Starting phenix.real_space_refine on Sun Jul 5 18:44:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vq0_32078/07_2026/7vq0_32078.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vq0_32078/07_2026/7vq0_32078.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vq0_32078/07_2026/7vq0_32078.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vq0_32078/07_2026/7vq0_32078.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7vq0_32078/07_2026/7vq0_32078.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vq0_32078/07_2026/7vq0_32078.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vq0_32078/07_2026/7vq0_32078.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vq0_32078/07_2026/7vq0_32078.map" } resolution = 3.03 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= 0.067 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 128 5.16 5 C 18712 2.51 5 N 4837 2.21 5 O 5840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.03s 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: 29517 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 8554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1093, 8554 Classifications: {'peptide': 1093} Link IDs: {'PTRANS': 54, 'TRANS': 1038} Chain breaks: 6 Chain: "B" Number of atoms: 8524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1091, 8524 Classifications: {'peptide': 1091} Link IDs: {'PTRANS': 54, 'TRANS': 1036} Chain breaks: 7 Chain: "C" Number of atoms: 8540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1092, 8540 Classifications: {'peptide': 1092} Link IDs: {'PTRANS': 54, 'TRANS': 1037} Chain breaks: 5 Chain: "D" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 885 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "E" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 885 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "F" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 885 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 7.42, per 1000 atoms: 0.25 Number of scatterers: 29517 At special positions: 0 Unit cell: (147.03, 153.12, 225.33, 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 128 16.00 O 5840 8.00 N 4837 7.00 C 18712 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 94 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 94 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 94 " 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=2, symmetry=0 Links applied ALPHA1-4 " NAG O 2 " - " MAN O 3 " " NAG P 2 " - " MAN P 3 " " NAG W 2 " - " MAN W 3 " " NAG X 2 " - " MAN X 3 " " NAG e 2 " - " MAN e 3 " " NAG f 2 " - " MAN f 3 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " BETA1-6 " NAG N 1 " - " FUC N 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG V 1 " - " FUC V 3 " " NAG d 1 " - " FUC d 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1404 " - " ASN A 331 " " NAG A1405 " - " ASN A 343 " " NAG A1406 " - " ASN A 603 " " NAG A1407 " - " ASN A 657 " " NAG A1408 " - " ASN A 709 " " NAG A1409 " - " ASN A1158 " " NAG B1402 " - " ASN B 122 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 657 " " NAG B1408 " - " ASN B 709 " " NAG B1409 " - " ASN B1158 " " NAG C1408 " - " ASN C 603 " " NAG C1409 " - " ASN C 657 " " NAG C1410 " - " ASN C 709 " " NAG C1411 " - " ASN C1158 " " NAG H 1 " - " ASN A 122 " " NAG J 1 " - " ASN A 282 " " NAG K 1 " - " ASN A 616 " " NAG L 1 " - " ASN A 717 " " NAG M 1 " - " ASN A 801 " " NAG N 1 " - " ASN A1074 " " NAG O 1 " - " ASN A1098 " " NAG P 1 " - " ASN A1134 " " NAG Q 1 " - " ASN B 17 " " NAG R 1 " - " ASN B 331 " " NAG S 1 " - " ASN B 616 " " NAG T 1 " - " ASN B 717 " " NAG U 1 " - " ASN B 801 " " NAG V 1 " - " ASN B1074 " " NAG W 1 " - " ASN B1098 " " NAG X 1 " - " ASN B1134 " " NAG Z 1 " - " ASN C 331 " " NAG a 1 " - " ASN C 616 " " NAG b 1 " - " ASN C 717 " " NAG c 1 " - " ASN C 801 " " NAG d 1 " - " ASN C1074 " " NAG e 1 " - " ASN C1098 " " NAG f 1 " - " ASN C1134 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.96 Conformation dependent library (CDL) restraints added in 1.4 seconds 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6762 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 58 sheets defined 23.5% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.523A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.536A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.559A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (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 616 through 620 removed outlier: 3.567A pdb=" N GLU A 619 " --> pdb=" O ASN A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.740A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 783 removed outlier: 3.567A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 830 through 835 removed outlier: 3.871A pdb=" N ILE A 834 " --> pdb=" O ASP A 830 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS A 835 " --> pdb=" O ALA A 831 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 830 through 835' Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.170A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.931A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1161 removed outlier: 3.691A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.967A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 411 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 618 through 623 removed outlier: 3.911A pdb=" N VAL B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.866A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.528A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 851 through 856 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 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.048A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.891A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.255A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1161 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.779A 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 619 through 623 removed outlier: 4.074A pdb=" N ALA C 623 " --> pdb=" O VAL C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.069A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.803A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (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 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.648A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1161 removed outlier: 4.017A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.767A pdb=" N THR D 89 " --> pdb=" O PRO D 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 89 Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 85 through 89 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 8.099A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.611A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.848A pdb=" N GLN A 271 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.956A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.630A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.630A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 140 through 143 removed outlier: 4.906A pdb=" N GLU A 156 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.174A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL A 595 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.899A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.623A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 542 through 543 removed outlier: 3.693A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 551 through 554 removed outlier: 3.519A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.300A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.257A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.784A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.268A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.385A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.566A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.344A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.915A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.997A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.649A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 131 through 140 removed outlier: 6.585A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.220A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL B 595 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC9, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.593A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.615A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.270A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.186A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.697A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.598A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.693A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.779A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.276A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.097A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.606A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 51 removed outlier: 6.488A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 12.716A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 12.209A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 9.866A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.463A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 9.670A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.617A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.629A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.647A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.014A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL C 595 " --> pdb=" O SER C 316 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.525A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.792A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.525A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.792A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 653 through 655 removed outlier: 3.816A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AF3, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.277A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.369A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF6, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF7, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.601A pdb=" N SER D 7 " --> pdb=" O SER D 21 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER D 21 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D 18 " --> pdb=" O MET D 81 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET D 81 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU D 20 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL D 77 " --> pdb=" O CYS D 22 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 36 through 39 removed outlier: 6.409A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 91 through 92 Processing sheet with id=AG1, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.589A pdb=" N GLN E 5 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER E 7 " --> pdb=" O SER E 21 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR E 67 " --> pdb=" O GLN E 80 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.839A pdb=" N VAL E 12 " --> pdb=" O SER E 115 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL E 91 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN E 39 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE E 34 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ARG E 38 " --> pdb=" O PHE E 47 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N PHE E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA E 50 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA E 57 " --> pdb=" O ALA E 50 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 5 through 7 removed outlier: 3.752A pdb=" N GLN F 5 " --> pdb=" O VAL F 23 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL F 23 " --> pdb=" O GLN F 5 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER F 7 " --> pdb=" O SER F 21 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU F 18 " --> pdb=" O MET F 81 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU F 20 " --> pdb=" O LEU F 79 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.892A pdb=" N THR F 110 " --> pdb=" O TYR F 92 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR F 92 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE F 34 " --> pdb=" O ALA F 50 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ALA F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) 1088 hydrogen bonds defined for protein. 2976 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.72 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9341 1.34 - 1.47: 7674 1.47 - 1.59: 12980 1.59 - 1.71: 0 1.71 - 1.83: 164 Bond restraints: 30159 Sorted by residual: bond pdb=" C5 MAN O 3 " pdb=" O5 MAN O 3 " ideal model delta sigma weight residual 1.418 1.465 -0.047 2.00e-02 2.50e+03 5.64e+00 bond pdb=" C5 MAN P 3 " pdb=" O5 MAN P 3 " ideal model delta sigma weight residual 1.418 1.464 -0.046 2.00e-02 2.50e+03 5.36e+00 bond pdb=" C5 MAN e 3 " pdb=" O5 MAN e 3 " ideal model delta sigma weight residual 1.418 1.463 -0.045 2.00e-02 2.50e+03 5.01e+00 bond pdb=" C5 MAN W 3 " pdb=" O5 MAN W 3 " ideal model delta sigma weight residual 1.418 1.462 -0.044 2.00e-02 2.50e+03 4.93e+00 bond pdb=" C5 MAN f 3 " pdb=" O5 MAN f 3 " ideal model delta sigma weight residual 1.418 1.458 -0.040 2.00e-02 2.50e+03 3.91e+00 ... (remaining 30154 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 39923 1.66 - 3.32: 945 3.32 - 4.98: 91 4.98 - 6.64: 29 6.64 - 8.30: 10 Bond angle restraints: 40998 Sorted by residual: angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 115.16 -4.46 1.22e+00 6.72e-01 1.33e+01 angle pdb=" CA PRO A 986 " pdb=" C PRO A 986 " pdb=" N PRO A 987 " ideal model delta sigma weight residual 117.93 121.64 -3.71 1.20e+00 6.94e-01 9.57e+00 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 114.19 -3.49 1.22e+00 6.72e-01 8.20e+00 angle pdb=" C ASP E 53 " pdb=" CA ASP E 53 " pdb=" CB ASP E 53 " ideal model delta sigma weight residual 110.42 115.98 -5.56 1.99e+00 2.53e-01 7.79e+00 angle pdb=" N VAL C1128 " pdb=" CA VAL C1128 " pdb=" C VAL C1128 " ideal model delta sigma weight residual 113.53 110.86 2.67 9.80e-01 1.04e+00 7.41e+00 ... (remaining 40993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 15630 17.97 - 35.93: 1301 35.93 - 53.90: 204 53.90 - 71.87: 55 71.87 - 89.83: 39 Dihedral angle restraints: 17229 sinusoidal: 6711 harmonic: 10518 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -162.03 76.03 1 1.00e+01 1.00e-02 7.28e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -12.41 -73.59 1 1.00e+01 1.00e-02 6.89e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -157.01 71.01 1 1.00e+01 1.00e-02 6.48e+01 ... (remaining 17226 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 4248 0.070 - 0.141: 608 0.141 - 0.211: 7 0.211 - 0.281: 2 0.281 - 0.352: 3 Chirality restraints: 4868 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN A 282 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CB ILE D 51 " pdb=" CA ILE D 51 " pdb=" CG1 ILE D 51 " pdb=" CG2 ILE D 51 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" C1 NAG B1402 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG B1402 " pdb=" O5 NAG B1402 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 4865 not shown) Planarity restraints: 5224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 526 " -0.044 5.00e-02 4.00e+02 6.75e-02 7.29e+00 pdb=" N PRO A 527 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 616 " -0.001 2.00e-02 2.50e+03 2.28e-02 6.52e+00 pdb=" CG ASN A 616 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 616 " 0.026 2.00e-02 2.50e+03 pdb=" ND2 ASN A 616 " -0.030 2.00e-02 2.50e+03 pdb=" C1 NAG K 1 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 560 " 0.030 5.00e-02 4.00e+02 4.57e-02 3.33e+00 pdb=" N PRO A 561 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 561 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 561 " 0.025 5.00e-02 4.00e+02 ... (remaining 5221 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 636 2.68 - 3.23: 27914 3.23 - 3.79: 45765 3.79 - 4.34: 61508 4.34 - 4.90: 101858 Nonbonded interactions: 237681 Sorted by model distance: nonbonded pdb=" OG SER A 884 " pdb=" OG1 THR A 887 " model vdw 2.124 3.040 nonbonded pdb=" NH2 ARG A 34 " pdb=" OE2 GLU A 191 " model vdw 2.183 3.120 nonbonded pdb=" OG SER B 469 " pdb=" OE1 GLU B 471 " model vdw 2.192 3.040 nonbonded pdb=" OG1 THR C 470 " pdb=" O TYR F 58 " model vdw 2.200 3.040 nonbonded pdb=" O SER A 937 " pdb=" OG1 THR A 941 " model vdw 2.204 3.040 ... (remaining 237676 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 145 or resid 152 through 623 or resid 636 throu \ gh 836 or resid 854 through 1409)) selection = (chain 'B' and (resid 14 through 68 or resid 77 through 836 or resid 854 through \ 1409)) selection = (chain 'C' and (resid 14 through 68 or resid 77 through 145 or resid 152 through \ 177 or resid 185 through 1409)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' } ncs_group { reference = (chain 'N' and resid 1 through 2) selection = (chain 'O' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.670 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 31.100 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 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 : 0.004 0.047 30279 Z= 0.181 Angle : 0.614 9.932 41308 Z= 0.289 Chirality : 0.045 0.352 4868 Planarity : 0.003 0.068 5185 Dihedral : 13.947 89.834 10335 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.61 % Favored : 95.30 % Rotamer: Outliers : 0.03 % Allowed : 0.22 % Favored : 99.75 % 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: -0.40 (0.14), residues: 3576 helix: 1.91 (0.20), residues: 741 sheet: -0.18 (0.19), residues: 752 loop : -1.14 (0.13), residues: 2083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 237 TYR 0.019 0.001 TYR A 170 PHE 0.025 0.001 PHE A 168 TRP 0.016 0.001 TRP A 64 HIS 0.006 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 (30159) covalent geometry : angle 0.59385 / 0.28 (40998) SS BOND : bond 0.00298 / 0.19 ( 44) SS BOND : angle 1.33541 / 0.83 ( 88) hydrogen bonds : bond 0.19194 / 12.46 ( 1067) hydrogen bonds : angle 8.35111 / 5.75 ( 2976) Misc. bond : bond 0.00148 / 0.08 ( 2) link_ALPHA1-4 : bond 0.00704 / 0.40 ( 6) link_ALPHA1-4 : angle 2.28604 / 1.38 ( 18) link_BETA1-4 : bond 0.00542 / 0.38 ( 26) link_BETA1-4 : angle 1.31046 / 0.86 ( 78) link_BETA1-6 : bond 0.00716 / 0.37 ( 3) link_BETA1-6 : angle 1.43163 / 0.93 ( 9) link_NAG-ASN : bond 0.00345 / 0.23 ( 39) link_NAG-ASN : angle 2.47592 / 1.73 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 280 time to evaluate : 1.074 Fit side-chains REVERT: B 237 ARG cc_start: 0.7453 (mtp-110) cc_final: 0.7121 (ttp-110) REVERT: B 568 ASP cc_start: 0.7065 (t0) cc_final: 0.6782 (t0) REVERT: B 904 TYR cc_start: 0.7881 (m-10) cc_final: 0.7542 (m-10) REVERT: C 52 GLN cc_start: 0.7740 (pp30) cc_final: 0.7534 (pp30) REVERT: C 586 ASP cc_start: 0.8041 (m-30) cc_final: 0.7775 (m-30) outliers start: 1 outliers final: 0 residues processed: 281 average time/residue: 0.1921 time to fit residues: 87.7319 Evaluate side-chains 196 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 40.0000 chunk 244 optimal weight: 0.0270 chunk 183 optimal weight: 0.3980 chunk 298 optimal weight: 1.9990 overall best weight: 1.0042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN A 613 GLN A 907 ASN A1010 GLN B 607 GLN ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B 914 ASN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN D 39 GLN D 55 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.206978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.137156 restraints weight = 41731.398| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 3.10 r_work: 0.3407 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.0875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30279 Z= 0.127 Angle : 0.569 10.858 41308 Z= 0.286 Chirality : 0.044 0.277 4868 Planarity : 0.004 0.049 5185 Dihedral : 4.213 20.003 3884 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.47 % Favored : 95.44 % Rotamer: Outliers : 0.35 % Allowed : 6.15 % Favored : 93.50 % 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: -0.28 (0.14), residues: 3576 helix: 2.05 (0.20), residues: 743 sheet: -0.00 (0.19), residues: 746 loop : -1.13 (0.13), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 34 TYR 0.024 0.001 TYR A 453 PHE 0.014 0.001 PHE A 168 TRP 0.016 0.001 TRP C 64 HIS 0.005 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (30159) covalent geometry : angle 0.55363 / 0.28 (40998) SS BOND : bond 0.00273 / 0.17 ( 44) SS BOND : angle 1.18263 / 0.81 ( 88) hydrogen bonds : bond 0.04631 / 3.06 ( 1067) hydrogen bonds : angle 6.52999 / 4.44 ( 2976) Misc. bond : bond 0.00113 / 0.06 ( 2) link_ALPHA1-4 : bond 0.00887 / 0.49 ( 6) link_ALPHA1-4 : angle 1.87600 / 1.12 ( 18) link_BETA1-4 : bond 0.00491 / 0.33 ( 26) link_BETA1-4 : angle 0.99580 / 0.66 ( 78) link_BETA1-6 : bond 0.00674 / 0.34 ( 3) link_BETA1-6 : angle 1.05490 / 0.67 ( 9) link_NAG-ASN : bond 0.00370 / 0.26 ( 39) link_NAG-ASN : angle 2.09860 / 1.38 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 226 time to evaluate : 1.110 Fit side-chains REVERT: A 406 GLU cc_start: 0.8455 (mp0) cc_final: 0.8214 (mp0) REVERT: A 619 GLU cc_start: 0.5301 (mp0) cc_final: 0.5084 (mm-30) REVERT: A 935 GLN cc_start: 0.8803 (pp30) cc_final: 0.8562 (tm-30) REVERT: B 675 GLN cc_start: 0.7102 (tm-30) cc_final: 0.6865 (tm-30) REVERT: B 904 TYR cc_start: 0.8586 (m-10) cc_final: 0.8338 (m-10) REVERT: C 52 GLN cc_start: 0.8039 (pp30) cc_final: 0.7722 (pp30) outliers start: 11 outliers final: 5 residues processed: 236 average time/residue: 0.1907 time to fit residues: 74.4070 Evaluate side-chains 204 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 199 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 959 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 138 optimal weight: 7.9990 chunk 265 optimal weight: 0.7980 chunk 315 optimal weight: 4.9990 chunk 220 optimal weight: 9.9990 chunk 164 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN A1010 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.203750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.131624 restraints weight = 41861.394| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 3.21 r_work: 0.3310 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 30279 Z= 0.224 Angle : 0.618 9.632 41308 Z= 0.308 Chirality : 0.045 0.260 4868 Planarity : 0.004 0.045 5185 Dihedral : 4.494 22.432 3884 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.03 % Favored : 94.88 % Rotamer: Outliers : 0.86 % Allowed : 9.46 % Favored : 89.68 % 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: -0.51 (0.14), residues: 3576 helix: 1.79 (0.19), residues: 743 sheet: -0.17 (0.18), residues: 772 loop : -1.26 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 983 TYR 0.020 0.002 TYR B1067 PHE 0.019 0.002 PHE B 238 TRP 0.018 0.002 TRP A 64 HIS 0.006 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.22 (30159) covalent geometry : angle 0.60297 / 0.30 (40998) SS BOND : bond 0.00395 / 0.26 ( 44) SS BOND : angle 1.34485 / 0.86 ( 88) hydrogen bonds : bond 0.04756 / 3.18 ( 1067) hydrogen bonds : angle 6.24242 / 4.24 ( 2976) Misc. bond : bond 0.00212 / 0.11 ( 2) link_ALPHA1-4 : bond 0.00773 / 0.43 ( 6) link_ALPHA1-4 : angle 1.97477 / 1.20 ( 18) link_BETA1-4 : bond 0.00330 / 0.23 ( 26) link_BETA1-4 : angle 1.17417 / 0.75 ( 78) link_BETA1-6 : bond 0.00557 / 0.29 ( 3) link_BETA1-6 : angle 1.16065 / 0.79 ( 9) link_NAG-ASN : bond 0.00380 / 0.26 ( 39) link_NAG-ASN : angle 2.15706 / 1.42 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 210 time to evaluate : 1.137 Fit side-chains REVERT: A 49 HIS cc_start: 0.8404 (t-170) cc_final: 0.8157 (t-170) REVERT: A 271 GLN cc_start: 0.8079 (pm20) cc_final: 0.7752 (pm20) REVERT: A 392 PHE cc_start: 0.7196 (m-80) cc_final: 0.6883 (m-80) REVERT: A 935 GLN cc_start: 0.8744 (pp30) cc_final: 0.8512 (tm-30) REVERT: B 239 GLN cc_start: 0.7927 (tt0) cc_final: 0.7521 (mt0) REVERT: B 568 ASP cc_start: 0.7667 (t0) cc_final: 0.7237 (t0) REVERT: B 904 TYR cc_start: 0.8397 (m-10) cc_final: 0.8179 (m-10) REVERT: C 52 GLN cc_start: 0.8196 (pp30) cc_final: 0.7894 (pp30) outliers start: 27 outliers final: 18 residues processed: 233 average time/residue: 0.1837 time to fit residues: 71.2563 Evaluate side-chains 219 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 201 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain D residue 23 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 208 optimal weight: 1.9990 chunk 279 optimal weight: 6.9990 chunk 115 optimal weight: 20.0000 chunk 142 optimal weight: 20.0000 chunk 51 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 195 optimal weight: 3.9990 chunk 330 optimal weight: 8.9990 chunk 326 optimal weight: 5.9990 chunk 284 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN B 544 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 360 ASN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1011 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.201842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.127509 restraints weight = 41605.149| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 3.05 r_work: 0.3293 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.110 30279 Z= 0.298 Angle : 0.678 11.973 41308 Z= 0.336 Chirality : 0.047 0.278 4868 Planarity : 0.004 0.046 5185 Dihedral : 4.786 23.439 3884 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.84 % Favored : 94.04 % Rotamer: Outliers : 1.91 % Allowed : 11.91 % Favored : 86.18 % 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: -0.82 (0.13), residues: 3576 helix: 1.39 (0.19), residues: 748 sheet: -0.32 (0.18), residues: 781 loop : -1.43 (0.13), residues: 2047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 403 TYR 0.020 0.002 TYR B1067 PHE 0.022 0.002 PHE C1148 TRP 0.029 0.002 TRP A 64 HIS 0.007 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00721 / 0.30 (30159) covalent geometry : angle 0.66075 / 0.33 (40998) SS BOND : bond 0.00573 / 0.37 ( 44) SS BOND : angle 1.54350 / 0.99 ( 88) hydrogen bonds : bond 0.04950 / 3.32 ( 1067) hydrogen bonds : angle 6.25592 / 4.25 ( 2976) Misc. bond : bond 0.00245 / 0.13 ( 2) link_ALPHA1-4 : bond 0.00743 / 0.41 ( 6) link_ALPHA1-4 : angle 2.08403 / 1.27 ( 18) link_BETA1-4 : bond 0.00306 / 0.22 ( 26) link_BETA1-4 : angle 1.29133 / 0.82 ( 78) link_BETA1-6 : bond 0.00467 / 0.24 ( 3) link_BETA1-6 : angle 1.23315 / 0.88 ( 9) link_NAG-ASN : bond 0.00449 / 0.31 ( 39) link_NAG-ASN : angle 2.32756 / 1.55 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 213 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8708 (mt) REVERT: A 271 GLN cc_start: 0.8154 (pm20) cc_final: 0.7828 (pm20) REVERT: A 392 PHE cc_start: 0.7390 (m-80) cc_final: 0.6999 (m-80) REVERT: A 515 PHE cc_start: 0.8318 (OUTLIER) cc_final: 0.6376 (p90) REVERT: A 935 GLN cc_start: 0.8798 (pp30) cc_final: 0.8590 (tm-30) REVERT: B 568 ASP cc_start: 0.7898 (t0) cc_final: 0.7479 (t0) REVERT: B 726 ILE cc_start: 0.9269 (OUTLIER) cc_final: 0.8792 (mp) REVERT: C 52 GLN cc_start: 0.8216 (pp30) cc_final: 0.7948 (pp30) REVERT: C 118 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7556 (tp) REVERT: C 220 PHE cc_start: 0.7577 (t80) cc_final: 0.7357 (t80) REVERT: C 878 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8468 (tt) outliers start: 60 outliers final: 34 residues processed: 261 average time/residue: 0.1738 time to fit residues: 75.8826 Evaluate side-chains 229 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 190 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain D residue 23 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 144 optimal weight: 7.9990 chunk 340 optimal weight: 40.0000 chunk 249 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 175 optimal weight: 0.7980 chunk 233 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 299 optimal weight: 0.9990 chunk 201 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 914 ASN A1010 GLN ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 ASN B1054 GLN C 360 ASN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.204849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.132976 restraints weight = 41688.056| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 3.29 r_work: 0.3326 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30279 Z= 0.131 Angle : 0.562 9.257 41308 Z= 0.279 Chirality : 0.043 0.271 4868 Planarity : 0.004 0.045 5185 Dihedral : 4.421 21.830 3884 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.61 % Favored : 95.27 % Rotamer: Outliers : 1.46 % Allowed : 13.47 % Favored : 85.06 % 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: -0.55 (0.14), residues: 3576 helix: 1.82 (0.19), residues: 749 sheet: -0.23 (0.18), residues: 759 loop : -1.29 (0.13), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 214 TYR 0.017 0.001 TYR C1067 PHE 0.016 0.001 PHE C 194 TRP 0.023 0.001 TRP A 64 HIS 0.002 0.000 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (30159) covalent geometry : angle 0.54802 / 0.28 (40998) SS BOND : bond 0.00294 / 0.19 ( 44) SS BOND : angle 1.14106 / 0.74 ( 88) hydrogen bonds : bond 0.03974 / 2.64 ( 1067) hydrogen bonds : angle 5.87909 / 3.99 ( 2976) Misc. bond : bond 0.00112 / 0.06 ( 2) link_ALPHA1-4 : bond 0.00754 / 0.43 ( 6) link_ALPHA1-4 : angle 1.78057 / 1.08 ( 18) link_BETA1-4 : bond 0.00402 / 0.28 ( 26) link_BETA1-4 : angle 1.02596 / 0.67 ( 78) link_BETA1-6 : bond 0.00553 / 0.28 ( 3) link_BETA1-6 : angle 1.12189 / 0.78 ( 9) link_NAG-ASN : bond 0.00325 / 0.22 ( 39) link_NAG-ASN : angle 2.01550 / 1.33 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 214 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: A 357 ARG cc_start: 0.8023 (tpp80) cc_final: 0.7798 (tpp80) REVERT: A 392 PHE cc_start: 0.7405 (m-80) cc_final: 0.6987 (m-80) REVERT: A 406 GLU cc_start: 0.8641 (mp0) cc_final: 0.8397 (mp0) REVERT: A 515 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.6310 (p90) REVERT: A 935 GLN cc_start: 0.8711 (pp30) cc_final: 0.8462 (tm-30) REVERT: B 239 GLN cc_start: 0.7825 (tt0) cc_final: 0.7299 (tt0) REVERT: B 568 ASP cc_start: 0.7640 (t0) cc_final: 0.7319 (t0) REVERT: C 52 GLN cc_start: 0.8076 (pp30) cc_final: 0.7828 (pp30) REVERT: C 118 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7501 (tp) REVERT: C 537 LYS cc_start: 0.8583 (mmpt) cc_final: 0.8254 (mtmm) outliers start: 46 outliers final: 28 residues processed: 251 average time/residue: 0.1722 time to fit residues: 72.4652 Evaluate side-chains 226 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 23 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 34 optimal weight: 1.9990 chunk 277 optimal weight: 0.9990 chunk 329 optimal weight: 10.0000 chunk 135 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 320 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 205 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 chunk 321 optimal weight: 0.8980 chunk 223 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 914 ASN A1010 GLN ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 ASN C 360 ASN C 501 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.204905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.133049 restraints weight = 41443.060| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 3.09 r_work: 0.3372 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30279 Z= 0.134 Angle : 0.557 9.192 41308 Z= 0.276 Chirality : 0.043 0.267 4868 Planarity : 0.004 0.050 5185 Dihedral : 4.327 21.219 3884 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.81 % Favored : 95.08 % Rotamer: Outliers : 1.75 % Allowed : 14.36 % Favored : 83.89 % 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: -0.44 (0.14), residues: 3576 helix: 1.95 (0.19), residues: 741 sheet: -0.18 (0.18), residues: 766 loop : -1.22 (0.13), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 403 TYR 0.021 0.001 TYR A 423 PHE 0.018 0.001 PHE A 342 TRP 0.018 0.001 TRP A 64 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (30159) covalent geometry : angle 0.54343 / 0.27 (40998) SS BOND : bond 0.00282 / 0.18 ( 44) SS BOND : angle 1.13016 / 0.70 ( 88) hydrogen bonds : bond 0.03879 / 2.58 ( 1067) hydrogen bonds : angle 5.75349 / 3.91 ( 2976) Misc. bond : bond 0.00276 / 0.15 ( 2) link_ALPHA1-4 : bond 0.00734 / 0.41 ( 6) link_ALPHA1-4 : angle 1.77406 / 1.09 ( 18) link_BETA1-4 : bond 0.00399 / 0.27 ( 26) link_BETA1-4 : angle 1.04391 / 0.68 ( 78) link_BETA1-6 : bond 0.00567 / 0.29 ( 3) link_BETA1-6 : angle 1.11393 / 0.77 ( 9) link_NAG-ASN : bond 0.00313 / 0.21 ( 39) link_NAG-ASN : angle 1.95691 / 1.29 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 216 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8655 (mt) REVERT: A 49 HIS cc_start: 0.8575 (t-170) cc_final: 0.8350 (t-170) REVERT: A 271 GLN cc_start: 0.8162 (pm20) cc_final: 0.7804 (pm20) REVERT: A 324 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7397 (tm-30) REVERT: A 357 ARG cc_start: 0.8106 (tpp80) cc_final: 0.7886 (tpp80) REVERT: A 392 PHE cc_start: 0.7507 (m-80) cc_final: 0.7106 (m-80) REVERT: A 406 GLU cc_start: 0.8641 (mp0) cc_final: 0.8379 (mp0) REVERT: A 462 LYS cc_start: 0.8415 (mmtt) cc_final: 0.7913 (ttpp) REVERT: A 515 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.6371 (p90) REVERT: A 820 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.7971 (t0) REVERT: A 935 GLN cc_start: 0.8782 (pp30) cc_final: 0.8541 (tm-30) REVERT: B 568 ASP cc_start: 0.7719 (t0) cc_final: 0.7338 (t0) REVERT: B 726 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8769 (mp) REVERT: C 52 GLN cc_start: 0.8081 (pp30) cc_final: 0.7832 (pp30) REVERT: C 118 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7517 (tp) REVERT: C 537 LYS cc_start: 0.8613 (mmpt) cc_final: 0.8305 (mtmm) REVERT: D 77 VAL cc_start: 0.6653 (m) cc_final: 0.5212 (p) outliers start: 55 outliers final: 30 residues processed: 259 average time/residue: 0.1636 time to fit residues: 71.6622 Evaluate side-chains 242 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 206 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain F residue 95 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 17 optimal weight: 0.3980 chunk 219 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 154 optimal weight: 8.9990 chunk 96 optimal weight: 0.5980 chunk 41 optimal weight: 9.9990 chunk 254 optimal weight: 10.0000 chunk 229 optimal weight: 5.9990 chunk 123 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 853 GLN B 914 ASN ** B1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C1010 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.204690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.133130 restraints weight = 41510.144| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 3.20 r_work: 0.3345 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30279 Z= 0.145 Angle : 0.560 9.147 41308 Z= 0.277 Chirality : 0.043 0.262 4868 Planarity : 0.004 0.049 5185 Dihedral : 4.297 21.223 3884 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.67 % Favored : 95.22 % Rotamer: Outliers : 1.75 % Allowed : 15.06 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.14), residues: 3576 helix: 1.99 (0.19), residues: 737 sheet: -0.28 (0.18), residues: 790 loop : -1.22 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 70 TYR 0.018 0.001 TYR B1067 PHE 0.015 0.001 PHE B 565 TRP 0.014 0.001 TRP A 64 HIS 0.005 0.001 HIS D 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 (30159) covalent geometry : angle 0.54551 / 0.27 (40998) SS BOND : bond 0.00295 / 0.19 ( 44) SS BOND : angle 1.19850 / 0.82 ( 88) hydrogen bonds : bond 0.03882 / 2.59 ( 1067) hydrogen bonds : angle 5.67185 / 3.85 ( 2976) Misc. bond : bond 0.00208 / 0.11 ( 2) link_ALPHA1-4 : bond 0.00720 / 0.40 ( 6) link_ALPHA1-4 : angle 1.77196 / 1.09 ( 18) link_BETA1-4 : bond 0.00366 / 0.25 ( 26) link_BETA1-4 : angle 1.04976 / 0.68 ( 78) link_BETA1-6 : bond 0.00556 / 0.29 ( 3) link_BETA1-6 : angle 1.12903 / 0.78 ( 9) link_NAG-ASN : bond 0.00308 / 0.21 ( 39) link_NAG-ASN : angle 1.99723 / 1.32 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 206 time to evaluate : 1.195 Fit side-chains revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8656 (mt) REVERT: A 49 HIS cc_start: 0.8568 (t-170) cc_final: 0.8321 (t-170) REVERT: A 140 PHE cc_start: 0.6111 (p90) cc_final: 0.5826 (p90) REVERT: A 271 GLN cc_start: 0.8150 (pm20) cc_final: 0.7774 (pm20) REVERT: A 324 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7382 (tm-30) REVERT: A 392 PHE cc_start: 0.7651 (m-80) cc_final: 0.7178 (m-80) REVERT: A 406 GLU cc_start: 0.8617 (mp0) cc_final: 0.8343 (mp0) REVERT: A 462 LYS cc_start: 0.8292 (mmtt) cc_final: 0.7753 (ttpp) REVERT: A 515 PHE cc_start: 0.8271 (OUTLIER) cc_final: 0.6417 (p90) REVERT: A 661 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8049 (pm20) REVERT: A 820 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7981 (t0) REVERT: A 935 GLN cc_start: 0.8769 (pp30) cc_final: 0.8520 (tm-30) REVERT: A 1004 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8868 (tt) REVERT: B 235 ILE cc_start: 0.5932 (OUTLIER) cc_final: 0.5719 (tp) REVERT: B 239 GLN cc_start: 0.8001 (tt0) cc_final: 0.7616 (mt0) REVERT: B 726 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8762 (mp) REVERT: C 52 GLN cc_start: 0.8128 (pp30) cc_final: 0.7870 (pp30) REVERT: C 118 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7511 (tp) REVERT: C 537 LYS cc_start: 0.8569 (mmpt) cc_final: 0.8243 (mtmm) outliers start: 55 outliers final: 38 residues processed: 250 average time/residue: 0.1732 time to fit residues: 73.4012 Evaluate side-chains 247 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 200 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain F residue 95 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 129 optimal weight: 10.0000 chunk 271 optimal weight: 10.0000 chunk 264 optimal weight: 9.9990 chunk 302 optimal weight: 0.6980 chunk 279 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 224 optimal weight: 0.8980 chunk 357 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 343 ASN C 360 ASN C1010 GLN D 72 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.204068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.133236 restraints weight = 41718.025| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 3.30 r_work: 0.3325 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 30279 Z= 0.177 Angle : 0.576 9.220 41308 Z= 0.285 Chirality : 0.044 0.266 4868 Planarity : 0.004 0.052 5185 Dihedral : 4.350 21.616 3884 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.01 % Favored : 94.88 % Rotamer: Outliers : 2.04 % Allowed : 15.25 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.14), residues: 3576 helix: 1.89 (0.19), residues: 743 sheet: -0.28 (0.18), residues: 788 loop : -1.27 (0.13), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 70 TYR 0.018 0.001 TYR B1067 PHE 0.016 0.001 PHE B 565 TRP 0.012 0.001 TRP A 64 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (30159) covalent geometry : angle 0.56135 / 0.28 (40998) SS BOND : bond 0.00347 / 0.21 ( 44) SS BOND : angle 1.23674 / 0.83 ( 88) hydrogen bonds : bond 0.04039 / 2.70 ( 1067) hydrogen bonds : angle 5.67464 / 3.85 ( 2976) Misc. bond : bond 0.00168 / 0.09 ( 2) link_ALPHA1-4 : bond 0.00732 / 0.41 ( 6) link_ALPHA1-4 : angle 1.83217 / 1.13 ( 18) link_BETA1-4 : bond 0.00346 / 0.24 ( 26) link_BETA1-4 : angle 1.09864 / 0.71 ( 78) link_BETA1-6 : bond 0.00533 / 0.27 ( 3) link_BETA1-6 : angle 1.15800 / 0.81 ( 9) link_NAG-ASN : bond 0.00320 / 0.22 ( 39) link_NAG-ASN : angle 2.02589 / 1.35 ( 117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 205 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8671 (mt) REVERT: A 140 PHE cc_start: 0.6073 (p90) cc_final: 0.5789 (p90) REVERT: A 271 GLN cc_start: 0.8166 (pm20) cc_final: 0.7850 (pm20) REVERT: A 324 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7393 (tm-30) REVERT: A 338 PHE cc_start: 0.8482 (m-10) cc_final: 0.8160 (m-80) REVERT: A 392 PHE cc_start: 0.7641 (m-80) cc_final: 0.7239 (m-80) REVERT: A 406 GLU cc_start: 0.8608 (mp0) cc_final: 0.8324 (mp0) REVERT: A 462 LYS cc_start: 0.8258 (mmtt) cc_final: 0.7636 (ttpp) REVERT: A 515 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.6411 (p90) REVERT: A 661 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8056 (pm20) REVERT: A 820 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.8008 (t0) REVERT: A 935 GLN cc_start: 0.8787 (pp30) cc_final: 0.8535 (tm-30) REVERT: A 1004 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8896 (tt) REVERT: B 239 GLN cc_start: 0.8059 (tt0) cc_final: 0.7531 (tt0) REVERT: B 271 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.7725 (mp10) REVERT: B 568 ASP cc_start: 0.7860 (t0) cc_final: 0.7405 (t0) REVERT: B 726 ILE cc_start: 0.9214 (OUTLIER) cc_final: 0.8791 (mp) REVERT: C 52 GLN cc_start: 0.8123 (pp30) cc_final: 0.7873 (pp30) REVERT: C 118 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7491 (tp) REVERT: C 537 LYS cc_start: 0.8561 (mmpt) cc_final: 0.8267 (mtmm) outliers start: 64 outliers final: 43 residues processed: 254 average time/residue: 0.1711 time to fit residues: 74.1425 Evaluate side-chains 254 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 202 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain F residue 95 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 233 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 295 optimal weight: 6.9990 chunk 350 optimal weight: 40.0000 chunk 121 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 168 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 259 optimal weight: 9.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C1010 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.202831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.130390 restraints weight = 41533.611| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 3.18 r_work: 0.3297 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 30279 Z= 0.234 Angle : 0.618 9.469 41308 Z= 0.306 Chirality : 0.045 0.272 4868 Planarity : 0.004 0.059 5185 Dihedral : 4.525 22.373 3884 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.17 % Favored : 94.71 % Rotamer: Outliers : 1.91 % Allowed : 15.48 % Favored : 82.61 % 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: -0.63 (0.14), residues: 3576 helix: 1.70 (0.19), residues: 748 sheet: -0.27 (0.18), residues: 781 loop : -1.34 (0.13), residues: 2047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 70 TYR 0.019 0.001 TYR A 423 PHE 0.016 0.002 PHE B 565 TRP 0.010 0.001 TRP B 886 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.23 (30159) covalent geometry : angle 0.60169 / 0.30 (40998) SS BOND : bond 0.00423 / 0.26 ( 44) SS BOND : angle 1.64430 / 1.05 ( 88) hydrogen bonds : bond 0.04366 / 2.92 ( 1067) hydrogen bonds : angle 5.76184 / 3.91 ( 2976) Misc. bond : bond 0.00221 / 0.12 ( 2) link_ALPHA1-4 : bond 0.00678 / 0.38 ( 6) link_ALPHA1-4 : angle 1.92196 / 1.18 ( 18) link_BETA1-4 : bond 0.00328 / 0.24 ( 26) link_BETA1-4 : angle 1.19420 / 0.76 ( 78) link_BETA1-6 : bond 0.00496 / 0.26 ( 3) link_BETA1-6 : angle 1.20718 / 0.85 ( 9) link_NAG-ASN : bond 0.00363 / 0.25 ( 39) link_NAG-ASN : angle 2.11985 / 1.42 ( 117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 199 time to evaluate : 1.111 Fit side-chains revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8640 (mt) REVERT: A 140 PHE cc_start: 0.5998 (p90) cc_final: 0.5723 (p90) REVERT: A 271 GLN cc_start: 0.8076 (pm20) cc_final: 0.7749 (pm20) REVERT: A 324 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7333 (tm-30) REVERT: A 338 PHE cc_start: 0.8486 (m-10) cc_final: 0.8170 (m-80) REVERT: A 392 PHE cc_start: 0.7530 (m-80) cc_final: 0.7117 (m-80) REVERT: A 406 GLU cc_start: 0.8614 (mp0) cc_final: 0.8315 (mp0) REVERT: A 515 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.6360 (p90) REVERT: A 935 GLN cc_start: 0.8725 (pp30) cc_final: 0.8468 (tm-30) REVERT: A 1004 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8897 (tt) REVERT: B 239 GLN cc_start: 0.7936 (tt0) cc_final: 0.7361 (tt0) REVERT: B 271 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.7672 (mp10) REVERT: B 568 ASP cc_start: 0.7712 (t0) cc_final: 0.7171 (t0) REVERT: B 726 ILE cc_start: 0.9214 (OUTLIER) cc_final: 0.8759 (mp) REVERT: C 52 GLN cc_start: 0.8115 (pp30) cc_final: 0.7882 (pp30) REVERT: C 118 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7517 (tp) REVERT: C 537 LYS cc_start: 0.8567 (mmpt) cc_final: 0.8249 (mtmm) REVERT: C 1010 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8304 (pt0) outliers start: 60 outliers final: 45 residues processed: 243 average time/residue: 0.1676 time to fit residues: 69.2655 Evaluate side-chains 251 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 198 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain F residue 95 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 45 optimal weight: 7.9990 chunk 201 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 181 optimal weight: 0.4980 chunk 168 optimal weight: 0.8980 chunk 195 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 337 optimal weight: 10.0000 chunk 304 optimal weight: 0.8980 chunk 42 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 388 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C1010 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.206072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.135943 restraints weight = 41445.967| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 3.14 r_work: 0.3379 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 30279 Z= 0.106 Angle : 0.543 9.978 41308 Z= 0.270 Chirality : 0.043 0.270 4868 Planarity : 0.003 0.050 5185 Dihedral : 4.227 20.817 3884 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.36 % Favored : 95.53 % Rotamer: Outliers : 1.46 % Allowed : 15.99 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.14), residues: 3576 helix: 2.04 (0.19), residues: 743 sheet: -0.32 (0.18), residues: 781 loop : -1.19 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 70 TYR 0.016 0.001 TYR A1067 PHE 0.018 0.001 PHE B 565 TRP 0.017 0.001 TRP A 436 HIS 0.004 0.000 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (30159) covalent geometry : angle 0.52984 / 0.27 (40998) SS BOND : bond 0.00281 / 0.16 ( 44) SS BOND : angle 1.21263 / 0.78 ( 88) hydrogen bonds : bond 0.03583 / 2.37 ( 1067) hydrogen bonds : angle 5.48714 / 3.72 ( 2976) Misc. bond : bond 0.00107 / 0.06 ( 2) link_ALPHA1-4 : bond 0.00744 / 0.43 ( 6) link_ALPHA1-4 : angle 1.66280 / 1.02 ( 18) link_BETA1-4 : bond 0.00431 / 0.28 ( 26) link_BETA1-4 : angle 0.97531 / 0.64 ( 78) link_BETA1-6 : bond 0.00589 / 0.30 ( 3) link_BETA1-6 : angle 1.09342 / 0.74 ( 9) link_NAG-ASN : bond 0.00322 / 0.22 ( 39) link_NAG-ASN : angle 1.89704 / 1.25 ( 117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 216 time to evaluate : 0.895 Fit side-chains revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8687 (mt) REVERT: A 49 HIS cc_start: 0.8575 (t-170) cc_final: 0.8338 (t-170) REVERT: A 140 PHE cc_start: 0.6011 (p90) cc_final: 0.5732 (p90) REVERT: A 324 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7388 (tm-30) REVERT: A 338 PHE cc_start: 0.8473 (m-10) cc_final: 0.8220 (m-80) REVERT: A 392 PHE cc_start: 0.7566 (m-80) cc_final: 0.7154 (m-80) REVERT: A 406 GLU cc_start: 0.8631 (mp0) cc_final: 0.8370 (mp0) REVERT: A 515 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.6326 (p90) REVERT: A 661 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7977 (pm20) REVERT: A 935 GLN cc_start: 0.8760 (pp30) cc_final: 0.8516 (tm-30) REVERT: B 239 GLN cc_start: 0.7969 (tt0) cc_final: 0.7576 (mt0) REVERT: B 568 ASP cc_start: 0.7757 (t0) cc_final: 0.7255 (t0) REVERT: C 52 GLN cc_start: 0.8038 (pp30) cc_final: 0.7814 (pp30) REVERT: C 118 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7504 (tp) REVERT: C 269 TYR cc_start: 0.7367 (m-80) cc_final: 0.6711 (m-80) REVERT: C 537 LYS cc_start: 0.8577 (mmpt) cc_final: 0.8251 (mtmm) outliers start: 46 outliers final: 36 residues processed: 253 average time/residue: 0.1681 time to fit residues: 72.1790 Evaluate side-chains 244 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 203 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain F residue 95 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 80 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 210 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 319 optimal weight: 3.9990 chunk 341 optimal weight: 20.0000 chunk 102 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 chunk 239 optimal weight: 20.0000 chunk 101 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN ** B1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 564 GLN C 774 GLN C1010 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.204910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.134311 restraints weight = 41683.345| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 3.20 r_work: 0.3354 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 30279 Z= 0.142 Angle : 0.554 9.659 41308 Z= 0.274 Chirality : 0.043 0.266 4868 Planarity : 0.003 0.049 5185 Dihedral : 4.233 20.153 3884 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.56 % Favored : 95.33 % Rotamer: Outliers : 1.50 % Allowed : 16.18 % Favored : 82.32 % 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: -0.44 (0.14), residues: 3576 helix: 1.99 (0.19), residues: 744 sheet: -0.29 (0.18), residues: 807 loop : -1.21 (0.13), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 70 TYR 0.018 0.001 TYR B1067 PHE 0.017 0.001 PHE B 565 TRP 0.011 0.001 TRP A 436 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (30159) covalent geometry : angle 0.54022 / 0.27 (40998) SS BOND : bond 0.00318 / 0.19 ( 44) SS BOND : angle 1.25896 / 0.81 ( 88) hydrogen bonds : bond 0.03788 / 2.53 ( 1067) hydrogen bonds : angle 5.48131 / 3.72 ( 2976) Misc. bond : bond 0.00135 / 0.07 ( 2) link_ALPHA1-4 : bond 0.00709 / 0.40 ( 6) link_ALPHA1-4 : angle 1.75202 / 1.08 ( 18) link_BETA1-4 : bond 0.00356 / 0.25 ( 26) link_BETA1-4 : angle 1.05792 / 0.68 ( 78) link_BETA1-6 : bond 0.00558 / 0.29 ( 3) link_BETA1-6 : angle 1.13387 / 0.78 ( 9) link_NAG-ASN : bond 0.00301 / 0.21 ( 39) link_NAG-ASN : angle 1.93240 / 1.28 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10853.77 seconds wall clock time: 185 minutes 35.07 seconds (11135.07 seconds total)