Starting phenix.real_space_refine on Sun Jul 5 19:46:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7nd4_12275/07_2026/7nd4_12275.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nd4_12275/07_2026/7nd4_12275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nd4_12275/07_2026/7nd4_12275.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nd4_12275/07_2026/7nd4_12275.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7nd4_12275/07_2026/7nd4_12275.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7nd4_12275/07_2026/7nd4_12275.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nd4_12275/07_2026/7nd4_12275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nd4_12275/07_2026/7nd4_12275.map" } resolution = 3.6 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= 0.002 sd= 0.021 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 126 5.16 5 C 18918 2.51 5 N 4884 2.21 5 O 5920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 29848 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "B" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "C" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "H" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 968 Classifications: {'peptide': 128} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 122} Chain: "L" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 832 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 105} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 968 Classifications: {'peptide': 128} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 122} Chain: "E" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 832 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 105} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 968 Classifications: {'peptide': 128} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 122} Chain: "G" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 832 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 105} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "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: 6.53, per 1000 atoms: 0.22 Number of scatterers: 29848 At special positions: 0 Unit cell: (141.04, 139.4, 227.96, 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 126 16.00 O 5920 8.00 N 4884 7.00 C 18918 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=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 106 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 101 " - pdb=" SG CYS D 106 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 97 " distance=2.03 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 106 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 89 " 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 ALPHA1-3 " BMA Y 3 " - " MAN Y 4 " ALPHA1-6 " BMA Y 3 " - " MAN Y 5 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 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 Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 603 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 603 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C1074 " " NAG C1310 " - " ASN C 165 " " NAG I 1 " - " ASN A 234 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 234 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN C 234 " " NAG U 1 " - " ASN C 717 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1098 " " NAG X 1 " - " ASN C1134 " " NAG Y 1 " - " ASN H 35 " " NAG Z 1 " - " ASN D 35 " " NAG a 1 " - " ASN F 35 " Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 1.3 seconds 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6930 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 60 sheets defined 21.9% alpha, 33.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 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 365 through 371 removed outlier: 3.563A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.248A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 4.363A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 759 removed outlier: 7.053A pdb=" N SER A 758 " --> pdb=" O GLN A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 783 removed outlier: 3.595A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.772A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.070A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.898A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.602A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.563A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.248A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 4.362A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 759 removed outlier: 7.054A pdb=" N SER B 758 " --> pdb=" O GLN B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.595A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.773A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.069A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.898A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.602A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.563A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 removed outlier: 4.247A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 removed outlier: 4.363A pdb=" N ARG C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 408' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 759 removed outlier: 7.054A pdb=" N SER C 758 " --> pdb=" O GLN C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.596A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.772A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.069A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.898A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.602A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'H' and resid 63 through 66 Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.526A pdb=" N GLU L 84 " --> pdb=" O SER L 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 66 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.526A pdb=" N GLU E 84 " --> pdb=" O SER E 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 66 Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'G' and resid 80 through 84 removed outlier: 3.527A pdb=" N GLU G 84 " --> pdb=" O SER G 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.504A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.747A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 52 removed outlier: 3.588A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.331A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.902A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 316 removed outlier: 6.892A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.386A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.645A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.954A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.380A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.380A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.560A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.492A 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: 3.504A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.589A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.330A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.902A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 316 removed outlier: 6.892A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.386A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.646A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.955A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.381A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.552A 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: 6.381A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.544A 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: 4.559A 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: 4.491A 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: 3.504A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 47 through 52 removed outlier: 3.589A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.331A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.902A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 316 removed outlier: 6.893A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.645A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.954A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.613A 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: 6.380A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.552A 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: 6.380A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.559A 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 1125 removed outlier: 4.491A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE8, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.480A pdb=" N TRP H 36 " --> pdb=" O ARG H 52 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ARG H 52 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TRP H 38 " --> pdb=" O ILE H 50 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.488A pdb=" N VAL H 116 " --> pdb=" O ARG H 99 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N CYS H 101 " --> pdb=" O MET H 114 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N MET H 114 " --> pdb=" O CYS H 101 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.869A pdb=" N GLU L 12 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.869A pdb=" N GLU L 12 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL L 98 " --> pdb=" O ASP L 93 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 17 through 23 removed outlier: 3.564A pdb=" N VAL L 18 " --> pdb=" O ILE L 76 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.480A pdb=" N TRP D 36 " --> pdb=" O ARG D 52 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ARG D 52 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TRP D 38 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 11 through 12 removed outlier: 4.487A pdb=" N VAL D 116 " --> pdb=" O ARG D 99 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N CYS D 101 " --> pdb=" O MET D 114 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N MET D 114 " --> pdb=" O CYS D 101 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 9 through 12 removed outlier: 3.870A pdb=" N GLU E 12 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 9 through 12 removed outlier: 3.870A pdb=" N GLU E 12 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL E 98 " --> pdb=" O ASP E 93 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 17 through 23 removed outlier: 3.564A pdb=" N VAL E 18 " --> pdb=" O ILE E 76 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AG2, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.481A pdb=" N TRP F 36 " --> pdb=" O ARG F 52 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ARG F 52 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TRP F 38 " --> pdb=" O ILE F 50 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 11 through 12 removed outlier: 4.488A pdb=" N VAL F 116 " --> pdb=" O ARG F 99 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N CYS F 101 " --> pdb=" O MET F 114 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N MET F 114 " --> pdb=" O CYS F 101 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 9 through 12 removed outlier: 3.869A pdb=" N GLU G 12 " --> pdb=" O THR G 108 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 9 through 12 removed outlier: 3.869A pdb=" N GLU G 12 " --> pdb=" O THR G 108 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL G 98 " --> pdb=" O ASP G 93 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 17 through 23 removed outlier: 3.565A pdb=" N VAL G 18 " --> pdb=" O ILE G 76 " (cutoff:3.500A) 1253 hydrogen bonds defined for protein. 3390 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: 8.07 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9474 1.35 - 1.47: 7747 1.47 - 1.59: 13122 1.59 - 1.71: 0 1.71 - 1.83: 153 Bond restraints: 30496 Sorted by residual: bond pdb=" C5 BMA a 3 " pdb=" O5 BMA a 3 " ideal model delta sigma weight residual 1.417 1.492 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C5 BMA Y 3 " pdb=" O5 BMA Y 3 " ideal model delta sigma weight residual 1.417 1.492 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C5 BMA Z 3 " pdb=" O5 BMA Z 3 " ideal model delta sigma weight residual 1.417 1.492 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C4 BMA Y 3 " pdb=" C5 BMA Y 3 " ideal model delta sigma weight residual 1.528 1.575 -0.047 2.00e-02 2.50e+03 5.46e+00 bond pdb=" C4 BMA a 3 " pdb=" C5 BMA a 3 " ideal model delta sigma weight residual 1.528 1.574 -0.046 2.00e-02 2.50e+03 5.37e+00 ... (remaining 30491 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 40546 1.86 - 3.72: 869 3.72 - 5.58: 57 5.58 - 7.44: 27 7.44 - 9.30: 6 Bond angle restraints: 41505 Sorted by residual: angle pdb=" C SER A 698 " pdb=" N LEU A 699 " pdb=" CA LEU A 699 " ideal model delta sigma weight residual 121.54 130.84 -9.30 1.91e+00 2.74e-01 2.37e+01 angle pdb=" C SER B 698 " pdb=" N LEU B 699 " pdb=" CA LEU B 699 " ideal model delta sigma weight residual 121.54 130.83 -9.29 1.91e+00 2.74e-01 2.37e+01 angle pdb=" C SER C 698 " pdb=" N LEU C 699 " pdb=" CA LEU C 699 " ideal model delta sigma weight residual 121.54 130.83 -9.29 1.91e+00 2.74e-01 2.36e+01 angle pdb=" CA PRO B 527 " pdb=" N PRO B 527 " pdb=" CD PRO B 527 " ideal model delta sigma weight residual 112.00 106.73 5.27 1.40e+00 5.10e-01 1.42e+01 angle pdb=" CA PRO C 527 " pdb=" N PRO C 527 " pdb=" CD PRO C 527 " ideal model delta sigma weight residual 112.00 106.73 5.27 1.40e+00 5.10e-01 1.42e+01 ... (remaining 41500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 16780 17.45 - 34.91: 574 34.91 - 52.36: 133 52.36 - 69.81: 63 69.81 - 87.26: 30 Dihedral angle restraints: 17580 sinusoidal: 6780 harmonic: 10800 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -163.35 77.35 1 1.00e+01 1.00e-02 7.50e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -163.35 77.35 1 1.00e+01 1.00e-02 7.50e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -163.34 77.34 1 1.00e+01 1.00e-02 7.50e+01 ... (remaining 17577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 4456 0.088 - 0.176: 452 0.176 - 0.265: 10 0.265 - 0.353: 3 0.353 - 0.441: 3 Chirality restraints: 4924 Sorted by residual: chirality pdb=" CA ASN B 331 " pdb=" N ASN B 331 " pdb=" C ASN B 331 " pdb=" CB ASN B 331 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.86e+00 chirality pdb=" CA ASN A 331 " pdb=" N ASN A 331 " pdb=" C ASN A 331 " pdb=" CB ASN A 331 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.81e+00 chirality pdb=" CA ASN C 331 " pdb=" N ASN C 331 " pdb=" C ASN C 331 " pdb=" CB ASN C 331 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.78e+00 ... (remaining 4921 not shown) Planarity restraints: 5313 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 526 " 0.092 5.00e-02 4.00e+02 1.38e-01 3.03e+01 pdb=" N PRO A 527 " -0.238 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 526 " 0.092 5.00e-02 4.00e+02 1.37e-01 3.02e+01 pdb=" N PRO C 527 " -0.238 5.00e-02 4.00e+02 pdb=" CA PRO C 527 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO C 527 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 526 " -0.092 5.00e-02 4.00e+02 1.37e-01 3.02e+01 pdb=" N PRO B 527 " 0.238 5.00e-02 4.00e+02 pdb=" CA PRO B 527 " -0.073 5.00e-02 4.00e+02 pdb=" CD PRO B 527 " -0.072 5.00e-02 4.00e+02 ... (remaining 5310 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 4509 2.77 - 3.30: 27386 3.30 - 3.83: 49230 3.83 - 4.37: 58642 4.37 - 4.90: 101735 Nonbonded interactions: 241502 Sorted by model distance: nonbonded pdb=" O PHE B 565 " pdb=" N PHE C 43 " model vdw 2.233 3.120 nonbonded pdb=" O ASP L 83 " pdb=" OH TYR L 87 " model vdw 2.279 3.040 nonbonded pdb=" O ASP E 83 " pdb=" OH TYR E 87 " model vdw 2.279 3.040 nonbonded pdb=" NZ LYS B 417 " pdb=" OH TYR G 51 " model vdw 2.280 3.120 nonbonded pdb=" O ASP G 83 " pdb=" OH TYR G 87 " model vdw 2.280 3.040 ... (remaining 241497 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' 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' } ncs_group { reference = chain 'Z' selection = chain 'a' } 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 group one per residue 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: 4.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.610 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 29.830 Find NCS groups from input model: 0.750 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: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 30615 Z= 0.185 Angle : 0.642 9.301 41814 Z= 0.325 Chirality : 0.048 0.441 4924 Planarity : 0.005 0.138 5265 Dihedral : 11.023 87.262 10506 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.12 % Favored : 95.64 % Rotamer: Outliers : 0.28 % Allowed : 2.51 % Favored : 97.21 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.13), residues: 3669 helix: 0.66 (0.19), residues: 660 sheet: 0.36 (0.15), residues: 990 loop : -0.50 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1000 TYR 0.014 0.001 TYR C 904 PHE 0.016 0.001 PHE C 55 TRP 0.018 0.001 TRP A 886 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.19 (30496) covalent geometry : angle 0.62023 / 0.32 (41505) SS BOND : bond 0.00250 / 0.15 ( 48) SS BOND : angle 1.11231 / 0.71 ( 96) hydrogen bonds : bond 0.20123 / 13.23 ( 1187) hydrogen bonds : angle 8.26819 / 5.75 ( 3390) link_ALPHA1-3 : bond 0.00770 / 0.41 ( 1) link_ALPHA1-3 : angle 5.60254 / 3.69 ( 3) link_ALPHA1-6 : bond 0.00675 / 0.36 ( 1) link_ALPHA1-6 : angle 0.87223 / 0.47 ( 3) link_BETA1-4 : bond 0.00414 / 0.25 ( 21) link_BETA1-4 : angle 1.13542 / 0.73 ( 63) link_NAG-ASN : bond 0.00222 / 0.12 ( 48) link_NAG-ASN : angle 2.58819 / 1.73 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 343 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 THR cc_start: 0.8921 (m) cc_final: 0.8705 (t) REVERT: A 675 GLN cc_start: 0.7367 (mt0) cc_final: 0.7104 (mt0) REVERT: B 307 THR cc_start: 0.8952 (m) cc_final: 0.8690 (t) REVERT: B 562 PHE cc_start: 0.7905 (p90) cc_final: 0.7672 (p90) REVERT: B 675 GLN cc_start: 0.7369 (mt0) cc_final: 0.7128 (mt0) REVERT: B 975 SER cc_start: 0.8684 (p) cc_final: 0.8402 (t) REVERT: C 239 GLN cc_start: 0.6904 (tt0) cc_final: 0.6342 (mt0) REVERT: C 307 THR cc_start: 0.8973 (m) cc_final: 0.8742 (t) REVERT: C 562 PHE cc_start: 0.7861 (p90) cc_final: 0.7383 (p90) outliers start: 9 outliers final: 1 residues processed: 352 average time/residue: 0.1933 time to fit residues: 109.6421 Evaluate side-chains 166 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 55 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 40.0000 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.3980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 762 GLN A 935 GLN A 949 GLN B 317 ASN B 762 GLN B 935 GLN B 949 GLN C 87 ASN C 317 ASN C 762 GLN C 907 ASN C 935 GLN C 949 GLN C1002 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.204230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.191570 restraints weight = 42293.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.189933 restraints weight = 87925.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.188084 restraints weight = 95017.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.186657 restraints weight = 98291.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.184973 restraints weight = 105574.284| |-----------------------------------------------------------------------------| r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30615 Z= 0.135 Angle : 0.564 7.335 41814 Z= 0.297 Chirality : 0.045 0.229 4924 Planarity : 0.004 0.079 5265 Dihedral : 4.031 34.765 3992 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.83 % Favored : 98.09 % Rotamer: Outliers : 1.36 % Allowed : 5.55 % Favored : 93.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.13), residues: 3669 helix: 2.06 (0.20), residues: 642 sheet: 0.58 (0.15), residues: 957 loop : -0.45 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 646 TYR 0.020 0.001 TYR B1067 PHE 0.013 0.001 PHE A 329 TRP 0.010 0.001 TRP A 886 HIS 0.004 0.001 HIS F 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (30496) covalent geometry : angle 0.54866 / 0.29 (41505) SS BOND : bond 0.00260 / 0.15 ( 48) SS BOND : angle 0.89596 / 0.61 ( 96) hydrogen bonds : bond 0.04292 / 2.79 ( 1187) hydrogen bonds : angle 6.08465 / 4.21 ( 3390) link_ALPHA1-3 : bond 0.00921 / 0.48 ( 1) link_ALPHA1-3 : angle 3.93576 / 2.54 ( 3) link_ALPHA1-6 : bond 0.00255 / 0.13 ( 1) link_ALPHA1-6 : angle 1.61878 / 0.76 ( 3) link_BETA1-4 : bond 0.00417 / 0.24 ( 21) link_BETA1-4 : angle 1.20474 / 0.81 ( 63) link_NAG-ASN : bond 0.00405 / 0.26 ( 48) link_NAG-ASN : angle 2.02890 / 1.37 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 176 time to evaluate : 1.051 Fit side-chains REVERT: A 1100 THR cc_start: 0.8342 (OUTLIER) cc_final: 0.8046 (m) REVERT: B 740 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.7613 (ttt) REVERT: C 562 PHE cc_start: 0.7798 (p90) cc_final: 0.7430 (p90) REVERT: C 1050 MET cc_start: 0.8256 (ptm) cc_final: 0.8038 (ptm) REVERT: D 114 MET cc_start: -0.0120 (mmt) cc_final: -0.0525 (mmt) outliers start: 44 outliers final: 22 residues processed: 206 average time/residue: 0.1682 time to fit residues: 59.7431 Evaluate side-chains 174 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1100 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 299 optimal weight: 0.6980 chunk 148 optimal weight: 4.9990 chunk 134 optimal weight: 50.0000 chunk 303 optimal weight: 50.0000 chunk 178 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 216 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 301 optimal weight: 50.0000 chunk 18 optimal weight: 0.9980 chunk 176 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 762 GLN A 907 ASN A1002 GLN B 207 HIS B 762 GLN B 949 GLN C 949 GLN C1002 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.201556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.187873 restraints weight = 42165.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.186227 restraints weight = 96022.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.181063 restraints weight = 93984.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.174866 restraints weight = 108301.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.171056 restraints weight = 73529.732| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30615 Z= 0.179 Angle : 0.552 7.590 41814 Z= 0.288 Chirality : 0.045 0.249 4924 Planarity : 0.004 0.038 5265 Dihedral : 4.029 18.595 3990 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.58 % Allowed : 6.60 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.13), residues: 3669 helix: 1.98 (0.21), residues: 639 sheet: 0.64 (0.15), residues: 969 loop : -0.45 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 646 TYR 0.019 0.001 TYR B1067 PHE 0.024 0.002 PHE A 168 TRP 0.011 0.001 TRP A 886 HIS 0.008 0.001 HIS A1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (30496) covalent geometry : angle 0.53842 / 0.29 (41505) SS BOND : bond 0.00323 / 0.18 ( 48) SS BOND : angle 0.88366 / 0.62 ( 96) hydrogen bonds : bond 0.04131 / 2.68 ( 1187) hydrogen bonds : angle 5.63997 / 3.89 ( 3390) link_ALPHA1-3 : bond 0.01266 / 0.67 ( 1) link_ALPHA1-3 : angle 3.72036 / 2.40 ( 3) link_ALPHA1-6 : bond 0.00433 / 0.23 ( 1) link_ALPHA1-6 : angle 1.45039 / 0.73 ( 3) link_BETA1-4 : bond 0.00306 / 0.17 ( 21) link_BETA1-4 : angle 1.17477 / 0.77 ( 63) link_NAG-ASN : bond 0.00293 / 0.19 ( 48) link_NAG-ASN : angle 1.88719 / 1.27 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 161 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1100 THR cc_start: 0.8317 (OUTLIER) cc_final: 0.8086 (m) REVERT: B 740 MET cc_start: 0.7918 (ttt) cc_final: 0.7681 (ttt) REVERT: C 562 PHE cc_start: 0.7848 (p90) cc_final: 0.7523 (p90) outliers start: 51 outliers final: 32 residues processed: 197 average time/residue: 0.1497 time to fit residues: 51.7332 Evaluate side-chains 174 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 949 GLN Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain G residue 51 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 347 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 chunk 214 optimal weight: 8.9990 chunk 172 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 259 optimal weight: 0.9980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN A 907 ASN B 762 GLN B 949 GLN C 935 GLN C 949 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.200897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.186930 restraints weight = 41820.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.185440 restraints weight = 97675.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.179384 restraints weight = 92767.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.172806 restraints weight = 108539.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.169334 restraints weight = 74946.989| |-----------------------------------------------------------------------------| r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 30615 Z= 0.178 Angle : 0.543 12.855 41814 Z= 0.280 Chirality : 0.045 0.246 4924 Planarity : 0.004 0.041 5265 Dihedral : 4.037 20.627 3990 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.18 % Favored : 97.77 % Rotamer: Outliers : 1.49 % Allowed : 7.96 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.13), residues: 3669 helix: 1.78 (0.21), residues: 657 sheet: 0.60 (0.15), residues: 966 loop : -0.47 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 905 TYR 0.018 0.001 TYR B1067 PHE 0.018 0.001 PHE C 643 TRP 0.009 0.001 TRP A 886 HIS 0.005 0.001 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (30496) covalent geometry : angle 0.52911 / 0.28 (41505) SS BOND : bond 0.00311 / 0.18 ( 48) SS BOND : angle 0.87442 / 0.60 ( 96) hydrogen bonds : bond 0.03890 / 2.53 ( 1187) hydrogen bonds : angle 5.48792 / 3.78 ( 3390) link_ALPHA1-3 : bond 0.01098 / 0.58 ( 1) link_ALPHA1-3 : angle 3.76874 / 2.44 ( 3) link_ALPHA1-6 : bond 0.00425 / 0.22 ( 1) link_ALPHA1-6 : angle 1.45420 / 0.73 ( 3) link_BETA1-4 : bond 0.00313 / 0.18 ( 21) link_BETA1-4 : angle 1.18674 / 0.77 ( 63) link_NAG-ASN : bond 0.00276 / 0.18 ( 48) link_NAG-ASN : angle 1.86322 / 1.26 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 152 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 36 residues processed: 188 average time/residue: 0.1597 time to fit residues: 53.7279 Evaluate side-chains 175 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain G residue 51 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 237 optimal weight: 0.8980 chunk 355 optimal weight: 40.0000 chunk 234 optimal weight: 9.9990 chunk 272 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 149 optimal weight: 0.6980 chunk 274 optimal weight: 0.5980 chunk 158 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 935 GLN B 949 GLN C 949 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.201827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.174457 restraints weight = 41958.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.172557 restraints weight = 91076.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.169092 restraints weight = 85296.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.166952 restraints weight = 89927.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.164995 restraints weight = 76206.865| |-----------------------------------------------------------------------------| r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30615 Z= 0.114 Angle : 0.493 10.472 41814 Z= 0.255 Chirality : 0.043 0.254 4924 Planarity : 0.003 0.039 5265 Dihedral : 3.862 20.338 3990 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.26 % Favored : 97.68 % Rotamer: Outliers : 1.18 % Allowed : 8.64 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.14), residues: 3669 helix: 1.93 (0.21), residues: 657 sheet: 0.70 (0.16), residues: 975 loop : -0.43 (0.14), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 319 TYR 0.018 0.001 TYR B1067 PHE 0.020 0.001 PHE C 643 TRP 0.008 0.001 TRP H 36 HIS 0.002 0.001 HIS A1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (30496) covalent geometry : angle 0.48080 / 0.25 (41505) SS BOND : bond 0.00210 / 0.12 ( 48) SS BOND : angle 0.70637 / 0.49 ( 96) hydrogen bonds : bond 0.03490 / 2.26 ( 1187) hydrogen bonds : angle 5.24426 / 3.61 ( 3390) link_ALPHA1-3 : bond 0.00935 / 0.49 ( 1) link_ALPHA1-3 : angle 3.70209 / 2.39 ( 3) link_ALPHA1-6 : bond 0.00431 / 0.23 ( 1) link_ALPHA1-6 : angle 1.44965 / 0.74 ( 3) link_BETA1-4 : bond 0.00342 / 0.20 ( 21) link_BETA1-4 : angle 1.10912 / 0.73 ( 63) link_NAG-ASN : bond 0.00316 / 0.22 ( 48) link_NAG-ASN : angle 1.68023 / 1.15 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 151 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 28 residues processed: 176 average time/residue: 0.1583 time to fit residues: 49.1615 Evaluate side-chains 172 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain G residue 51 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 194 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 357 optimal weight: 50.0000 chunk 149 optimal weight: 0.9990 chunk 249 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 239 optimal weight: 8.9990 chunk 138 optimal weight: 50.0000 chunk 32 optimal weight: 50.0000 chunk 130 optimal weight: 30.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN A 907 ASN A1002 GLN B 949 GLN C 949 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.198567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.184957 restraints weight = 41666.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.183364 restraints weight = 95631.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.174094 restraints weight = 99053.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.167214 restraints weight = 107194.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.163477 restraints weight = 77756.882| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 30615 Z= 0.275 Angle : 0.585 9.531 41814 Z= 0.302 Chirality : 0.047 0.252 4924 Planarity : 0.004 0.043 5265 Dihedral : 4.192 21.765 3990 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.13 % Favored : 96.81 % Rotamer: Outliers : 1.64 % Allowed : 8.86 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.14), residues: 3669 helix: 1.59 (0.21), residues: 654 sheet: 0.47 (0.16), residues: 975 loop : -0.54 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1014 TYR 0.018 0.001 TYR B1067 PHE 0.023 0.002 PHE C 643 TRP 0.013 0.001 TRP B 886 HIS 0.007 0.002 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00658 / 0.27 (30496) covalent geometry : angle 0.57140 / 0.30 (41505) SS BOND : bond 0.00442 / 0.25 ( 48) SS BOND : angle 0.97844 / 0.67 ( 96) hydrogen bonds : bond 0.04273 / 2.78 ( 1187) hydrogen bonds : angle 5.55536 / 3.82 ( 3390) link_ALPHA1-3 : bond 0.00995 / 0.52 ( 1) link_ALPHA1-3 : angle 3.68056 / 2.37 ( 3) link_ALPHA1-6 : bond 0.00415 / 0.22 ( 1) link_ALPHA1-6 : angle 1.45921 / 0.76 ( 3) link_BETA1-4 : bond 0.00288 / 0.17 ( 21) link_BETA1-4 : angle 1.26887 / 0.82 ( 63) link_NAG-ASN : bond 0.00346 / 0.22 ( 48) link_NAG-ASN : angle 1.91324 / 1.30 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 155 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 THR cc_start: 0.9382 (OUTLIER) cc_final: 0.8947 (p) REVERT: B 192 PHE cc_start: 0.7783 (m-80) cc_final: 0.7561 (m-80) REVERT: B 284 THR cc_start: 0.9396 (OUTLIER) cc_final: 0.8946 (p) REVERT: B 735 SER cc_start: 0.8707 (t) cc_final: 0.8380 (m) REVERT: C 284 THR cc_start: 0.9345 (OUTLIER) cc_final: 0.8935 (p) outliers start: 53 outliers final: 38 residues processed: 195 average time/residue: 0.1565 time to fit residues: 53.9845 Evaluate side-chains 177 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 136 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 949 GLN Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain G residue 51 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 265 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 chunk 361 optimal weight: 10.0000 chunk 285 optimal weight: 0.7980 chunk 38 optimal weight: 50.0000 chunk 107 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 35 optimal weight: 30.0000 chunk 314 optimal weight: 50.0000 chunk 365 optimal weight: 10.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN B 949 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.199329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.171742 restraints weight = 41651.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.169348 restraints weight = 89099.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.166642 restraints weight = 85513.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.164539 restraints weight = 82893.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.162286 restraints weight = 87686.503| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 30615 Z= 0.194 Angle : 0.532 8.958 41814 Z= 0.275 Chirality : 0.045 0.260 4924 Planarity : 0.004 0.043 5265 Dihedral : 4.042 20.505 3990 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.64 % Favored : 97.30 % Rotamer: Outliers : 1.77 % Allowed : 9.05 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.14), residues: 3669 helix: 1.68 (0.21), residues: 657 sheet: 0.48 (0.16), residues: 966 loop : -0.56 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 905 TYR 0.017 0.001 TYR B1067 PHE 0.022 0.001 PHE C 643 TRP 0.009 0.001 TRP B 886 HIS 0.005 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.19 (30496) covalent geometry : angle 0.51967 / 0.27 (41505) SS BOND : bond 0.00337 / 0.19 ( 48) SS BOND : angle 0.88072 / 0.59 ( 96) hydrogen bonds : bond 0.03811 / 2.47 ( 1187) hydrogen bonds : angle 5.35101 / 3.68 ( 3390) link_ALPHA1-3 : bond 0.00881 / 0.46 ( 1) link_ALPHA1-3 : angle 3.67989 / 2.36 ( 3) link_ALPHA1-6 : bond 0.00421 / 0.22 ( 1) link_ALPHA1-6 : angle 1.46286 / 0.77 ( 3) link_BETA1-4 : bond 0.00270 / 0.16 ( 21) link_BETA1-4 : angle 1.16056 / 0.75 ( 63) link_NAG-ASN : bond 0.00247 / 0.17 ( 48) link_NAG-ASN : angle 1.73673 / 1.19 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 146 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 284 THR cc_start: 0.9402 (OUTLIER) cc_final: 0.8923 (p) REVERT: B 735 SER cc_start: 0.8588 (t) cc_final: 0.8275 (m) REVERT: B 1100 THR cc_start: 0.8632 (OUTLIER) cc_final: 0.8385 (m) REVERT: C 284 THR cc_start: 0.9363 (OUTLIER) cc_final: 0.8940 (p) REVERT: F 114 MET cc_start: 0.0327 (mmt) cc_final: -0.0002 (mmt) outliers start: 57 outliers final: 43 residues processed: 192 average time/residue: 0.1417 time to fit residues: 48.1515 Evaluate side-chains 186 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 140 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain G residue 51 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 313 optimal weight: 30.0000 chunk 69 optimal weight: 2.9990 chunk 235 optimal weight: 30.0000 chunk 330 optimal weight: 20.0000 chunk 344 optimal weight: 40.0000 chunk 28 optimal weight: 6.9990 chunk 137 optimal weight: 9.9990 chunk 35 optimal weight: 30.0000 chunk 221 optimal weight: 0.6980 chunk 177 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN C 949 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.198117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.155303 restraints weight = 41808.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.156030 restraints weight = 88581.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.155721 restraints weight = 38455.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.156030 restraints weight = 42505.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.155778 restraints weight = 28125.880| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 30615 Z= 0.259 Angle : 0.575 8.489 41814 Z= 0.295 Chirality : 0.046 0.262 4924 Planarity : 0.004 0.044 5265 Dihedral : 4.170 21.794 3990 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.27 % Favored : 96.67 % Rotamer: Outliers : 1.73 % Allowed : 9.48 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.14), residues: 3669 helix: 1.53 (0.20), residues: 657 sheet: 0.39 (0.16), residues: 966 loop : -0.61 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 983 TYR 0.018 0.001 TYR B1067 PHE 0.025 0.002 PHE C 643 TRP 0.011 0.001 TRP B 886 HIS 0.006 0.001 HIS A1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.26 (30496) covalent geometry : angle 0.56231 / 0.29 (41505) SS BOND : bond 0.00444 / 0.25 ( 48) SS BOND : angle 0.97573 / 0.65 ( 96) hydrogen bonds : bond 0.04103 / 2.65 ( 1187) hydrogen bonds : angle 5.45461 / 3.74 ( 3390) link_ALPHA1-3 : bond 0.00715 / 0.38 ( 1) link_ALPHA1-3 : angle 3.60178 / 2.30 ( 3) link_ALPHA1-6 : bond 0.00433 / 0.23 ( 1) link_ALPHA1-6 : angle 1.43642 / 0.75 ( 3) link_BETA1-4 : bond 0.00253 / 0.16 ( 21) link_BETA1-4 : angle 1.20003 / 0.78 ( 63) link_NAG-ASN : bond 0.00298 / 0.20 ( 48) link_NAG-ASN : angle 1.82187 / 1.25 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 146 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 284 THR cc_start: 0.9358 (OUTLIER) cc_final: 0.8834 (p) REVERT: B 735 SER cc_start: 0.8707 (t) cc_final: 0.8359 (m) REVERT: C 284 THR cc_start: 0.9316 (OUTLIER) cc_final: 0.8852 (p) REVERT: C 735 SER cc_start: 0.8637 (t) cc_final: 0.8347 (m) outliers start: 56 outliers final: 42 residues processed: 188 average time/residue: 0.1563 time to fit residues: 52.2159 Evaluate side-chains 183 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 139 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain G residue 51 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 51 optimal weight: 0.8980 chunk 314 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 284 optimal weight: 8.9990 chunk 211 optimal weight: 10.0000 chunk 294 optimal weight: 0.7980 chunk 184 optimal weight: 4.9990 chunk 255 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 361 optimal weight: 50.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN B 901 GLN B 949 GLN C 613 GLN C 949 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.200391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.186939 restraints weight = 41608.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.185398 restraints weight = 90642.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.181059 restraints weight = 92032.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.173408 restraints weight = 105008.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.168541 restraints weight = 76848.105| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30615 Z= 0.125 Angle : 0.498 8.249 41814 Z= 0.258 Chirality : 0.043 0.263 4924 Planarity : 0.004 0.042 5265 Dihedral : 3.903 19.502 3990 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.48 % Favored : 97.47 % Rotamer: Outliers : 1.18 % Allowed : 10.29 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.14), residues: 3669 helix: 2.05 (0.21), residues: 642 sheet: 0.48 (0.16), residues: 993 loop : -0.55 (0.14), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 983 TYR 0.017 0.001 TYR C1067 PHE 0.022 0.001 PHE C 643 TRP 0.009 0.001 TRP B 104 HIS 0.002 0.001 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 (30496) covalent geometry : angle 0.48611 / 0.26 (41505) SS BOND : bond 0.00236 / 0.14 ( 48) SS BOND : angle 0.77049 / 0.52 ( 96) hydrogen bonds : bond 0.03449 / 2.23 ( 1187) hydrogen bonds : angle 5.13617 / 3.53 ( 3390) link_ALPHA1-3 : bond 0.00807 / 0.42 ( 1) link_ALPHA1-3 : angle 3.56336 / 2.26 ( 3) link_ALPHA1-6 : bond 0.00460 / 0.24 ( 1) link_ALPHA1-6 : angle 1.41940 / 0.74 ( 3) link_BETA1-4 : bond 0.00311 / 0.19 ( 21) link_BETA1-4 : angle 1.08322 / 0.71 ( 63) link_NAG-ASN : bond 0.00248 / 0.17 ( 48) link_NAG-ASN : angle 1.60388 / 1.11 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 154 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 735 SER cc_start: 0.8646 (t) cc_final: 0.8408 (m) outliers start: 38 outliers final: 32 residues processed: 183 average time/residue: 0.1611 time to fit residues: 52.6955 Evaluate side-chains 182 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain G residue 51 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 194 optimal weight: 0.5980 chunk 200 optimal weight: 10.0000 chunk 301 optimal weight: 50.0000 chunk 234 optimal weight: 9.9990 chunk 293 optimal weight: 0.5980 chunk 367 optimal weight: 9.9990 chunk 169 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 365 optimal weight: 50.0000 chunk 275 optimal weight: 0.5980 chunk 140 optimal weight: 50.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.199709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.186082 restraints weight = 41465.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.184666 restraints weight = 94297.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.172881 restraints weight = 95243.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.166444 restraints weight = 101726.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.162743 restraints weight = 70252.260| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 30615 Z= 0.162 Angle : 0.512 8.139 41814 Z= 0.263 Chirality : 0.044 0.260 4924 Planarity : 0.004 0.041 5265 Dihedral : 3.911 20.072 3990 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.86 % Favored : 97.08 % Rotamer: Outliers : 1.18 % Allowed : 10.29 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.14), residues: 3669 helix: 2.10 (0.21), residues: 639 sheet: 0.50 (0.16), residues: 987 loop : -0.55 (0.14), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 983 TYR 0.018 0.001 TYR B1067 PHE 0.029 0.001 PHE C 643 TRP 0.008 0.001 TRP H 36 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 (30496) covalent geometry : angle 0.50031 / 0.26 (41505) SS BOND : bond 0.00301 / 0.17 ( 48) SS BOND : angle 0.82895 / 0.55 ( 96) hydrogen bonds : bond 0.03581 / 2.31 ( 1187) hydrogen bonds : angle 5.14966 / 3.54 ( 3390) link_ALPHA1-3 : bond 0.00772 / 0.41 ( 1) link_ALPHA1-3 : angle 3.51386 / 2.22 ( 3) link_ALPHA1-6 : bond 0.00461 / 0.24 ( 1) link_ALPHA1-6 : angle 1.41300 / 0.74 ( 3) link_BETA1-4 : bond 0.00283 / 0.17 ( 21) link_BETA1-4 : angle 1.09121 / 0.71 ( 63) link_NAG-ASN : bond 0.00230 / 0.16 ( 48) link_NAG-ASN : angle 1.61936 / 1.12 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 154 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 735 SER cc_start: 0.8639 (t) cc_final: 0.8304 (m) REVERT: C 735 SER cc_start: 0.8634 (t) cc_final: 0.8418 (m) outliers start: 38 outliers final: 35 residues processed: 182 average time/residue: 0.1465 time to fit residues: 47.7886 Evaluate side-chains 188 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 153 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain G residue 51 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 111 optimal weight: 8.9990 chunk 197 optimal weight: 1.9990 chunk 288 optimal weight: 0.5980 chunk 102 optimal weight: 0.4980 chunk 121 optimal weight: 0.8980 chunk 354 optimal weight: 50.0000 chunk 93 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 164 optimal weight: 0.6980 chunk 180 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.200733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.180883 restraints weight = 41930.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.178810 restraints weight = 91531.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.177365 restraints weight = 83213.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.175892 restraints weight = 69309.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.174375 restraints weight = 78436.801| |-----------------------------------------------------------------------------| r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30615 Z= 0.113 Angle : 0.483 8.030 41814 Z= 0.249 Chirality : 0.043 0.259 4924 Planarity : 0.003 0.037 5265 Dihedral : 3.765 18.912 3990 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.45 % Favored : 97.49 % Rotamer: Outliers : 1.21 % Allowed : 10.22 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.14), residues: 3669 helix: 2.20 (0.21), residues: 642 sheet: 0.58 (0.16), residues: 987 loop : -0.49 (0.14), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 983 TYR 0.018 0.001 TYR A1067 PHE 0.024 0.001 PHE C 643 TRP 0.008 0.001 TRP H 36 HIS 0.005 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (30496) covalent geometry : angle 0.47222 / 0.25 (41505) SS BOND : bond 0.00212 / 0.12 ( 48) SS BOND : angle 0.75951 / 0.51 ( 96) hydrogen bonds : bond 0.03300 / 2.13 ( 1187) hydrogen bonds : angle 4.98182 / 3.43 ( 3390) link_ALPHA1-3 : bond 0.00798 / 0.42 ( 1) link_ALPHA1-3 : angle 3.42724 / 2.14 ( 3) link_ALPHA1-6 : bond 0.00502 / 0.26 ( 1) link_ALPHA1-6 : angle 1.40198 / 0.73 ( 3) link_BETA1-4 : bond 0.00349 / 0.21 ( 21) link_BETA1-4 : angle 1.06642 / 0.70 ( 63) link_NAG-ASN : bond 0.00236 / 0.16 ( 48) link_NAG-ASN : angle 1.51354 / 1.05 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3904.23 seconds wall clock time: 69 minutes 8.46 seconds (4148.46 seconds total)