Starting phenix.real_space_refine on Sun Jul 5 04:11:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7v8c_31798/07_2026/7v8c_31798.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v8c_31798/07_2026/7v8c_31798.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v8c_31798/07_2026/7v8c_31798.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v8c_31798/07_2026/7v8c_31798.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v8c_31798/07_2026/7v8c_31798.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v8c_31798/07_2026/7v8c_31798.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7v8c_31798/07_2026/7v8c_31798.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7v8c_31798/07_2026/7v8c_31798.cif" } resolution = 3.4 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= -0.001 sd= 0.040 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 111 5.16 5 C 16030 2.51 5 N 4088 2.21 5 O 4968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25197 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 8016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8016 Classifications: {'peptide': 1026} Link IDs: {'PTRANS': 50, 'TRANS': 975} Chain breaks: 7 Chain: "B" Number of atoms: 8072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8072 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 51, 'TRANS': 980} Chain breaks: 7 Chain: "C" Number of atoms: 8059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 8059 Classifications: {'peptide': 1030} Link IDs: {'PTRANS': 51, 'TRANS': 978} Chain breaks: 7 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 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 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 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 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 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 chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 5.78, per 1000 atoms: 0.23 Number of scatterers: 25197 At special positions: 0 Unit cell: (141.9, 146.3, 196.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 4968 8.00 N 4088 7.00 C 16030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.04 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.04 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.04 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.02 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.02 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.04 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.02 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.02 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2003 " - " ASN A 234 " " NAG A2004 " - " ASN A 600 " " NAG A2005 " - " ASN A 654 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 122 " " NAG B2003 " - " ASN B 234 " " NAG B2004 " - " ASN B 328 " " NAG B2005 " - " ASN B 600 " " NAG B2006 " - " ASN B 654 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 165 " " NAG C2003 " - " ASN C 328 " " NAG C2004 " - " ASN C 600 " " NAG C2005 " - " ASN C 613 " " NAG C2006 " - " ASN C 654 " " NAG D 1 " - " ASN A 165 " " NAG E 1 " - " ASN A 279 " " NAG F 1 " - " ASN A 328 " " NAG G 1 " - " ASN A 340 " " NAG H 1 " - " ASN A 613 " " NAG I 1 " - " ASN A 706 " " NAG J 1 " - " ASN A 714 " " NAG K 1 " - " ASN A 798 " " NAG L 1 " - " ASN A1071 " " NAG M 1 " - " ASN A1095 " " NAG N 1 " - " ASN A1131 " " NAG P 1 " - " ASN B 279 " " NAG Q 1 " - " ASN B 340 " " NAG R 1 " - " ASN B 613 " " NAG S 1 " - " ASN B 706 " " NAG T 1 " - " ASN B 714 " " NAG U 1 " - " ASN B 798 " " NAG V 1 " - " ASN B1071 " " NAG W 1 " - " ASN B1095 " " NAG X 1 " - " ASN B1131 " " NAG Y 1 " - " ASN C 279 " " NAG Z 1 " - " ASN C 340 " " NAG a 1 " - " ASN C 706 " " NAG b 1 " - " ASN C 714 " " NAG c 1 " - " ASN C 798 " " NAG d 1 " - " ASN C1071 " " NAG e 1 " - " ASN C1095 " " NAG f 1 " - " ASN C1131 " Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 1.0 seconds 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5780 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 45 sheets defined 25.1% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 removed outlier: 3.546A pdb=" N GLU A 295 " --> pdb=" O ASP A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 361 through 368 removed outlier: 4.377A pdb=" N LEU A 365 " --> pdb=" O ASP A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 386 removed outlier: 4.190A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 734 through 740 removed outlier: 3.551A pdb=" N TYR A 738 " --> pdb=" O ASP A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.837A pdb=" N GLN A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 780 Processing helix chain 'A' and resid 813 through 823 Processing helix chain 'A' and resid 863 through 881 Processing helix chain 'A' and resid 883 through 887 Processing helix chain 'A' and resid 895 through 906 removed outlier: 4.441A pdb=" N TYR A 901 " --> pdb=" O MET A 897 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A 906 " --> pdb=" O ARG A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 916 removed outlier: 3.554A pdb=" N TYR A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 938 Processing helix chain 'A' and resid 942 through 962 removed outlier: 3.602A pdb=" N GLN A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 980 removed outlier: 3.612A pdb=" N ILE A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 1030 removed outlier: 4.629A pdb=" N VAL A 988 " --> pdb=" O VAL A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1143 Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 334 through 340 removed outlier: 4.062A pdb=" N VAL B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 368 removed outlier: 4.383A pdb=" N LEU B 365 " --> pdb=" O ASP B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 385 removed outlier: 3.928A pdb=" N LEU B 384 " --> pdb=" O PRO B 381 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 407 removed outlier: 3.809A pdb=" N VAL B 404 " --> pdb=" O GLY B 401 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG B 405 " --> pdb=" O ASP B 402 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE B 407 " --> pdb=" O VAL B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 735 through 740 Processing helix chain 'B' and resid 743 through 752 removed outlier: 3.939A pdb=" N GLN B 752 " --> pdb=" O ASN B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 780 Processing helix chain 'B' and resid 813 through 823 Processing helix chain 'B' and resid 863 through 881 Processing helix chain 'B' and resid 883 through 887 removed outlier: 3.636A pdb=" N ALA B 887 " --> pdb=" O THR B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 904 removed outlier: 3.722A pdb=" N ALA B 900 " --> pdb=" O ALA B 896 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR B 901 " --> pdb=" O MET B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 915 removed outlier: 4.161A pdb=" N TYR B 914 " --> pdb=" O ASN B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 Processing helix chain 'B' and resid 942 through 962 Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 981 removed outlier: 3.615A pdb=" N LEU B 981 " --> pdb=" O ILE B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 1029 removed outlier: 3.790A pdb=" N ALA B 986 " --> pdb=" O ASP B 982 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU B 987 " --> pdb=" O LYS B 983 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N VAL B 988 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1113 through 1115 No H-bonds generated for 'chain 'B' and resid 1113 through 1115' Processing helix chain 'B' and resid 1137 through 1143 removed outlier: 3.690A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 346 through 350 removed outlier: 3.617A pdb=" N TRP C 350 " --> pdb=" O VAL C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 367 Processing helix chain 'C' and resid 381 through 387 removed outlier: 3.886A pdb=" N LEU C 384 " --> pdb=" O PRO C 381 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP C 386 " --> pdb=" O LYS C 383 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU C 387 " --> pdb=" O LEU C 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 381 through 387' Processing helix chain 'C' and resid 402 through 407 removed outlier: 4.199A pdb=" N ARG C 405 " --> pdb=" O ASP C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 419 Processing helix chain 'C' and resid 435 through 440 Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.857A pdb=" N THR C 635 " --> pdb=" O VAL C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 740 Processing helix chain 'C' and resid 743 through 752 removed outlier: 3.997A pdb=" N GLN C 752 " --> pdb=" O ASN C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 780 removed outlier: 3.599A pdb=" N GLN C 771 " --> pdb=" O ILE C 767 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP C 772 " --> pdb=" O ALA C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 823 Processing helix chain 'C' and resid 863 through 881 removed outlier: 3.582A pdb=" N ILE C 879 " --> pdb=" O LEU C 875 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR C 880 " --> pdb=" O ALA C 876 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 887 Processing helix chain 'C' and resid 894 through 904 removed outlier: 3.823A pdb=" N ALA C 900 " --> pdb=" O ALA C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 915 Processing helix chain 'C' and resid 916 through 938 Processing helix chain 'C' and resid 942 through 962 Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 981 removed outlier: 3.582A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1030 removed outlier: 4.175A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1143 removed outlier: 3.554A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.566A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.919A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.852A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.272A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 308 through 316 removed outlier: 5.350A pdb=" N ILE A 309 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N THR A 596 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N GLN A 311 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL A 594 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER A 313 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 322 through 323 Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 355 Processing sheet with id=AA8, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AA9, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AB1, first strand: chain 'A' and resid 570 through 573 removed outlier: 3.835A pdb=" N ALA A 572 " --> pdb=" O GLY A 563 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N PHE A 562 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.399A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 714 through 725 removed outlier: 3.600A pdb=" N GLY A1056 " --> pdb=" O ALA A1053 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.561A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1083 through 1087 removed outlier: 4.689A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER A1120 " --> pdb=" O ALA A1084 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1091 through 1094 Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.156A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.855A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 10.460A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.456A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 224 through 229 removed outlier: 5.796A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 308 through 316 removed outlier: 5.710A pdb=" N ILE B 309 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N THR B 596 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N GLN B 311 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL B 594 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER B 313 " --> pdb=" O VAL B 592 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 322 through 325 removed outlier: 3.662A pdb=" N ARG B 325 " --> pdb=" O ASN B 539 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ASP B 571 " --> pdb=" O ILE B 584 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 351 through 355 Processing sheet with id=AC5, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AC6, first strand: chain 'B' and resid 651 through 657 removed outlier: 4.994A pdb=" N THR B 693 " --> pdb=" O VAL B 653 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASN B 655 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 699 through 700 Processing sheet with id=AC8, first strand: chain 'B' and resid 714 through 716 Processing sheet with id=AC9, first strand: chain 'B' and resid 714 through 716 removed outlier: 5.915A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.445A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 3.612A pdb=" N SER B1120 " --> pdb=" O ALA B1084 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA B1077 " --> pdb=" O VAL B1130 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1091 through 1094 Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 30 removed outlier: 5.907A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.871A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.500A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 308 through 313 removed outlier: 5.673A pdb=" N ILE C 309 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N THR C 596 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N GLN C 311 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL C 594 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER C 313 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 322 through 325 removed outlier: 3.607A pdb=" N ARG C 325 " --> pdb=" O ASN C 539 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ASP C 571 " --> pdb=" O ILE C 584 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLY C 563 " --> pdb=" O ASP C 571 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 351 through 355 Processing sheet with id=AE1, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.226A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AE3, first strand: chain 'C' and resid 470 through 471 removed outlier: 3.513A pdb=" N TYR C 470 " --> pdb=" O TYR C 486 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR C 486 " --> pdb=" O TYR C 470 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 651 through 657 removed outlier: 3.512A pdb=" N ALA C 691 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N THR C 693 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASN C 655 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ALA C 669 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 709 through 725 removed outlier: 6.979A pdb=" N GLN C1068 " --> pdb=" O THR C 713 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N PHE C 715 " --> pdb=" O PRO C1066 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE C 717 " --> pdb=" O TYR C1064 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N TYR C1064 " --> pdb=" O ILE C 717 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL C 719 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL C1062 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR C 721 " --> pdb=" O LEU C1060 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU C1060 " --> pdb=" O THR C 721 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILE C 723 " --> pdb=" O VAL C1058 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL C1058 " --> pdb=" O ILE C 723 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLY C1056 " --> pdb=" O PRO C 725 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY C1056 " --> pdb=" O ALA C1053 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET C1047 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 732 through 733 Processing sheet with id=AE7, first strand: chain 'C' and resid 1078 through 1079 Processing sheet with id=AE8, first strand: chain 'C' and resid 1085 through 1087 Processing sheet with id=AE9, first strand: chain 'C' and resid 1091 through 1094 947 hydrogen bonds defined for protein. 2574 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.94 Time building geometry restraints manager: 3.30 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: 7935 1.34 - 1.46: 6418 1.46 - 1.58: 11258 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 25749 Sorted by residual: bond pdb=" C ILE A 739 " pdb=" N CYS A 740 " ideal model delta sigma weight residual 1.332 1.308 0.025 1.40e-02 5.10e+03 3.13e+00 bond pdb=" C LEU A 229 " pdb=" N PRO A 230 " ideal model delta sigma weight residual 1.334 1.293 0.041 2.34e-02 1.83e+03 3.03e+00 bond pdb=" C1 NAG A2001 " pdb=" O5 NAG A2001 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.68e+00 bond pdb=" C1 NAG Z 2 " pdb=" O5 NAG Z 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.68e+00 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.62e+00 ... (remaining 25744 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 33839 1.66 - 3.32: 1075 3.32 - 4.98: 98 4.98 - 6.63: 15 6.63 - 8.29: 8 Bond angle restraints: 35035 Sorted by residual: angle pdb=" N VAL B 984 " pdb=" CA VAL B 984 " pdb=" C VAL B 984 " ideal model delta sigma weight residual 106.21 109.94 -3.73 1.07e+00 8.73e-01 1.22e+01 angle pdb=" C ASN A 328 " pdb=" N ILE A 329 " pdb=" CA ILE A 329 " ideal model delta sigma weight residual 121.97 127.92 -5.95 1.80e+00 3.09e-01 1.09e+01 angle pdb=" N ASP B 198 " pdb=" CA ASP B 198 " pdb=" C ASP B 198 " ideal model delta sigma weight residual 111.17 115.42 -4.25 1.41e+00 5.03e-01 9.10e+00 angle pdb=" C ILE B 197 " pdb=" N ASP B 198 " pdb=" CA ASP B 198 " ideal model delta sigma weight residual 122.82 127.00 -4.18 1.42e+00 4.96e-01 8.65e+00 angle pdb=" CA THR A1114 " pdb=" C THR A1114 " pdb=" N ASP A1115 " ideal model delta sigma weight residual 116.84 121.58 -4.74 1.71e+00 3.42e-01 7.67e+00 ... (remaining 35030 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 13338 17.90 - 35.81: 1115 35.81 - 53.71: 198 53.71 - 71.61: 36 71.61 - 89.51: 27 Dihedral angle restraints: 14714 sinusoidal: 5726 harmonic: 8988 Sorted by residual: dihedral pdb=" CB CYS C 131 " pdb=" SG CYS C 131 " pdb=" SG CYS C 166 " pdb=" CB CYS C 166 " ideal model delta sinusoidal sigma weight residual -86.00 2.73 -88.73 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sinusoidal sigma weight residual 93.00 5.04 87.96 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" CB CYS A 659 " pdb=" SG CYS A 659 " pdb=" SG CYS A 668 " pdb=" CB CYS A 668 " ideal model delta sinusoidal sigma weight residual 93.00 -179.41 -87.59 1 1.00e+01 1.00e-02 9.20e+01 ... (remaining 14711 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 4094 0.110 - 0.220: 98 0.220 - 0.330: 3 0.330 - 0.440: 2 0.440 - 0.550: 2 Chirality restraints: 4199 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.56e+00 chirality pdb=" C1 NAG V 1 " pdb=" ND2 ASN B1071 " pdb=" C2 NAG V 1 " pdb=" O5 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.41e+00 chirality pdb=" C1 NAG C2003 " pdb=" ND2 ASN C 328 " pdb=" C2 NAG C2003 " pdb=" O5 NAG C2003 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.28e+00 ... (remaining 4196 not shown) Planarity restraints: 4468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B1071 " 0.030 2.00e-02 2.50e+03 2.81e-02 9.87e+00 pdb=" CG ASN B1071 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN B1071 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B1071 " -0.034 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 216 " 0.033 5.00e-02 4.00e+02 5.11e-02 4.17e+00 pdb=" N PRO C 217 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 217 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 217 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 903 " 0.015 2.00e-02 2.50e+03 1.27e-02 2.83e+00 pdb=" CG PHE C 903 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE C 903 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE C 903 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 903 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 903 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 903 " 0.003 2.00e-02 2.50e+03 ... (remaining 4465 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 558 2.66 - 3.22: 24351 3.22 - 3.78: 37474 3.78 - 4.34: 49172 4.34 - 4.90: 81656 Nonbonded interactions: 193211 Sorted by model distance: nonbonded pdb=" OD2 ASP A 575 " pdb=" OG1 THR A 578 " model vdw 2.102 3.040 nonbonded pdb=" O PRO A 230 " pdb=" NH1 ARG C 354 " model vdw 2.109 3.120 nonbonded pdb=" O GLY C 877 " pdb=" OG SER C 881 " model vdw 2.149 3.040 nonbonded pdb=" O GLU A 658 " pdb=" OH TYR A 692 " model vdw 2.149 3.040 nonbonded pdb=" OG1 THR B 615 " pdb=" OE1 GLU B 616 " model vdw 2.169 3.040 ... (remaining 193206 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 260 or resid 262 through 2005)) selection = (chain 'B' and (resid 14 through 260 or resid 262 through 618 or resid 632 throu \ gh 824 or resid 852 through 2005)) selection = (chain 'C' and (resid 14 through 618 or resid 632 through 824 or resid 852 throu \ gh 2005)) } 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' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' } 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: 5.670 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: 0.080 Set scattering table: 0.070 Process input model: 25.370 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 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 : 0.005 0.047 25862 Z= 0.252 Angle : 0.704 12.906 35334 Z= 0.353 Chirality : 0.048 0.550 4199 Planarity : 0.003 0.051 4424 Dihedral : 13.513 89.514 8814 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.81 % Favored : 93.03 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % 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: -0.58 (0.15), residues: 3040 helix: 1.52 (0.21), residues: 685 sheet: -0.14 (0.19), residues: 698 loop : -1.35 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 354 TYR 0.021 0.001 TYR C 870 PHE 0.029 0.002 PHE C 903 TRP 0.009 0.001 TRP A 883 HIS 0.003 0.001 HIS B1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.25 (25749) covalent geometry : angle 0.66924 / 0.34 (35035) SS BOND : bond 0.00435 / 0.26 ( 40) SS BOND : angle 2.15248 / 1.37 ( 80) hydrogen bonds : bond 0.12147 / 8.19 ( 943) hydrogen bonds : angle 6.14270 / 4.17 ( 2574) link_BETA1-4 : bond 0.00436 / 0.29 ( 29) link_BETA1-4 : angle 1.95828 / 1.46 ( 87) link_NAG-ASN : bond 0.00478 / 0.33 ( 44) link_NAG-ASN : angle 2.91140 / 1.93 ( 132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0054 (pmm) cc_final: -0.0187 (pmm) REVERT: A 1026 MET cc_start: 0.8157 (tpp) cc_final: 0.7854 (ttp) REVERT: B 242 HIS cc_start: 0.7469 (t70) cc_final: 0.7085 (t70) REVERT: B 461 PHE cc_start: 0.9130 (m-80) cc_final: 0.8410 (m-10) REVERT: B 737 MET cc_start: 0.8202 (tpt) cc_final: 0.7955 (tpt) REVERT: B 852 PHE cc_start: 0.7695 (m-10) cc_final: 0.7430 (m-10) REVERT: B 983 LYS cc_start: 0.9382 (mmpt) cc_final: 0.9122 (tppt) REVERT: C 462 GLU cc_start: 0.8922 (tp30) cc_final: 0.8068 (tm-30) REVERT: C 1047 MET cc_start: 0.7541 (ptm) cc_final: 0.7138 (ptm) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1601 time to fit residues: 43.4891 Evaluate side-chains 93 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1007 GLN B 318 GLN ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 759 GLN ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.118202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.074811 restraints weight = 60698.616| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.82 r_work: 0.3226 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 25862 Z= 0.162 Angle : 0.631 13.389 35334 Z= 0.315 Chirality : 0.046 0.311 4199 Planarity : 0.004 0.047 4424 Dihedral : 4.492 25.378 3312 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.46 % Favored : 94.41 % Rotamer: Outliers : 0.67 % Allowed : 5.91 % Favored : 93.42 % 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: -0.60 (0.15), residues: 3040 helix: 1.51 (0.21), residues: 678 sheet: -0.01 (0.19), residues: 681 loop : -1.42 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 354 TYR 0.016 0.001 TYR C1064 PHE 0.025 0.002 PHE A1118 TRP 0.009 0.001 TRP C 104 HIS 0.004 0.001 HIS B1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (25749) covalent geometry : angle 0.60344 / 0.31 (35035) SS BOND : bond 0.00401 / 0.24 ( 40) SS BOND : angle 1.95822 / 1.23 ( 80) hydrogen bonds : bond 0.04633 / 3.13 ( 943) hydrogen bonds : angle 5.34780 / 3.62 ( 2574) link_BETA1-4 : bond 0.00480 / 0.33 ( 29) link_BETA1-4 : angle 1.54744 / 1.23 ( 87) link_NAG-ASN : bond 0.00442 / 0.32 ( 44) link_NAG-ASN : angle 2.46945 / 1.70 ( 132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7905 (t0) cc_final: 0.7649 (t0) REVERT: A 153 MET cc_start: 0.0246 (pmm) cc_final: -0.0078 (pmm) REVERT: A 335 PHE cc_start: 0.7948 (m-80) cc_final: 0.7355 (m-80) REVERT: A 962 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8772 (mp10) REVERT: A 985 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8156 (pm20) REVERT: A 1026 MET cc_start: 0.8001 (tpp) cc_final: 0.7670 (ttp) REVERT: B 453 PHE cc_start: 0.8567 (m-80) cc_final: 0.7824 (m-10) REVERT: B 461 PHE cc_start: 0.8891 (m-80) cc_final: 0.8283 (m-10) REVERT: B 983 LYS cc_start: 0.9401 (mmpt) cc_final: 0.9136 (tppt) REVERT: C 462 GLU cc_start: 0.8996 (tp30) cc_final: 0.8195 (tm-30) outliers start: 18 outliers final: 10 residues processed: 122 average time/residue: 0.1504 time to fit residues: 31.4795 Evaluate side-chains 108 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 852 PHE Chi-restraints excluded: chain A residue 962 GLN Chi-restraints excluded: chain A residue 985 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 318 GLN Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 1094 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 158 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 185 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 257 optimal weight: 2.9990 chunk 110 optimal weight: 20.0000 chunk 270 optimal weight: 1.9990 chunk 279 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 chunk 143 optimal weight: 0.7980 chunk 271 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** 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 = 0.4087 r_free = 0.4087 target = 0.118830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.075640 restraints weight = 60287.091| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 3.83 r_work: 0.3241 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25862 Z= 0.118 Angle : 0.580 13.139 35334 Z= 0.285 Chirality : 0.044 0.306 4199 Planarity : 0.003 0.049 4424 Dihedral : 4.253 23.794 3312 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.39 % Favored : 94.47 % Rotamer: Outliers : 0.96 % Allowed : 8.21 % Favored : 90.83 % 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: -0.46 (0.15), residues: 3040 helix: 1.50 (0.21), residues: 685 sheet: 0.15 (0.19), residues: 692 loop : -1.34 (0.15), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 354 TYR 0.012 0.001 TYR B1064 PHE 0.024 0.001 PHE A 389 TRP 0.011 0.001 TRP C 104 HIS 0.007 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (25749) covalent geometry : angle 0.55229 / 0.28 (35035) SS BOND : bond 0.00468 / 0.34 ( 40) SS BOND : angle 1.78264 / 1.11 ( 80) hydrogen bonds : bond 0.04116 / 2.78 ( 943) hydrogen bonds : angle 5.09577 / 3.45 ( 2574) link_BETA1-4 : bond 0.00515 / 0.35 ( 29) link_BETA1-4 : angle 1.53626 / 1.22 ( 87) link_NAG-ASN : bond 0.00431 / 0.32 ( 44) link_NAG-ASN : angle 2.35305 / 1.63 ( 132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.0278 (pmm) cc_final: -0.0058 (pmm) REVERT: A 335 PHE cc_start: 0.8007 (m-80) cc_final: 0.7519 (m-80) REVERT: A 985 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8117 (pm20) REVERT: A 1026 MET cc_start: 0.8023 (tpp) cc_final: 0.7666 (ttp) REVERT: B 449 LEU cc_start: 0.8917 (pt) cc_final: 0.8294 (tt) REVERT: B 453 PHE cc_start: 0.8673 (m-80) cc_final: 0.8012 (m-10) REVERT: B 461 PHE cc_start: 0.8882 (m-80) cc_final: 0.8281 (m-10) REVERT: B 983 LYS cc_start: 0.9393 (mmpt) cc_final: 0.9160 (tppt) REVERT: B 1086 PHE cc_start: 0.7503 (OUTLIER) cc_final: 0.7166 (m-80) REVERT: C 449 LEU cc_start: 0.9339 (tp) cc_final: 0.9129 (tp) REVERT: C 462 GLU cc_start: 0.8937 (tp30) cc_final: 0.8275 (tm-30) REVERT: C 722 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7869 (pt0) REVERT: C 931 ILE cc_start: 0.8557 (mm) cc_final: 0.8350 (mm) outliers start: 26 outliers final: 14 residues processed: 129 average time/residue: 0.1556 time to fit residues: 34.2848 Evaluate side-chains 110 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 852 PHE Chi-restraints excluded: chain A residue 985 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 1086 PHE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 1094 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 263 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 113 optimal weight: 0.0270 chunk 114 optimal weight: 6.9990 chunk 303 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 210 optimal weight: 7.9990 overall best weight: 2.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1007 GLN A1020 ASN A1085 HIS B 242 HIS ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.115645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.073696 restraints weight = 60939.773| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 4.71 r_work: 0.3122 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.131 25862 Z= 0.262 Angle : 0.690 13.033 35334 Z= 0.347 Chirality : 0.047 0.298 4199 Planarity : 0.004 0.051 4424 Dihedral : 4.682 29.711 3312 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.55 % Favored : 93.32 % Rotamer: Outliers : 1.59 % Allowed : 10.72 % Favored : 87.69 % 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: -0.79 (0.15), residues: 3040 helix: 1.18 (0.20), residues: 679 sheet: 0.02 (0.19), residues: 713 loop : -1.57 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 902 TYR 0.025 0.002 TYR B 91 PHE 0.040 0.002 PHE A1118 TRP 0.009 0.002 TRP C 64 HIS 0.011 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.26 (25749) covalent geometry : angle 0.66469 / 0.34 (35035) SS BOND : bond 0.00638 / 0.37 ( 40) SS BOND : angle 2.13602 / 1.37 ( 80) hydrogen bonds : bond 0.05059 / 3.40 ( 943) hydrogen bonds : angle 5.38934 / 3.65 ( 2574) link_BETA1-4 : bond 0.00488 / 0.33 ( 29) link_BETA1-4 : angle 1.55905 / 1.22 ( 87) link_NAG-ASN : bond 0.00401 / 0.29 ( 44) link_NAG-ASN : angle 2.44429 / 1.67 ( 132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 108 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.0392 (pmm) cc_final: -0.0008 (pmm) REVERT: A 694 MET cc_start: 0.8015 (mtp) cc_final: 0.7700 (mpp) REVERT: A 985 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8240 (pm20) REVERT: A 1086 PHE cc_start: 0.7625 (OUTLIER) cc_final: 0.7346 (m-80) REVERT: B 318 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7636 (mm-40) REVERT: B 449 LEU cc_start: 0.9021 (pt) cc_final: 0.8537 (tt) REVERT: B 453 PHE cc_start: 0.8642 (m-80) cc_final: 0.7987 (m-80) REVERT: B 461 PHE cc_start: 0.8925 (m-80) cc_final: 0.8287 (m-10) REVERT: B 739 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8747 (mp) REVERT: B 983 LYS cc_start: 0.9452 (mmpt) cc_final: 0.9154 (tppt) REVERT: B 1086 PHE cc_start: 0.8033 (OUTLIER) cc_final: 0.7319 (m-10) REVERT: C 462 GLU cc_start: 0.8969 (tp30) cc_final: 0.8319 (tm-30) outliers start: 43 outliers final: 22 residues processed: 144 average time/residue: 0.1445 time to fit residues: 36.0766 Evaluate side-chains 123 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 852 PHE Chi-restraints excluded: chain A residue 985 GLU Chi-restraints excluded: chain A residue 1086 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 739 ILE Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 1086 PHE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 722 GLU Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1094 SER Chi-restraints excluded: chain C residue 1127 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 125 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 191 optimal weight: 0.8980 chunk 295 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 184 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 221 optimal weight: 7.9990 chunk 102 optimal weight: 20.0000 chunk 137 optimal weight: 1.9990 chunk 175 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 239 GLN ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.117423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.076039 restraints weight = 60496.491| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 4.69 r_work: 0.3171 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 25862 Z= 0.133 Angle : 0.601 12.851 35334 Z= 0.296 Chirality : 0.044 0.301 4199 Planarity : 0.003 0.052 4424 Dihedral : 4.373 26.293 3312 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.53 % Favored : 94.31 % Rotamer: Outliers : 1.52 % Allowed : 11.90 % Favored : 86.58 % 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: -0.60 (0.15), residues: 3040 helix: 1.47 (0.21), residues: 671 sheet: 0.10 (0.20), residues: 699 loop : -1.46 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 405 TYR 0.013 0.001 TYR C1064 PHE 0.022 0.001 PHE B1118 TRP 0.013 0.001 TRP C 104 HIS 0.005 0.001 HIS B1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (25749) covalent geometry : angle 0.57404 / 0.29 (35035) SS BOND : bond 0.00382 / 0.22 ( 40) SS BOND : angle 2.08449 / 1.30 ( 80) hydrogen bonds : bond 0.04177 / 2.81 ( 943) hydrogen bonds : angle 5.15737 / 3.49 ( 2574) link_BETA1-4 : bond 0.00487 / 0.34 ( 29) link_BETA1-4 : angle 1.48391 / 1.19 ( 87) link_NAG-ASN : bond 0.00396 / 0.29 ( 44) link_NAG-ASN : angle 2.28694 / 1.57 ( 132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 105 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0485 (pmm) cc_final: 0.0061 (pmm) REVERT: A 875 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7759 (tt) REVERT: A 985 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8186 (pm20) REVERT: A 1026 MET cc_start: 0.8091 (tpp) cc_final: 0.7608 (ttp) REVERT: B 318 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7547 (mm-40) REVERT: B 449 LEU cc_start: 0.9024 (pt) cc_final: 0.8532 (tt) REVERT: B 453 PHE cc_start: 0.8634 (m-80) cc_final: 0.7957 (m-80) REVERT: B 461 PHE cc_start: 0.8915 (m-80) cc_final: 0.8314 (m-10) REVERT: B 739 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8738 (mp) REVERT: B 983 LYS cc_start: 0.9442 (mmpt) cc_final: 0.9145 (tppt) REVERT: B 1086 PHE cc_start: 0.7707 (OUTLIER) cc_final: 0.7356 (m-80) REVERT: B 1129 ILE cc_start: 0.7875 (OUTLIER) cc_final: 0.7587 (tp) REVERT: C 462 GLU cc_start: 0.8921 (tp30) cc_final: 0.8299 (tm-30) REVERT: C 722 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7926 (pt0) REVERT: C 875 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8319 (tp) REVERT: C 1086 PHE cc_start: 0.7472 (OUTLIER) cc_final: 0.7132 (m-80) outliers start: 41 outliers final: 21 residues processed: 139 average time/residue: 0.1465 time to fit residues: 35.0974 Evaluate side-chains 126 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 852 PHE Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 985 GLU Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 614 CYS Chi-restraints excluded: chain B residue 739 ILE Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 903 PHE Chi-restraints excluded: chain B residue 1086 PHE Chi-restraints excluded: chain B residue 1129 ILE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1086 PHE Chi-restraints excluded: chain C residue 1094 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 303 optimal weight: 0.5980 chunk 250 optimal weight: 0.0370 chunk 180 optimal weight: 0.6980 chunk 46 optimal weight: 10.0000 chunk 174 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 102 optimal weight: 20.0000 chunk 176 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 140 optimal weight: 10.0000 overall best weight: 1.0662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** 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 = 0.4070 r_free = 0.4070 target = 0.117525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.076061 restraints weight = 60537.219| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 4.68 r_work: 0.3178 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25862 Z= 0.132 Angle : 0.591 12.992 35334 Z= 0.289 Chirality : 0.044 0.291 4199 Planarity : 0.003 0.053 4424 Dihedral : 4.270 26.087 3312 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.89 % Favored : 93.95 % Rotamer: Outliers : 1.81 % Allowed : 12.38 % Favored : 85.80 % 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: -0.56 (0.15), residues: 3040 helix: 1.51 (0.21), residues: 674 sheet: 0.08 (0.20), residues: 666 loop : -1.41 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 214 TYR 0.013 0.001 TYR B1064 PHE 0.022 0.001 PHE B1118 TRP 0.011 0.001 TRP C 104 HIS 0.005 0.001 HIS B1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (25749) covalent geometry : angle 0.56447 / 0.28 (35035) SS BOND : bond 0.00355 / 0.20 ( 40) SS BOND : angle 1.95559 / 1.23 ( 80) hydrogen bonds : bond 0.04005 / 2.68 ( 943) hydrogen bonds : angle 5.05351 / 3.42 ( 2574) link_BETA1-4 : bond 0.00488 / 0.33 ( 29) link_BETA1-4 : angle 1.47730 / 1.17 ( 87) link_NAG-ASN : bond 0.00391 / 0.29 ( 44) link_NAG-ASN : angle 2.24466 / 1.53 ( 132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 107 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0482 (pmm) cc_final: -0.0036 (mpp) REVERT: A 875 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7816 (tt) REVERT: A 1026 MET cc_start: 0.8087 (tpp) cc_final: 0.7569 (ttp) REVERT: B 318 GLN cc_start: 0.8008 (mm-40) cc_final: 0.7521 (mm-40) REVERT: B 449 LEU cc_start: 0.9020 (pt) cc_final: 0.8506 (tt) REVERT: B 453 PHE cc_start: 0.8598 (m-80) cc_final: 0.7961 (m-80) REVERT: B 461 PHE cc_start: 0.8866 (m-80) cc_final: 0.8255 (m-10) REVERT: B 739 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8706 (mp) REVERT: B 983 LYS cc_start: 0.9453 (mmpt) cc_final: 0.9171 (tppt) REVERT: B 1086 PHE cc_start: 0.7657 (OUTLIER) cc_final: 0.7311 (m-80) REVERT: B 1129 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7516 (tp) REVERT: C 462 GLU cc_start: 0.8927 (tp30) cc_final: 0.8176 (tm-30) REVERT: C 722 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7910 (pt0) REVERT: C 931 ILE cc_start: 0.8601 (mm) cc_final: 0.8381 (mm) REVERT: C 1086 PHE cc_start: 0.7487 (OUTLIER) cc_final: 0.7138 (m-80) outliers start: 49 outliers final: 30 residues processed: 147 average time/residue: 0.1458 time to fit residues: 37.0463 Evaluate side-chains 133 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 98 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 852 PHE Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 614 CYS Chi-restraints excluded: chain B residue 739 ILE Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 903 PHE Chi-restraints excluded: chain B residue 1086 PHE Chi-restraints excluded: chain B residue 1129 ILE Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1086 PHE Chi-restraints excluded: chain C residue 1101 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 112 optimal weight: 7.9990 chunk 183 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 chunk 217 optimal weight: 9.9990 chunk 100 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 178 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** 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 = 0.4098 r_free = 0.4098 target = 0.127922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.086640 restraints weight = 58662.928| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 4.50 r_work: 0.3169 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 25862 Z= 0.182 Angle : 0.627 12.961 35334 Z= 0.308 Chirality : 0.045 0.277 4199 Planarity : 0.004 0.053 4424 Dihedral : 4.392 27.935 3312 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.05 % Favored : 93.78 % Rotamer: Outliers : 1.81 % Allowed : 13.42 % Favored : 84.77 % 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: -0.67 (0.15), residues: 3040 helix: 1.44 (0.21), residues: 672 sheet: 0.06 (0.20), residues: 650 loop : -1.49 (0.15), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 902 TYR 0.018 0.001 TYR B 91 PHE 0.029 0.001 PHE A1118 TRP 0.007 0.001 TRP C 104 HIS 0.006 0.001 HIS C1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 (25749) covalent geometry : angle 0.60078 / 0.30 (35035) SS BOND : bond 0.00450 / 0.26 ( 40) SS BOND : angle 2.19049 / 1.54 ( 80) hydrogen bonds : bond 0.04326 / 2.91 ( 943) hydrogen bonds : angle 5.12424 / 3.47 ( 2574) link_BETA1-4 : bond 0.00484 / 0.33 ( 29) link_BETA1-4 : angle 1.47962 / 1.17 ( 87) link_NAG-ASN : bond 0.00377 / 0.28 ( 44) link_NAG-ASN : angle 2.24891 / 1.51 ( 132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 101 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0372 (pmm) cc_final: -0.0110 (mpp) REVERT: A 875 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7795 (tt) REVERT: A 993 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8405 (mt) REVERT: A 1026 MET cc_start: 0.8084 (tpp) cc_final: 0.7557 (ttp) REVERT: B 318 GLN cc_start: 0.8031 (mm-40) cc_final: 0.7521 (mm-40) REVERT: B 449 LEU cc_start: 0.9005 (pt) cc_final: 0.8512 (tt) REVERT: B 453 PHE cc_start: 0.8678 (m-80) cc_final: 0.8060 (m-10) REVERT: B 461 PHE cc_start: 0.8912 (m-80) cc_final: 0.8301 (m-10) REVERT: B 739 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8721 (mp) REVERT: B 983 LYS cc_start: 0.9435 (mmpt) cc_final: 0.9169 (tppt) REVERT: B 1086 PHE cc_start: 0.7859 (OUTLIER) cc_final: 0.7254 (m-10) REVERT: B 1129 ILE cc_start: 0.7907 (OUTLIER) cc_final: 0.7657 (tp) REVERT: C 462 GLU cc_start: 0.8900 (tp30) cc_final: 0.8127 (tm-30) REVERT: C 722 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7867 (pt0) REVERT: C 931 ILE cc_start: 0.8654 (mm) cc_final: 0.8440 (mm) REVERT: C 1047 MET cc_start: 0.8141 (ptm) cc_final: 0.7848 (ptm) outliers start: 49 outliers final: 34 residues processed: 144 average time/residue: 0.1294 time to fit residues: 32.1626 Evaluate side-chains 140 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 101 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 852 PHE Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1103 GLN Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 614 CYS Chi-restraints excluded: chain B residue 739 ILE Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 903 PHE Chi-restraints excluded: chain B residue 1086 PHE Chi-restraints excluded: chain B residue 1129 ILE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1101 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 259 optimal weight: 1.9990 chunk 241 optimal weight: 6.9990 chunk 160 optimal weight: 0.7980 chunk 195 optimal weight: 0.6980 chunk 37 optimal weight: 20.0000 chunk 62 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 282 optimal weight: 0.1980 chunk 139 optimal weight: 10.0000 chunk 286 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 ASN ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.129015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.086411 restraints weight = 59675.441| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 4.68 r_work: 0.3182 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25862 Z= 0.121 Angle : 0.586 12.974 35334 Z= 0.286 Chirality : 0.044 0.276 4199 Planarity : 0.003 0.054 4424 Dihedral : 4.222 26.368 3312 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.69 % Favored : 94.14 % Rotamer: Outliers : 1.81 % Allowed : 13.68 % Favored : 84.51 % 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: -0.52 (0.15), residues: 3040 helix: 1.55 (0.21), residues: 675 sheet: 0.11 (0.20), residues: 659 loop : -1.38 (0.15), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 354 TYR 0.012 0.001 TYR A1064 PHE 0.021 0.001 PHE A 389 TRP 0.012 0.001 TRP C 104 HIS 0.004 0.001 HIS B1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (25749) covalent geometry : angle 0.56064 / 0.28 (35035) SS BOND : bond 0.00369 / 0.20 ( 40) SS BOND : angle 1.99450 / 1.34 ( 80) hydrogen bonds : bond 0.03870 / 2.60 ( 943) hydrogen bonds : angle 5.00140 / 3.38 ( 2574) link_BETA1-4 : bond 0.00503 / 0.34 ( 29) link_BETA1-4 : angle 1.45240 / 1.15 ( 87) link_NAG-ASN : bond 0.00394 / 0.30 ( 44) link_NAG-ASN : angle 2.18308 / 1.47 ( 132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 108 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0314 (pmm) cc_final: -0.0131 (mpp) REVERT: A 310 TYR cc_start: 0.8406 (m-80) cc_final: 0.8061 (m-80) REVERT: A 875 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7901 (tt) REVERT: A 998 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8351 (mm) REVERT: A 1026 MET cc_start: 0.8064 (tpp) cc_final: 0.7524 (ttp) REVERT: B 318 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7499 (mm-40) REVERT: B 449 LEU cc_start: 0.9023 (pt) cc_final: 0.8546 (tt) REVERT: B 453 PHE cc_start: 0.8710 (m-80) cc_final: 0.8125 (m-80) REVERT: B 461 PHE cc_start: 0.8952 (m-80) cc_final: 0.8331 (m-10) REVERT: B 739 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8704 (mp) REVERT: B 983 LYS cc_start: 0.9459 (mmpt) cc_final: 0.9167 (tppt) REVERT: B 1086 PHE cc_start: 0.7575 (OUTLIER) cc_final: 0.7178 (m-80) REVERT: C 29 THR cc_start: 0.7174 (OUTLIER) cc_final: 0.6853 (p) REVERT: C 462 GLU cc_start: 0.8898 (tp30) cc_final: 0.8091 (tm-30) REVERT: C 722 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7910 (pt0) REVERT: C 931 ILE cc_start: 0.8620 (mm) cc_final: 0.8397 (mm) outliers start: 49 outliers final: 38 residues processed: 146 average time/residue: 0.1446 time to fit residues: 36.5297 Evaluate side-chains 148 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 105 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 852 PHE Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1103 GLN Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 614 CYS Chi-restraints excluded: chain B residue 739 ILE Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 903 PHE Chi-restraints excluded: chain B residue 1086 PHE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 486 TYR Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1101 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 146 optimal weight: 1.9990 chunk 303 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 231 optimal weight: 0.4980 chunk 131 optimal weight: 7.9990 chunk 237 optimal weight: 8.9990 chunk 5 optimal weight: 0.8980 chunk 282 optimal weight: 0.0770 chunk 218 optimal weight: 20.0000 chunk 240 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** 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 = 0.4123 r_free = 0.4123 target = 0.129739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.087245 restraints weight = 59408.593| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 4.72 r_work: 0.3187 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25862 Z= 0.106 Angle : 0.575 12.872 35334 Z= 0.279 Chirality : 0.044 0.272 4199 Planarity : 0.003 0.054 4424 Dihedral : 4.075 25.371 3312 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.20 % Favored : 94.64 % Rotamer: Outliers : 1.77 % Allowed : 13.86 % Favored : 84.36 % 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: -0.43 (0.15), residues: 3040 helix: 1.60 (0.21), residues: 677 sheet: 0.17 (0.20), residues: 659 loop : -1.31 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 354 TYR 0.012 0.001 TYR A1064 PHE 0.021 0.001 PHE A 389 TRP 0.013 0.001 TRP C 104 HIS 0.004 0.000 HIS B1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (25749) covalent geometry : angle 0.55014 / 0.27 (35035) SS BOND : bond 0.00295 / 0.17 ( 40) SS BOND : angle 1.90931 / 1.26 ( 80) hydrogen bonds : bond 0.03667 / 2.45 ( 943) hydrogen bonds : angle 4.92050 / 3.32 ( 2574) link_BETA1-4 : bond 0.00514 / 0.35 ( 29) link_BETA1-4 : angle 1.44489 / 1.14 ( 87) link_NAG-ASN : bond 0.00403 / 0.30 ( 44) link_NAG-ASN : angle 2.13972 / 1.43 ( 132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 107 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0398 (pmm) cc_final: -0.0049 (mpp) REVERT: A 310 TYR cc_start: 0.8399 (m-80) cc_final: 0.8029 (m-80) REVERT: A 998 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8363 (mm) REVERT: A 1026 MET cc_start: 0.8082 (tpp) cc_final: 0.7546 (ttp) REVERT: B 449 LEU cc_start: 0.9017 (pt) cc_final: 0.8530 (tt) REVERT: B 453 PHE cc_start: 0.8715 (m-80) cc_final: 0.8148 (m-80) REVERT: B 461 PHE cc_start: 0.8910 (m-80) cc_final: 0.8303 (m-10) REVERT: B 739 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8712 (mp) REVERT: B 983 LYS cc_start: 0.9409 (mmpt) cc_final: 0.9159 (tppt) REVERT: C 29 THR cc_start: 0.7097 (OUTLIER) cc_final: 0.6798 (p) REVERT: C 153 MET cc_start: 0.1309 (OUTLIER) cc_final: 0.0839 (ptp) REVERT: C 453 PHE cc_start: 0.8707 (m-10) cc_final: 0.8478 (m-10) REVERT: C 462 GLU cc_start: 0.8921 (tp30) cc_final: 0.8137 (tm-30) REVERT: C 875 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8262 (tp) REVERT: C 931 ILE cc_start: 0.8630 (mm) cc_final: 0.8410 (mm) outliers start: 48 outliers final: 38 residues processed: 145 average time/residue: 0.1364 time to fit residues: 34.4169 Evaluate side-chains 145 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 102 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 852 PHE Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1103 GLN Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 614 CYS Chi-restraints excluded: chain B residue 739 ILE Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 903 PHE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1101 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 131 optimal weight: 8.9990 chunk 149 optimal weight: 4.9990 chunk 228 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 242 optimal weight: 6.9990 chunk 155 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 144 optimal weight: 20.0000 chunk 99 optimal weight: 0.7980 chunk 44 optimal weight: 30.0000 chunk 109 optimal weight: 0.4980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 898 GLN ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.129725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.087840 restraints weight = 59945.950| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 4.63 r_work: 0.3190 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 25862 Z= 0.115 Angle : 0.580 12.832 35334 Z= 0.282 Chirality : 0.044 0.268 4199 Planarity : 0.003 0.053 4424 Dihedral : 4.053 24.522 3312 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.26 % Favored : 94.57 % Rotamer: Outliers : 1.66 % Allowed : 14.20 % Favored : 84.14 % 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: -0.41 (0.15), residues: 3040 helix: 1.58 (0.21), residues: 678 sheet: 0.21 (0.20), residues: 658 loop : -1.30 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 354 TYR 0.012 0.001 TYR A1064 PHE 0.021 0.001 PHE B1118 TRP 0.011 0.001 TRP C 104 HIS 0.005 0.001 HIS C1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (25749) covalent geometry : angle 0.55580 / 0.28 (35035) SS BOND : bond 0.00311 / 0.18 ( 40) SS BOND : angle 1.88604 / 1.25 ( 80) hydrogen bonds : bond 0.03695 / 2.48 ( 943) hydrogen bonds : angle 4.91199 / 3.32 ( 2574) link_BETA1-4 : bond 0.00506 / 0.34 ( 29) link_BETA1-4 : angle 1.44151 / 1.14 ( 87) link_NAG-ASN : bond 0.00393 / 0.30 ( 44) link_NAG-ASN : angle 2.12470 / 1.42 ( 132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 105 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0323 (pmm) cc_final: -0.0088 (mpp) REVERT: A 310 TYR cc_start: 0.8429 (m-80) cc_final: 0.8052 (m-80) REVERT: A 998 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8342 (mm) REVERT: A 1026 MET cc_start: 0.8080 (tpp) cc_final: 0.7534 (ttp) REVERT: B 449 LEU cc_start: 0.9042 (pt) cc_final: 0.8586 (tt) REVERT: B 453 PHE cc_start: 0.8765 (m-80) cc_final: 0.8214 (m-80) REVERT: B 461 PHE cc_start: 0.8957 (m-80) cc_final: 0.8343 (m-10) REVERT: B 739 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8704 (mp) REVERT: B 983 LYS cc_start: 0.9449 (mmpt) cc_final: 0.9175 (tppt) REVERT: C 29 THR cc_start: 0.6955 (OUTLIER) cc_final: 0.6642 (p) REVERT: C 153 MET cc_start: 0.0999 (OUTLIER) cc_final: 0.0648 (ptp) REVERT: C 462 GLU cc_start: 0.8879 (tp30) cc_final: 0.8018 (tm-30) REVERT: C 931 ILE cc_start: 0.8631 (mm) cc_final: 0.8409 (mm) REVERT: C 985 GLU cc_start: 0.8060 (pm20) cc_final: 0.7783 (pm20) outliers start: 45 outliers final: 40 residues processed: 141 average time/residue: 0.1388 time to fit residues: 34.0268 Evaluate side-chains 144 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 100 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 852 PHE Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1103 GLN Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 614 CYS Chi-restraints excluded: chain B residue 739 ILE Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 903 PHE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1101 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 67 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 263 optimal weight: 2.9990 chunk 227 optimal weight: 0.0570 chunk 252 optimal weight: 5.9990 chunk 273 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 206 optimal weight: 4.9990 chunk 215 optimal weight: 0.9980 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 898 GLN ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.128523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.086203 restraints weight = 58544.818| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 4.57 r_work: 0.3181 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 25862 Z= 0.155 Angle : 0.608 12.788 35334 Z= 0.298 Chirality : 0.044 0.264 4199 Planarity : 0.003 0.053 4424 Dihedral : 4.204 32.789 3312 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.92 % Favored : 93.95 % Rotamer: Outliers : 1.74 % Allowed : 14.31 % Favored : 83.96 % 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: -0.51 (0.15), residues: 3040 helix: 1.49 (0.21), residues: 675 sheet: 0.14 (0.20), residues: 659 loop : -1.34 (0.15), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1036 TYR 0.015 0.001 TYR B 91 PHE 0.027 0.001 PHE A1118 TRP 0.008 0.001 TRP C 64 HIS 0.005 0.001 HIS C1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 (25749) covalent geometry : angle 0.58481 / 0.29 (35035) SS BOND : bond 0.00410 / 0.24 ( 40) SS BOND : angle 1.95301 / 1.30 ( 80) hydrogen bonds : bond 0.04021 / 2.70 ( 943) hydrogen bonds : angle 4.98755 / 3.37 ( 2574) link_BETA1-4 : bond 0.00483 / 0.33 ( 29) link_BETA1-4 : angle 1.44354 / 1.14 ( 87) link_NAG-ASN : bond 0.00370 / 0.28 ( 44) link_NAG-ASN : angle 2.13485 / 1.41 ( 132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7395.54 seconds wall clock time: 127 minutes 16.26 seconds (7636.26 seconds total)