Starting phenix.real_space_refine on Sun Jul 5 04:47:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7fce_31525/07_2026/7fce_31525.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fce_31525/07_2026/7fce_31525.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7fce_31525/07_2026/7fce_31525.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7fce_31525/07_2026/7fce_31525.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7fce_31525/07_2026/7fce_31525.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fce_31525/07_2026/7fce_31525.map" model { file = "/net/cci-nas-00/data/ceres_data/7fce_31525/07_2026/7fce_31525.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fce_31525/07_2026/7fce_31525.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 114 5.16 5 C 16239 2.51 5 N 4157 2.21 5 O 5032 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 25542 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 8158 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1043, 8142 Classifications: {'peptide': 1043} Link IDs: {'PTRANS': 51, 'TRANS': 991} Chain breaks: 8 Conformer: "B" Number of residues, atoms: 1043, 8142 Classifications: {'peptide': 1043} Link IDs: {'PTRANS': 51, 'TRANS': 991} Chain breaks: 8 bond proxies already assigned to first conformer: 8305 Chain: "B" Number of atoms: 8146 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1041, 8130 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 51, 'TRANS': 989} Chain breaks: 8 Conformer: "B" Number of residues, atoms: 1041, 8130 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 51, 'TRANS': 989} Chain breaks: 8 bond proxies already assigned to first conformer: 8293 Chain: "C" Number of atoms: 8146 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1041, 8130 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 51, 'TRANS': 989} Chain breaks: 8 Conformer: "B" Number of residues, atoms: 1041, 8130 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 51, 'TRANS': 989} Chain breaks: 8 bond proxies already assigned to first conformer: 8293 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: "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: "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: "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: "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: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 9.08, per 1000 atoms: 0.36 Number of scatterers: 25542 At special positions: 0 Unit cell: (135.042, 136.14, 162.489, 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 114 16.00 O 5032 8.00 N 4157 7.00 C 16239 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, 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=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.05 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.06 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.05 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.06 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.05 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.06 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.05 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG 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 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 g 1 " - " NAG g 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A 370 " " NAG A1308 " - " ASN A 616 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 343 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B 370 " " NAG B1308 " - " ASN B 61 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C 370 " " NAG C1308 " - " ASN C 61 " " NAG D 1 " - " ASN A 61 " " NAG E 1 " - " ASN A 17 " " NAG F 1 " - " ASN A 122 " " NAG G 1 " - " ASN A 165 " " NAG H 1 " - " ASN A 234 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 17 " " NAG P 1 " - " ASN B 122 " " NAG Q 1 " - " ASN B 165 " " NAG R 1 " - " ASN B 234 " " NAG S 1 " - " ASN B 616 " " NAG T 1 " - " ASN B 717 " " NAG U 1 " - " ASN B 801 " " NAG V 1 " - " ASN B1098 " " NAG W 1 " - " ASN B1134 " " NAG Y 1 " - " ASN C 17 " " NAG Z 1 " - " ASN C 122 " " NAG a 1 " - " ASN C 165 " " NAG b 1 " - " ASN C 234 " " NAG c 1 " - " ASN C 616 " " NAG d 1 " - " ASN C 717 " " NAG e 1 " - " ASN C 801 " " NAG f 1 " - " ASN C1098 " " NAG g 1 " - " ASN C1134 " Time building additional restraints: 2.42 Conformation dependent library (CDL) restraints added in 1.5 seconds 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5864 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 42 sheets defined 25.6% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.704A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.671A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.191A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 756 through 783 removed outlier: 3.752A pdb=" N CYS A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 836 through 840 Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.137A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.210A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.438A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.653A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.671A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.190A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 756 through 783 removed outlier: 3.751A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 836 through 840 Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.137A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.209A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.438A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 366 through 372 removed outlier: 4.094A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.671A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.191A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 756 through 783 removed outlier: 3.750A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 836 through 840 Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.137A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.210A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.438A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.205A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.030A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.877A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 133 through 135 removed outlier: 6.136A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.418A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.334A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.322A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 712 through 715 removed outlier: 3.629A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.070A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.405A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB6, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.204A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.031A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.876A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 133 through 135 removed outlier: 6.645A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC2, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.418A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.334A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.321A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.629A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.070A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.406A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD2, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.204A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.030A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.876A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 133 through 135 removed outlier: 6.644A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AD7, first strand: chain 'C' and resid 324 through 328 removed outlier: 6.417A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.333A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.321A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 712 through 715 removed outlier: 3.629A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.071A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.406A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1122 1037 hydrogen bonds defined for protein. 2796 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.45 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7816 1.34 - 1.47: 6740 1.47 - 1.59: 11403 1.59 - 1.72: 0 1.72 - 1.85: 138 Bond restraints: 26097 Sorted by residual: bond pdb=" C ASP A 138 " pdb=" N PRO A 139 " ideal model delta sigma weight residual 1.329 1.372 -0.043 1.25e-02 6.40e+03 1.16e+01 bond pdb=" C LYS A 462 " pdb=" N PRO A 463 " ideal model delta sigma weight residual 1.332 1.373 -0.041 1.30e-02 5.92e+03 1.01e+01 bond pdb=" N ARG B 457 " pdb=" CA ARG B 457 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.21e-02 6.83e+03 8.84e+00 bond pdb=" N SER A 494 " pdb=" CA SER A 494 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.18e-02 7.18e+03 8.52e+00 bond pdb=" N ILE A 472 " pdb=" CA ILE A 472 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.09e+00 ... (remaining 26092 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 34165 2.35 - 4.70: 1252 4.70 - 7.04: 82 7.04 - 9.39: 10 9.39 - 11.74: 6 Bond angle restraints: 35515 Sorted by residual: angle pdb=" N CYS A 525 " pdb=" CA CYS A 525 " pdb=" C CYS A 525 " ideal model delta sigma weight residual 110.80 119.21 -8.41 2.13e+00 2.20e-01 1.56e+01 angle pdb=" N CYS C 525 " pdb=" CA CYS C 525 " pdb=" C CYS C 525 " ideal model delta sigma weight residual 110.80 119.21 -8.41 2.13e+00 2.20e-01 1.56e+01 angle pdb=" N CYS B 525 " pdb=" CA CYS B 525 " pdb=" C CYS B 525 " ideal model delta sigma weight residual 110.80 119.17 -8.37 2.13e+00 2.20e-01 1.55e+01 angle pdb=" N LEU A 455 " pdb=" CA LEU A 455 " pdb=" C LEU A 455 " ideal model delta sigma weight residual 113.50 108.67 4.83 1.23e+00 6.61e-01 1.54e+01 angle pdb=" C TYR A 495 " pdb=" CA TYR A 495 " pdb=" CB TYR A 495 " ideal model delta sigma weight residual 109.75 103.39 6.36 1.65e+00 3.67e-01 1.49e+01 ... (remaining 35510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 13889 17.58 - 35.16: 832 35.16 - 52.74: 127 52.74 - 70.32: 64 70.32 - 87.90: 28 Dihedral angle restraints: 14940 sinusoidal: 5828 harmonic: 9112 Sorted by residual: dihedral pdb=" CA LEU B 368 " pdb=" C LEU B 368 " pdb=" N TYR B 369 " pdb=" CA TYR B 369 " ideal model delta harmonic sigma weight residual -180.00 -156.33 -23.67 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA SER C 371 " pdb=" C SER C 371 " pdb=" N THR C 372 " pdb=" CA THR C 372 " ideal model delta harmonic sigma weight residual -180.00 -156.62 -23.38 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA SER A 371 " pdb=" C SER A 371 " pdb=" N THR A 372 " pdb=" CA THR A 372 " ideal model delta harmonic sigma weight residual -180.00 -156.96 -23.04 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 14937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3265 0.079 - 0.159: 955 0.159 - 0.238: 46 0.238 - 0.318: 2 0.318 - 0.397: 2 Chirality restraints: 4270 Sorted by residual: chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B 370 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CA TYR A 495 " pdb=" N TYR A 495 " pdb=" C TYR A 495 " pdb=" CB TYR A 495 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" C1 NAG C1307 " pdb=" ND2 ASN C 370 " pdb=" C2 NAG C1307 " pdb=" O5 NAG C1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 4267 not shown) Planarity restraints: 4542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1307 " 0.333 2.00e-02 2.50e+03 2.88e-01 1.04e+03 pdb=" C7 NAG B1307 " -0.077 2.00e-02 2.50e+03 pdb=" C8 NAG B1307 " 0.042 2.00e-02 2.50e+03 pdb=" N2 NAG B1307 " -0.504 2.00e-02 2.50e+03 pdb=" O7 NAG B1307 " 0.205 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1307 " 0.330 2.00e-02 2.50e+03 2.82e-01 9.91e+02 pdb=" C7 NAG A1307 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG A1307 " 0.177 2.00e-02 2.50e+03 pdb=" N2 NAG A1307 " -0.494 2.00e-02 2.50e+03 pdb=" O7 NAG A1307 " 0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1307 " 0.135 2.00e-02 2.50e+03 1.11e-01 1.53e+02 pdb=" C7 NAG C1307 " -0.037 2.00e-02 2.50e+03 pdb=" C8 NAG C1307 " 0.101 2.00e-02 2.50e+03 pdb=" N2 NAG C1307 " -0.175 2.00e-02 2.50e+03 pdb=" O7 NAG C1307 " -0.023 2.00e-02 2.50e+03 ... (remaining 4539 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 8440 2.85 - 3.37: 20721 3.37 - 3.88: 40988 3.88 - 4.39: 47432 4.39 - 4.90: 82022 Nonbonded interactions: 199603 Sorted by model distance: nonbonded pdb=" OD1 ASN A 777 " pdb=" NH1BARG A1019 " model vdw 2.343 3.120 nonbonded pdb=" OD1 ASN C 777 " pdb=" NH1BARG C1019 " model vdw 2.344 3.120 nonbonded pdb=" OD1 ASN B 777 " pdb=" NH1BARG B1019 " model vdw 2.345 3.120 nonbonded pdb=" O SER B 477 " pdb=" OG1 THR B 478 " model vdw 2.346 3.040 nonbonded pdb=" O SER A 477 " pdb=" OG1 THR A 478 " model vdw 2.347 3.040 ... (remaining 199598 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 70 or resid 81 through 245 or resid 262 through \ 822 or resid 824 through 1018 or resid 1020 through 1308)) selection = (chain 'B' and (resid 14 through 822 or resid 824 through 1018 or resid 1020 thr \ ough 1308)) selection = (chain 'C' and (resid 14 through 822 or resid 824 through 1018 or resid 1020 thr \ ough 1308)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' 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 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 28.440 Find NCS groups from input model: 0.860 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.081 26220 Z= 0.439 Angle : 1.003 11.739 35839 Z= 0.548 Chirality : 0.065 0.397 4270 Planarity : 0.008 0.288 4491 Dihedral : 12.914 87.899 8941 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.56 % Favored : 95.28 % Rotamer: Outliers : 0.99 % Allowed : 3.47 % Favored : 95.54 % 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: -0.85 (0.14), residues: 3077 helix: 0.89 (0.20), residues: 711 sheet: 0.63 (0.20), residues: 664 loop : -1.79 (0.13), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1039 TYR 0.024 0.004 TYR C 265 PHE 0.022 0.004 PHE A 592 TRP 0.017 0.004 TRP B 886 HIS 0.008 0.002 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.01013 / 0.44 (26097) covalent geometry : angle 0.97828 / 0.54 (35515) SS BOND : bond 0.01175 / 0.82 ( 45) SS BOND : angle 2.27823 / 1.62 ( 90) hydrogen bonds : bond 0.14391 / 9.91 ( 1037) hydrogen bonds : angle 6.37837 / 4.40 ( 2796) link_BETA1-4 : bond 0.00498 / 0.30 ( 27) link_BETA1-4 : angle 1.55286 / 1.05 ( 81) link_NAG-ASN : bond 0.00575 / 0.41 ( 51) link_NAG-ASN : angle 3.02835 / 2.09 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 577 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 904 TYR cc_start: 0.6157 (m-10) cc_final: 0.5529 (m-10) REVERT: B 844 ILE cc_start: 0.6885 (mt) cc_final: 0.6506 (mt) REVERT: C 14 GLN cc_start: 0.5295 (OUTLIER) cc_final: 0.4344 (mm-40) REVERT: C 751 ASN cc_start: 0.7140 (m110) cc_final: 0.6936 (m-40) REVERT: C 912 THR cc_start: 0.6991 (p) cc_final: 0.6786 (p) outliers start: 27 outliers final: 2 residues processed: 598 average time/residue: 0.1625 time to fit residues: 155.2634 Evaluate side-chains 292 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 289 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 331 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN A 207 HIS A 218 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 ASN A 501 ASN A 563 GLN A 580 GLN A 641 ASN A 703 ASN A 751 ASN ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN A1023 ASN A1036 GLN A1054 GLN A1064 HIS A1083 HIS A1101 HIS B 87 ASN ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 245 HIS B 394 ASN B 540 ASN B 563 GLN B 580 GLN B 641 ASN B 658 ASN B 751 ASN B 925 ASN B 935 GLN B1023 ASN B1036 GLN B1054 GLN B1064 HIS C 66 HIS ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN C 188 ASN C 218 GLN C 271 GLN C 394 ASN C 540 ASN C 563 GLN C 580 GLN C 607 GLN C 658 ASN C 703 ASN C 751 ASN C 925 ASN C1023 ASN C1036 GLN C1064 HIS Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.162574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.134946 restraints weight = 60177.645| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 4.59 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3590 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3590 r_free = 0.3590 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3590 r_free = 0.3590 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3590 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 26220 Z= 0.167 Angle : 0.712 19.001 35839 Z= 0.353 Chirality : 0.049 0.546 4270 Planarity : 0.005 0.056 4491 Dihedral : 5.080 48.890 3363 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.58 % Favored : 96.26 % Rotamer: Outliers : 1.10 % Allowed : 9.03 % Favored : 89.87 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % 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 (0.14), residues: 3077 helix: 1.25 (0.20), residues: 711 sheet: 0.63 (0.19), residues: 670 loop : -1.62 (0.13), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1091 TYR 0.019 0.002 TYR C 756 PHE 0.029 0.002 PHE C 59 TRP 0.014 0.002 TRP B 353 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (26097) covalent geometry : angle 0.66998 / 0.34 (35515) SS BOND : bond 0.00804 / 0.46 ( 45) SS BOND : angle 2.64112 / 2.07 ( 90) hydrogen bonds : bond 0.05014 / 3.36 ( 1037) hydrogen bonds : angle 5.42751 / 3.74 ( 2796) link_BETA1-4 : bond 0.00607 / 0.42 ( 27) link_BETA1-4 : angle 1.32510 / 0.87 ( 81) link_NAG-ASN : bond 0.00456 / 0.29 ( 51) link_NAG-ASN : angle 3.11006 / 2.20 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 337 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 ARG cc_start: 0.6326 (mmm-85) cc_final: 0.6042 (mmt-90) REVERT: A 904 TYR cc_start: 0.6500 (m-10) cc_final: 0.5914 (m-10) REVERT: B 190 ARG cc_start: 0.6268 (mtt-85) cc_final: 0.5679 (mtm180) REVERT: B 221 SER cc_start: 0.6293 (t) cc_final: 0.6086 (p) REVERT: B 233 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8204 (pp) REVERT: B 844 ILE cc_start: 0.6640 (mt) cc_final: 0.6369 (mt) REVERT: B 936 ASP cc_start: 0.6818 (OUTLIER) cc_final: 0.6534 (m-30) REVERT: C 14 GLN cc_start: 0.4783 (OUTLIER) cc_final: 0.3712 (mm-40) REVERT: C 643 PHE cc_start: 0.7625 (t80) cc_final: 0.7409 (t80) outliers start: 30 outliers final: 20 residues processed: 356 average time/residue: 0.1594 time to fit residues: 90.6321 Evaluate side-chains 290 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 267 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 118 optimal weight: 2.9990 chunk 149 optimal weight: 0.0010 chunk 215 optimal weight: 0.9990 chunk 221 optimal weight: 3.9990 chunk 191 optimal weight: 0.8980 chunk 279 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 100 optimal weight: 0.0570 overall best weight: 0.7908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 207 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1011 GLN B 115 GLN B 137 ASN B 164 ASN B 188 ASN B1101 HIS C 137 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.151116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.119414 restraints weight = 68900.249| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 4.51 r_work: 0.3077 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 26220 Z= 0.144 Angle : 0.620 15.454 35839 Z= 0.317 Chirality : 0.046 0.303 4270 Planarity : 0.004 0.049 4491 Dihedral : 4.700 50.317 3361 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.29 % Favored : 96.52 % Rotamer: Outliers : 1.50 % Allowed : 10.50 % Favored : 88.00 % 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: -0.27 (0.15), residues: 3077 helix: 1.68 (0.20), residues: 693 sheet: 0.79 (0.20), residues: 623 loop : -1.39 (0.13), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 577 TYR 0.016 0.001 TYR A 495 PHE 0.034 0.001 PHE A 392 TRP 0.014 0.001 TRP C1102 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (26097) covalent geometry : angle 0.59422 / 0.31 (35515) SS BOND : bond 0.00937 / 0.44 ( 45) SS BOND : angle 2.04949 / 1.52 ( 90) hydrogen bonds : bond 0.04504 / 3.02 ( 1037) hydrogen bonds : angle 5.16847 / 3.56 ( 2796) link_BETA1-4 : bond 0.00504 / 0.32 ( 27) link_BETA1-4 : angle 1.16365 / 0.80 ( 81) link_NAG-ASN : bond 0.00414 / 0.27 ( 51) link_NAG-ASN : angle 2.17914 / 1.63 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 266 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.7766 (m-40) cc_final: 0.7169 (m-40) REVERT: A 273 ARG cc_start: 0.6385 (mmm-85) cc_final: 0.6094 (mmt-90) REVERT: A 428 ASP cc_start: 0.8249 (p0) cc_final: 0.7884 (p0) REVERT: A 470 THR cc_start: 0.8946 (p) cc_final: 0.8733 (p) REVERT: A 675 GLN cc_start: 0.6090 (pp30) cc_final: 0.5692 (pp30) REVERT: B 190 ARG cc_start: 0.6661 (mtt-85) cc_final: 0.6045 (mtt-85) REVERT: B 470 THR cc_start: 0.8106 (p) cc_final: 0.7780 (p) REVERT: B 503 VAL cc_start: 0.9192 (p) cc_final: 0.8929 (t) REVERT: B 821 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8419 (mt) REVERT: B 844 ILE cc_start: 0.6183 (mt) cc_final: 0.5896 (mt) REVERT: B 1118 ASP cc_start: 0.8279 (t0) cc_final: 0.7675 (m-30) REVERT: C 14 GLN cc_start: 0.4985 (OUTLIER) cc_final: 0.4111 (mm-40) REVERT: C 108 THR cc_start: 0.8234 (m) cc_final: 0.7970 (p) REVERT: C 319 ARG cc_start: 0.8182 (mtp85) cc_final: 0.6396 (mtt90) REVERT: C 505 TYR cc_start: 0.8415 (m-80) cc_final: 0.8113 (m-80) REVERT: C 643 PHE cc_start: 0.7624 (t80) cc_final: 0.7201 (t80) outliers start: 41 outliers final: 23 residues processed: 291 average time/residue: 0.1641 time to fit residues: 76.8984 Evaluate side-chains 258 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 233 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 126 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 265 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 9 optimal weight: 0.0980 chunk 211 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 263 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A 540 ASN A 703 ASN ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A1005 GLN B 66 HIS B 137 ASN B 207 HIS B1101 HIS C 137 ASN C 271 GLN C 641 ASN C1054 GLN C1083 HIS C1135 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.135891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.103367 restraints weight = 58514.880| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 3.74 r_work: 0.2885 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (12 function evaluations) r_final: 0.2875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.5752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 26220 Z= 0.158 Angle : 0.656 16.399 35839 Z= 0.328 Chirality : 0.048 0.341 4270 Planarity : 0.004 0.054 4491 Dihedral : 4.814 55.375 3359 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.78 % Favored : 96.19 % Rotamer: Outliers : 1.35 % Allowed : 11.05 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.31 % 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: -0.24 (0.15), residues: 3077 helix: 1.59 (0.20), residues: 704 sheet: 0.75 (0.20), residues: 618 loop : -1.30 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 577 TYR 0.020 0.002 TYR C 756 PHE 0.033 0.002 PHE B 643 TRP 0.020 0.001 TRP A1102 HIS 0.014 0.001 HIS A1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (26097) covalent geometry : angle 0.63361 / 0.32 (35515) SS BOND : bond 0.00497 / 0.32 ( 45) SS BOND : angle 2.26750 / 1.61 ( 90) hydrogen bonds : bond 0.04430 / 2.95 ( 1037) hydrogen bonds : angle 5.19329 / 3.59 ( 2796) link_BETA1-4 : bond 0.00580 / 0.36 ( 27) link_BETA1-4 : angle 1.45057 / 1.06 ( 81) link_NAG-ASN : bond 0.00367 / 0.26 ( 51) link_NAG-ASN : angle 1.87303 / 1.30 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 252 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.7814 (m-40) cc_final: 0.7177 (m-40) REVERT: A 428 ASP cc_start: 0.8729 (p0) cc_final: 0.8221 (p0) REVERT: A 449 TYR cc_start: 0.8812 (m-80) cc_final: 0.8570 (m-80) REVERT: A 703 ASN cc_start: 0.7114 (OUTLIER) cc_final: 0.6786 (p0) REVERT: A 935 GLN cc_start: 0.8081 (tm-30) cc_final: 0.7787 (tt0) REVERT: B 190 ARG cc_start: 0.7166 (mtt-85) cc_final: 0.6541 (mtt180) REVERT: B 393 THR cc_start: 0.9166 (m) cc_final: 0.8938 (m) REVERT: B 503 VAL cc_start: 0.9325 (p) cc_final: 0.9108 (t) REVERT: B 606 ASN cc_start: 0.8171 (m-40) cc_final: 0.7665 (t0) REVERT: B 646 ARG cc_start: 0.7586 (mtm180) cc_final: 0.7075 (mtm180) REVERT: B 821 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8490 (mt) REVERT: B 844 ILE cc_start: 0.6184 (mt) cc_final: 0.5978 (mt) REVERT: C 489 TYR cc_start: 0.8582 (m-80) cc_final: 0.8251 (m-80) REVERT: C 503 VAL cc_start: 0.9436 (p) cc_final: 0.9197 (t) REVERT: C 787 GLN cc_start: 0.8863 (mm-40) cc_final: 0.8290 (mm-40) REVERT: C 1141 LEU cc_start: 0.6859 (mp) cc_final: 0.6449 (tp) outliers start: 37 outliers final: 22 residues processed: 283 average time/residue: 0.1545 time to fit residues: 70.8846 Evaluate side-chains 219 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 195 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 267 optimal weight: 0.6980 chunk 308 optimal weight: 4.9990 chunk 183 optimal weight: 0.8980 chunk 279 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 234 optimal weight: 0.9980 chunk 202 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 270 optimal weight: 0.6980 chunk 237 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 207 HIS C 271 GLN ** C1135 ASN ** 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 = 0.3603 r_free = 0.3603 target = 0.134937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.104046 restraints weight = 55132.670| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 4.69 r_work: 0.2751 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.6051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 26220 Z= 0.130 Angle : 0.590 15.631 35839 Z= 0.297 Chirality : 0.045 0.327 4270 Planarity : 0.004 0.047 4491 Dihedral : 4.478 27.264 3356 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.16 % Favored : 96.74 % Rotamer: Outliers : 1.10 % Allowed : 12.18 % Favored : 86.72 % 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: -0.09 (0.15), residues: 3077 helix: 1.74 (0.20), residues: 706 sheet: 0.81 (0.20), residues: 624 loop : -1.21 (0.14), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 577 TYR 0.016 0.001 TYR C 756 PHE 0.028 0.001 PHE B 643 TRP 0.012 0.001 TRP C1102 HIS 0.012 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (26097) covalent geometry : angle 0.56972 / 0.29 (35515) SS BOND : bond 0.00555 / 0.33 ( 45) SS BOND : angle 1.89566 / 1.35 ( 90) hydrogen bonds : bond 0.04203 / 2.79 ( 1037) hydrogen bonds : angle 5.08401 / 3.51 ( 2796) link_BETA1-4 : bond 0.00409 / 0.27 ( 27) link_BETA1-4 : angle 1.20675 / 0.84 ( 81) link_NAG-ASN : bond 0.00283 / 0.17 ( 51) link_NAG-ASN : angle 1.81754 / 1.30 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 206 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 CYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7498 (m) REVERT: A 428 ASP cc_start: 0.8878 (p0) cc_final: 0.8398 (p0) REVERT: A 449 TYR cc_start: 0.8859 (m-80) cc_final: 0.8657 (m-80) REVERT: B 190 ARG cc_start: 0.7304 (mtt-85) cc_final: 0.6483 (mtt180) REVERT: B 393 THR cc_start: 0.9176 (m) cc_final: 0.8976 (m) REVERT: B 503 VAL cc_start: 0.9379 (p) cc_final: 0.9139 (t) REVERT: B 606 ASN cc_start: 0.8339 (m-40) cc_final: 0.7738 (t0) REVERT: B 646 ARG cc_start: 0.7638 (mtm180) cc_final: 0.7180 (mtm180) REVERT: B 814 LYS cc_start: 0.7087 (mmtt) cc_final: 0.6795 (mttm) REVERT: B 821 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8581 (mp) REVERT: B 844 ILE cc_start: 0.6091 (mt) cc_final: 0.5829 (mt) REVERT: B 904 TYR cc_start: 0.8307 (m-10) cc_final: 0.7972 (m-10) REVERT: C 489 TYR cc_start: 0.8716 (m-80) cc_final: 0.8391 (m-80) REVERT: C 503 VAL cc_start: 0.9470 (p) cc_final: 0.9245 (t) REVERT: C 690 GLN cc_start: 0.6346 (mm110) cc_final: 0.5975 (mm-40) REVERT: C 787 GLN cc_start: 0.8944 (mm-40) cc_final: 0.8317 (mm-40) REVERT: C 1141 LEU cc_start: 0.6908 (mp) cc_final: 0.6554 (tp) outliers start: 30 outliers final: 24 residues processed: 229 average time/residue: 0.1704 time to fit residues: 63.0358 Evaluate side-chains 219 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 193 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1132 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 72 optimal weight: 0.8980 chunk 172 optimal weight: 1.9990 chunk 287 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 135 optimal weight: 0.7980 chunk 166 optimal weight: 0.8980 chunk 115 optimal weight: 6.9990 chunk 144 optimal weight: 6.9990 chunk 184 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS B 137 ASN C 271 GLN C 394 ASN C 751 ASN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.133872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.100693 restraints weight = 65561.667| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 4.24 r_work: 0.2843 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2767 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.6273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 26220 Z= 0.130 Angle : 0.574 15.650 35839 Z= 0.289 Chirality : 0.045 0.274 4270 Planarity : 0.004 0.040 4491 Dihedral : 4.467 34.104 3356 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.26 % Favored : 96.71 % Rotamer: Outliers : 1.35 % Allowed : 12.29 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % 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: -0.06 (0.15), residues: 3077 helix: 1.78 (0.20), residues: 706 sheet: 0.77 (0.20), residues: 631 loop : -1.19 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 577 TYR 0.018 0.001 TYR C 756 PHE 0.030 0.001 PHE B 643 TRP 0.011 0.001 TRP C1102 HIS 0.025 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (26097) covalent geometry : angle 0.55608 / 0.28 (35515) SS BOND : bond 0.00484 / 0.31 ( 45) SS BOND : angle 1.75181 / 1.27 ( 90) hydrogen bonds : bond 0.04200 / 2.79 ( 1037) hydrogen bonds : angle 5.04838 / 3.48 ( 2796) link_BETA1-4 : bond 0.00450 / 0.30 ( 27) link_BETA1-4 : angle 1.18924 / 0.84 ( 81) link_NAG-ASN : bond 0.00241 / 0.16 ( 51) link_NAG-ASN : angle 1.72310 / 1.21 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 201 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ILE cc_start: 0.7921 (mp) cc_final: 0.7570 (mt) REVERT: A 131 CYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7308 (m) REVERT: A 449 TYR cc_start: 0.8799 (m-80) cc_final: 0.8594 (m-80) REVERT: A 935 GLN cc_start: 0.8454 (tm-30) cc_final: 0.8138 (tt0) REVERT: B 190 ARG cc_start: 0.7433 (mtt-85) cc_final: 0.6583 (mtt180) REVERT: B 503 VAL cc_start: 0.9366 (p) cc_final: 0.9142 (t) REVERT: B 606 ASN cc_start: 0.8379 (m-40) cc_final: 0.7766 (t0) REVERT: B 646 ARG cc_start: 0.7549 (mtm180) cc_final: 0.7104 (mtm180) REVERT: B 821 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8563 (mp) REVERT: B 844 ILE cc_start: 0.6188 (mt) cc_final: 0.5938 (mt) REVERT: C 14 GLN cc_start: 0.4703 (OUTLIER) cc_final: 0.4297 (mm-40) REVERT: C 489 TYR cc_start: 0.8754 (m-80) cc_final: 0.8387 (m-80) REVERT: C 690 GLN cc_start: 0.6535 (mm110) cc_final: 0.6218 (mm-40) REVERT: C 1141 LEU cc_start: 0.6885 (mp) cc_final: 0.6562 (tp) outliers start: 37 outliers final: 30 residues processed: 228 average time/residue: 0.1691 time to fit residues: 61.8708 Evaluate side-chains 217 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1132 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 147 optimal weight: 2.9990 chunk 252 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 242 optimal weight: 0.0970 chunk 230 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 16 optimal weight: 0.5980 chunk 175 optimal weight: 6.9990 chunk 76 optimal weight: 0.0980 chunk 297 optimal weight: 0.6980 chunk 137 optimal weight: 0.8980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 925 ASN A1101 HIS B 207 HIS B 394 ASN C 271 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.135268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.103173 restraints weight = 70649.267| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 4.20 r_work: 0.2795 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.6439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 26220 Z= 0.097 Angle : 0.531 14.876 35839 Z= 0.267 Chirality : 0.044 0.242 4270 Planarity : 0.004 0.042 4491 Dihedral : 4.242 29.324 3356 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.13 % Favored : 96.84 % Rotamer: Outliers : 0.95 % Allowed : 12.73 % Favored : 86.32 % 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: 0.11 (0.15), residues: 3077 helix: 1.98 (0.20), residues: 706 sheet: 0.86 (0.20), residues: 630 loop : -1.09 (0.14), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 577 TYR 0.016 0.001 TYR C1067 PHE 0.032 0.001 PHE B 643 TRP 0.010 0.001 TRP A1102 HIS 0.008 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (26097) covalent geometry : angle 0.51570 / 0.26 (35515) SS BOND : bond 0.00549 / 0.32 ( 45) SS BOND : angle 1.47188 / 1.08 ( 90) hydrogen bonds : bond 0.03592 / 2.39 ( 1037) hydrogen bonds : angle 4.89931 / 3.37 ( 2796) link_BETA1-4 : bond 0.00441 / 0.29 ( 27) link_BETA1-4 : angle 1.10475 / 0.77 ( 81) link_NAG-ASN : bond 0.00246 / 0.16 ( 51) link_NAG-ASN : angle 1.56331 / 1.10 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 210 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ILE cc_start: 0.7899 (mp) cc_final: 0.7542 (mt) REVERT: A 131 CYS cc_start: 0.7489 (OUTLIER) cc_final: 0.7175 (m) REVERT: A 935 GLN cc_start: 0.8569 (tm-30) cc_final: 0.8135 (tt0) REVERT: B 190 ARG cc_start: 0.7352 (mtt-85) cc_final: 0.6549 (mtt180) REVERT: B 606 ASN cc_start: 0.8441 (m-40) cc_final: 0.7774 (t0) REVERT: B 646 ARG cc_start: 0.7474 (mtm180) cc_final: 0.7038 (mtm180) REVERT: B 821 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8601 (mp) REVERT: B 844 ILE cc_start: 0.6105 (mt) cc_final: 0.5874 (mt) REVERT: B 904 TYR cc_start: 0.8309 (m-10) cc_final: 0.8002 (m-10) REVERT: C 489 TYR cc_start: 0.8795 (m-80) cc_final: 0.8442 (m-80) REVERT: C 690 GLN cc_start: 0.6510 (mm110) cc_final: 0.6172 (mm-40) REVERT: C 1141 LEU cc_start: 0.6834 (mp) cc_final: 0.6510 (tp) outliers start: 26 outliers final: 15 residues processed: 225 average time/residue: 0.1629 time to fit residues: 59.2000 Evaluate side-chains 203 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 186 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 754 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 146 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 251 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 229 optimal weight: 4.9990 chunk 306 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN A 422 ASN ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 925 ASN C 271 GLN C 474 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.131790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.098764 restraints weight = 61022.645| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.98 r_work: 0.2784 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.6645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 26220 Z= 0.142 Angle : 0.576 15.628 35839 Z= 0.290 Chirality : 0.045 0.265 4270 Planarity : 0.004 0.046 4491 Dihedral : 4.369 32.986 3356 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.61 % Favored : 96.35 % Rotamer: Outliers : 1.17 % Allowed : 12.44 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % 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: 0.05 (0.15), residues: 3077 helix: 1.88 (0.20), residues: 706 sheet: 0.76 (0.20), residues: 644 loop : -1.10 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1039 TYR 0.020 0.001 TYR C 756 PHE 0.025 0.001 PHE B 643 TRP 0.009 0.001 TRP A 353 HIS 0.017 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 (26097) covalent geometry : angle 0.55853 / 0.29 (35515) SS BOND : bond 0.00567 / 0.34 ( 45) SS BOND : angle 1.76657 / 1.27 ( 90) hydrogen bonds : bond 0.04281 / 2.84 ( 1037) hydrogen bonds : angle 5.00353 / 3.45 ( 2796) link_BETA1-4 : bond 0.00398 / 0.27 ( 27) link_BETA1-4 : angle 1.14123 / 0.80 ( 81) link_NAG-ASN : bond 0.00227 / 0.14 ( 51) link_NAG-ASN : angle 1.66063 / 1.15 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 193 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ILE cc_start: 0.7945 (mp) cc_final: 0.7571 (mt) REVERT: A 319 ARG cc_start: 0.7076 (mtt-85) cc_final: 0.6812 (mtt90) REVERT: A 422 ASN cc_start: 0.9472 (OUTLIER) cc_final: 0.9190 (m110) REVERT: A 489 TYR cc_start: 0.8682 (m-80) cc_final: 0.8476 (m-80) REVERT: A 828 LEU cc_start: 0.8657 (mm) cc_final: 0.8400 (mt) REVERT: A 935 GLN cc_start: 0.8721 (tm-30) cc_final: 0.8206 (tt0) REVERT: A 936 ASP cc_start: 0.7897 (t70) cc_final: 0.7516 (m-30) REVERT: B 190 ARG cc_start: 0.7396 (mtt-85) cc_final: 0.6600 (mtt180) REVERT: B 223 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8576 (mt) REVERT: B 606 ASN cc_start: 0.8413 (m-40) cc_final: 0.7768 (t0) REVERT: B 646 ARG cc_start: 0.7500 (mtm180) cc_final: 0.7059 (mtm180) REVERT: B 821 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8574 (mp) REVERT: B 844 ILE cc_start: 0.6160 (mt) cc_final: 0.5935 (mt) REVERT: C 489 TYR cc_start: 0.8796 (m-80) cc_final: 0.8430 (m-80) REVERT: C 690 GLN cc_start: 0.6545 (mm110) cc_final: 0.6199 (mm-40) REVERT: C 1141 LEU cc_start: 0.6878 (mp) cc_final: 0.6623 (tp) outliers start: 32 outliers final: 26 residues processed: 220 average time/residue: 0.1702 time to fit residues: 60.7848 Evaluate side-chains 214 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 1132 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 84 optimal weight: 4.9990 chunk 266 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 206 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 chunk 303 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 278 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 261 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 481 ASN C 271 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.131404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.098435 restraints weight = 63837.442| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 4.17 r_work: 0.2749 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.6653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 26220 Z= 0.160 Angle : 0.716 59.200 35839 Z= 0.391 Chirality : 0.046 0.549 4270 Planarity : 0.004 0.046 4491 Dihedral : 4.372 32.937 3356 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.24 % Allowed : 12.44 % Favored : 86.32 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % 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: 0.04 (0.15), residues: 3077 helix: 1.87 (0.20), residues: 706 sheet: 0.76 (0.20), residues: 644 loop : -1.11 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 102 TYR 0.020 0.001 TYR C 756 PHE 0.021 0.001 PHE B 643 TRP 0.009 0.001 TRP A 353 HIS 0.019 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (26097) covalent geometry : angle 0.69769 / 0.39 (35515) SS BOND : bond 0.01369 / 0.71 ( 45) SS BOND : angle 2.47270 / 1.79 ( 90) hydrogen bonds : bond 0.04338 / 2.87 ( 1037) hydrogen bonds : angle 5.02170 / 3.47 ( 2796) link_BETA1-4 : bond 0.00352 / 0.24 ( 27) link_BETA1-4 : angle 1.14056 / 0.80 ( 81) link_NAG-ASN : bond 0.00228 / 0.14 ( 51) link_NAG-ASN : angle 1.65944 / 1.15 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 189 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ILE cc_start: 0.7840 (mp) cc_final: 0.7479 (mt) REVERT: A 319 ARG cc_start: 0.7056 (mtt-85) cc_final: 0.6711 (mtt90) REVERT: A 489 TYR cc_start: 0.8601 (m-80) cc_final: 0.8377 (m-80) REVERT: A 828 LEU cc_start: 0.8626 (mm) cc_final: 0.8352 (mt) REVERT: A 935 GLN cc_start: 0.8714 (tm-30) cc_final: 0.8175 (tt0) REVERT: A 936 ASP cc_start: 0.7868 (t70) cc_final: 0.7450 (m-30) REVERT: A 1136 THR cc_start: 0.9056 (OUTLIER) cc_final: 0.8849 (p) REVERT: B 190 ARG cc_start: 0.7262 (mtt-85) cc_final: 0.6455 (mtt180) REVERT: B 223 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8409 (mt) REVERT: B 606 ASN cc_start: 0.8438 (m-40) cc_final: 0.7728 (t0) REVERT: B 646 ARG cc_start: 0.7517 (mtm180) cc_final: 0.7051 (mtm180) REVERT: B 821 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8497 (mp) REVERT: B 844 ILE cc_start: 0.5979 (mt) cc_final: 0.5762 (mt) REVERT: C 489 TYR cc_start: 0.8732 (m-80) cc_final: 0.8321 (m-80) REVERT: C 690 GLN cc_start: 0.6496 (mm110) cc_final: 0.6172 (mm-40) REVERT: C 1141 LEU cc_start: 0.6814 (mp) cc_final: 0.6519 (tp) outliers start: 34 outliers final: 29 residues processed: 216 average time/residue: 0.1724 time to fit residues: 60.5211 Evaluate side-chains 218 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1132 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 38 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 270 optimal weight: 0.7980 chunk 292 optimal weight: 0.6980 chunk 220 optimal weight: 7.9990 chunk 226 optimal weight: 2.9990 chunk 269 optimal weight: 4.9990 chunk 277 optimal weight: 0.2980 chunk 80 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 265 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 481 ASN C 271 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.132760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.103518 restraints weight = 50517.640| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 4.33 r_work: 0.2740 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.6655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.176 26220 Z= 0.420 Angle : 0.756 59.200 35839 Z= 0.408 Chirality : 0.046 0.549 4270 Planarity : 0.004 0.046 4491 Dihedral : 4.372 32.937 3356 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.21 % Allowed : 12.55 % Favored : 86.25 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % 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: 0.04 (0.15), residues: 3077 helix: 1.87 (0.20), residues: 706 sheet: 0.76 (0.20), residues: 644 loop : -1.11 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 102 TYR 0.020 0.001 TYR C 756 PHE 0.021 0.001 PHE B 643 TRP 0.009 0.001 TRP A 353 HIS 0.019 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (26097) covalent geometry : angle 0.69769 / 0.39 (35515) SS BOND : bond 0.18784 / 9.01 ( 45) SS BOND : angle 5.46576 / 3.42 ( 90) hydrogen bonds : bond 0.04338 / 2.87 ( 1037) hydrogen bonds : angle 5.02170 / 3.47 ( 2796) link_BETA1-4 : bond 0.00352 / 0.24 ( 27) link_BETA1-4 : angle 1.14056 / 0.80 ( 81) link_NAG-ASN : bond 0.00228 / 0.14 ( 51) link_NAG-ASN : angle 1.65944 / 1.15 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 187 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ILE cc_start: 0.7950 (mp) cc_final: 0.7581 (mt) REVERT: A 319 ARG cc_start: 0.7138 (mtt-85) cc_final: 0.6824 (mtt90) REVERT: A 489 TYR cc_start: 0.8679 (m-80) cc_final: 0.8466 (m-80) REVERT: A 828 LEU cc_start: 0.8645 (mm) cc_final: 0.8381 (mt) REVERT: A 935 GLN cc_start: 0.8749 (tm-30) cc_final: 0.8228 (tt0) REVERT: A 936 ASP cc_start: 0.7962 (t70) cc_final: 0.7560 (m-30) REVERT: B 190 ARG cc_start: 0.7365 (mtt-85) cc_final: 0.6596 (mtt180) REVERT: B 223 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8571 (mt) REVERT: B 606 ASN cc_start: 0.8440 (m-40) cc_final: 0.7785 (t0) REVERT: B 646 ARG cc_start: 0.7558 (mtm180) cc_final: 0.7112 (mtm180) REVERT: B 821 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8587 (mp) REVERT: B 844 ILE cc_start: 0.6081 (mt) cc_final: 0.5856 (mt) REVERT: C 489 TYR cc_start: 0.8826 (m-80) cc_final: 0.8437 (m-80) REVERT: C 690 GLN cc_start: 0.6552 (mm110) cc_final: 0.6212 (mm-40) REVERT: C 1141 LEU cc_start: 0.6873 (mp) cc_final: 0.6609 (tp) outliers start: 33 outliers final: 29 residues processed: 214 average time/residue: 0.1730 time to fit residues: 59.9798 Evaluate side-chains 217 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1132 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 127 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 112 optimal weight: 0.0670 chunk 18 optimal weight: 8.9990 chunk 181 optimal weight: 0.7980 chunk 214 optimal weight: 0.0980 chunk 174 optimal weight: 0.0770 chunk 132 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 481 ASN C 271 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.131344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.092964 restraints weight = 70236.319| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.23 r_work: 0.2811 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.6655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.176 26220 Z= 0.420 Angle : 0.756 59.200 35839 Z= 0.408 Chirality : 0.046 0.549 4270 Planarity : 0.004 0.046 4491 Dihedral : 4.372 32.937 3356 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.17 % Allowed : 12.58 % Favored : 86.25 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % 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: 0.04 (0.15), residues: 3077 helix: 1.87 (0.20), residues: 706 sheet: 0.76 (0.20), residues: 644 loop : -1.11 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 102 TYR 0.020 0.001 TYR C 756 PHE 0.021 0.001 PHE B 643 TRP 0.009 0.001 TRP A 353 HIS 0.019 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (26097) covalent geometry : angle 0.69769 / 0.39 (35515) SS BOND : bond 0.18784 / 9.01 ( 45) SS BOND : angle 5.46576 / 3.42 ( 90) hydrogen bonds : bond 0.04338 / 2.87 ( 1037) hydrogen bonds : angle 5.02170 / 3.47 ( 2796) link_BETA1-4 : bond 0.00352 / 0.24 ( 27) link_BETA1-4 : angle 1.14056 / 0.80 ( 81) link_NAG-ASN : bond 0.00228 / 0.14 ( 51) link_NAG-ASN : angle 1.65944 / 1.15 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6003.23 seconds wall clock time: 103 minutes 52.33 seconds (6232.33 seconds total)