Starting phenix.real_space_refine on Sun Jul 5 19:05:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xic_33202/07_2026/7xic_33202.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xic_33202/07_2026/7xic_33202.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7xic_33202/07_2026/7xic_33202.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xic_33202/07_2026/7xic_33202.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xic_33202/07_2026/7xic_33202.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xic_33202/07_2026/7xic_33202.map" model { file = "/net/cci-nas-00/data/ceres_data/7xic_33202/07_2026/7xic_33202.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xic_33202/07_2026/7xic_33202.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.085 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 135 5.16 5 C 19039 2.51 5 N 4908 2.21 5 O 5859 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 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: 29941 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 7848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 999, 7848 Classifications: {'peptide': 999} Link IDs: {'PTRANS': 54, 'TRANS': 944} Chain breaks: 9 Chain: "B" Number of atoms: 7842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7842 Classifications: {'peptide': 998} Link IDs: {'PTRANS': 54, 'TRANS': 943} Chain breaks: 9 Chain: "C" Number of atoms: 7842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7842 Classifications: {'peptide': 998} Link IDs: {'PTRANS': 54, 'TRANS': 943} Chain breaks: 9 Chain: "E" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 968 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "F" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 837 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 100} Chain: "H" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 968 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "I" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 837 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 100} Chain: "K" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 968 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "L" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 837 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 100} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "C" 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 Time building chain proxies: 7.22, per 1000 atoms: 0.24 Number of scatterers: 29941 At special positions: 0 Unit cell: (168.485, 160.876, 194.573, 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 135 16.00 O 5859 8.00 N 4908 7.00 C 19039 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.19 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=1.97 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.12 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.00 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.15 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.07 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.15 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.15 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.12 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.18 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.07 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.14 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.10 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.12 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.00 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.14 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.07 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.20 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=1.99 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.17 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.26 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=1.97 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.17 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.10 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.09 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.18 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.12 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.00 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.09 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.07 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.01 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.06 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.05 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.08 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.20 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 102 " - pdb=" SG CYS E 106 " distance=2.09 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 102 " - pdb=" SG CYS H 106 " distance=2.09 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 102 " - pdb=" SG CYS K 106 " distance=2.09 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A1406 " - " NAG A1407 " " NAG B1406 " - " NAG B1407 " " NAG B1411 " - " NAG B1412 " " NAG C1406 " - " NAG C1407 " " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG J 1 " - " NAG J 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-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 343 " " NAG A1408 " - " ASN A 603 " " NAG A1409 " - " ASN A 616 " " NAG A1410 " - " ASN A 657 " " NAG A1411 " - " ASN A 709 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 343 " " NAG B1408 " - " ASN B 603 " " NAG B1409 " - " ASN B 616 " " NAG B1410 " - " ASN B 657 " " NAG B1411 " - " ASN B1074 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 343 " " NAG C1408 " - " ASN C 603 " " NAG C1409 " - " ASN C 616 " " NAG C1410 " - " ASN C 657 " " NAG D 1 " - " ASN A 331 " " NAG G 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1074 " " NAG N 1 " - " ASN A1098 " " NAG O 1 " - " ASN A1134 " " NAG P 1 " - " ASN B 331 " " NAG Q 1 " - " ASN B 709 " " NAG R 1 " - " ASN B 717 " " NAG S 1 " - " ASN B 801 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 331 " " NAG W 1 " - " ASN C 709 " " NAG X 1 " - " ASN C 717 " " NAG Y 1 " - " ASN C 801 " " NAG Z 1 " - " ASN C1074 " " NAG a 1 " - " ASN C1098 " " NAG b 1 " - " ASN C1134 " Time building additional restraints: 2.78 Conformation dependent library (CDL) restraints added in 1.3 seconds 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6884 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 60 sheets defined 22.5% alpha, 33.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.689A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A 368 " --> pdb=" O TYR A 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 364 through 368' Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.479A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.542A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.530A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.790A pdb=" N LYS A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.701A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.252A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 932 Processing helix chain 'A' and resid 933 through 940 Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.761A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 968 removed outlier: 3.702A pdb=" N SER A 968 " --> pdb=" O GLN A 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 965 through 968' Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.757A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.982A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.686A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU B 368 " --> pdb=" O TYR B 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 364 through 368' Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.479A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.542A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 removed outlier: 4.087A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.985A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 removed outlier: 3.589A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.514A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.576A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.651A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.591A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 4.078A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.757A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 983 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.323A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.688A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU C 368 " --> pdb=" O TYR C 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 364 through 368' Processing helix chain 'C' and resid 383 through 388 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.478A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.542A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 753 Processing helix chain 'C' and resid 754 through 756 No H-bonds generated for 'chain 'C' and resid 754 through 756' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.612A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.655A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 933 Processing helix chain 'C' and resid 933 through 939 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.322A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 981 removed outlier: 3.810A pdb=" N PHE C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.931A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 50 through 52 No H-bonds generated for 'chain 'F' and resid 50 through 52' Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.895A pdb=" N PHE F 83 " --> pdb=" O SER F 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 50 through 52 No H-bonds generated for 'chain 'I' and resid 50 through 52' Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.896A pdb=" N PHE I 83 " --> pdb=" O SER I 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 87 through 91 Processing helix chain 'L' and resid 50 through 52 No H-bonds generated for 'chain 'L' and resid 50 through 52' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.896A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.514A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 7.395A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.326A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 92 removed outlier: 6.306A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.469A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 323 through 328 removed outlier: 5.676A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.962A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.292A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.753A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.753A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.485A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.768A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.851A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.589A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 49 through 55 removed outlier: 7.471A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.512A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.696A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER B 596 " --> pdb=" O LEU B 611 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU B 611 " --> pdb=" O SER B 596 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 323 through 328 removed outlier: 5.857A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.962A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.239A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.577A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.546A pdb=" N ASN B 703 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.152A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.152A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.499A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.943A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.685A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 49 through 55 removed outlier: 7.498A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.421A 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: 6.887A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.924A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU C 117 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLU C 132 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 90 through 92 removed outlier: 3.738A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.478A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 323 through 328 removed outlier: 5.456A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.962A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.307A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.892A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.892A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.301A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE7, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AE8, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.286A pdb=" N GLY E 33 " --> pdb=" O VAL E 99 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.629A pdb=" N TYR E 117 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.551A pdb=" N GLU F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.528A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 10 through 13 Processing sheet with id=AF4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.287A pdb=" N GLY H 33 " --> pdb=" O VAL H 99 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.630A pdb=" N TYR H 117 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.550A pdb=" N GLU I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.528A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 10 through 13 Processing sheet with id=AG1, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AG2, first strand: chain 'K' and resid 10 through 12 removed outlier: 4.286A pdb=" N GLY K 33 " --> pdb=" O VAL K 99 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N MET K 34 " --> pdb=" O GLY K 50 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLY K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.630A pdb=" N TYR K 117 " --> pdb=" O ARG K 98 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.550A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.528A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 10 through 13 1181 hydrogen bonds defined for protein. 3117 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: 8.32 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6644 1.33 - 1.45: 8265 1.45 - 1.58: 15539 1.58 - 1.71: 0 1.71 - 1.84: 171 Bond restraints: 30619 Sorted by residual: bond pdb=" CA SER A 698 " pdb=" C SER A 698 " ideal model delta sigma weight residual 1.522 1.442 0.080 1.20e-02 6.94e+03 4.40e+01 bond pdb=" C THR C 208 " pdb=" N PRO C 209 " ideal model delta sigma weight residual 1.329 1.387 -0.058 1.20e-02 6.94e+03 2.36e+01 bond pdb=" C THR A 208 " pdb=" N PRO A 209 " ideal model delta sigma weight residual 1.329 1.386 -0.057 1.25e-02 6.40e+03 2.07e+01 bond pdb=" C THR B 208 " pdb=" N PRO B 209 " ideal model delta sigma weight residual 1.329 1.386 -0.057 1.25e-02 6.40e+03 2.05e+01 bond pdb=" N PRO B 521 " pdb=" CD PRO B 521 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.87e+01 ... (remaining 30614 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 39963 2.63 - 5.26: 1533 5.26 - 7.89: 94 7.89 - 10.53: 18 10.53 - 13.16: 12 Bond angle restraints: 41620 Sorted by residual: angle pdb=" N PHE A 375 " pdb=" CA PHE A 375 " pdb=" C PHE A 375 " ideal model delta sigma weight residual 110.28 123.15 -12.87 1.48e+00 4.57e-01 7.56e+01 angle pdb=" N PHE C 375 " pdb=" CA PHE C 375 " pdb=" C PHE C 375 " ideal model delta sigma weight residual 110.28 123.14 -12.86 1.48e+00 4.57e-01 7.55e+01 angle pdb=" N PHE B 375 " pdb=" CA PHE B 375 " pdb=" C PHE B 375 " ideal model delta sigma weight residual 110.28 123.12 -12.84 1.48e+00 4.57e-01 7.53e+01 angle pdb=" N ILE A 794 " pdb=" CA ILE A 794 " pdb=" C ILE A 794 " ideal model delta sigma weight residual 110.05 103.16 6.89 1.09e+00 8.42e-01 3.99e+01 angle pdb=" C THR C 208 " pdb=" N PRO C 209 " pdb=" CA PRO C 209 " ideal model delta sigma weight residual 120.31 114.31 6.00 9.80e-01 1.04e+00 3.75e+01 ... (remaining 41615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 16699 17.67 - 35.34: 684 35.34 - 53.02: 175 53.02 - 70.69: 55 70.69 - 88.36: 28 Dihedral angle restraints: 17641 sinusoidal: 6907 harmonic: 10734 Sorted by residual: 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 -16.74 -69.26 1 1.00e+01 1.00e-02 6.20e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -23.70 -62.30 1 1.00e+01 1.00e-02 5.14e+01 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 -132.52 46.52 1 1.00e+01 1.00e-02 2.99e+01 ... (remaining 17638 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.330: 4837 0.330 - 0.660: 6 0.660 - 0.990: 6 0.990 - 1.321: 3 1.321 - 1.651: 1 Chirality restraints: 4853 Sorted by residual: chirality pdb=" C1 NAG C1407 " pdb=" O4 NAG C1406 " pdb=" C2 NAG C1407 " pdb=" O5 NAG C1407 " both_signs ideal model delta sigma weight residual False -2.40 -1.40 -1.00 2.00e-02 2.50e+03 2.52e+03 chirality pdb=" C1 NAG A1407 " pdb=" O4 NAG A1406 " pdb=" C2 NAG A1407 " pdb=" O5 NAG A1407 " both_signs ideal model delta sigma weight residual False -2.40 -1.40 -1.00 2.00e-02 2.50e+03 2.52e+03 chirality pdb=" C1 NAG B1407 " pdb=" O4 NAG B1406 " pdb=" C2 NAG B1407 " pdb=" O5 NAG B1407 " both_signs ideal model delta sigma weight residual False -2.40 -1.40 -1.00 2.00e-02 2.50e+03 2.50e+03 ... (remaining 4850 not shown) Planarity restraints: 5337 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " 0.252 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" CG ASN C 331 " -0.104 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " -0.041 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " -0.480 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " 0.372 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " 0.197 2.00e-02 2.50e+03 2.43e-01 7.41e+02 pdb=" CG ASN A 343 " -0.077 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " -0.415 2.00e-02 2.50e+03 pdb=" C1 NAG A1406 " 0.281 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 343 " 0.197 2.00e-02 2.50e+03 2.43e-01 7.40e+02 pdb=" CG ASN C 343 " -0.077 2.00e-02 2.50e+03 pdb=" OD1 ASN C 343 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN C 343 " -0.415 2.00e-02 2.50e+03 pdb=" C1 NAG C1406 " 0.281 2.00e-02 2.50e+03 ... (remaining 5334 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 102 2.53 - 3.12: 22539 3.12 - 3.71: 42510 3.71 - 4.31: 65103 4.31 - 4.90: 105803 Nonbonded interactions: 236057 Sorted by model distance: nonbonded pdb=" O ARG A 328 " pdb=" CD1 PHE A 329 " model vdw 1.933 3.340 nonbonded pdb=" O ASN B 334 " pdb=" O VAL B 362 " model vdw 2.210 3.040 nonbonded pdb=" CG PRO B 521 " pdb=" OH TYR C 200 " model vdw 2.233 3.440 nonbonded pdb=" O GLY H 104 " pdb=" N CYS H 106 " model vdw 2.238 3.120 nonbonded pdb=" O GLY K 104 " pdb=" N CYS K 106 " model vdw 2.238 3.120 ... (remaining 236052 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 939 or resid 944 through 1410)) selection = (chain 'B' and resid 27 through 1410) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'L' } 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: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.620 Check model and map are aligned: 0.140 Set scattering table: 0.070 Process input model: 30.530 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6481 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.232 30738 Z= 0.586 Angle : 1.427 48.957 41929 Z= 0.781 Chirality : 0.080 1.651 4853 Planarity : 0.007 0.098 5289 Dihedral : 11.357 88.361 10613 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 1.84 % Allowed : 5.64 % Favored : 92.52 % Rotamer: Outliers : 1.40 % Allowed : 2.46 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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: -2.01 (0.13), residues: 3634 helix: -1.27 (0.17), residues: 676 sheet: -0.43 (0.15), residues: 966 loop : -1.85 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 54 TYR 0.070 0.004 TYR L 36 PHE 0.034 0.002 PHE K 29 TRP 0.130 0.012 TRP H 53 HIS 0.006 0.001 HIS E 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00949 / 0.55 (30619) covalent geometry : angle 1.13861 / 0.71 (41620) SS BOND : bond 0.08732 / 5.47 ( 48) SS BOND : angle 11.18266 / 7.20 ( 96) hydrogen bonds : bond 0.20544 / 13.52 ( 1116) hydrogen bonds : angle 8.57384 / 5.88 ( 3117) link_BETA1-4 : bond 0.06777 / 4.89 ( 23) link_BETA1-4 : angle 11.54640 / 7.46 ( 69) link_NAG-ASN : bond 0.04573 / 2.99 ( 48) link_NAG-ASN : angle 8.44113 / 5.45 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 452 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ILE cc_start: 0.7706 (mm) cc_final: 0.7505 (tp) REVERT: B 408 ARG cc_start: 0.1885 (OUTLIER) cc_final: 0.1148 (ptm160) REVERT: B 569 ILE cc_start: 0.8825 (tt) cc_final: 0.8519 (tt) outliers start: 45 outliers final: 13 residues processed: 497 average time/residue: 0.1987 time to fit residues: 156.7649 Evaluate side-chains 220 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 206 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 102 CYS Chi-restraints excluded: chain H residue 99 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 5.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 HIS A 207 HIS A 239 GLN A 388 ASN A1088 HIS B 52 GLN B 239 GLN B 388 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN C 321 GLN C 388 ASN C 690 GLN C 907 ASN C 913 GLN C 992 GLN C1010 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.204614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.136618 restraints weight = 54281.403| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 4.83 r_work: 0.3524 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.133 30738 Z= 0.238 Angle : 0.853 15.801 41929 Z= 0.420 Chirality : 0.052 0.433 4853 Planarity : 0.006 0.062 5289 Dihedral : 5.772 59.022 4021 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.37 % Favored : 94.41 % Rotamer: Outliers : 2.49 % Allowed : 6.58 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.13), residues: 3634 helix: 0.01 (0.20), residues: 659 sheet: -0.62 (0.16), residues: 965 loop : -1.40 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 995 TYR 0.027 0.002 TYR B 369 PHE 0.035 0.003 PHE B 823 TRP 0.020 0.002 TRP H 53 HIS 0.007 0.002 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.24 (30619) covalent geometry : angle 0.81232 / 0.41 (41620) SS BOND : bond 0.00673 / 0.40 ( 48) SS BOND : angle 3.21093 / 2.12 ( 96) hydrogen bonds : bond 0.05392 / 3.61 ( 1116) hydrogen bonds : angle 6.12393 / 4.23 ( 3117) link_BETA1-4 : bond 0.01318 / 0.90 ( 23) link_BETA1-4 : angle 2.77308 / 1.97 ( 69) link_NAG-ASN : bond 0.01039 / 0.77 ( 48) link_NAG-ASN : angle 3.23486 / 2.17 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 213 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6551 (mpp) cc_final: 0.5145 (tpt) REVERT: A 207 HIS cc_start: 0.7261 (OUTLIER) cc_final: 0.6769 (m90) REVERT: A 654 GLU cc_start: 0.8400 (tt0) cc_final: 0.8133 (tp30) REVERT: A 787 GLN cc_start: 0.8645 (mp10) cc_final: 0.8417 (mp10) REVERT: A 820 ASP cc_start: 0.8622 (t70) cc_final: 0.8378 (t0) REVERT: A 979 ASP cc_start: 0.8232 (t0) cc_final: 0.7990 (t70) REVERT: A 1002 GLN cc_start: 0.7727 (mm110) cc_final: 0.7516 (mm110) REVERT: B 58 PHE cc_start: 0.7995 (m-10) cc_final: 0.7770 (m-80) REVERT: B 331 ASN cc_start: 0.2395 (OUTLIER) cc_final: 0.2012 (m-40) REVERT: B 332 ILE cc_start: 0.6274 (OUTLIER) cc_final: 0.5679 (mp) REVERT: B 376 THR cc_start: 0.2051 (OUTLIER) cc_final: 0.1769 (p) REVERT: B 407 VAL cc_start: 0.1207 (OUTLIER) cc_final: 0.0859 (m) REVERT: B 755 GLN cc_start: 0.8620 (mm110) cc_final: 0.7696 (pt0) REVERT: B 902 MET cc_start: 0.8655 (tpt) cc_final: 0.8313 (tpt) REVERT: B 955 ASN cc_start: 0.8250 (m-40) cc_final: 0.7969 (m-40) REVERT: C 204 TYR cc_start: 0.7799 (m-80) cc_final: 0.7388 (m-80) REVERT: C 725 GLU cc_start: 0.7748 (tt0) cc_final: 0.7478 (tt0) REVERT: L 33 LEU cc_start: 0.4445 (tt) cc_final: 0.4237 (tp) REVERT: L 98 THR cc_start: 0.3553 (m) cc_final: 0.2935 (p) outliers start: 80 outliers final: 44 residues processed: 285 average time/residue: 0.1876 time to fit residues: 87.3024 Evaluate side-chains 208 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 159 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 313 TYR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain K residue 48 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 360 optimal weight: 5.9990 chunk 275 optimal weight: 0.5980 chunk 185 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 290 optimal weight: 2.9990 chunk 37 optimal weight: 40.0000 chunk 351 optimal weight: 8.9990 chunk 265 optimal weight: 3.9990 chunk 215 optimal weight: 8.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B 913 GLN C 690 GLN C 762 GLN C 907 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.204122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.137273 restraints weight = 53744.416| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 4.72 r_work: 0.3498 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 30738 Z= 0.144 Angle : 0.675 16.537 41929 Z= 0.330 Chirality : 0.046 0.345 4853 Planarity : 0.005 0.050 5289 Dihedral : 5.079 57.975 4008 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.51 % Favored : 95.27 % Rotamer: Outliers : 2.31 % Allowed : 7.86 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.13), residues: 3634 helix: 0.72 (0.20), residues: 672 sheet: -0.34 (0.16), residues: 942 loop : -1.15 (0.13), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 983 TYR 0.018 0.001 TYR L 91 PHE 0.024 0.002 PHE C 329 TRP 0.019 0.001 TRP H 53 HIS 0.011 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (30619) covalent geometry : angle 0.64280 / 0.32 (41620) SS BOND : bond 0.00705 / 0.51 ( 48) SS BOND : angle 2.49510 / 1.59 ( 96) hydrogen bonds : bond 0.04405 / 2.98 ( 1116) hydrogen bonds : angle 5.63854 / 3.89 ( 3117) link_BETA1-4 : bond 0.00712 / 0.40 ( 23) link_BETA1-4 : angle 2.01037 / 1.31 ( 69) link_NAG-ASN : bond 0.00434 / 0.29 ( 48) link_NAG-ASN : angle 2.66366 / 1.76 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 186 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6674 (mpp) cc_final: 0.5916 (ttp) REVERT: A 207 HIS cc_start: 0.6776 (OUTLIER) cc_final: 0.6121 (m90) REVERT: A 377 PHE cc_start: 0.3968 (OUTLIER) cc_final: 0.3619 (m-80) REVERT: A 654 GLU cc_start: 0.8345 (tt0) cc_final: 0.8092 (tp30) REVERT: A 787 GLN cc_start: 0.8595 (mp10) cc_final: 0.8270 (mp10) REVERT: A 820 ASP cc_start: 0.8609 (t70) cc_final: 0.8254 (t0) REVERT: A 1002 GLN cc_start: 0.7674 (mm110) cc_final: 0.7464 (mm110) REVERT: B 755 GLN cc_start: 0.8723 (mm110) cc_final: 0.7803 (pt0) REVERT: B 955 ASN cc_start: 0.8184 (m-40) cc_final: 0.7960 (m-40) REVERT: C 204 TYR cc_start: 0.7913 (m-80) cc_final: 0.6999 (m-80) REVERT: C 725 GLU cc_start: 0.7872 (tt0) cc_final: 0.7636 (tt0) REVERT: C 959 LEU cc_start: 0.8864 (mt) cc_final: 0.8527 (tp) REVERT: C 965 GLN cc_start: 0.8288 (mm110) cc_final: 0.8023 (tp40) REVERT: E 105 ASP cc_start: -0.2340 (OUTLIER) cc_final: -0.2635 (m-30) outliers start: 74 outliers final: 40 residues processed: 252 average time/residue: 0.1836 time to fit residues: 76.5078 Evaluate side-chains 200 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 157 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain K residue 48 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 310 optimal weight: 6.9990 chunk 264 optimal weight: 1.9990 chunk 220 optimal weight: 0.8980 chunk 288 optimal weight: 0.8980 chunk 119 optimal weight: 0.0770 chunk 2 optimal weight: 6.9990 chunk 253 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 270 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 141 optimal weight: 40.0000 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS B 544 ASN B 907 ASN B1135 ASN C 690 GLN C 762 GLN C 907 ASN I 92 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.203087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.129233 restraints weight = 53805.858| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 4.38 r_work: 0.3430 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 30738 Z= 0.130 Angle : 0.628 10.256 41929 Z= 0.308 Chirality : 0.045 0.310 4853 Planarity : 0.004 0.060 5289 Dihedral : 4.763 48.424 4002 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.68 % Favored : 95.13 % Rotamer: Outliers : 2.09 % Allowed : 8.42 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.14), residues: 3634 helix: 1.07 (0.21), residues: 662 sheet: -0.26 (0.16), residues: 965 loop : -1.02 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 983 TYR 0.018 0.001 TYR I 91 PHE 0.021 0.001 PHE C 329 TRP 0.016 0.001 TRP H 53 HIS 0.003 0.001 HIS A 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (30619) covalent geometry : angle 0.59947 / 0.30 (41620) SS BOND : bond 0.00682 / 0.42 ( 48) SS BOND : angle 2.33917 / 1.51 ( 96) hydrogen bonds : bond 0.03888 / 2.63 ( 1116) hydrogen bonds : angle 5.36419 / 3.72 ( 3117) link_BETA1-4 : bond 0.00586 / 0.32 ( 23) link_BETA1-4 : angle 1.84723 / 1.20 ( 69) link_NAG-ASN : bond 0.00371 / 0.24 ( 48) link_NAG-ASN : angle 2.38204 / 1.56 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 175 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6756 (mpp) cc_final: 0.5985 (ttp) REVERT: A 207 HIS cc_start: 0.6721 (OUTLIER) cc_final: 0.6114 (m90) REVERT: A 377 PHE cc_start: 0.3973 (OUTLIER) cc_final: 0.3667 (m-80) REVERT: A 787 GLN cc_start: 0.8651 (mp10) cc_final: 0.8331 (mp10) REVERT: A 820 ASP cc_start: 0.8560 (t70) cc_final: 0.7963 (m-30) REVERT: B 558 LYS cc_start: 0.6869 (tmtt) cc_final: 0.6638 (tmtt) REVERT: B 580 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.6931 (mp10) REVERT: B 755 GLN cc_start: 0.8701 (mm110) cc_final: 0.7934 (pt0) REVERT: B 955 ASN cc_start: 0.8126 (m-40) cc_final: 0.7886 (m-40) REVERT: C 204 TYR cc_start: 0.7900 (m-80) cc_final: 0.6907 (m-80) REVERT: C 725 GLU cc_start: 0.7904 (tt0) cc_final: 0.7658 (tt0) REVERT: C 965 GLN cc_start: 0.8346 (mm110) cc_final: 0.8065 (tp40) REVERT: E 105 ASP cc_start: -0.2467 (OUTLIER) cc_final: -0.2729 (m-30) outliers start: 67 outliers final: 45 residues processed: 230 average time/residue: 0.1577 time to fit residues: 61.6511 Evaluate side-chains 202 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 153 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain I residue 92 ASN Chi-restraints excluded: chain K residue 48 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 214 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 123 optimal weight: 20.0000 chunk 206 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 268 optimal weight: 0.6980 chunk 196 optimal weight: 3.9990 chunk 299 optimal weight: 20.0000 chunk 20 optimal weight: 7.9990 chunk 300 optimal weight: 40.0000 chunk 68 optimal weight: 3.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 245 HIS A 271 GLN B 580 GLN B 914 ASN C 690 GLN C 762 GLN C 907 ASN C1071 GLN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.195787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.122553 restraints weight = 53735.881| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 4.37 r_work: 0.3365 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.5048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.112 30738 Z= 0.312 Angle : 0.793 16.814 41929 Z= 0.396 Chirality : 0.050 0.291 4853 Planarity : 0.005 0.048 5289 Dihedral : 5.124 51.000 4000 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.38 % Favored : 93.42 % Rotamer: Outliers : 2.77 % Allowed : 8.63 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.13), residues: 3634 helix: 0.59 (0.20), residues: 655 sheet: -0.53 (0.16), residues: 960 loop : -1.21 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 983 TYR 0.024 0.002 TYR C 873 PHE 0.032 0.003 PHE C 275 TRP 0.020 0.002 TRP B 64 HIS 0.026 0.002 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00758 / 0.31 (30619) covalent geometry : angle 0.76266 / 0.39 (41620) SS BOND : bond 0.00740 / 0.43 ( 48) SS BOND : angle 3.14542 / 2.32 ( 96) hydrogen bonds : bond 0.05402 / 3.64 ( 1116) hydrogen bonds : angle 5.70900 / 3.94 ( 3117) link_BETA1-4 : bond 0.00564 / 0.29 ( 23) link_BETA1-4 : angle 1.90461 / 1.24 ( 69) link_NAG-ASN : bond 0.00476 / 0.32 ( 48) link_NAG-ASN : angle 2.60052 / 1.69 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 161 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.6572 (m-90) cc_final: 0.6181 (m-90) REVERT: A 153 MET cc_start: 0.6926 (mpp) cc_final: 0.6039 (ttp) REVERT: A 377 PHE cc_start: 0.4061 (OUTLIER) cc_final: 0.3498 (m-80) REVERT: A 787 GLN cc_start: 0.9029 (mp10) cc_final: 0.8557 (mp10) REVERT: A 1002 GLN cc_start: 0.7884 (mm110) cc_final: 0.7547 (mm110) REVERT: B 200 TYR cc_start: 0.7169 (m-80) cc_final: 0.6886 (m-80) REVERT: B 755 GLN cc_start: 0.8760 (mm110) cc_final: 0.7965 (pt0) REVERT: B 762 GLN cc_start: 0.7904 (tp40) cc_final: 0.7587 (tp40) REVERT: B 955 ASN cc_start: 0.8277 (m-40) cc_final: 0.8019 (m-40) REVERT: B 1092 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7463 (mm-30) REVERT: C 153 MET cc_start: 0.2448 (tmm) cc_final: 0.2248 (tmm) REVERT: C 204 TYR cc_start: 0.8198 (m-80) cc_final: 0.7475 (m-80) REVERT: C 725 GLU cc_start: 0.8003 (tt0) cc_final: 0.7723 (tt0) REVERT: C 959 LEU cc_start: 0.8997 (mt) cc_final: 0.8777 (tp) outliers start: 89 outliers final: 61 residues processed: 237 average time/residue: 0.1741 time to fit residues: 69.7743 Evaluate side-chains 198 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 136 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain K residue 48 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 340 optimal weight: 30.0000 chunk 337 optimal weight: 8.9990 chunk 184 optimal weight: 0.9990 chunk 296 optimal weight: 7.9990 chunk 323 optimal weight: 50.0000 chunk 167 optimal weight: 0.6980 chunk 242 optimal weight: 7.9990 chunk 126 optimal weight: 20.0000 chunk 251 optimal weight: 1.9990 chunk 349 optimal weight: 20.0000 chunk 81 optimal weight: 0.4980 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 690 GLN A 762 GLN B 580 GLN C 690 GLN C 762 GLN C 907 ASN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.196704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.124601 restraints weight = 53528.785| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 4.89 r_work: 0.3316 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.5319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 30738 Z= 0.184 Angle : 0.672 12.322 41929 Z= 0.333 Chirality : 0.046 0.279 4853 Planarity : 0.005 0.052 5289 Dihedral : 4.870 49.430 3998 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.98 % Favored : 94.85 % Rotamer: Outliers : 1.93 % Allowed : 10.01 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.14), residues: 3634 helix: 0.78 (0.21), residues: 652 sheet: -0.54 (0.16), residues: 954 loop : -1.11 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 983 TYR 0.020 0.001 TYR A1067 PHE 0.022 0.002 PHE A 86 TRP 0.014 0.001 TRP H 53 HIS 0.007 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.18 (30619) covalent geometry : angle 0.64505 / 0.32 (41620) SS BOND : bond 0.00441 / 0.27 ( 48) SS BOND : angle 2.62404 / 1.75 ( 96) hydrogen bonds : bond 0.04407 / 2.97 ( 1116) hydrogen bonds : angle 5.44004 / 3.76 ( 3117) link_BETA1-4 : bond 0.00605 / 0.33 ( 23) link_BETA1-4 : angle 1.74144 / 1.13 ( 69) link_NAG-ASN : bond 0.00344 / 0.22 ( 48) link_NAG-ASN : angle 2.29698 / 1.48 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 153 time to evaluate : 0.820 Fit side-chains revert: symmetry clash REVERT: A 104 TRP cc_start: 0.6431 (m-90) cc_final: 0.5116 (m-90) REVERT: A 140 PHE cc_start: 0.4894 (OUTLIER) cc_final: 0.4123 (m-80) REVERT: A 153 MET cc_start: 0.6756 (mpp) cc_final: 0.6043 (ttp) REVERT: A 191 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7372 (mp0) REVERT: A 377 PHE cc_start: 0.3855 (OUTLIER) cc_final: 0.3388 (m-80) REVERT: A 787 GLN cc_start: 0.9042 (mp10) cc_final: 0.8566 (mp10) REVERT: A 820 ASP cc_start: 0.8588 (t70) cc_final: 0.8147 (m-30) REVERT: A 1029 MET cc_start: 0.9066 (tpp) cc_final: 0.8774 (tpp) REVERT: B 580 GLN cc_start: 0.8008 (mt0) cc_final: 0.7679 (mp10) REVERT: B 755 GLN cc_start: 0.8765 (mm110) cc_final: 0.7985 (pt0) REVERT: B 955 ASN cc_start: 0.8284 (m-40) cc_final: 0.8044 (m-40) REVERT: B 1092 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7535 (mm-30) REVERT: C 204 TYR cc_start: 0.8166 (m-80) cc_final: 0.7382 (m-80) REVERT: C 725 GLU cc_start: 0.8049 (tt0) cc_final: 0.7776 (tt0) REVERT: C 959 LEU cc_start: 0.8907 (mt) cc_final: 0.8598 (tp) REVERT: L 4 MET cc_start: 0.2909 (ttt) cc_final: 0.2416 (tpp) outliers start: 62 outliers final: 45 residues processed: 211 average time/residue: 0.1644 time to fit residues: 59.3585 Evaluate side-chains 185 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 137 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain K residue 48 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 63 optimal weight: 0.0170 chunk 287 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 282 optimal weight: 5.9990 chunk 256 optimal weight: 7.9990 chunk 265 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 252 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 214 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 overall best weight: 1.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 121 ASN C 690 GLN C 762 GLN C 907 ASN C1054 GLN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.197188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.125966 restraints weight = 53619.167| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 4.76 r_work: 0.3359 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.5543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 30738 Z= 0.141 Angle : 0.643 15.893 41929 Z= 0.315 Chirality : 0.045 0.265 4853 Planarity : 0.004 0.047 5289 Dihedral : 4.683 47.444 3998 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.42 % Favored : 94.41 % Rotamer: Outliers : 2.06 % Allowed : 10.38 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.14), residues: 3634 helix: 1.03 (0.21), residues: 653 sheet: -0.41 (0.16), residues: 978 loop : -1.06 (0.14), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 983 TYR 0.020 0.001 TYR C 904 PHE 0.027 0.001 PHE B 429 TRP 0.013 0.001 TRP E 53 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (30619) covalent geometry : angle 0.61917 / 0.31 (41620) SS BOND : bond 0.00404 / 0.25 ( 48) SS BOND : angle 2.41090 / 1.66 ( 96) hydrogen bonds : bond 0.03987 / 2.68 ( 1116) hydrogen bonds : angle 5.27433 / 3.65 ( 3117) link_BETA1-4 : bond 0.00562 / 0.30 ( 23) link_BETA1-4 : angle 1.66741 / 1.08 ( 69) link_NAG-ASN : bond 0.00320 / 0.21 ( 48) link_NAG-ASN : angle 2.11778 / 1.36 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 154 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.6375 (m-90) cc_final: 0.5103 (m-90) REVERT: A 140 PHE cc_start: 0.4542 (OUTLIER) cc_final: 0.3890 (m-80) REVERT: A 153 MET cc_start: 0.6700 (mpp) cc_final: 0.6079 (ttp) REVERT: A 244 LEU cc_start: 0.5420 (pp) cc_final: 0.5054 (pp) REVERT: A 377 PHE cc_start: 0.4182 (OUTLIER) cc_final: 0.3703 (m-80) REVERT: A 787 GLN cc_start: 0.9021 (mp10) cc_final: 0.8530 (mp10) REVERT: A 820 ASP cc_start: 0.8473 (t70) cc_final: 0.8111 (m-30) REVERT: A 869 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.7914 (mtt) REVERT: B 53 ASP cc_start: 0.7587 (t0) cc_final: 0.7169 (t0) REVERT: B 755 GLN cc_start: 0.8683 (mm110) cc_final: 0.7976 (pt0) REVERT: B 955 ASN cc_start: 0.8266 (m-40) cc_final: 0.8021 (m-40) REVERT: C 204 TYR cc_start: 0.8167 (m-80) cc_final: 0.7465 (m-80) REVERT: C 725 GLU cc_start: 0.7956 (tt0) cc_final: 0.7690 (tt0) REVERT: L 4 MET cc_start: 0.2655 (ttt) cc_final: 0.2191 (tpp) outliers start: 66 outliers final: 45 residues processed: 212 average time/residue: 0.1771 time to fit residues: 64.0955 Evaluate side-chains 188 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 140 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain K residue 48 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 352 optimal weight: 20.0000 chunk 298 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 151 optimal weight: 0.2980 chunk 271 optimal weight: 1.9990 chunk 345 optimal weight: 3.9990 chunk 257 optimal weight: 0.9980 chunk 145 optimal weight: 10.0000 chunk 20 optimal weight: 0.4980 chunk 155 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 762 GLN B 907 ASN C 239 GLN C 690 GLN C 762 GLN C 907 ASN C1010 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.197683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.126996 restraints weight = 53957.204| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 4.88 r_work: 0.3376 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.5677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30738 Z= 0.113 Angle : 0.607 10.518 41929 Z= 0.299 Chirality : 0.044 0.257 4853 Planarity : 0.004 0.051 5289 Dihedral : 4.525 43.776 3998 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.46 % Favored : 95.40 % Rotamer: Outliers : 1.71 % Allowed : 10.97 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.14), residues: 3634 helix: 1.28 (0.21), residues: 651 sheet: -0.31 (0.16), residues: 991 loop : -0.94 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 983 TYR 0.019 0.001 TYR C1067 PHE 0.021 0.001 PHE B 86 TRP 0.013 0.001 TRP E 53 HIS 0.004 0.000 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (30619) covalent geometry : angle 0.58521 / 0.29 (41620) SS BOND : bond 0.00447 / 0.25 ( 48) SS BOND : angle 2.20619 / 1.46 ( 96) hydrogen bonds : bond 0.03557 / 2.39 ( 1116) hydrogen bonds : angle 5.10953 / 3.55 ( 3117) link_BETA1-4 : bond 0.00497 / 0.27 ( 23) link_BETA1-4 : angle 1.60587 / 1.05 ( 69) link_NAG-ASN : bond 0.00318 / 0.21 ( 48) link_NAG-ASN : angle 1.97546 / 1.27 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 152 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.6300 (m-90) cc_final: 0.5107 (m-90) REVERT: A 140 PHE cc_start: 0.4488 (OUTLIER) cc_final: 0.3788 (m-80) REVERT: A 153 MET cc_start: 0.6710 (mpp) cc_final: 0.6090 (ttp) REVERT: A 377 PHE cc_start: 0.4210 (OUTLIER) cc_final: 0.3771 (m-80) REVERT: A 544 ASN cc_start: 0.7908 (p0) cc_final: 0.7679 (m-40) REVERT: A 787 GLN cc_start: 0.9003 (mp10) cc_final: 0.8740 (mp10) REVERT: A 820 ASP cc_start: 0.8385 (t70) cc_final: 0.8080 (m-30) REVERT: A 869 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.7843 (mtt) REVERT: B 755 GLN cc_start: 0.8663 (mm110) cc_final: 0.8028 (pt0) REVERT: B 955 ASN cc_start: 0.8229 (m-40) cc_final: 0.7988 (m-40) REVERT: C 204 TYR cc_start: 0.8192 (m-80) cc_final: 0.7509 (m-80) REVERT: C 725 GLU cc_start: 0.7899 (tt0) cc_final: 0.7652 (tt0) REVERT: L 4 MET cc_start: 0.2464 (ttt) cc_final: 0.2046 (tpp) outliers start: 55 outliers final: 37 residues processed: 200 average time/residue: 0.1721 time to fit residues: 58.5297 Evaluate side-chains 184 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 144 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 228 optimal weight: 40.0000 chunk 170 optimal weight: 0.0050 chunk 256 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 286 optimal weight: 0.7980 chunk 232 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 323 optimal weight: 8.9990 chunk 339 optimal weight: 20.0000 overall best weight: 1.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS B 907 ASN C 690 GLN C 762 GLN C 907 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.197295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.124537 restraints weight = 53403.633| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 4.38 r_work: 0.3359 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.5821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 30738 Z= 0.127 Angle : 0.614 17.609 41929 Z= 0.302 Chirality : 0.045 0.253 4853 Planarity : 0.004 0.054 5289 Dihedral : 4.489 41.293 3998 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.28 % Favored : 94.55 % Rotamer: Outliers : 1.68 % Allowed : 11.07 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.14), residues: 3634 helix: 1.36 (0.21), residues: 651 sheet: -0.28 (0.16), residues: 992 loop : -0.90 (0.14), residues: 1991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 983 TYR 0.020 0.001 TYR A1067 PHE 0.022 0.001 PHE C 970 TRP 0.013 0.001 TRP E 53 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (30619) covalent geometry : angle 0.59137 / 0.29 (41620) SS BOND : bond 0.00327 / 0.22 ( 48) SS BOND : angle 2.39494 / 1.65 ( 96) hydrogen bonds : bond 0.03636 / 2.44 ( 1116) hydrogen bonds : angle 5.13015 / 3.56 ( 3117) link_BETA1-4 : bond 0.00525 / 0.28 ( 23) link_BETA1-4 : angle 1.59219 / 1.04 ( 69) link_NAG-ASN : bond 0.00306 / 0.20 ( 48) link_NAG-ASN : angle 1.94552 / 1.26 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 146 time to evaluate : 1.074 Fit side-chains revert: symmetry clash REVERT: A 104 TRP cc_start: 0.6406 (m-90) cc_final: 0.5220 (m-90) REVERT: A 140 PHE cc_start: 0.4596 (OUTLIER) cc_final: 0.3843 (m-80) REVERT: A 153 MET cc_start: 0.6654 (mpp) cc_final: 0.6003 (ttp) REVERT: A 207 HIS cc_start: 0.6984 (OUTLIER) cc_final: 0.6429 (m90) REVERT: A 377 PHE cc_start: 0.4362 (OUTLIER) cc_final: 0.3955 (m-80) REVERT: A 787 GLN cc_start: 0.9017 (mp10) cc_final: 0.8738 (mp10) REVERT: A 820 ASP cc_start: 0.8386 (t70) cc_final: 0.8081 (m-30) REVERT: A 869 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.7849 (mtt) REVERT: B 200 TYR cc_start: 0.7206 (OUTLIER) cc_final: 0.6146 (m-80) REVERT: B 755 GLN cc_start: 0.8611 (mm110) cc_final: 0.8034 (pt0) REVERT: B 950 ASP cc_start: 0.7804 (m-30) cc_final: 0.7544 (t0) REVERT: B 955 ASN cc_start: 0.8237 (m-40) cc_final: 0.7996 (m-40) REVERT: C 158 ARG cc_start: 0.5950 (OUTLIER) cc_final: 0.4645 (ptp90) REVERT: C 204 TYR cc_start: 0.8228 (m-80) cc_final: 0.7521 (m-80) REVERT: C 725 GLU cc_start: 0.7895 (tt0) cc_final: 0.7647 (tt0) REVERT: L 4 MET cc_start: 0.2988 (ttt) cc_final: 0.2554 (tpp) outliers start: 54 outliers final: 40 residues processed: 195 average time/residue: 0.1626 time to fit residues: 54.3472 Evaluate side-chains 184 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 138 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 87 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 277 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 204 optimal weight: 4.9990 chunk 69 optimal weight: 0.0970 chunk 218 optimal weight: 0.6980 chunk 112 optimal weight: 0.8980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 907 ASN C 690 GLN C 762 GLN C 907 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.197952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.126234 restraints weight = 53343.044| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 4.23 r_work: 0.3406 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.5918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 30738 Z= 0.102 Angle : 0.588 14.951 41929 Z= 0.289 Chirality : 0.044 0.250 4853 Planarity : 0.004 0.062 5289 Dihedral : 4.365 39.185 3998 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.43 % Favored : 95.40 % Rotamer: Outliers : 1.50 % Allowed : 11.35 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.14), residues: 3634 helix: 1.59 (0.21), residues: 652 sheet: -0.17 (0.16), residues: 981 loop : -0.84 (0.14), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 983 TYR 0.018 0.001 TYR A1067 PHE 0.024 0.001 PHE A 168 TRP 0.014 0.001 TRP E 53 HIS 0.018 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (30619) covalent geometry : angle 0.56841 / 0.28 (41620) SS BOND : bond 0.00297 / 0.18 ( 48) SS BOND : angle 2.06808 / 1.43 ( 96) hydrogen bonds : bond 0.03325 / 2.24 ( 1116) hydrogen bonds : angle 5.03358 / 3.50 ( 3117) link_BETA1-4 : bond 0.00562 / 0.30 ( 23) link_BETA1-4 : angle 1.57926 / 1.02 ( 69) link_NAG-ASN : bond 0.00317 / 0.21 ( 48) link_NAG-ASN : angle 1.84270 / 1.19 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 148 time to evaluate : 1.102 Fit side-chains revert: symmetry clash REVERT: A 104 TRP cc_start: 0.6325 (m-90) cc_final: 0.5164 (m-90) REVERT: A 140 PHE cc_start: 0.4359 (OUTLIER) cc_final: 0.3530 (m-80) REVERT: A 153 MET cc_start: 0.6496 (mpp) cc_final: 0.5862 (ttp) REVERT: A 377 PHE cc_start: 0.4347 (OUTLIER) cc_final: 0.3957 (m-80) REVERT: A 787 GLN cc_start: 0.8916 (mp10) cc_final: 0.8368 (mp10) REVERT: A 820 ASP cc_start: 0.8322 (t70) cc_final: 0.7928 (m-30) REVERT: A 869 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.7721 (mtt) REVERT: B 200 TYR cc_start: 0.6997 (OUTLIER) cc_final: 0.5934 (m-80) REVERT: B 755 GLN cc_start: 0.8537 (mm110) cc_final: 0.7968 (pt0) REVERT: B 950 ASP cc_start: 0.7745 (m-30) cc_final: 0.7491 (t0) REVERT: B 955 ASN cc_start: 0.8165 (m-40) cc_final: 0.7957 (m-40) REVERT: C 158 ARG cc_start: 0.6041 (OUTLIER) cc_final: 0.4692 (ptp90) REVERT: C 204 TYR cc_start: 0.8164 (m-80) cc_final: 0.7433 (m-80) REVERT: L 4 MET cc_start: 0.2994 (ttt) cc_final: 0.2565 (tpp) outliers start: 48 outliers final: 36 residues processed: 192 average time/residue: 0.1744 time to fit residues: 57.1653 Evaluate side-chains 184 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 143 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 211 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 42 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 69 optimal weight: 0.0040 chunk 357 optimal weight: 20.0000 chunk 139 optimal weight: 40.0000 chunk 121 optimal weight: 2.9990 chunk 162 optimal weight: 0.0040 chunk 163 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.5806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS B 907 ASN C 196 ASN C 690 GLN C 762 GLN C 907 ASN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.198825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.127370 restraints weight = 53963.447| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 4.31 r_work: 0.3413 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.6020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 30738 Z= 0.099 Angle : 0.580 15.745 41929 Z= 0.282 Chirality : 0.044 0.245 4853 Planarity : 0.004 0.063 5289 Dihedral : 4.244 39.045 3998 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.62 % Favored : 95.24 % Rotamer: Outliers : 1.43 % Allowed : 11.75 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.14), residues: 3634 helix: 1.70 (0.21), residues: 660 sheet: -0.10 (0.16), residues: 998 loop : -0.79 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 983 TYR 0.018 0.001 TYR C1067 PHE 0.019 0.001 PHE B 86 TRP 0.015 0.001 TRP E 53 HIS 0.005 0.000 HIS A 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (30619) covalent geometry : angle 0.56254 / 0.28 (41620) SS BOND : bond 0.00298 / 0.19 ( 48) SS BOND : angle 1.83419 / 1.27 ( 96) hydrogen bonds : bond 0.03098 / 2.08 ( 1116) hydrogen bonds : angle 4.93197 / 3.43 ( 3117) link_BETA1-4 : bond 0.00546 / 0.29 ( 23) link_BETA1-4 : angle 1.55196 / 1.01 ( 69) link_NAG-ASN : bond 0.00317 / 0.21 ( 48) link_NAG-ASN : angle 1.75890 / 1.15 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8840.96 seconds wall clock time: 151 minutes 41.97 seconds (9101.97 seconds total)