Starting phenix.real_space_refine on Mon Aug 25 19:10:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hec_34687/08_2025/8hec_34687.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hec_34687/08_2025/8hec_34687.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hec_34687/08_2025/8hec_34687.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hec_34687/08_2025/8hec_34687.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hec_34687/08_2025/8hec_34687.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hec_34687/08_2025/8hec_34687.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.037 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 141 5.16 5 C 18999 2.51 5 N 4894 2.21 5 O 5891 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29925 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 8000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 8000 Classifications: {'peptide': 1031} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 51, 'TRANS': 979} Chain breaks: 7 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 7992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 7992 Classifications: {'peptide': 1028} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 51, 'TRANS': 976} Chain breaks: 7 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 7985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 7985 Classifications: {'peptide': 1029} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 51, 'TRANS': 977} Chain breaks: 7 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 3, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "D" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 815 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 105} Chain: "E" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 883 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "F" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 815 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 105} Chain: "G" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 883 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "H" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 815 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 105} Chain: "I" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 883 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 6.37, per 1000 atoms: 0.21 Number of scatterers: 29925 At special positions: 0 Unit cell: (146.78, 156.62, 223.86, 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 141 16.00 O 5891 8.00 N 4894 7.00 C 18999 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 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 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 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 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 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 87 " distance=2.04 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 92 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 87 " distance=2.03 Simple disulfide: pdb=" SG CYS G 21 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 87 " distance=2.04 Simple disulfide: pdb=" SG CYS I 21 " - pdb=" SG CYS I 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C1074 " " NAG J 1 " - " ASN A 343 " " NAG K 1 " - " ASN A 717 " " NAG L 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN A 17 " " NAG P 1 " - " ASN B 17 " " NAG Q 1 " - " ASN B 343 " " NAG R 1 " - " ASN B 717 " " NAG S 1 " - " ASN B 801 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 17 " " NAG W 1 " - " ASN C 717 " " NAG X 1 " - " ASN C 801 " " NAG Y 1 " - " ASN C1098 " " NAG Z 1 " - " ASN C1134 " Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 953.7 nanoseconds 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6998 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 66 sheets defined 21.1% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.607A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.179A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.973A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.556A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 744 removed outlier: 3.642A pdb=" N CYS A 743 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.776A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.799A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.178A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.819A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.326A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.647A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.551A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.045A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.659A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 752 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.685A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.117A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY B 891 " --> pdb=" O THR B 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 891' Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.090A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.292A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.617A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.164A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.027A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.785A pdb=" N ASN C 343 " --> pdb=" O GLY C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.705A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.262A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.605A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.189A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.725A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 761 through 783 removed outlier: 3.538A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.528A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.197A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.811A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.653A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.531A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.277A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 82 removed outlier: 3.799A pdb=" N ALA D 82 " --> pdb=" O CYS D 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 82 removed outlier: 3.860A pdb=" N ALA F 82 " --> pdb=" O CYS F 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 31 removed outlier: 3.505A pdb=" N ARG G 30 " --> pdb=" O SER G 27 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.678A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.979A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.608A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 135 through 142 removed outlier: 10.776A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE A 140 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 317 removed outlier: 5.451A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 327 through 328 removed outlier: 3.678A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 5.890A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 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 660 removed outlier: 5.882A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 7.093A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.859A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 727 " --> pdb=" O VAL A1060 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A1060 " --> pdb=" O LEU A 727 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.641A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.736A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.570A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.322A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.834A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC2, first strand: chain 'B' and resid 132 through 134 removed outlier: 3.689A pdb=" N GLU B 132 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN B 164 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 140 through 142 Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.631A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.260A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.095A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.902A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 713 through 715 Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.979A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.476A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.871A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.662A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.462A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.937A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD9, first strand: chain 'C' and resid 132 through 135 removed outlier: 4.180A pdb=" N GLU C 132 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN C 164 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.947A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 327 through 328 Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.269A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.691A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 538 through 540 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 659 removed outlier: 6.077A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 712 removed outlier: 3.612A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 717 through 719 removed outlier: 6.458A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 717 through 719 removed outlier: 6.458A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 4.428A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.836A pdb=" N HIS D 69 " --> pdb=" O SER D 66 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 9 through 13 removed outlier: 3.682A pdb=" N VAL D 108 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA D 12 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS D 110 " --> pdb=" O ALA D 12 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE D 47 " --> pdb=" O TRP D 34 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLN D 36 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N LEU D 45 " --> pdb=" O GLN D 36 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 9 through 13 removed outlier: 3.682A pdb=" N VAL D 108 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA D 12 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS D 110 " --> pdb=" O ALA D 12 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY D 89 " --> pdb=" O ALA D 100 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA D 100 " --> pdb=" O GLY D 89 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 2 through 6 removed outlier: 3.866A pdb=" N LEU E 17 " --> pdb=" O MET E 79 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.938A pdb=" N MET E 33 " --> pdb=" O ILE E 49 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ILE E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N TRP E 35 " --> pdb=" O ILE E 47 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.869A pdb=" N PHE E 106 " --> pdb=" O ARG E 94 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.719A pdb=" N HIS F 69 " --> pdb=" O SER F 66 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 9 through 12 removed outlier: 3.830A pdb=" N VAL F 108 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA F 12 " --> pdb=" O VAL F 108 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 9 through 12 removed outlier: 3.830A pdb=" N VAL F 108 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA F 12 " --> pdb=" O VAL F 108 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY F 89 " --> pdb=" O ALA F 100 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA F 100 " --> pdb=" O GLY F 89 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 47 through 48 Processing sheet with id=AG5, first strand: chain 'G' and resid 2 through 6 removed outlier: 3.596A pdb=" N LEU G 17 " --> pdb=" O MET G 79 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 10 through 11 removed outlier: 7.157A pdb=" N MET G 33 " --> pdb=" O ILE G 49 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ILE G 49 " --> pdb=" O MET G 33 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TRP G 35 " --> pdb=" O ILE G 47 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.724A pdb=" N HIS H 69 " --> pdb=" O SER H 66 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 9 through 13 removed outlier: 3.650A pdb=" N VAL H 108 " --> pdb=" O VAL H 10 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA H 12 " --> pdb=" O VAL H 108 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS H 110 " --> pdb=" O ALA H 12 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 9 through 13 removed outlier: 3.650A pdb=" N VAL H 108 " --> pdb=" O VAL H 10 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA H 12 " --> pdb=" O VAL H 108 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS H 110 " --> pdb=" O ALA H 12 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY H 89 " --> pdb=" O ALA H 100 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA H 100 " --> pdb=" O GLY H 89 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 47 through 48 Processing sheet with id=AH2, first strand: chain 'I' and resid 2 through 6 Processing sheet with id=AH3, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.643A pdb=" N TRP I 35 " --> pdb=" O ILE I 47 " (cutoff:3.500A) 1120 hydrogen bonds defined for protein. 3042 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: 8.26 Time building geometry restraints manager: 3.38 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: 9523 1.35 - 1.47: 7843 1.47 - 1.59: 13039 1.59 - 1.71: 0 1.71 - 1.83: 177 Bond restraints: 30582 Sorted by residual: bond pdb=" N GLY D 96 " pdb=" CA GLY D 96 " ideal model delta sigma weight residual 1.451 1.479 -0.029 8.60e-03 1.35e+04 1.10e+01 bond pdb=" N ASP D 97 " pdb=" CA ASP D 97 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.55e+00 bond pdb=" N SER F 94 " pdb=" CA SER F 94 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.16e+00 bond pdb=" N SER H 95 " pdb=" CA SER H 95 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.19e-02 7.06e+03 5.72e+00 bond pdb=" N SER F 95 " pdb=" CA SER F 95 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.23e-02 6.61e+03 5.52e+00 ... (remaining 30577 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 40898 2.03 - 4.05: 678 4.05 - 6.08: 55 6.08 - 8.11: 4 8.11 - 10.13: 7 Bond angle restraints: 41642 Sorted by residual: angle pdb=" N ILE D 28 " pdb=" CA ILE D 28 " pdb=" C ILE D 28 " ideal model delta sigma weight residual 113.53 109.12 4.41 9.80e-01 1.04e+00 2.02e+01 angle pdb=" C SER F 92 " pdb=" CA SER F 92 " pdb=" CB SER F 92 " ideal model delta sigma weight residual 116.54 111.70 4.84 1.15e+00 7.56e-01 1.77e+01 angle pdb=" CA GLY D 96 " pdb=" C GLY D 96 " pdb=" O GLY D 96 " ideal model delta sigma weight residual 121.78 118.12 3.66 9.10e-01 1.21e+00 1.61e+01 angle pdb=" C SER H 92 " pdb=" CA SER H 92 " pdb=" CB SER H 92 " ideal model delta sigma weight residual 116.63 112.04 4.59 1.16e+00 7.43e-01 1.56e+01 angle pdb=" C SER D 92 " pdb=" N CYS D 93 " pdb=" CA CYS D 93 " ideal model delta sigma weight residual 121.54 114.03 7.51 1.91e+00 2.74e-01 1.55e+01 ... (remaining 41637 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 16631 17.64 - 35.27: 1735 35.27 - 52.91: 410 52.91 - 70.54: 70 70.54 - 88.18: 34 Dihedral angle restraints: 18880 sinusoidal: 7985 harmonic: 10895 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 93.00 175.26 -82.26 1 1.00e+01 1.00e-02 8.31e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -5.10 -80.90 1 1.00e+01 1.00e-02 8.08e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -163.45 77.45 1 1.00e+01 1.00e-02 7.51e+01 ... (remaining 18877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.169: 4923 0.169 - 0.338: 9 0.338 - 0.506: 1 0.506 - 0.675: 0 0.675 - 0.844: 1 Chirality restraints: 4934 Sorted by residual: chirality pdb=" C1 NAG Z 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG Z 1 " pdb=" O5 NAG Z 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.56 -0.84 2.00e-01 2.50e+01 1.78e+01 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.37e+00 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 4931 not shown) Planarity restraints: 5338 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 81 " -0.015 2.00e-02 2.50e+03 2.95e-02 8.72e+00 pdb=" C ASN C 81 " 0.051 2.00e-02 2.50e+03 pdb=" O ASN C 81 " -0.019 2.00e-02 2.50e+03 pdb=" N PRO C 82 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 92 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.48e+00 pdb=" C SER D 92 " -0.041 2.00e-02 2.50e+03 pdb=" O SER D 92 " 0.015 2.00e-02 2.50e+03 pdb=" N CYS D 93 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 614 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.60e+00 pdb=" C ASP C 614 " -0.037 2.00e-02 2.50e+03 pdb=" O ASP C 614 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL C 615 " 0.012 2.00e-02 2.50e+03 ... (remaining 5335 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2730 2.74 - 3.28: 28994 3.28 - 3.82: 47777 3.82 - 4.36: 53254 4.36 - 4.90: 95296 Nonbonded interactions: 228051 Sorted by model distance: nonbonded pdb=" N GLU B 583 " pdb=" OE1 GLU B 583 " model vdw 2.203 3.120 nonbonded pdb=" OD1 ASP A 663 " pdb=" OG SER A 673 " model vdw 2.211 3.040 nonbonded pdb=" O PHE A 329 " pdb=" NE2 GLN A 580 " model vdw 2.224 3.120 nonbonded pdb=" O PRO A 85 " pdb=" OH TYR A 269 " model vdw 2.226 3.040 nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.227 3.040 ... (remaining 228046 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 518 or (resid 519 through 520 and (name N or na \ me CA or name C or name O or name CB )) or resid 521 through 527 or (resid 528 a \ nd (name N or name CA or name C or name O or name CB )) or resid 529 through 555 \ or (resid 556 and (name N or name CA or name C or name O or name CB )) or resid \ 557 through 827 or resid 854 through 1309)) selection = (chain 'B' and (resid 15 through 527 or (resid 528 and (name N or name CA or nam \ e C or name O or name CB )) or resid 529 through 555 or (resid 556 and (name N o \ r name CA or name C or name O or name CB )) or resid 557 or (resid 558 through 5 \ 59 and (name N or name CA or name C or name O or name CB )) or resid 560 through \ 785 or (resid 786 and (name N or name CA or name C or name O or name CB )) or r \ esid 787 through 827 or (resid 854 and (name N or name CA or name C or name O or \ name CB )) or resid 855 through 903 or (resid 904 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ )) or resid 905 through 1309)) selection = (chain 'C' and (resid 15 through 557 or (resid 558 through 559 and (name N or na \ me CA or name C or name O or name CB )) or resid 560 through 827 or resid 854 th \ rough 903 or (resid 904 and (name N or name CA or name C or name O or name CB or \ name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or resid \ 905 through 1309)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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: 9.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 28.370 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 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 0.045 30686 Z= 0.183 Angle : 0.620 14.803 41911 Z= 0.314 Chirality : 0.047 0.844 4934 Planarity : 0.003 0.048 5294 Dihedral : 14.799 88.180 11753 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.75 % Favored : 95.15 % Rotamer: Outliers : 0.12 % Allowed : 18.48 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.14), residues: 3709 helix: 2.02 (0.22), residues: 643 sheet: 0.51 (0.17), residues: 963 loop : -1.30 (0.13), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 346 TYR 0.015 0.001 TYR B1067 PHE 0.016 0.001 PHE D 91 TRP 0.029 0.001 TRP B 353 HIS 0.003 0.001 HIS E 55 Details of bonding type rmsd covalent geometry : bond 0.00366 (30582) covalent geometry : angle 0.59751 (41642) SS BOND : bond 0.00366 ( 43) SS BOND : angle 1.12840 ( 86) hydrogen bonds : bond 0.15027 ( 1103) hydrogen bonds : angle 6.80514 ( 3042) link_BETA1-4 : bond 0.00374 ( 17) link_BETA1-4 : angle 1.44496 ( 51) link_NAG-ASN : bond 0.00449 ( 44) link_NAG-ASN : angle 2.77220 ( 132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 140 time to evaluate : 1.002 Fit side-chains REVERT: E 33 MET cc_start: 0.6239 (tpt) cc_final: 0.6013 (tpt) REVERT: H 74 MET cc_start: 0.0934 (pmm) cc_final: -0.1723 (ttp) outliers start: 4 outliers final: 2 residues processed: 142 average time/residue: 0.1519 time to fit residues: 36.9352 Evaluate side-chains 116 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 114 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 50.0000 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 804 GLN B 935 GLN C 901 GLN C1106 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.129885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.074579 restraints weight = 86791.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.073419 restraints weight = 38028.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.074342 restraints weight = 23624.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.075206 restraints weight = 18532.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.075744 restraints weight = 15435.797| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 30686 Z= 0.229 Angle : 0.626 14.562 41911 Z= 0.314 Chirality : 0.046 0.595 4934 Planarity : 0.004 0.047 5294 Dihedral : 6.774 59.907 5315 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.63 % Favored : 94.31 % Rotamer: Outliers : 3.61 % Allowed : 17.14 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.14), residues: 3709 helix: 1.89 (0.21), residues: 660 sheet: 0.35 (0.17), residues: 981 loop : -1.30 (0.13), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1019 TYR 0.020 0.001 TYR C1067 PHE 0.017 0.001 PHE C 888 TRP 0.011 0.001 TRP B 353 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00533 (30582) covalent geometry : angle 0.60314 (41642) SS BOND : bond 0.00419 ( 43) SS BOND : angle 1.41553 ( 86) hydrogen bonds : bond 0.04935 ( 1103) hydrogen bonds : angle 5.62936 ( 3042) link_BETA1-4 : bond 0.00422 ( 17) link_BETA1-4 : angle 1.12289 ( 51) link_NAG-ASN : bond 0.00463 ( 44) link_NAG-ASN : angle 2.78308 ( 132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 124 time to evaluate : 1.151 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.4071 (tmm) cc_final: 0.3404 (tmm) REVERT: B 214 ARG cc_start: 0.6272 (OUTLIER) cc_final: 0.5739 (tpt90) REVERT: B 726 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.9054 (tp) REVERT: B 727 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9350 (pp) REVERT: G 33 MET cc_start: 0.1161 (mmm) cc_final: 0.0733 (mmt) REVERT: I 33 MET cc_start: 0.3842 (mmp) cc_final: 0.2725 (ppp) outliers start: 116 outliers final: 67 residues processed: 227 average time/residue: 0.1424 time to fit residues: 56.8081 Evaluate side-chains 187 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 117 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 55 HIS Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain H residue 108 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 60 optimal weight: 0.9990 chunk 345 optimal weight: 40.0000 chunk 184 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 121 optimal weight: 7.9990 chunk 334 optimal weight: 20.0000 chunk 330 optimal weight: 20.0000 chunk 66 optimal weight: 4.9990 chunk 331 optimal weight: 30.0000 chunk 42 optimal weight: 7.9990 chunk 249 optimal weight: 50.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.128865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.074182 restraints weight = 87395.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.073680 restraints weight = 38471.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.074835 restraints weight = 24192.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.074337 restraints weight = 18495.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.074821 restraints weight = 16139.878| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 30686 Z= 0.276 Angle : 0.643 15.202 41911 Z= 0.323 Chirality : 0.046 0.549 4934 Planarity : 0.004 0.047 5294 Dihedral : 6.446 59.198 5315 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.50 % Favored : 94.47 % Rotamer: Outliers : 4.27 % Allowed : 18.17 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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 aren not related in a simple way. whole: -0.50 (0.14), residues: 3709 helix: 1.75 (0.21), residues: 665 sheet: 0.26 (0.17), residues: 997 loop : -1.41 (0.13), residues: 2047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.019 0.001 TYR C 170 PHE 0.020 0.002 PHE E 106 TRP 0.014 0.001 TRP A 104 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00640 (30582) covalent geometry : angle 0.61876 (41642) SS BOND : bond 0.00599 ( 43) SS BOND : angle 1.60914 ( 86) hydrogen bonds : bond 0.05125 ( 1103) hydrogen bonds : angle 5.61403 ( 3042) link_BETA1-4 : bond 0.00308 ( 17) link_BETA1-4 : angle 1.25622 ( 51) link_NAG-ASN : bond 0.00505 ( 44) link_NAG-ASN : angle 2.87481 ( 132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 123 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8507 (t70) cc_final: 0.8295 (t70) REVERT: A 141 LEU cc_start: 0.8809 (mp) cc_final: 0.8560 (mt) REVERT: A 153 MET cc_start: 0.4076 (tmm) cc_final: 0.3543 (tmm) REVERT: B 214 ARG cc_start: 0.6309 (OUTLIER) cc_final: 0.5817 (tpt90) REVERT: B 726 ILE cc_start: 0.9249 (OUTLIER) cc_final: 0.9035 (tp) REVERT: B 727 LEU cc_start: 0.9619 (OUTLIER) cc_final: 0.9388 (pp) REVERT: I 33 MET cc_start: 0.3693 (mmp) cc_final: 0.2895 (ppp) outliers start: 137 outliers final: 92 residues processed: 250 average time/residue: 0.1327 time to fit residues: 58.6323 Evaluate side-chains 211 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 116 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 55 HIS Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 108 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 302 optimal weight: 1.9990 chunk 293 optimal weight: 1.9990 chunk 222 optimal weight: 8.9990 chunk 228 optimal weight: 0.9980 chunk 337 optimal weight: 30.0000 chunk 7 optimal weight: 10.0000 chunk 281 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 255 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 361 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.130282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.075537 restraints weight = 89082.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.076924 restraints weight = 37944.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.078149 restraints weight = 23397.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.078868 restraints weight = 17792.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.079367 restraints weight = 15137.294| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 30686 Z= 0.133 Angle : 0.553 13.713 41911 Z= 0.276 Chirality : 0.045 0.489 4934 Planarity : 0.003 0.046 5294 Dihedral : 5.833 59.796 5315 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.55 % Allowed : 19.66 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.14), residues: 3709 helix: 2.11 (0.21), residues: 654 sheet: 0.42 (0.17), residues: 998 loop : -1.31 (0.13), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 94 TYR 0.017 0.001 TYR A1067 PHE 0.019 0.001 PHE C 855 TRP 0.020 0.001 TRP B 353 HIS 0.004 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00306 (30582) covalent geometry : angle 0.52907 (41642) SS BOND : bond 0.00374 ( 43) SS BOND : angle 1.18349 ( 86) hydrogen bonds : bond 0.04270 ( 1103) hydrogen bonds : angle 5.22792 ( 3042) link_BETA1-4 : bond 0.00349 ( 17) link_BETA1-4 : angle 1.19563 ( 51) link_NAG-ASN : bond 0.00430 ( 44) link_NAG-ASN : angle 2.67422 ( 132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 124 time to evaluate : 1.113 Fit side-chains revert: symmetry clash REVERT: A 505 TYR cc_start: 0.6226 (m-80) cc_final: 0.6018 (m-80) REVERT: B 214 ARG cc_start: 0.6085 (OUTLIER) cc_final: 0.5638 (tpt90) REVERT: B 726 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8959 (tp) REVERT: B 727 LEU cc_start: 0.9565 (OUTLIER) cc_final: 0.9323 (pp) REVERT: C 948 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8843 (mp) REVERT: H 74 MET cc_start: 0.1015 (pmm) cc_final: 0.0733 (pmm) REVERT: I 33 MET cc_start: 0.3563 (mmp) cc_final: 0.2863 (ppp) outliers start: 114 outliers final: 74 residues processed: 229 average time/residue: 0.1331 time to fit residues: 53.7664 Evaluate side-chains 194 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 116 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 55 HIS Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain I residue 112 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 264 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 80 optimal weight: 2.9990 chunk 179 optimal weight: 0.9980 chunk 113 optimal weight: 20.0000 chunk 311 optimal weight: 20.0000 chunk 155 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 50 optimal weight: 0.3980 chunk 336 optimal weight: 30.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.129465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.073852 restraints weight = 88485.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.075862 restraints weight = 37638.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.077150 restraints weight = 23208.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.077353 restraints weight = 17975.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.077741 restraints weight = 15384.617| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 30686 Z= 0.207 Angle : 0.590 14.309 41911 Z= 0.294 Chirality : 0.045 0.511 4934 Planarity : 0.003 0.045 5294 Dihedral : 5.694 59.362 5315 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.08 % Allowed : 19.63 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.14), residues: 3709 helix: 1.93 (0.21), residues: 667 sheet: 0.33 (0.17), residues: 980 loop : -1.34 (0.13), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 94 TYR 0.017 0.001 TYR C1067 PHE 0.016 0.001 PHE C 888 TRP 0.015 0.001 TRP B 353 HIS 0.002 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00481 (30582) covalent geometry : angle 0.56629 (41642) SS BOND : bond 0.00402 ( 43) SS BOND : angle 1.37075 ( 86) hydrogen bonds : bond 0.04547 ( 1103) hydrogen bonds : angle 5.27378 ( 3042) link_BETA1-4 : bond 0.00295 ( 17) link_BETA1-4 : angle 1.22220 ( 51) link_NAG-ASN : bond 0.00448 ( 44) link_NAG-ASN : angle 2.74103 ( 132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 120 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4078 (tmm) cc_final: 0.3281 (tmm) REVERT: A 271 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8433 (mp10) REVERT: A 1029 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.7923 (ttp) REVERT: B 725 GLU cc_start: 0.7536 (tt0) cc_final: 0.7264 (tt0) REVERT: B 726 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.9004 (tp) REVERT: B 727 LEU cc_start: 0.9605 (OUTLIER) cc_final: 0.9377 (pp) REVERT: H 74 MET cc_start: 0.1496 (pmm) cc_final: 0.1196 (pmm) REVERT: I 33 MET cc_start: 0.3847 (mmp) cc_final: 0.3083 (ppp) outliers start: 131 outliers final: 92 residues processed: 241 average time/residue: 0.1378 time to fit residues: 58.7343 Evaluate side-chains 210 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 114 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 55 HIS Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain I residue 112 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 44 optimal weight: 9.9990 chunk 347 optimal weight: 7.9990 chunk 212 optimal weight: 0.3980 chunk 295 optimal weight: 0.8980 chunk 194 optimal weight: 0.8980 chunk 263 optimal weight: 0.0170 chunk 338 optimal weight: 2.9990 chunk 271 optimal weight: 5.9990 chunk 266 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN B 777 ASN C 901 GLN C 907 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.131320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.077405 restraints weight = 88485.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.078698 restraints weight = 37125.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.079999 restraints weight = 22679.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.080499 restraints weight = 17097.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.080876 restraints weight = 14402.471| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 30686 Z= 0.094 Angle : 0.531 11.145 41911 Z= 0.264 Chirality : 0.044 0.605 4934 Planarity : 0.003 0.045 5294 Dihedral : 5.180 59.911 5315 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.12 % Allowed : 20.91 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.14), residues: 3709 helix: 2.20 (0.22), residues: 659 sheet: 0.49 (0.17), residues: 971 loop : -1.23 (0.13), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 346 TYR 0.018 0.001 TYR A1067 PHE 0.016 0.001 PHE B 157 TRP 0.018 0.001 TRP B 353 HIS 0.002 0.000 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00204 (30582) covalent geometry : angle 0.50863 (41642) SS BOND : bond 0.00412 ( 43) SS BOND : angle 0.99989 ( 86) hydrogen bonds : bond 0.03818 ( 1103) hydrogen bonds : angle 4.96418 ( 3042) link_BETA1-4 : bond 0.00399 ( 17) link_BETA1-4 : angle 1.25598 ( 51) link_NAG-ASN : bond 0.00466 ( 44) link_NAG-ASN : angle 2.56870 ( 132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 131 time to evaluate : 0.754 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.4221 (tmm) cc_final: 0.3511 (tmm) REVERT: A 271 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8387 (mp10) REVERT: A 1029 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.7798 (ttp) REVERT: B 214 ARG cc_start: 0.5921 (OUTLIER) cc_final: 0.5695 (tpm170) REVERT: B 727 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9292 (pp) REVERT: C 614 ASP cc_start: 0.7746 (t0) cc_final: 0.7308 (t0) REVERT: C 948 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8862 (mp) REVERT: H 74 MET cc_start: 0.1684 (pmm) cc_final: 0.1320 (pmm) REVERT: I 33 MET cc_start: 0.3741 (mmp) cc_final: 0.3051 (ppp) outliers start: 100 outliers final: 71 residues processed: 222 average time/residue: 0.1303 time to fit residues: 50.1607 Evaluate side-chains 193 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 117 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 55 HIS Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain I residue 112 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 245 optimal weight: 0.2980 chunk 93 optimal weight: 0.5980 chunk 256 optimal weight: 0.8980 chunk 13 optimal weight: 20.0000 chunk 318 optimal weight: 5.9990 chunk 203 optimal weight: 2.9990 chunk 149 optimal weight: 20.0000 chunk 240 optimal weight: 9.9990 chunk 177 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 176 optimal weight: 7.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN C 901 GLN C 907 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.130428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.075231 restraints weight = 88792.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.077375 restraints weight = 37542.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.078807 restraints weight = 22731.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.079443 restraints weight = 17705.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.079525 restraints weight = 15173.627| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30686 Z= 0.144 Angle : 0.546 12.192 41911 Z= 0.271 Chirality : 0.044 0.568 4934 Planarity : 0.003 0.045 5294 Dihedral : 5.067 59.645 5315 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.46 % Allowed : 20.54 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.14), residues: 3709 helix: 2.20 (0.21), residues: 661 sheet: 0.39 (0.17), residues: 1002 loop : -1.19 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 94 TYR 0.015 0.001 TYR C1067 PHE 0.016 0.001 PHE B 157 TRP 0.018 0.001 TRP A 104 HIS 0.002 0.000 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00333 (30582) covalent geometry : angle 0.52441 (41642) SS BOND : bond 0.00340 ( 43) SS BOND : angle 1.13920 ( 86) hydrogen bonds : bond 0.03978 ( 1103) hydrogen bonds : angle 4.99607 ( 3042) link_BETA1-4 : bond 0.00339 ( 17) link_BETA1-4 : angle 1.20751 ( 51) link_NAG-ASN : bond 0.00441 ( 44) link_NAG-ASN : angle 2.58081 ( 132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 120 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4334 (tmm) cc_final: 0.3669 (tmm) REVERT: A 271 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8391 (mp10) REVERT: A 1029 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.7766 (ttp) REVERT: B 726 ILE cc_start: 0.9220 (OUTLIER) cc_final: 0.8952 (tp) REVERT: B 727 LEU cc_start: 0.9575 (OUTLIER) cc_final: 0.9341 (pp) REVERT: C 614 ASP cc_start: 0.7776 (t0) cc_final: 0.7334 (t0) REVERT: C 948 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8839 (mp) REVERT: I 33 MET cc_start: 0.3780 (mmp) cc_final: 0.3062 (ppp) outliers start: 111 outliers final: 86 residues processed: 221 average time/residue: 0.1226 time to fit residues: 47.3161 Evaluate side-chains 210 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 119 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 55 HIS Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain I residue 112 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 291 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 131 optimal weight: 20.0000 chunk 198 optimal weight: 4.9990 chunk 116 optimal weight: 8.9990 chunk 101 optimal weight: 4.9990 chunk 300 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 313 optimal weight: 50.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN C 907 ASN D 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.128634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.077534 restraints weight = 88555.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.079396 restraints weight = 43816.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.078949 restraints weight = 25298.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.079595 restraints weight = 19520.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.079383 restraints weight = 17645.333| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 30686 Z= 0.289 Angle : 0.648 13.749 41911 Z= 0.323 Chirality : 0.047 0.629 4934 Planarity : 0.004 0.048 5294 Dihedral : 5.449 59.100 5315 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.96 % Allowed : 19.98 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.14), residues: 3709 helix: 1.79 (0.21), residues: 672 sheet: 0.23 (0.17), residues: 1002 loop : -1.33 (0.13), residues: 2035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 94 TYR 0.020 0.001 TYR C 170 PHE 0.021 0.002 PHE C 888 TRP 0.021 0.001 TRP B 353 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00673 (30582) covalent geometry : angle 0.62553 (41642) SS BOND : bond 0.00436 ( 43) SS BOND : angle 1.59599 ( 86) hydrogen bonds : bond 0.04835 ( 1103) hydrogen bonds : angle 5.29795 ( 3042) link_BETA1-4 : bond 0.00271 ( 17) link_BETA1-4 : angle 1.26634 ( 51) link_NAG-ASN : bond 0.00503 ( 44) link_NAG-ASN : angle 2.77773 ( 132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 119 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 271 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8403 (mp10) REVERT: A 1029 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8029 (ttp) REVERT: B 153 MET cc_start: 0.5910 (tpp) cc_final: 0.5605 (tpt) REVERT: B 726 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.9010 (tp) REVERT: B 727 LEU cc_start: 0.9599 (OUTLIER) cc_final: 0.9377 (pp) REVERT: B 988 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8329 (tm-30) REVERT: C 614 ASP cc_start: 0.8005 (t0) cc_final: 0.7538 (t0) REVERT: C 948 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8774 (mp) REVERT: E 45 GLU cc_start: 0.7243 (tp30) cc_final: 0.7024 (tp30) REVERT: I 33 MET cc_start: 0.3367 (mmp) cc_final: 0.2601 (ppp) outliers start: 127 outliers final: 99 residues processed: 238 average time/residue: 0.1327 time to fit residues: 55.2536 Evaluate side-chains 219 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 115 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain I residue 112 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 143 optimal weight: 0.6980 chunk 220 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 277 optimal weight: 0.6980 chunk 213 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 297 optimal weight: 1.9990 chunk 300 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.130720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.078901 restraints weight = 88886.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.080819 restraints weight = 38145.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.080484 restraints weight = 27069.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.081704 restraints weight = 19037.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.081825 restraints weight = 14916.368| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 30686 Z= 0.106 Angle : 0.547 11.680 41911 Z= 0.272 Chirality : 0.044 0.540 4934 Planarity : 0.003 0.048 5294 Dihedral : 5.066 59.804 5315 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.12 % Allowed : 20.82 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.14), residues: 3709 helix: 2.10 (0.22), residues: 667 sheet: 0.32 (0.17), residues: 1014 loop : -1.19 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 346 TYR 0.017 0.001 TYR A1067 PHE 0.016 0.001 PHE B 157 TRP 0.023 0.001 TRP B 353 HIS 0.002 0.000 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00237 (30582) covalent geometry : angle 0.52571 (41642) SS BOND : bond 0.00306 ( 43) SS BOND : angle 1.04611 ( 86) hydrogen bonds : bond 0.03934 ( 1103) hydrogen bonds : angle 4.93886 ( 3042) link_BETA1-4 : bond 0.00414 ( 17) link_BETA1-4 : angle 1.23086 ( 51) link_NAG-ASN : bond 0.00463 ( 44) link_NAG-ASN : angle 2.55796 ( 132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 117 time to evaluate : 0.827 Fit side-chains revert: symmetry clash REVERT: A 271 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8367 (mp10) REVERT: A 1029 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.7886 (ttp) REVERT: B 726 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8977 (tp) REVERT: B 727 LEU cc_start: 0.9548 (OUTLIER) cc_final: 0.9281 (pp) REVERT: B 1017 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8350 (tm-30) REVERT: C 614 ASP cc_start: 0.7782 (t0) cc_final: 0.7351 (t0) REVERT: I 33 MET cc_start: 0.3544 (mmp) cc_final: 0.2761 (ppp) outliers start: 100 outliers final: 86 residues processed: 210 average time/residue: 0.1279 time to fit residues: 48.1394 Evaluate side-chains 205 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 115 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 55 HIS Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain I residue 112 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 166 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 239 optimal weight: 0.9990 chunk 358 optimal weight: 30.0000 chunk 42 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 chunk 252 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 99 optimal weight: 0.4980 chunk 360 optimal weight: 30.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.130287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.078367 restraints weight = 88610.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.080670 restraints weight = 38660.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.080342 restraints weight = 25500.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.081391 restraints weight = 18349.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.081484 restraints weight = 15319.327| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30686 Z= 0.136 Angle : 0.551 11.771 41911 Z= 0.273 Chirality : 0.044 0.546 4934 Planarity : 0.003 0.047 5294 Dihedral : 4.966 59.455 5315 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.02 % Allowed : 20.75 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.14), residues: 3709 helix: 2.10 (0.21), residues: 673 sheet: 0.31 (0.17), residues: 1022 loop : -1.20 (0.14), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 346 TYR 0.015 0.001 TYR A1067 PHE 0.015 0.001 PHE B 157 TRP 0.024 0.001 TRP B 353 HIS 0.002 0.000 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00312 (30582) covalent geometry : angle 0.52888 (41642) SS BOND : bond 0.00328 ( 43) SS BOND : angle 1.15344 ( 86) hydrogen bonds : bond 0.03987 ( 1103) hydrogen bonds : angle 4.93016 ( 3042) link_BETA1-4 : bond 0.00341 ( 17) link_BETA1-4 : angle 1.21575 ( 51) link_NAG-ASN : bond 0.00438 ( 44) link_NAG-ASN : angle 2.56808 ( 132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 115 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4707 (tmm) cc_final: 0.4299 (tmm) REVERT: A 271 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8377 (mp10) REVERT: A 1029 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.7824 (ttp) REVERT: B 726 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8965 (tp) REVERT: B 727 LEU cc_start: 0.9555 (OUTLIER) cc_final: 0.9322 (pp) REVERT: C 614 ASP cc_start: 0.7854 (t0) cc_final: 0.7428 (t0) REVERT: I 33 MET cc_start: 0.3532 (mmp) cc_final: 0.2679 (ppp) outliers start: 97 outliers final: 90 residues processed: 204 average time/residue: 0.1233 time to fit residues: 45.3218 Evaluate side-chains 208 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 114 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 55 HIS Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain I residue 112 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 293 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 325 optimal weight: 40.0000 chunk 141 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 203 optimal weight: 2.9990 chunk 146 optimal weight: 0.0670 chunk 160 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.129683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.075198 restraints weight = 89387.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.076768 restraints weight = 38257.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.078000 restraints weight = 23693.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.078797 restraints weight = 17988.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.079145 restraints weight = 15501.645| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 30686 Z= 0.215 Angle : 0.605 12.845 41911 Z= 0.301 Chirality : 0.046 0.580 4934 Planarity : 0.003 0.049 5294 Dihedral : 5.190 59.723 5315 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.30 % Allowed : 20.50 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.14), residues: 3709 helix: 1.91 (0.21), residues: 672 sheet: 0.21 (0.17), residues: 1034 loop : -1.27 (0.14), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 346 TYR 0.016 0.001 TYR C1067 PHE 0.018 0.001 PHE A 106 TRP 0.024 0.001 TRP B 353 HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00500 (30582) covalent geometry : angle 0.58324 (41642) SS BOND : bond 0.00387 ( 43) SS BOND : angle 1.38556 ( 86) hydrogen bonds : bond 0.04505 ( 1103) hydrogen bonds : angle 5.10229 ( 3042) link_BETA1-4 : bond 0.00299 ( 17) link_BETA1-4 : angle 1.23828 ( 51) link_NAG-ASN : bond 0.00463 ( 44) link_NAG-ASN : angle 2.68707 ( 132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7182.79 seconds wall clock time: 123 minutes 40.63 seconds (7420.63 seconds total)