_NAG-ASN : angle 1.60229 ( 138) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 221 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 SER cc_start: 0.9081 (t) cc_final: 0.8838 (p) REVERT: A 519 HIS cc_start: 0.4861 (OUTLIER) cc_final: 0.3547 (m-70) REVERT: B 239 GLN cc_start: 0.7902 (tt0) cc_final: 0.7357 (tm-30) REVERT: B 324 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7933 (tt0) REVERT: B 369 TYR cc_start: 0.7932 (p90) cc_final: 0.7599 (p90) REVERT: B 408 ARG cc_start: 0.8206 (ptm-80) cc_final: 0.7994 (tmm160) REVERT: B 471 GLU cc_start: 0.8533 (tp30) cc_final: 0.8235 (tp30) REVERT: B 472 ILE cc_start: 0.8931 (mt) cc_final: 0.8358 (tt) REVERT: B 489 TYR cc_start: 0.7715 (m-10) cc_final: 0.7323 (m-10) REVERT: B 508 TYR cc_start: 0.7506 (m-80) cc_final: 0.6490 (m-80) REVERT: B 643 PHE cc_start: 0.8733 (t80) cc_final: 0.8465 (t80) REVERT: B 776 LYS cc_start: 0.9114 (tttt) cc_final: 0.8754 (tttm) REVERT: B 994 ASP cc_start: 0.8640 (t70) cc_final: 0.8242 (t0) REVERT: C 86 PHE cc_start: 0.7304 (t80) cc_final: 0.6968 (t80) REVERT: C 190 ARG cc_start: 0.6377 (mmt180) cc_final: 0.5976 (mmt180) REVERT: C 239 GLN cc_start: 0.8715 (tt0) cc_final: 0.8049 (tm-30) REVERT: C 400 PHE cc_start: 0.8806 (p90) cc_final: 0.8460 (p90) REVERT: C 424 LYS cc_start: 0.8432 (tptt) cc_final: 0.8062 (tttp) REVERT: C 462 LYS cc_start: 0.9066 (tmmt) cc_final: 0.8772 (tptt) REVERT: C 643 PHE cc_start: 0.8649 (t80) cc_final: 0.8440 (t80) REVERT: C 758 SER cc_start: 0.8665 (m) cc_final: 0.8099 (p) REVERT: C 878 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8981 (mt) REVERT: X 34 MET cc_start: -0.4424 (OUTLIER) cc_final: -0.5091 (ptt) REVERT: Y 12 MET cc_start: 0.6936 (pmm) cc_final: 0.6661 (pmm) REVERT: Y 34 MET cc_start: 0.6908 (mmm) cc_final: 0.6415 (mmm) REVERT: Y 52 ARG cc_start: 0.8219 (mtp-110) cc_final: 0.7830 (mtp-110) REVERT: Y 103 ARG cc_start: 0.8478 (tpp-160) cc_final: 0.8235 (tpp-160) REVERT: Y 108 ASP cc_start: 0.8488 (m-30) cc_final: 0.8251 (m-30) REVERT: Z 34 MET cc_start: 0.6579 (OUTLIER) cc_final: 0.2644 (pmm) outliers start: 53 outliers final: 39 residues processed: 262 average time/residue: 0.1526 time to fit residues: 66.3914 Evaluate side-chains 255 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 211 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain X residue 34 MET Chi-restraints excluded: chain Y residue 78 THR Chi-restraints excluded: chain Z residue 34 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 196 optimal weight: 0.9980 chunk 149 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 232 optimal weight: 20.0000 chunk 108 optimal weight: 9.9990 chunk 195 optimal weight: 0.1980 chunk 71 optimal weight: 0.1980 chunk 40 optimal weight: 10.0000 chunk 303 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.179094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.105345 restraints weight = 39912.991| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.96 r_work: 0.2918 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27416 Z= 0.135 Angle : 0.531 9.463 37456 Z= 0.268 Chirality : 0.043 0.235 4432 Planarity : 0.004 0.047 4701 Dihedral : 4.597 55.669 4983 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.64 % Allowed : 11.48 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.15), residues: 3291 helix: 1.78 (0.21), residues: 669 sheet: 0.49 (0.18), residues: 800 loop : -0.25 (0.15), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 357 TYR 0.031 0.001 TYR A 369 PHE 0.021 0.001 PHE A 168 TRP 0.012 0.001 TRP Y 112 HIS 0.002 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00315 (27308) covalent geometry : angle 0.52066 (37174) SS BOND : bond 0.00229 ( 42) SS BOND : angle 0.91015 ( 84) hydrogen bonds : bond 0.03728 ( 1154) hydrogen bonds : angle 5.21028 ( 3090) link_BETA1-4 : bond 0.00268 ( 20) link_BETA1-4 : angle 1.27381 ( 60) link_NAG-ASN : bond 0.00164 ( 46) link_NAG-ASN : angle 1.51363 ( 138) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 225 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8011 (ptmt) cc_final: 0.7617 (ptmt) REVERT: A 305 SER cc_start: 0.9072 (t) cc_final: 0.8821 (p) REVERT: A 519 HIS cc_start: 0.4845 (OUTLIER) cc_final: 0.3535 (m-70) REVERT: B 239 GLN cc_start: 0.7856 (tt0) cc_final: 0.7293 (tm-30) REVERT: B 324 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7953 (tt0) REVERT: B 369 TYR cc_start: 0.7894 (p90) cc_final: 0.7691 (p90) REVERT: B 472 ILE cc_start: 0.8926 (mt) cc_final: 0.8628 (tt) REVERT: B 489 TYR cc_start: 0.7634 (m-10) cc_final: 0.7280 (m-10) REVERT: B 508 TYR cc_start: 0.7474 (m-80) cc_final: 0.6450 (m-80) REVERT: B 643 PHE cc_start: 0.8727 (t80) cc_final: 0.8459 (t80) REVERT: B 776 LYS cc_start: 0.9062 (tttt) cc_final: 0.8618 (tttm) REVERT: B 994 ASP cc_start: 0.8615 (t70) cc_final: 0.8212 (t0) REVERT: C 86 PHE cc_start: 0.7179 (t80) cc_final: 0.6896 (t80) REVERT: C 190 ARG cc_start: 0.6441 (mmt180) cc_final: 0.6032 (mmt180) REVERT: C 239 GLN cc_start: 0.8747 (tt0) cc_final: 0.8055 (tm-30) REVERT: C 400 PHE cc_start: 0.8747 (p90) cc_final: 0.8289 (p90) REVERT: C 424 LYS cc_start: 0.8392 (tptt) cc_final: 0.8019 (tttp) REVERT: C 462 LYS cc_start: 0.9011 (tmmt) cc_final: 0.8713 (tptt) REVERT: C 643 PHE cc_start: 0.8598 (t80) cc_final: 0.8378 (t80) REVERT: C 758 SER cc_start: 0.8616 (m) cc_final: 0.8042 (p) REVERT: C 878 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8954 (mt) REVERT: X 34 MET cc_start: -0.4202 (OUTLIER) cc_final: -0.4919 (ptt) REVERT: Y 12 MET cc_start: 0.6820 (pmm) cc_final: 0.6589 (pmm) REVERT: Y 52 ARG cc_start: 0.8143 (mtp-110) cc_final: 0.7744 (mtp-110) REVERT: Y 103 ARG cc_start: 0.8430 (tpp-160) cc_final: 0.8189 (tpp-160) REVERT: Y 108 ASP cc_start: 0.8482 (m-30) cc_final: 0.8259 (m-30) REVERT: Z 34 MET cc_start: 0.6554 (OUTLIER) cc_final: 0.2813 (pmm) outliers start: 46 outliers final: 37 residues processed: 260 average time/residue: 0.1593 time to fit residues: 68.9627 Evaluate side-chains 257 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 215 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain X residue 34 MET Chi-restraints excluded: chain Y residue 78 THR Chi-restraints excluded: chain Z residue 34 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 246 optimal weight: 0.9980 chunk 247 optimal weight: 0.8980 chunk 66 optimal weight: 0.0970 chunk 98 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 190 optimal weight: 0.3980 chunk 153 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 232 optimal weight: 20.0000 chunk 64 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.178721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.105200 restraints weight = 39560.767| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.25 r_work: 0.2867 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27416 Z= 0.140 Angle : 0.533 11.366 37456 Z= 0.269 Chirality : 0.043 0.236 4432 Planarity : 0.004 0.045 4701 Dihedral : 4.541 55.610 4983 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.72 % Allowed : 11.66 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.15), residues: 3291 helix: 1.85 (0.21), residues: 663 sheet: 0.46 (0.17), residues: 810 loop : -0.23 (0.15), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 357 TYR 0.035 0.001 TYR A 369 PHE 0.022 0.001 PHE B 201 TRP 0.012 0.001 TRP Y 112 HIS 0.002 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00329 (27308) covalent geometry : angle 0.52317 (37174) SS BOND : bond 0.00245 ( 42) SS BOND : angle 0.89274 ( 84) hydrogen bonds : bond 0.03724 ( 1154) hydrogen bonds : angle 5.17913 ( 3090) link_BETA1-4 : bond 0.00251 ( 20) link_BETA1-4 : angle 1.26058 ( 60) link_NAG-ASN : bond 0.00159 ( 46) link_NAG-ASN : angle 1.49794 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9209.68 seconds wall clock time: 157 minutes 41.44 seconds (9461.44 seconds total)