Starting phenix.real_space_refine on Fri Sep 19 11:39:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9elo_48157/09_2025/9elo_48157.cif Found real_map, /net/cci-nas-00/data/ceres_data/9elo_48157/09_2025/9elo_48157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9elo_48157/09_2025/9elo_48157.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9elo_48157/09_2025/9elo_48157.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9elo_48157/09_2025/9elo_48157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9elo_48157/09_2025/9elo_48157.map" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 16239 2.51 5 N 4140 2.21 5 O 4953 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25446 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1050, 8236 Classifications: {'peptide': 1050} Link IDs: {'PTRANS': 56, 'TRANS': 993} Chain breaks: 6 Chain: "B" Number of atoms: 8236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1050, 8236 Classifications: {'peptide': 1050} Link IDs: {'PTRANS': 56, 'TRANS': 993} Chain breaks: 6 Chain: "C" Number of atoms: 8236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1050, 8236 Classifications: {'peptide': 1050} Link IDs: {'PTRANS': 56, 'TRANS': 993} Chain breaks: 6 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 5.72, per 1000 atoms: 0.22 Number of scatterers: 25446 At special positions: 0 Unit cell: (134.266, 140.728, 185.962, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 4953 8.00 N 4140 7.00 C 16239 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 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 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " 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 M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " 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 R 2 " - " BMA R 3 " NAG-ASN " NAG A1301 " - " ASN A 616 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 354 " " NAG A1304 " - " ASN A 343 " " NAG A1306 " - " ASN A 30 " " NAG B1301 " - " ASN B 616 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 354 " " NAG B1304 " - " ASN B 343 " " NAG B1306 " - " ASN B 30 " " NAG C1301 " - " ASN C 616 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 354 " " NAG C1304 " - " ASN C 343 " " NAG C1306 " - " ASN C 30 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A1098 " " NAG F 1 " - " ASN A1134 " " NAG G 1 " - " ASN A 282 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN B 717 " " NAG J 1 " - " ASN B1098 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN B 282 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN C 717 " " NAG O 1 " - " ASN C1098 " " NAG P 1 " - " ASN C1134 " " NAG Q 1 " - " ASN C 282 " " NAG R 1 " - " ASN C 801 " NAG-THR " NAG A1305 " - " THR A 236 " " NAG B1305 " - " THR B 236 " " NAG C1305 " - " THR C 236 " Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 936.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5904 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 42 sheets defined 26.2% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.683A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 372 removed outlier: 3.830A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.579A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 626 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.047A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.178A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1150 removed outlier: 3.842A pdb=" N GLU A1150 " --> pdb=" O ASP A1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.683A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 372 removed outlier: 3.830A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.579A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 626 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.046A 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 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.178A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1139 through 1150 removed outlier: 3.842A pdb=" N GLU B1150 " --> pdb=" O ASP B1146 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.683A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 372 removed outlier: 3.830A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.579A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 626 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.046A 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 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.178A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1139 through 1150 removed outlier: 3.842A pdb=" N GLU C1150 " --> pdb=" O ASP C1146 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.277A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.857A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 65 removed outlier: 5.793A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.674A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.434A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.429A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.222A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.418A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.577A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.586A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.586A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.528A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 removed outlier: 6.049A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.489A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.858A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 63 through 65 removed outlier: 5.793A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.674A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.434A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.429A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.222A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.418A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.577A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.586A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.586A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.528A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.489A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.858A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 63 through 65 removed outlier: 5.793A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.674A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.434A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.222A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.418A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.577A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.585A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.585A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.528A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.488A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1091 hydrogen bonds defined for protein. 3075 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: 4.83 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5814 1.33 - 1.46: 7558 1.46 - 1.59: 12521 1.59 - 1.71: 0 1.71 - 1.84: 144 Bond restraints: 26037 Sorted by residual: bond pdb=" CA SER C 746 " pdb=" CB SER C 746 " ideal model delta sigma weight residual 1.529 1.463 0.066 1.43e-02 4.89e+03 2.12e+01 bond pdb=" CA SER A 746 " pdb=" CB SER A 746 " ideal model delta sigma weight residual 1.529 1.464 0.065 1.43e-02 4.89e+03 2.09e+01 bond pdb=" CA SER B 746 " pdb=" CB SER B 746 " ideal model delta sigma weight residual 1.529 1.464 0.065 1.43e-02 4.89e+03 2.08e+01 bond pdb=" N PHE C 855 " pdb=" CA PHE C 855 " ideal model delta sigma weight residual 1.464 1.514 -0.050 1.30e-02 5.92e+03 1.49e+01 bond pdb=" N PHE A 855 " pdb=" CA PHE A 855 " ideal model delta sigma weight residual 1.464 1.513 -0.050 1.30e-02 5.92e+03 1.46e+01 ... (remaining 26032 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 33306 2.58 - 5.16: 1860 5.16 - 7.74: 213 7.74 - 10.31: 27 10.31 - 12.89: 12 Bond angle restraints: 35418 Sorted by residual: angle pdb=" CA PHE B 855 " pdb=" CB PHE B 855 " pdb=" CG PHE B 855 " ideal model delta sigma weight residual 113.80 123.34 -9.54 1.00e+00 1.00e+00 9.09e+01 angle pdb=" CA PHE C 855 " pdb=" CB PHE C 855 " pdb=" CG PHE C 855 " ideal model delta sigma weight residual 113.80 123.33 -9.53 1.00e+00 1.00e+00 9.09e+01 angle pdb=" CA PHE A 855 " pdb=" CB PHE A 855 " pdb=" CG PHE A 855 " ideal model delta sigma weight residual 113.80 123.32 -9.52 1.00e+00 1.00e+00 9.06e+01 angle pdb=" N PHE A 855 " pdb=" CA PHE A 855 " pdb=" CB PHE A 855 " ideal model delta sigma weight residual 110.53 119.00 -8.47 1.22e+00 6.72e-01 4.82e+01 angle pdb=" N PHE C 855 " pdb=" CA PHE C 855 " pdb=" CB PHE C 855 " ideal model delta sigma weight residual 110.53 118.99 -8.46 1.22e+00 6.72e-01 4.81e+01 ... (remaining 35413 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.98: 15420 20.98 - 41.96: 555 41.96 - 62.93: 135 62.93 - 83.91: 67 83.91 - 104.89: 41 Dihedral angle restraints: 16218 sinusoidal: 7044 harmonic: 9174 Sorted by residual: dihedral pdb=" CD ARG C 454 " pdb=" NE ARG C 454 " pdb=" CZ ARG C 454 " pdb=" NH1 ARG C 454 " ideal model delta sinusoidal sigma weight residual 0.00 78.37 -78.37 1 1.00e+01 1.00e-02 7.67e+01 dihedral pdb=" CD ARG A 454 " pdb=" NE ARG A 454 " pdb=" CZ ARG A 454 " pdb=" NH1 ARG A 454 " ideal model delta sinusoidal sigma weight residual 0.00 78.34 -78.34 1 1.00e+01 1.00e-02 7.66e+01 dihedral pdb=" CD ARG B 454 " pdb=" NE ARG B 454 " pdb=" CZ ARG B 454 " pdb=" NH1 ARG B 454 " ideal model delta sinusoidal sigma weight residual 0.00 78.33 -78.33 1 1.00e+01 1.00e-02 7.66e+01 ... (remaining 16215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 3551 0.099 - 0.199: 541 0.199 - 0.298: 54 0.298 - 0.398: 6 0.398 - 0.497: 3 Chirality restraints: 4155 Sorted by residual: chirality pdb=" CA PHE A 855 " pdb=" N PHE A 855 " pdb=" C PHE A 855 " pdb=" CB PHE A 855 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.17e+00 chirality pdb=" CA PHE B 855 " pdb=" N PHE B 855 " pdb=" C PHE B 855 " pdb=" CB PHE B 855 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.14e+00 chirality pdb=" CA PHE C 855 " pdb=" N PHE C 855 " pdb=" C PHE C 855 " pdb=" CB PHE C 855 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.11e+00 ... (remaining 4152 not shown) Planarity restraints: 4527 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 454 " -1.076 9.50e-02 1.11e+02 4.82e-01 1.40e+02 pdb=" NE ARG B 454 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG B 454 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 454 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG B 454 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 454 " -1.076 9.50e-02 1.11e+02 4.82e-01 1.40e+02 pdb=" NE ARG C 454 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG C 454 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG C 454 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG C 454 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 454 " -1.076 9.50e-02 1.11e+02 4.82e-01 1.40e+02 pdb=" NE ARG A 454 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG A 454 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 454 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 454 " -0.020 2.00e-02 2.50e+03 ... (remaining 4524 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 12 2.23 - 2.90: 9851 2.90 - 3.57: 34454 3.57 - 4.23: 60324 4.23 - 4.90: 100868 Nonbonded interactions: 205509 Sorted by model distance: nonbonded pdb=" OD2 ASP A 745 " pdb=" NH2 ARG C 319 " model vdw 1.564 3.120 nonbonded pdb=" NH2 ARG B 319 " pdb=" OD2 ASP C 745 " model vdw 1.564 3.120 nonbonded pdb=" NH2 ARG A 319 " pdb=" OD2 ASP B 745 " model vdw 1.565 3.120 nonbonded pdb=" NH1 ARG C 454 " pdb=" CG2 THR C 470 " model vdw 1.942 3.540 nonbonded pdb=" NH1 ARG B 454 " pdb=" CG2 THR B 470 " model vdw 1.942 3.540 ... (remaining 205504 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.580 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: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 22.160 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.070 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:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 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 : 0.008 0.076 26130 Z= 0.378 Angle : 1.315 12.920 35655 Z= 0.783 Chirality : 0.071 0.497 4155 Planarity : 0.015 0.482 4497 Dihedral : 13.704 104.891 10197 Min Nonbonded Distance : 1.564 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.11 % Allowed : 5.96 % Favored : 93.93 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.14), residues: 3108 helix: 1.02 (0.17), residues: 723 sheet: 1.60 (0.21), residues: 555 loop : 0.06 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG A 328 TYR 0.058 0.005 TYR C 451 PHE 0.037 0.004 PHE C 216 TRP 0.037 0.007 TRP A 436 HIS 0.010 0.002 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00754 (26037) covalent geometry : angle 1.29275 (35418) SS BOND : bond 0.00460 ( 39) SS BOND : angle 2.56251 ( 78) hydrogen bonds : bond 0.13718 ( 1055) hydrogen bonds : angle 7.64749 ( 3075) link_BETA1-4 : bond 0.01548 ( 21) link_BETA1-4 : angle 4.21726 ( 63) link_NAG-ASN : bond 0.00677 ( 30) link_NAG-ASN : angle 2.38458 ( 90) link_NAG-THR : bond 0.01417 ( 3) link_NAG-THR : angle 7.20920 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 467 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.6116 (p90) cc_final: 0.5817 (p90) REVERT: A 282 ASN cc_start: 0.7265 (m-40) cc_final: 0.6952 (t0) REVERT: A 399 SER cc_start: 0.7127 (t) cc_final: 0.6607 (m) REVERT: A 513 LEU cc_start: 0.7850 (mt) cc_final: 0.7564 (mt) REVERT: A 534 VAL cc_start: 0.8077 (m) cc_final: 0.7765 (p) REVERT: A 540 ASN cc_start: 0.8288 (m-40) cc_final: 0.7983 (m110) REVERT: A 646 ARG cc_start: 0.8088 (mmm-85) cc_final: 0.7772 (tpp80) REVERT: A 654 GLU cc_start: 0.7807 (tt0) cc_final: 0.7484 (tm-30) REVERT: A 779 GLN cc_start: 0.8019 (tp40) cc_final: 0.7679 (tm-30) REVERT: A 780 GLU cc_start: 0.8323 (mm-30) cc_final: 0.8099 (mm-30) REVERT: A 904 TYR cc_start: 0.7162 (t80) cc_final: 0.6753 (t80) REVERT: A 964 LYS cc_start: 0.7989 (tptt) cc_final: 0.7549 (mtmt) REVERT: A 1005 GLN cc_start: 0.8682 (mt0) cc_final: 0.8464 (mt0) REVERT: A 1045 LYS cc_start: 0.8277 (mmmt) cc_final: 0.7625 (ttpt) REVERT: A 1073 LYS cc_start: 0.8387 (tttt) cc_final: 0.8115 (ttmt) REVERT: A 1125 ASN cc_start: 0.8105 (m-40) cc_final: 0.7851 (p0) REVERT: B 88 ASP cc_start: 0.7611 (m-30) cc_final: 0.7406 (m-30) REVERT: B 190 ARG cc_start: 0.6273 (mtt90) cc_final: 0.5848 (mtp85) REVERT: B 282 ASN cc_start: 0.7220 (m-40) cc_final: 0.6966 (t0) REVERT: B 399 SER cc_start: 0.7146 (t) cc_final: 0.6813 (m) REVERT: B 534 VAL cc_start: 0.8078 (m) cc_final: 0.7764 (p) REVERT: B 554 LYS cc_start: 0.7590 (tttm) cc_final: 0.7368 (ptmm) REVERT: B 646 ARG cc_start: 0.8109 (mmm-85) cc_final: 0.7810 (tpp80) REVERT: B 654 GLU cc_start: 0.7761 (tt0) cc_final: 0.7468 (tm-30) REVERT: B 779 GLN cc_start: 0.7990 (tp40) cc_final: 0.7664 (tm-30) REVERT: B 964 LYS cc_start: 0.8029 (tptt) cc_final: 0.7644 (mttt) REVERT: B 1005 GLN cc_start: 0.8638 (mt0) cc_final: 0.8389 (mt0) REVERT: B 1045 LYS cc_start: 0.8270 (mmmt) cc_final: 0.7648 (ttpt) REVERT: B 1073 LYS cc_start: 0.8404 (tttt) cc_final: 0.8106 (ttmt) REVERT: B 1092 GLU cc_start: 0.7770 (pt0) cc_final: 0.7517 (mt-10) REVERT: B 1101 HIS cc_start: 0.8124 (m90) cc_final: 0.7578 (m-70) REVERT: B 1125 ASN cc_start: 0.8182 (m-40) cc_final: 0.7843 (p0) REVERT: B 1127 ASP cc_start: 0.6981 (p0) cc_final: 0.6762 (m-30) REVERT: C 59 PHE cc_start: 0.8764 (m-80) cc_final: 0.8516 (m-80) REVERT: C 190 ARG cc_start: 0.6255 (mtt90) cc_final: 0.5808 (mtp85) REVERT: C 238 PHE cc_start: 0.6035 (p90) cc_final: 0.5645 (p90) REVERT: C 389 ASP cc_start: 0.8425 (m-30) cc_final: 0.8131 (m-30) REVERT: C 399 SER cc_start: 0.7179 (t) cc_final: 0.6649 (m) REVERT: C 513 LEU cc_start: 0.7853 (mt) cc_final: 0.7574 (mt) REVERT: C 534 VAL cc_start: 0.8037 (m) cc_final: 0.7698 (p) REVERT: C 554 LYS cc_start: 0.7575 (tttm) cc_final: 0.7331 (ptmm) REVERT: C 646 ARG cc_start: 0.8079 (mmm-85) cc_final: 0.7761 (tpp80) REVERT: C 779 GLN cc_start: 0.8107 (tp40) cc_final: 0.7747 (tm-30) REVERT: C 964 LYS cc_start: 0.7901 (tptt) cc_final: 0.7494 (mttt) REVERT: C 1005 GLN cc_start: 0.8696 (mt0) cc_final: 0.8471 (mt0) REVERT: C 1045 LYS cc_start: 0.8221 (mmmt) cc_final: 0.7607 (ttpt) REVERT: C 1073 LYS cc_start: 0.8360 (tttt) cc_final: 0.8048 (ttmt) REVERT: C 1101 HIS cc_start: 0.8094 (m90) cc_final: 0.7876 (m-70) REVERT: C 1125 ASN cc_start: 0.8079 (m-40) cc_final: 0.7773 (p0) outliers start: 3 outliers final: 0 residues processed: 470 average time/residue: 0.4652 time to fit residues: 261.2576 Evaluate side-chains 286 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1074 ASN A1101 HIS B 540 ASN B 606 ASN B 675 GLN B1074 ASN C 540 ASN C1074 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.193815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.124200 restraints weight = 27727.304| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.27 r_work: 0.3229 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26130 Z= 0.173 Angle : 0.738 9.828 35655 Z= 0.373 Chirality : 0.050 0.330 4155 Planarity : 0.005 0.037 4497 Dihedral : 8.049 64.751 4491 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.29 % Favored : 98.62 % Rotamer: Outliers : 2.20 % Allowed : 8.81 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.14), residues: 3108 helix: 2.52 (0.19), residues: 681 sheet: 1.00 (0.19), residues: 627 loop : -0.17 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 237 TYR 0.023 0.002 TYR A 636 PHE 0.026 0.002 PHE B 565 TRP 0.014 0.002 TRP C 64 HIS 0.007 0.001 HIS A1101 Details of bonding type rmsd covalent geometry : bond 0.00391 (26037) covalent geometry : angle 0.69909 (35418) SS BOND : bond 0.00483 ( 39) SS BOND : angle 1.57216 ( 78) hydrogen bonds : bond 0.05405 ( 1055) hydrogen bonds : angle 6.27859 ( 3075) link_BETA1-4 : bond 0.00925 ( 21) link_BETA1-4 : angle 3.59127 ( 63) link_NAG-ASN : bond 0.01036 ( 30) link_NAG-ASN : angle 3.31638 ( 90) link_NAG-THR : bond 0.01104 ( 3) link_NAG-THR : angle 4.59296 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 327 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.6749 (OUTLIER) cc_final: 0.6536 (tp) REVERT: A 282 ASN cc_start: 0.7164 (m-40) cc_final: 0.6879 (t0) REVERT: A 294 ASP cc_start: 0.7509 (m-30) cc_final: 0.7289 (m-30) REVERT: A 399 SER cc_start: 0.7217 (t) cc_final: 0.6541 (p) REVERT: A 534 VAL cc_start: 0.8275 (m) cc_final: 0.7981 (p) REVERT: A 540 ASN cc_start: 0.8254 (m-40) cc_final: 0.8009 (m110) REVERT: A 619 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7799 (mt-10) REVERT: A 646 ARG cc_start: 0.8436 (mmm-85) cc_final: 0.8099 (mpp80) REVERT: A 654 GLU cc_start: 0.7789 (tt0) cc_final: 0.7530 (tm-30) REVERT: A 740 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8614 (ttt) REVERT: A 779 GLN cc_start: 0.8203 (tp40) cc_final: 0.7773 (tm-30) REVERT: A 888 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7085 (t80) REVERT: A 964 LYS cc_start: 0.7988 (tptt) cc_final: 0.7602 (mttt) REVERT: A 1002 GLN cc_start: 0.8304 (tt0) cc_final: 0.7549 (tp-100) REVERT: A 1005 GLN cc_start: 0.8706 (mt0) cc_final: 0.8497 (mt0) REVERT: A 1010 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.7167 (mp10) REVERT: A 1045 LYS cc_start: 0.8340 (mmmt) cc_final: 0.7795 (ttpt) REVERT: A 1073 LYS cc_start: 0.8386 (tttt) cc_final: 0.8160 (ttmt) REVERT: A 1128 VAL cc_start: 0.8690 (OUTLIER) cc_final: 0.8434 (t) REVERT: B 88 ASP cc_start: 0.7797 (m-30) cc_final: 0.7493 (m-30) REVERT: B 282 ASN cc_start: 0.7255 (m-40) cc_final: 0.6929 (t0) REVERT: B 399 SER cc_start: 0.7275 (t) cc_final: 0.6544 (p) REVERT: B 534 VAL cc_start: 0.8220 (m) cc_final: 0.7926 (p) REVERT: B 554 LYS cc_start: 0.7674 (tttm) cc_final: 0.7463 (ptmm) REVERT: B 646 ARG cc_start: 0.8437 (mmm-85) cc_final: 0.8158 (tpp80) REVERT: B 654 GLU cc_start: 0.7830 (tt0) cc_final: 0.7499 (tm-30) REVERT: B 779 GLN cc_start: 0.8152 (tp40) cc_final: 0.7711 (tm-30) REVERT: B 888 PHE cc_start: 0.8170 (OUTLIER) cc_final: 0.6725 (t80) REVERT: B 964 LYS cc_start: 0.8052 (tptt) cc_final: 0.7697 (mttt) REVERT: B 1002 GLN cc_start: 0.8254 (tt0) cc_final: 0.7489 (tp-100) REVERT: B 1005 GLN cc_start: 0.8645 (mt0) cc_final: 0.8440 (mt0) REVERT: B 1010 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7155 (mp10) REVERT: B 1045 LYS cc_start: 0.8361 (mmmt) cc_final: 0.7811 (ttpt) REVERT: B 1073 LYS cc_start: 0.8392 (tttt) cc_final: 0.8118 (ttmt) REVERT: B 1125 ASN cc_start: 0.8180 (m-40) cc_final: 0.7958 (p0) REVERT: C 59 PHE cc_start: 0.8784 (m-80) cc_final: 0.8533 (m-80) REVERT: C 118 LEU cc_start: 0.6787 (OUTLIER) cc_final: 0.6585 (tp) REVERT: C 319 ARG cc_start: 0.8283 (mtp-110) cc_final: 0.7798 (ttm-80) REVERT: C 389 ASP cc_start: 0.8482 (m-30) cc_final: 0.8222 (m-30) REVERT: C 399 SER cc_start: 0.7338 (t) cc_final: 0.6625 (p) REVERT: C 513 LEU cc_start: 0.7831 (mt) cc_final: 0.7620 (mt) REVERT: C 528 LYS cc_start: 0.7709 (mttm) cc_final: 0.7500 (mtpp) REVERT: C 534 VAL cc_start: 0.8252 (m) cc_final: 0.7944 (p) REVERT: C 554 LYS cc_start: 0.7688 (tttm) cc_final: 0.7468 (ptmm) REVERT: C 558 LYS cc_start: 0.7711 (mmtt) cc_final: 0.7167 (mmtp) REVERT: C 654 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7669 (tt0) REVERT: C 779 GLN cc_start: 0.8210 (tp40) cc_final: 0.7750 (tm-30) REVERT: C 888 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.6896 (t80) REVERT: C 964 LYS cc_start: 0.7955 (tptt) cc_final: 0.7519 (mttt) REVERT: C 1002 GLN cc_start: 0.8307 (tt0) cc_final: 0.7549 (tp40) REVERT: C 1005 GLN cc_start: 0.8701 (mt0) cc_final: 0.8448 (mt0) REVERT: C 1010 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7182 (mp10) REVERT: C 1045 LYS cc_start: 0.8298 (mmmt) cc_final: 0.7758 (ttpt) REVERT: C 1073 LYS cc_start: 0.8360 (tttt) cc_final: 0.8079 (ttmt) REVERT: C 1101 HIS cc_start: 0.8339 (m90) cc_final: 0.8098 (m-70) outliers start: 61 outliers final: 24 residues processed: 364 average time/residue: 0.5254 time to fit residues: 226.9747 Evaluate side-chains 312 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 277 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 89 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 76 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 216 optimal weight: 6.9990 chunk 227 optimal weight: 5.9990 chunk 206 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 283 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 544 ASN A 935 GLN A1101 HIS B 544 ASN B1101 HIS B1119 ASN C 544 ASN C1002 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.186559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.115129 restraints weight = 27559.961| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.40 r_work: 0.3120 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 26130 Z= 0.306 Angle : 0.759 9.297 35655 Z= 0.389 Chirality : 0.053 0.356 4155 Planarity : 0.005 0.059 4497 Dihedral : 7.017 54.185 4491 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.03 % Allowed : 8.78 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.14), residues: 3108 helix: 2.02 (0.19), residues: 705 sheet: 0.64 (0.19), residues: 654 loop : -0.49 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 815 TYR 0.025 0.002 TYR B1067 PHE 0.023 0.003 PHE B 541 TRP 0.016 0.002 TRP A 64 HIS 0.008 0.002 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00744 (26037) covalent geometry : angle 0.73010 (35418) SS BOND : bond 0.00517 ( 39) SS BOND : angle 1.59608 ( 78) hydrogen bonds : bond 0.06239 ( 1055) hydrogen bonds : angle 6.38589 ( 3075) link_BETA1-4 : bond 0.01055 ( 21) link_BETA1-4 : angle 3.49188 ( 63) link_NAG-ASN : bond 0.00490 ( 30) link_NAG-ASN : angle 2.53712 ( 90) link_NAG-THR : bond 0.01071 ( 3) link_NAG-THR : angle 4.06770 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 280 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8481 (tt0) cc_final: 0.8232 (tt0) REVERT: A 282 ASN cc_start: 0.7285 (m-40) cc_final: 0.7018 (t0) REVERT: A 328 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.5608 (mmp-170) REVERT: A 399 SER cc_start: 0.7401 (t) cc_final: 0.6826 (p) REVERT: A 534 VAL cc_start: 0.8451 (m) cc_final: 0.8138 (p) REVERT: A 646 ARG cc_start: 0.8530 (mmm-85) cc_final: 0.8237 (mpp80) REVERT: A 654 GLU cc_start: 0.7791 (tt0) cc_final: 0.7415 (tm-30) REVERT: A 779 GLN cc_start: 0.8306 (tp40) cc_final: 0.7852 (tm-30) REVERT: A 955 ASN cc_start: 0.8337 (m-40) cc_final: 0.8119 (m110) REVERT: A 964 LYS cc_start: 0.8105 (tptt) cc_final: 0.7722 (mtmt) REVERT: A 1002 GLN cc_start: 0.8290 (tt0) cc_final: 0.7621 (tp-100) REVERT: A 1005 GLN cc_start: 0.8685 (mt0) cc_final: 0.8485 (mt0) REVERT: A 1010 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7105 (mp10) REVERT: A 1045 LYS cc_start: 0.8322 (mmmt) cc_final: 0.7959 (mppt) REVERT: B 88 ASP cc_start: 0.7774 (m-30) cc_final: 0.7432 (m-30) REVERT: B 282 ASN cc_start: 0.7296 (m-40) cc_final: 0.7021 (t0) REVERT: B 399 SER cc_start: 0.7457 (t) cc_final: 0.6862 (p) REVERT: B 534 VAL cc_start: 0.8374 (m) cc_final: 0.8089 (p) REVERT: B 554 LYS cc_start: 0.7859 (tttm) cc_final: 0.7607 (ptmm) REVERT: B 558 LYS cc_start: 0.7767 (mmtt) cc_final: 0.7488 (mmtp) REVERT: B 571 ASP cc_start: 0.7423 (m-30) cc_final: 0.7099 (m-30) REVERT: B 646 ARG cc_start: 0.8560 (mmm-85) cc_final: 0.8235 (mpp80) REVERT: B 654 GLU cc_start: 0.7871 (tt0) cc_final: 0.7418 (tm-30) REVERT: B 779 GLN cc_start: 0.8221 (tp40) cc_final: 0.7793 (tm-30) REVERT: B 964 LYS cc_start: 0.8193 (tptt) cc_final: 0.7807 (mttt) REVERT: B 1002 GLN cc_start: 0.8253 (tt0) cc_final: 0.7452 (tp-100) REVERT: B 1010 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7130 (mp10) REVERT: B 1045 LYS cc_start: 0.8341 (mmmt) cc_final: 0.7752 (ttpt) REVERT: B 1125 ASN cc_start: 0.8362 (m-40) cc_final: 0.8069 (p0) REVERT: C 319 ARG cc_start: 0.8138 (mtp-110) cc_final: 0.7732 (ttm-80) REVERT: C 378 LYS cc_start: 0.7370 (pttt) cc_final: 0.7150 (pttt) REVERT: C 399 SER cc_start: 0.7474 (t) cc_final: 0.6962 (p) REVERT: C 534 VAL cc_start: 0.8457 (m) cc_final: 0.8137 (p) REVERT: C 554 LYS cc_start: 0.7823 (tttm) cc_final: 0.7612 (ptmm) REVERT: C 558 LYS cc_start: 0.7772 (mmtt) cc_final: 0.7405 (mmtp) REVERT: C 646 ARG cc_start: 0.8401 (mmm-85) cc_final: 0.8152 (mpp80) REVERT: C 654 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7656 (tt0) REVERT: C 675 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7571 (mt0) REVERT: C 779 GLN cc_start: 0.8246 (tp40) cc_final: 0.7786 (tm-30) REVERT: C 964 LYS cc_start: 0.8036 (tptt) cc_final: 0.7577 (mttt) REVERT: C 1002 GLN cc_start: 0.8269 (tt0) cc_final: 0.7594 (tp40) REVERT: C 1010 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7225 (mp10) REVERT: C 1045 LYS cc_start: 0.8358 (mmmt) cc_final: 0.7767 (ttpt) REVERT: C 1073 LYS cc_start: 0.8350 (tttt) cc_final: 0.8011 (ttmt) outliers start: 84 outliers final: 51 residues processed: 336 average time/residue: 0.5775 time to fit residues: 229.6061 Evaluate side-chains 306 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 249 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 71 optimal weight: 0.6980 chunk 303 optimal weight: 0.5980 chunk 121 optimal weight: 0.5980 chunk 156 optimal weight: 2.9990 chunk 293 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 206 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 118 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 229 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN A1101 HIS A1119 ASN B1005 GLN B1101 HIS C1119 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.189473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.117503 restraints weight = 27476.322| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.09 r_work: 0.3165 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26130 Z= 0.141 Angle : 0.616 8.408 35655 Z= 0.313 Chirality : 0.046 0.319 4155 Planarity : 0.004 0.058 4497 Dihedral : 6.021 44.705 4491 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.81 % Allowed : 10.36 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.15), residues: 3108 helix: 2.34 (0.19), residues: 705 sheet: 0.47 (0.19), residues: 651 loop : -0.40 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 319 TYR 0.031 0.002 TYR B 636 PHE 0.015 0.001 PHE C 898 TRP 0.010 0.001 TRP A 64 HIS 0.002 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00314 (26037) covalent geometry : angle 0.58777 (35418) SS BOND : bond 0.00222 ( 39) SS BOND : angle 1.11515 ( 78) hydrogen bonds : bond 0.04779 ( 1055) hydrogen bonds : angle 5.99000 ( 3075) link_BETA1-4 : bond 0.01017 ( 21) link_BETA1-4 : angle 3.21069 ( 63) link_NAG-ASN : bond 0.00951 ( 30) link_NAG-ASN : angle 2.37465 ( 90) link_NAG-THR : bond 0.00699 ( 3) link_NAG-THR : angle 3.03343 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 284 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 ASN cc_start: 0.7264 (m-40) cc_final: 0.7010 (t0) REVERT: A 321 GLN cc_start: 0.8356 (mm110) cc_final: 0.8148 (mm110) REVERT: A 399 SER cc_start: 0.7338 (t) cc_final: 0.6822 (p) REVERT: A 534 VAL cc_start: 0.8360 (m) cc_final: 0.8079 (p) REVERT: A 646 ARG cc_start: 0.8524 (mmm-85) cc_final: 0.8195 (mpp80) REVERT: A 654 GLU cc_start: 0.7823 (tt0) cc_final: 0.7512 (tm-30) REVERT: A 779 GLN cc_start: 0.8210 (tp40) cc_final: 0.7728 (tm-30) REVERT: A 955 ASN cc_start: 0.8284 (m-40) cc_final: 0.8063 (m110) REVERT: A 964 LYS cc_start: 0.7981 (tptt) cc_final: 0.7611 (mttt) REVERT: A 1002 GLN cc_start: 0.8234 (tt0) cc_final: 0.7630 (tp-100) REVERT: A 1010 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7129 (mp10) REVERT: A 1045 LYS cc_start: 0.8355 (mmmt) cc_final: 0.7784 (ttpt) REVERT: A 1073 LYS cc_start: 0.8371 (tttt) cc_final: 0.8115 (ttmt) REVERT: A 1128 VAL cc_start: 0.8766 (OUTLIER) cc_final: 0.8477 (t) REVERT: A 1138 TYR cc_start: 0.8157 (m-80) cc_final: 0.7914 (m-80) REVERT: B 88 ASP cc_start: 0.7556 (m-30) cc_final: 0.7339 (m-30) REVERT: B 399 SER cc_start: 0.7390 (t) cc_final: 0.6808 (p) REVERT: B 534 VAL cc_start: 0.8330 (m) cc_final: 0.8051 (p) REVERT: B 554 LYS cc_start: 0.7831 (tttm) cc_final: 0.7614 (ptmm) REVERT: B 558 LYS cc_start: 0.7744 (mmtt) cc_final: 0.7505 (mmtp) REVERT: B 646 ARG cc_start: 0.8552 (mmm-85) cc_final: 0.8236 (mpp80) REVERT: B 654 GLU cc_start: 0.7815 (tt0) cc_final: 0.7410 (tm-30) REVERT: B 779 GLN cc_start: 0.8138 (tp40) cc_final: 0.7678 (tm-30) REVERT: B 921 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8378 (tttp) REVERT: B 955 ASN cc_start: 0.8235 (m-40) cc_final: 0.8020 (m-40) REVERT: B 964 LYS cc_start: 0.8054 (tptt) cc_final: 0.7639 (mttt) REVERT: B 1002 GLN cc_start: 0.8166 (tt0) cc_final: 0.7427 (tp-100) REVERT: B 1010 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7161 (mp10) REVERT: B 1045 LYS cc_start: 0.8345 (mmmt) cc_final: 0.7832 (ttpt) REVERT: B 1073 LYS cc_start: 0.8417 (tttt) cc_final: 0.8150 (ttmt) REVERT: B 1125 ASN cc_start: 0.8326 (m-40) cc_final: 0.8009 (p0) REVERT: C 319 ARG cc_start: 0.8107 (mtp-110) cc_final: 0.7628 (ttm-80) REVERT: C 378 LYS cc_start: 0.7370 (pttt) cc_final: 0.7130 (pttt) REVERT: C 399 SER cc_start: 0.7462 (t) cc_final: 0.6949 (p) REVERT: C 534 VAL cc_start: 0.8353 (m) cc_final: 0.8054 (p) REVERT: C 554 LYS cc_start: 0.7797 (tttm) cc_final: 0.7588 (ptmm) REVERT: C 558 LYS cc_start: 0.7748 (mmtt) cc_final: 0.7373 (mmtp) REVERT: C 646 ARG cc_start: 0.8376 (mmm-85) cc_final: 0.8122 (mpp80) REVERT: C 654 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7654 (tt0) REVERT: C 779 GLN cc_start: 0.8214 (tp40) cc_final: 0.7729 (tm-30) REVERT: C 964 LYS cc_start: 0.7977 (tptt) cc_final: 0.7556 (mttt) REVERT: C 1002 GLN cc_start: 0.8235 (tt0) cc_final: 0.7620 (tp40) REVERT: C 1010 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7153 (mp10) REVERT: C 1045 LYS cc_start: 0.8352 (mmmt) cc_final: 0.7843 (ttpt) REVERT: C 1073 LYS cc_start: 0.8325 (tttt) cc_final: 0.8017 (ttmt) REVERT: C 1101 HIS cc_start: 0.8577 (m90) cc_final: 0.8293 (m-70) outliers start: 50 outliers final: 31 residues processed: 315 average time/residue: 0.6085 time to fit residues: 225.5314 Evaluate side-chains 309 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 272 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 23 optimal weight: 2.9990 chunk 137 optimal weight: 8.9990 chunk 153 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 297 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 271 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 314 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1101 HIS B1101 HIS C 321 GLN C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.184920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.112603 restraints weight = 27467.955| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.08 r_work: 0.3097 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 26130 Z= 0.299 Angle : 0.716 9.091 35655 Z= 0.364 Chirality : 0.051 0.242 4155 Planarity : 0.005 0.070 4497 Dihedral : 6.254 46.116 4491 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.78 % Allowed : 10.58 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.15), residues: 3108 helix: 2.07 (0.19), residues: 684 sheet: 0.26 (0.18), residues: 699 loop : -0.67 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 319 TYR 0.025 0.002 TYR B1067 PHE 0.024 0.002 PHE A 329 TRP 0.016 0.003 TRP A 64 HIS 0.009 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00731 (26037) covalent geometry : angle 0.69213 (35418) SS BOND : bond 0.00492 ( 39) SS BOND : angle 1.25445 ( 78) hydrogen bonds : bond 0.06010 ( 1055) hydrogen bonds : angle 6.27125 ( 3075) link_BETA1-4 : bond 0.01031 ( 21) link_BETA1-4 : angle 3.18716 ( 63) link_NAG-ASN : bond 0.00551 ( 30) link_NAG-ASN : angle 2.37083 ( 90) link_NAG-THR : bond 0.00930 ( 3) link_NAG-THR : angle 3.04668 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 268 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8470 (tm-30) cc_final: 0.8216 (tt0) REVERT: A 328 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7007 (mmp-170) REVERT: A 399 SER cc_start: 0.7496 (t) cc_final: 0.7008 (p) REVERT: A 534 VAL cc_start: 0.8458 (m) cc_final: 0.8173 (p) REVERT: A 646 ARG cc_start: 0.8521 (mmm-85) cc_final: 0.8225 (mpp80) REVERT: A 654 GLU cc_start: 0.7877 (tt0) cc_final: 0.7443 (tm-30) REVERT: A 779 GLN cc_start: 0.8264 (tp40) cc_final: 0.7814 (tm-30) REVERT: A 955 ASN cc_start: 0.8338 (m-40) cc_final: 0.8115 (m110) REVERT: A 964 LYS cc_start: 0.8125 (tptt) cc_final: 0.7774 (mtmt) REVERT: A 1002 GLN cc_start: 0.8260 (tt0) cc_final: 0.7626 (tp-100) REVERT: A 1010 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7178 (mp10) REVERT: A 1045 LYS cc_start: 0.8368 (mmmt) cc_final: 0.7782 (ttpt) REVERT: B 88 ASP cc_start: 0.7588 (m-30) cc_final: 0.7378 (m-30) REVERT: B 281 GLU cc_start: 0.8029 (mp0) cc_final: 0.7782 (pm20) REVERT: B 328 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.5932 (mmp-170) REVERT: B 399 SER cc_start: 0.7464 (t) cc_final: 0.6948 (p) REVERT: B 534 VAL cc_start: 0.8391 (m) cc_final: 0.8140 (p) REVERT: B 554 LYS cc_start: 0.7943 (tttm) cc_final: 0.7725 (ptmm) REVERT: B 646 ARG cc_start: 0.8589 (mmm-85) cc_final: 0.8282 (mpp80) REVERT: B 654 GLU cc_start: 0.7863 (tt0) cc_final: 0.7368 (tm-30) REVERT: B 779 GLN cc_start: 0.8220 (tp40) cc_final: 0.7780 (tm-30) REVERT: B 955 ASN cc_start: 0.8278 (m-40) cc_final: 0.8054 (m110) REVERT: B 964 LYS cc_start: 0.8210 (tptt) cc_final: 0.7885 (mttt) REVERT: B 1002 GLN cc_start: 0.8224 (tt0) cc_final: 0.7501 (tp-100) REVERT: B 1010 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7204 (mp10) REVERT: B 1045 LYS cc_start: 0.8360 (mmmt) cc_final: 0.7837 (ttpt) REVERT: B 1073 LYS cc_start: 0.8425 (tttt) cc_final: 0.8136 (ttmt) REVERT: B 1125 ASN cc_start: 0.8431 (m-40) cc_final: 0.8137 (p0) REVERT: C 319 ARG cc_start: 0.8103 (mtp-110) cc_final: 0.7705 (ttm-80) REVERT: C 399 SER cc_start: 0.7473 (t) cc_final: 0.6972 (p) REVERT: C 534 VAL cc_start: 0.8441 (m) cc_final: 0.8150 (p) REVERT: C 554 LYS cc_start: 0.7919 (tttm) cc_final: 0.7697 (ptmm) REVERT: C 558 LYS cc_start: 0.7771 (mmtt) cc_final: 0.7402 (mmtp) REVERT: C 654 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7690 (tt0) REVERT: C 779 GLN cc_start: 0.8262 (tp40) cc_final: 0.7799 (tm-30) REVERT: C 964 LYS cc_start: 0.8090 (tptt) cc_final: 0.7696 (mttt) REVERT: C 1002 GLN cc_start: 0.8328 (tt0) cc_final: 0.7615 (tp40) REVERT: C 1010 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.7252 (mp10) REVERT: C 1045 LYS cc_start: 0.8382 (mmmt) cc_final: 0.7826 (ttpt) REVERT: C 1073 LYS cc_start: 0.8387 (tttt) cc_final: 0.8039 (ttmt) outliers start: 77 outliers final: 46 residues processed: 320 average time/residue: 0.5757 time to fit residues: 217.8973 Evaluate side-chains 301 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 249 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 301 optimal weight: 0.6980 chunk 109 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 288 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 26 optimal weight: 0.0670 chunk 251 optimal weight: 0.0020 chunk 290 optimal weight: 0.6980 chunk 205 optimal weight: 0.9980 overall best weight: 0.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1101 HIS A1119 ASN B 339 HIS B 580 GLN B1005 GLN B1119 ASN C 339 HIS C1119 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.189019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.117528 restraints weight = 27566.171| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.09 r_work: 0.3182 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26130 Z= 0.120 Angle : 0.581 7.976 35655 Z= 0.295 Chirality : 0.045 0.370 4155 Planarity : 0.004 0.058 4497 Dihedral : 5.528 45.199 4491 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.09 % Allowed : 11.45 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.15), residues: 3108 helix: 2.46 (0.19), residues: 702 sheet: 0.22 (0.19), residues: 651 loop : -0.52 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 319 TYR 0.026 0.001 TYR B 170 PHE 0.016 0.001 PHE A 32 TRP 0.010 0.001 TRP A 633 HIS 0.002 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00257 (26037) covalent geometry : angle 0.55517 (35418) SS BOND : bond 0.00181 ( 39) SS BOND : angle 0.95636 ( 78) hydrogen bonds : bond 0.04388 ( 1055) hydrogen bonds : angle 5.83711 ( 3075) link_BETA1-4 : bond 0.00947 ( 21) link_BETA1-4 : angle 2.93633 ( 63) link_NAG-ASN : bond 0.00834 ( 30) link_NAG-ASN : angle 2.24947 ( 90) link_NAG-THR : bond 0.00554 ( 3) link_NAG-THR : angle 2.49436 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 277 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 282 ASN cc_start: 0.7275 (m-40) cc_final: 0.7034 (t0) REVERT: A 328 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.6947 (mmp-170) REVERT: A 399 SER cc_start: 0.7339 (t) cc_final: 0.6873 (p) REVERT: A 534 VAL cc_start: 0.8361 (m) cc_final: 0.8102 (p) REVERT: A 646 ARG cc_start: 0.8520 (mmm-85) cc_final: 0.8192 (mpp80) REVERT: A 654 GLU cc_start: 0.7891 (tt0) cc_final: 0.7465 (tm-30) REVERT: A 779 GLN cc_start: 0.8152 (tp40) cc_final: 0.7644 (tm-30) REVERT: A 955 ASN cc_start: 0.8240 (m-40) cc_final: 0.8006 (m110) REVERT: A 964 LYS cc_start: 0.7972 (tptt) cc_final: 0.7589 (mttt) REVERT: A 1002 GLN cc_start: 0.8201 (tt0) cc_final: 0.7588 (tp40) REVERT: A 1010 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7141 (mp10) REVERT: A 1045 LYS cc_start: 0.8399 (mmmt) cc_final: 0.8031 (mppt) REVERT: A 1073 LYS cc_start: 0.8320 (tttt) cc_final: 0.8052 (ttmt) REVERT: B 88 ASP cc_start: 0.7461 (m-30) cc_final: 0.7238 (m-30) REVERT: B 190 ARG cc_start: 0.6810 (mtt90) cc_final: 0.6182 (ttp-110) REVERT: B 281 GLU cc_start: 0.7979 (mp0) cc_final: 0.7735 (pm20) REVERT: B 399 SER cc_start: 0.7376 (t) cc_final: 0.6868 (p) REVERT: B 534 VAL cc_start: 0.8311 (m) cc_final: 0.8069 (p) REVERT: B 554 LYS cc_start: 0.7857 (tttm) cc_final: 0.7615 (ptmm) REVERT: B 646 ARG cc_start: 0.8540 (mmm-85) cc_final: 0.8235 (mpp80) REVERT: B 654 GLU cc_start: 0.7850 (tt0) cc_final: 0.7396 (tm-30) REVERT: B 779 GLN cc_start: 0.8099 (tp40) cc_final: 0.7588 (tm-30) REVERT: B 955 ASN cc_start: 0.8219 (m-40) cc_final: 0.7966 (m-40) REVERT: B 964 LYS cc_start: 0.7957 (tptt) cc_final: 0.7529 (mttt) REVERT: B 1002 GLN cc_start: 0.8131 (tt0) cc_final: 0.7437 (tp-100) REVERT: B 1010 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7065 (mp10) REVERT: B 1045 LYS cc_start: 0.8388 (mmmt) cc_final: 0.8056 (mppt) REVERT: B 1073 LYS cc_start: 0.8401 (tttt) cc_final: 0.8110 (ttmt) REVERT: B 1125 ASN cc_start: 0.8347 (m-40) cc_final: 0.8017 (p0) REVERT: C 52 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.8065 (tt0) REVERT: C 190 ARG cc_start: 0.6686 (mtt90) cc_final: 0.6445 (ttm110) REVERT: C 319 ARG cc_start: 0.8047 (mtp-110) cc_final: 0.7616 (ttm-80) REVERT: C 399 SER cc_start: 0.7324 (t) cc_final: 0.6809 (p) REVERT: C 534 VAL cc_start: 0.8393 (m) cc_final: 0.8123 (p) REVERT: C 554 LYS cc_start: 0.7797 (tttm) cc_final: 0.7517 (ptmm) REVERT: C 558 LYS cc_start: 0.7739 (mmtt) cc_final: 0.7193 (mmtp) REVERT: C 654 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7658 (tt0) REVERT: C 740 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8268 (ttt) REVERT: C 779 GLN cc_start: 0.8173 (tp40) cc_final: 0.7668 (tm-30) REVERT: C 955 ASN cc_start: 0.8259 (m-40) cc_final: 0.8050 (m-40) REVERT: C 964 LYS cc_start: 0.7927 (tptt) cc_final: 0.7516 (mttt) REVERT: C 1002 GLN cc_start: 0.8157 (tt0) cc_final: 0.7522 (tp40) REVERT: C 1010 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7121 (mp10) REVERT: C 1045 LYS cc_start: 0.8365 (mmmt) cc_final: 0.7862 (ttpt) REVERT: C 1073 LYS cc_start: 0.8310 (tttt) cc_final: 0.7979 (ttmt) outliers start: 58 outliers final: 27 residues processed: 318 average time/residue: 0.5702 time to fit residues: 213.6822 Evaluate side-chains 291 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 257 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 142 optimal weight: 8.9990 chunk 234 optimal weight: 2.9990 chunk 198 optimal weight: 0.4980 chunk 98 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 210 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 227 optimal weight: 10.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS A1101 HIS B1005 GLN B1101 HIS C 339 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.186109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.114164 restraints weight = 27463.349| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.07 r_work: 0.3133 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 26130 Z= 0.225 Angle : 0.633 8.451 35655 Z= 0.321 Chirality : 0.048 0.375 4155 Planarity : 0.004 0.058 4497 Dihedral : 5.657 45.292 4491 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.46 % Allowed : 11.41 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.15), residues: 3108 helix: 2.35 (0.19), residues: 705 sheet: 0.15 (0.18), residues: 696 loop : -0.66 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 319 TYR 0.023 0.002 TYR B 170 PHE 0.019 0.002 PHE C 898 TRP 0.013 0.002 TRP A 64 HIS 0.006 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00550 (26037) covalent geometry : angle 0.60821 (35418) SS BOND : bond 0.00388 ( 39) SS BOND : angle 1.52046 ( 78) hydrogen bonds : bond 0.05187 ( 1055) hydrogen bonds : angle 5.97072 ( 3075) link_BETA1-4 : bond 0.00950 ( 21) link_BETA1-4 : angle 2.91761 ( 63) link_NAG-ASN : bond 0.00619 ( 30) link_NAG-ASN : angle 2.20533 ( 90) link_NAG-THR : bond 0.00716 ( 3) link_NAG-THR : angle 2.55018 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 255 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7020 (mmp-170) REVERT: A 399 SER cc_start: 0.7357 (t) cc_final: 0.6853 (p) REVERT: A 534 VAL cc_start: 0.8445 (m) cc_final: 0.8183 (p) REVERT: A 646 ARG cc_start: 0.8549 (mmm-85) cc_final: 0.8228 (mpp80) REVERT: A 654 GLU cc_start: 0.7877 (tt0) cc_final: 0.7452 (tm-30) REVERT: A 779 GLN cc_start: 0.8248 (tp40) cc_final: 0.7760 (tm-30) REVERT: A 955 ASN cc_start: 0.8271 (m-40) cc_final: 0.8043 (m110) REVERT: A 964 LYS cc_start: 0.8033 (tptt) cc_final: 0.7679 (mtmt) REVERT: A 1002 GLN cc_start: 0.8228 (tt0) cc_final: 0.7625 (tp-100) REVERT: A 1010 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7169 (mp10) REVERT: A 1045 LYS cc_start: 0.8391 (mmmt) cc_final: 0.8049 (mppt) REVERT: B 281 GLU cc_start: 0.8006 (mp0) cc_final: 0.7733 (pm20) REVERT: B 399 SER cc_start: 0.7334 (t) cc_final: 0.6821 (p) REVERT: B 534 VAL cc_start: 0.8379 (m) cc_final: 0.8136 (p) REVERT: B 554 LYS cc_start: 0.7882 (tttm) cc_final: 0.7631 (ptmm) REVERT: B 646 ARG cc_start: 0.8558 (mmm-85) cc_final: 0.8276 (mpp80) REVERT: B 654 GLU cc_start: 0.7859 (tt0) cc_final: 0.7371 (tm-30) REVERT: B 779 GLN cc_start: 0.8178 (tp40) cc_final: 0.7728 (tm-30) REVERT: B 955 ASN cc_start: 0.8257 (m-40) cc_final: 0.8022 (m110) REVERT: B 964 LYS cc_start: 0.8164 (tptt) cc_final: 0.7819 (mttt) REVERT: B 1002 GLN cc_start: 0.8183 (tt0) cc_final: 0.7480 (tp-100) REVERT: B 1010 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7126 (mp10) REVERT: B 1045 LYS cc_start: 0.8378 (mmmt) cc_final: 0.8037 (mppt) REVERT: B 1073 LYS cc_start: 0.8421 (tttt) cc_final: 0.8131 (ttmt) REVERT: B 1125 ASN cc_start: 0.8387 (m-40) cc_final: 0.8080 (p0) REVERT: C 52 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8140 (tt0) REVERT: C 319 ARG cc_start: 0.8000 (mtp-110) cc_final: 0.7695 (ttm-80) REVERT: C 399 SER cc_start: 0.7318 (t) cc_final: 0.6830 (p) REVERT: C 534 VAL cc_start: 0.8431 (m) cc_final: 0.8156 (p) REVERT: C 554 LYS cc_start: 0.7786 (tttm) cc_final: 0.7545 (ptmm) REVERT: C 558 LYS cc_start: 0.7764 (mmtt) cc_final: 0.7388 (mmtp) REVERT: C 654 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7679 (tt0) REVERT: C 779 GLN cc_start: 0.8225 (tp40) cc_final: 0.7729 (tm-30) REVERT: C 964 LYS cc_start: 0.8031 (tptt) cc_final: 0.7637 (mttt) REVERT: C 1002 GLN cc_start: 0.8197 (tt0) cc_final: 0.7549 (tp40) REVERT: C 1010 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7117 (mp10) REVERT: C 1045 LYS cc_start: 0.8355 (mmmt) cc_final: 0.7829 (ttpt) REVERT: C 1073 LYS cc_start: 0.8347 (tttt) cc_final: 0.8004 (ttmt) outliers start: 68 outliers final: 47 residues processed: 301 average time/residue: 0.5560 time to fit residues: 198.7758 Evaluate side-chains 301 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 248 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 298 optimal weight: 0.0980 chunk 53 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 314 optimal weight: 7.9990 chunk 281 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 271 optimal weight: 0.4980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1101 HIS B1005 GLN B1101 HIS C 339 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.188417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.118251 restraints weight = 27378.985| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.32 r_work: 0.3151 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26130 Z= 0.123 Angle : 0.570 9.617 35655 Z= 0.288 Chirality : 0.045 0.329 4155 Planarity : 0.004 0.044 4497 Dihedral : 5.280 44.438 4491 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.77 % Allowed : 12.24 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.15), residues: 3108 helix: 2.57 (0.19), residues: 705 sheet: 0.06 (0.18), residues: 678 loop : -0.60 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 319 TYR 0.028 0.001 TYR B 170 PHE 0.019 0.001 PHE B 238 TRP 0.010 0.001 TRP C 633 HIS 0.002 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00275 (26037) covalent geometry : angle 0.54169 (35418) SS BOND : bond 0.00203 ( 39) SS BOND : angle 1.18192 ( 78) hydrogen bonds : bond 0.04369 ( 1055) hydrogen bonds : angle 5.73711 ( 3075) link_BETA1-4 : bond 0.00905 ( 21) link_BETA1-4 : angle 2.82236 ( 63) link_NAG-ASN : bond 0.00559 ( 30) link_NAG-ASN : angle 2.44400 ( 90) link_NAG-THR : bond 0.00430 ( 3) link_NAG-THR : angle 2.12026 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 264 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.6788 (mmp-170) REVERT: A 399 SER cc_start: 0.7253 (t) cc_final: 0.6743 (p) REVERT: A 534 VAL cc_start: 0.8379 (m) cc_final: 0.8115 (p) REVERT: A 646 ARG cc_start: 0.8519 (mmm-85) cc_final: 0.8191 (mpp80) REVERT: A 654 GLU cc_start: 0.7873 (tt0) cc_final: 0.7399 (tm-30) REVERT: A 779 GLN cc_start: 0.8155 (tp40) cc_final: 0.7602 (tm-30) REVERT: A 964 LYS cc_start: 0.7918 (tptt) cc_final: 0.7517 (mtmt) REVERT: A 1002 GLN cc_start: 0.8187 (tt0) cc_final: 0.7547 (tp40) REVERT: A 1010 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7116 (mp10) REVERT: A 1045 LYS cc_start: 0.8420 (mmmt) cc_final: 0.8022 (mppt) REVERT: A 1073 LYS cc_start: 0.8312 (tttt) cc_final: 0.8008 (ttmt) REVERT: B 190 ARG cc_start: 0.6809 (mtt90) cc_final: 0.6509 (ttm110) REVERT: B 205 SER cc_start: 0.8792 (OUTLIER) cc_final: 0.8555 (t) REVERT: B 281 GLU cc_start: 0.7949 (mp0) cc_final: 0.7689 (pm20) REVERT: B 399 SER cc_start: 0.7261 (t) cc_final: 0.6756 (p) REVERT: B 534 VAL cc_start: 0.8332 (m) cc_final: 0.8085 (p) REVERT: B 554 LYS cc_start: 0.7763 (tttm) cc_final: 0.7474 (ptmm) REVERT: B 646 ARG cc_start: 0.8537 (mmm-85) cc_final: 0.8254 (mpp80) REVERT: B 654 GLU cc_start: 0.7862 (tt0) cc_final: 0.7361 (tm-30) REVERT: B 779 GLN cc_start: 0.8066 (tp40) cc_final: 0.7502 (tm-30) REVERT: B 955 ASN cc_start: 0.8182 (m-40) cc_final: 0.7927 (m-40) REVERT: B 964 LYS cc_start: 0.8039 (tptt) cc_final: 0.7584 (mttt) REVERT: B 1002 GLN cc_start: 0.8107 (tt0) cc_final: 0.7409 (tp-100) REVERT: B 1010 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7030 (mp10) REVERT: B 1045 LYS cc_start: 0.8401 (mmmt) cc_final: 0.8026 (mppt) REVERT: B 1073 LYS cc_start: 0.8375 (tttt) cc_final: 0.8061 (ttmt) REVERT: B 1125 ASN cc_start: 0.8371 (m-40) cc_final: 0.7980 (p0) REVERT: C 52 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.8084 (tt0) REVERT: C 319 ARG cc_start: 0.7964 (mtp-110) cc_final: 0.7652 (ttm-80) REVERT: C 399 SER cc_start: 0.7278 (t) cc_final: 0.6789 (p) REVERT: C 534 VAL cc_start: 0.8400 (m) cc_final: 0.8126 (p) REVERT: C 554 LYS cc_start: 0.7761 (tttm) cc_final: 0.7462 (pttp) REVERT: C 558 LYS cc_start: 0.7720 (mmtt) cc_final: 0.7341 (mmtp) REVERT: C 654 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7636 (tt0) REVERT: C 779 GLN cc_start: 0.8175 (tp40) cc_final: 0.7619 (tm-30) REVERT: C 964 LYS cc_start: 0.7926 (tptt) cc_final: 0.7464 (mttt) REVERT: C 1002 GLN cc_start: 0.8126 (tt0) cc_final: 0.7463 (tp40) REVERT: C 1010 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7094 (mp10) REVERT: C 1045 LYS cc_start: 0.8349 (mmmt) cc_final: 0.7798 (ttpt) REVERT: C 1073 LYS cc_start: 0.8290 (tttt) cc_final: 0.7922 (ttmt) outliers start: 49 outliers final: 33 residues processed: 297 average time/residue: 0.5913 time to fit residues: 206.8509 Evaluate side-chains 295 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 255 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 168 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 240 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 307 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 208 optimal weight: 5.9990 chunk 303 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 216 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS B 957 GLN B1005 GLN B1101 HIS C 339 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.186711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.116467 restraints weight = 27565.926| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.35 r_work: 0.3116 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 26130 Z= 0.189 Angle : 0.606 8.424 35655 Z= 0.307 Chirality : 0.046 0.322 4155 Planarity : 0.004 0.045 4497 Dihedral : 5.409 44.774 4491 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.17 % Allowed : 12.17 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.15), residues: 3108 helix: 2.46 (0.19), residues: 705 sheet: 0.13 (0.18), residues: 708 loop : -0.68 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 319 TYR 0.024 0.002 TYR C 170 PHE 0.019 0.002 PHE B 238 TRP 0.012 0.002 TRP A 64 HIS 0.005 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00453 (26037) covalent geometry : angle 0.58102 (35418) SS BOND : bond 0.00328 ( 39) SS BOND : angle 1.19228 ( 78) hydrogen bonds : bond 0.04916 ( 1055) hydrogen bonds : angle 5.84178 ( 3075) link_BETA1-4 : bond 0.00954 ( 21) link_BETA1-4 : angle 2.81113 ( 63) link_NAG-ASN : bond 0.00563 ( 30) link_NAG-ASN : angle 2.32363 ( 90) link_NAG-THR : bond 0.00598 ( 3) link_NAG-THR : angle 2.19277 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 256 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.6845 (mmp-170) REVERT: A 399 SER cc_start: 0.7234 (t) cc_final: 0.6755 (p) REVERT: A 534 VAL cc_start: 0.8453 (m) cc_final: 0.8191 (p) REVERT: A 646 ARG cc_start: 0.8558 (mmm-85) cc_final: 0.8243 (mpp80) REVERT: A 654 GLU cc_start: 0.7897 (tt0) cc_final: 0.7419 (tm-30) REVERT: A 779 GLN cc_start: 0.8235 (tp40) cc_final: 0.7751 (tm-30) REVERT: A 955 ASN cc_start: 0.8213 (m-40) cc_final: 0.7966 (m110) REVERT: A 964 LYS cc_start: 0.8018 (tptt) cc_final: 0.7671 (mtmt) REVERT: A 1002 GLN cc_start: 0.8280 (tt0) cc_final: 0.7672 (tp-100) REVERT: A 1010 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7193 (mp10) REVERT: A 1045 LYS cc_start: 0.8407 (mmmt) cc_final: 0.8064 (mppt) REVERT: A 1073 LYS cc_start: 0.8347 (tttt) cc_final: 0.8048 (ttmt) REVERT: B 205 SER cc_start: 0.8862 (OUTLIER) cc_final: 0.8632 (t) REVERT: B 281 GLU cc_start: 0.7929 (mp0) cc_final: 0.7663 (pm20) REVERT: B 399 SER cc_start: 0.7227 (t) cc_final: 0.6722 (p) REVERT: B 534 VAL cc_start: 0.8403 (m) cc_final: 0.8166 (p) REVERT: B 554 LYS cc_start: 0.7795 (tttm) cc_final: 0.7513 (pttp) REVERT: B 646 ARG cc_start: 0.8581 (mmm-85) cc_final: 0.8306 (mpp80) REVERT: B 654 GLU cc_start: 0.7910 (tt0) cc_final: 0.7401 (tm-30) REVERT: B 779 GLN cc_start: 0.8189 (tp40) cc_final: 0.7705 (tm-30) REVERT: B 955 ASN cc_start: 0.8221 (m-40) cc_final: 0.7960 (m-40) REVERT: B 964 LYS cc_start: 0.8161 (tptt) cc_final: 0.7810 (mttt) REVERT: B 1002 GLN cc_start: 0.8217 (tt0) cc_final: 0.7529 (tp-100) REVERT: B 1010 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7103 (mp10) REVERT: B 1045 LYS cc_start: 0.8391 (mmmt) cc_final: 0.8041 (mppt) REVERT: B 1073 LYS cc_start: 0.8418 (tttt) cc_final: 0.8141 (ttmt) REVERT: B 1125 ASN cc_start: 0.8404 (m-40) cc_final: 0.8090 (p0) REVERT: C 52 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8125 (tt0) REVERT: C 190 ARG cc_start: 0.6749 (mtt90) cc_final: 0.6525 (ttm110) REVERT: C 319 ARG cc_start: 0.8032 (mtp-110) cc_final: 0.7723 (ttm-80) REVERT: C 399 SER cc_start: 0.7229 (t) cc_final: 0.6794 (p) REVERT: C 534 VAL cc_start: 0.8447 (m) cc_final: 0.8163 (p) REVERT: C 554 LYS cc_start: 0.7778 (tttm) cc_final: 0.7526 (ptmm) REVERT: C 654 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7705 (tt0) REVERT: C 779 GLN cc_start: 0.8237 (tp40) cc_final: 0.7732 (tm-30) REVERT: C 964 LYS cc_start: 0.8044 (tptt) cc_final: 0.7640 (mttt) REVERT: C 1002 GLN cc_start: 0.8218 (tt0) cc_final: 0.7578 (tp40) REVERT: C 1010 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7140 (mp10) REVERT: C 1045 LYS cc_start: 0.8348 (mmmt) cc_final: 0.7806 (ttpt) REVERT: C 1073 LYS cc_start: 0.8347 (tttt) cc_final: 0.7996 (ttmt) outliers start: 60 outliers final: 42 residues processed: 299 average time/residue: 0.5728 time to fit residues: 203.1527 Evaluate side-chains 301 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 252 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 80 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 193 optimal weight: 0.9990 chunk 197 optimal weight: 0.8980 chunk 314 optimal weight: 10.0000 chunk 300 optimal weight: 2.9990 chunk 177 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 206 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 307 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS B 957 GLN B1005 GLN B1101 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.188176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.121648 restraints weight = 27331.311| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.28 r_work: 0.3160 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26130 Z= 0.133 Angle : 0.572 8.136 35655 Z= 0.291 Chirality : 0.045 0.302 4155 Planarity : 0.004 0.050 4497 Dihedral : 5.224 44.161 4491 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.73 % Allowed : 12.82 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.15), residues: 3108 helix: 2.58 (0.19), residues: 705 sheet: 0.09 (0.18), residues: 675 loop : -0.64 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 319 TYR 0.027 0.001 TYR B 170 PHE 0.019 0.001 PHE B 238 TRP 0.010 0.001 TRP B 633 HIS 0.002 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00302 (26037) covalent geometry : angle 0.54688 (35418) SS BOND : bond 0.00206 ( 39) SS BOND : angle 1.06712 ( 78) hydrogen bonds : bond 0.04403 ( 1055) hydrogen bonds : angle 5.68727 ( 3075) link_BETA1-4 : bond 0.00887 ( 21) link_BETA1-4 : angle 2.70824 ( 63) link_NAG-ASN : bond 0.00662 ( 30) link_NAG-ASN : angle 2.39744 ( 90) link_NAG-THR : bond 0.00449 ( 3) link_NAG-THR : angle 2.04264 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 261 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.6774 (mmp-170) REVERT: A 399 SER cc_start: 0.7137 (t) cc_final: 0.6658 (p) REVERT: A 534 VAL cc_start: 0.8400 (m) cc_final: 0.8136 (p) REVERT: A 646 ARG cc_start: 0.8499 (mmm-85) cc_final: 0.8177 (mpp80) REVERT: A 654 GLU cc_start: 0.7883 (tt0) cc_final: 0.7424 (tm-30) REVERT: A 779 GLN cc_start: 0.8159 (tp40) cc_final: 0.7616 (tm-30) REVERT: A 964 LYS cc_start: 0.7909 (tptt) cc_final: 0.7533 (mtmt) REVERT: A 1002 GLN cc_start: 0.8196 (tt0) cc_final: 0.7544 (tp40) REVERT: A 1010 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.7144 (mp10) REVERT: A 1045 LYS cc_start: 0.8411 (mmmt) cc_final: 0.8028 (mppt) REVERT: A 1073 LYS cc_start: 0.8316 (tttt) cc_final: 0.8013 (ttmt) REVERT: B 281 GLU cc_start: 0.7925 (mp0) cc_final: 0.7709 (pm20) REVERT: B 399 SER cc_start: 0.7161 (t) cc_final: 0.6649 (p) REVERT: B 534 VAL cc_start: 0.8371 (m) cc_final: 0.8133 (p) REVERT: B 554 LYS cc_start: 0.7716 (tttm) cc_final: 0.7449 (ptmm) REVERT: B 646 ARG cc_start: 0.8531 (mmm-85) cc_final: 0.8249 (mpp80) REVERT: B 654 GLU cc_start: 0.7860 (tt0) cc_final: 0.7353 (tm-30) REVERT: B 779 GLN cc_start: 0.8080 (tp40) cc_final: 0.7537 (tm-30) REVERT: B 955 ASN cc_start: 0.8181 (m-40) cc_final: 0.7918 (m-40) REVERT: B 964 LYS cc_start: 0.8022 (tptt) cc_final: 0.7607 (mttt) REVERT: B 1002 GLN cc_start: 0.8114 (tt0) cc_final: 0.7425 (tp-100) REVERT: B 1010 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7047 (mp10) REVERT: B 1045 LYS cc_start: 0.8393 (mmmt) cc_final: 0.8022 (mppt) REVERT: B 1073 LYS cc_start: 0.8375 (tttt) cc_final: 0.8091 (ttmt) REVERT: B 1125 ASN cc_start: 0.8382 (m-40) cc_final: 0.8008 (p0) REVERT: C 52 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.8052 (tt0) REVERT: C 190 ARG cc_start: 0.6715 (mtt90) cc_final: 0.6170 (ttm110) REVERT: C 319 ARG cc_start: 0.7994 (mtp-110) cc_final: 0.7622 (ttm-80) REVERT: C 399 SER cc_start: 0.7190 (t) cc_final: 0.6720 (p) REVERT: C 534 VAL cc_start: 0.8417 (m) cc_final: 0.8138 (p) REVERT: C 554 LYS cc_start: 0.7731 (tttm) cc_final: 0.7457 (ptmm) REVERT: C 654 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7670 (tt0) REVERT: C 779 GLN cc_start: 0.8165 (tp40) cc_final: 0.7635 (tm-30) REVERT: C 964 LYS cc_start: 0.7942 (tptt) cc_final: 0.7492 (mttt) REVERT: C 1002 GLN cc_start: 0.8134 (tt0) cc_final: 0.7482 (tp40) REVERT: C 1010 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7069 (mp10) REVERT: C 1045 LYS cc_start: 0.8368 (mmmt) cc_final: 0.7799 (ttpt) REVERT: C 1073 LYS cc_start: 0.8294 (tttt) cc_final: 0.7922 (ttmt) outliers start: 48 outliers final: 35 residues processed: 293 average time/residue: 0.5827 time to fit residues: 202.2308 Evaluate side-chains 294 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 253 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 258 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 231 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 chunk 24 optimal weight: 0.2980 chunk 9 optimal weight: 0.6980 chunk 213 optimal weight: 0.9980 chunk 187 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 236 optimal weight: 0.8980 chunk 252 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS B 87 ASN B 613 GLN B 804 GLN B1005 GLN B1101 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.189747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.123161 restraints weight = 27341.983| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.33 r_work: 0.3170 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 26130 Z= 0.114 Angle : 0.545 9.004 35655 Z= 0.277 Chirality : 0.044 0.284 4155 Planarity : 0.004 0.045 4497 Dihedral : 4.906 42.441 4491 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.63 % Allowed : 12.89 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.15), residues: 3108 helix: 2.76 (0.19), residues: 705 sheet: 0.20 (0.18), residues: 693 loop : -0.68 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 319 TYR 0.033 0.001 TYR C 170 PHE 0.017 0.001 PHE B 238 TRP 0.012 0.001 TRP C 633 HIS 0.002 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00252 (26037) covalent geometry : angle 0.52285 (35418) SS BOND : bond 0.00175 ( 39) SS BOND : angle 1.00391 ( 78) hydrogen bonds : bond 0.04021 ( 1055) hydrogen bonds : angle 5.47382 ( 3075) link_BETA1-4 : bond 0.00869 ( 21) link_BETA1-4 : angle 2.55140 ( 63) link_NAG-ASN : bond 0.00523 ( 30) link_NAG-ASN : angle 2.14189 ( 90) link_NAG-THR : bond 0.00398 ( 3) link_NAG-THR : angle 1.86037 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10284.25 seconds wall clock time: 175 minutes 43.02 seconds (10543.02 seconds total)