Starting phenix.real_space_refine on Sun Jun 22 05:07:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9elo_48157/06_2025/9elo_48157.cif Found real_map, /net/cci-nas-00/data/ceres_data/9elo_48157/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9elo_48157/06_2025/9elo_48157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9elo_48157/06_2025/9elo_48157.map" model { file = "/net/cci-nas-00/data/ceres_data/9elo_48157/06_2025/9elo_48157.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9elo_48157/06_2025/9elo_48157.cif" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.85, per 1000 atoms: 0.62 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: 6.35 Conformation dependent library (CDL) restraints added in 3.0 seconds 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: 3.74 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: 10.81 Time building geometry restraints manager: 7.53 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: 0.17 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: 7.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.010 Check model and map are aligned: 0.170 Set scattering table: 0.240 Process input model: 59.220 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.140 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:11.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.860 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.037 0.007 TRP A 436 HIS 0.010 0.002 HIS C1048 PHE 0.037 0.004 PHE C 216 TYR 0.058 0.005 TYR C 451 ARG 0.016 0.002 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00677 ( 30) link_NAG-ASN : angle 2.38458 ( 90) link_BETA1-4 : bond 0.01548 ( 21) link_BETA1-4 : angle 4.21726 ( 63) hydrogen bonds : bond 0.13718 ( 1055) hydrogen bonds : angle 7.64749 ( 3075) SS BOND : bond 0.00460 ( 39) SS BOND : angle 2.56251 ( 78) link_NAG-THR : bond 0.01417 ( 3) link_NAG-THR : angle 7.20920 ( 6) covalent geometry : bond 0.00754 (26037) covalent geometry : angle 1.29275 (35418) *********************** 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 : 2.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.3611 (mmt) cc_final: 0.3390 (tmm) REVERT: A 190 ARG cc_start: 0.6233 (mtt90) cc_final: 0.5746 (mtp85) 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: 0.7849 (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: 0.7577 (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: 0.6763 (m-30) REVERT: C 59 PHE cc_start: 0.8764 (m-80) cc_final: 0.8515 (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: 1.0655 time to fit residues: 601.8067 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 : 3.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 265 optimal weight: 4.9990 chunk 238 optimal weight: 0.8980 chunk 132 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 161 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 246 optimal weight: 7.9990 chunk 95 optimal weight: 0.6980 chunk 150 optimal weight: 7.9990 chunk 183 optimal weight: 0.9980 chunk 286 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4125 r_free = 0.4125 target = 0.193845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.124747 restraints weight = 27524.239| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.34 r_work: 0.3197 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26130 Z= 0.176 Angle : 0.738 10.476 35655 Z= 0.376 Chirality : 0.049 0.232 4155 Planarity : 0.005 0.039 4497 Dihedral : 8.042 64.842 4491 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.29 % Favored : 98.62 % Rotamer: Outliers : 2.24 % Allowed : 8.74 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.14), residues: 3108 helix: 2.51 (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 TRP 0.014 0.002 TRP A 64 HIS 0.007 0.001 HIS A1101 PHE 0.026 0.002 PHE B 565 TYR 0.025 0.002 TYR A 636 ARG 0.005 0.001 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.01491 ( 30) link_NAG-ASN : angle 3.37556 ( 90) link_BETA1-4 : bond 0.00969 ( 21) link_BETA1-4 : angle 3.56295 ( 63) hydrogen bonds : bond 0.05405 ( 1055) hydrogen bonds : angle 6.28207 ( 3075) SS BOND : bond 0.00328 ( 39) SS BOND : angle 1.51050 ( 78) link_NAG-THR : bond 0.01132 ( 3) link_NAG-THR : angle 4.62935 ( 6) covalent geometry : bond 0.00388 (26037) covalent geometry : angle 0.69829 (35418) *********************** 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 389 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 327 time to evaluate : 3.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.6714 (OUTLIER) cc_final: 0.6501 (tp) REVERT: A 190 ARG cc_start: 0.6296 (mtt90) cc_final: 0.5699 (mtp85) REVERT: A 294 ASP cc_start: 0.7498 (m-30) cc_final: 0.7276 (m-30) REVERT: A 399 SER cc_start: 0.7188 (t) cc_final: 0.6514 (p) REVERT: A 534 VAL cc_start: 0.8267 (m) cc_final: 0.7969 (p) REVERT: A 540 ASN cc_start: 0.8225 (m-40) cc_final: 0.7975 (m110) REVERT: A 619 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7772 (mt-10) REVERT: A 646 ARG cc_start: 0.8435 (mmm-85) cc_final: 0.8093 (mpp80) REVERT: A 654 GLU cc_start: 0.7786 (tt0) cc_final: 0.7503 (tm-30) REVERT: A 740 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8586 (ttt) REVERT: A 779 GLN cc_start: 0.8203 (tp40) cc_final: 0.7746 (tm-30) REVERT: A 888 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7072 (t80) REVERT: A 964 LYS cc_start: 0.7971 (tptt) cc_final: 0.7563 (mttt) REVERT: A 1002 GLN cc_start: 0.8290 (tt0) cc_final: 0.7512 (tp-100) REVERT: A 1005 GLN cc_start: 0.8705 (mt0) cc_final: 0.8500 (mt0) REVERT: A 1010 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7150 (mp10) REVERT: A 1045 LYS cc_start: 0.8354 (mmmt) cc_final: 0.7785 (ttpt) REVERT: A 1073 LYS cc_start: 0.8372 (tttt) cc_final: 0.8137 (ttmt) REVERT: A 1128 VAL cc_start: 0.8648 (OUTLIER) cc_final: 0.8430 (t) REVERT: B 88 ASP cc_start: 0.7799 (m-30) cc_final: 0.7500 (m-30) REVERT: B 282 ASN cc_start: 0.7244 (m-40) cc_final: 0.6903 (t0) REVERT: B 340 GLU cc_start: 0.7222 (mp0) cc_final: 0.7004 (mt-10) REVERT: B 399 SER cc_start: 0.7248 (t) cc_final: 0.6517 (p) REVERT: B 534 VAL cc_start: 0.8215 (m) cc_final: 0.7917 (p) REVERT: B 554 LYS cc_start: 0.7666 (tttm) cc_final: 0.7428 (ptmm) REVERT: B 646 ARG cc_start: 0.8434 (mmm-85) cc_final: 0.8153 (tpp80) REVERT: B 654 GLU cc_start: 0.7856 (tt0) cc_final: 0.7500 (tm-30) REVERT: B 779 GLN cc_start: 0.8158 (tp40) cc_final: 0.7687 (tm-30) REVERT: B 888 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.6784 (t80) REVERT: B 964 LYS cc_start: 0.8036 (tptt) cc_final: 0.7659 (mttt) REVERT: B 1002 GLN cc_start: 0.8222 (tt0) cc_final: 0.7429 (tp-100) REVERT: B 1005 GLN cc_start: 0.8646 (mt0) cc_final: 0.8444 (mt0) REVERT: B 1010 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7136 (mp10) REVERT: B 1045 LYS cc_start: 0.8371 (mmmt) cc_final: 0.7796 (ttpt) REVERT: B 1073 LYS cc_start: 0.8373 (tttt) cc_final: 0.8120 (ttmt) REVERT: B 1101 HIS cc_start: 0.8355 (m90) cc_final: 0.8152 (m-70) REVERT: B 1125 ASN cc_start: 0.8207 (m-40) cc_final: 0.7949 (p0) REVERT: C 59 PHE cc_start: 0.8779 (m-80) cc_final: 0.8522 (m-80) REVERT: C 319 ARG cc_start: 0.8270 (mtp-110) cc_final: 0.7770 (ttm-80) REVERT: C 389 ASP cc_start: 0.8469 (m-30) cc_final: 0.8201 (m-30) REVERT: C 399 SER cc_start: 0.7328 (t) cc_final: 0.6608 (p) REVERT: C 513 LEU cc_start: 0.7778 (mt) cc_final: 0.7560 (mt) REVERT: C 528 LYS cc_start: 0.7689 (mttm) cc_final: 0.7471 (mtpp) REVERT: C 534 VAL cc_start: 0.8267 (m) cc_final: 0.7956 (p) REVERT: C 554 LYS cc_start: 0.7679 (tttm) cc_final: 0.7448 (ptmm) REVERT: C 558 LYS cc_start: 0.7709 (mmtt) cc_final: 0.7355 (mmtp) REVERT: C 654 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7658 (tt0) REVERT: C 779 GLN cc_start: 0.8206 (tp40) cc_final: 0.7723 (tm-30) REVERT: C 888 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.6885 (t80) REVERT: C 964 LYS cc_start: 0.7939 (tptt) cc_final: 0.7475 (mttt) REVERT: C 1002 GLN cc_start: 0.8309 (tt0) cc_final: 0.7537 (tp40) REVERT: C 1005 GLN cc_start: 0.8700 (mt0) cc_final: 0.8463 (mt0) REVERT: C 1010 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7164 (mp10) REVERT: C 1045 LYS cc_start: 0.8310 (mmmt) cc_final: 0.7740 (ttpt) REVERT: C 1073 LYS cc_start: 0.8342 (tttt) cc_final: 0.8050 (ttmt) REVERT: C 1101 HIS cc_start: 0.8329 (m90) cc_final: 0.8076 (m-70) REVERT: C 1125 ASN cc_start: 0.8087 (m-40) cc_final: 0.7874 (p0) outliers start: 62 outliers final: 25 residues processed: 364 average time/residue: 1.6833 time to fit residues: 734.5954 Evaluate side-chains 314 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 279 time to evaluate : 3.557 ------------------------------------------------------------------------------- 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 189 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 514 SER 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 0 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 169 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 12 optimal weight: 0.0000 chunk 11 optimal weight: 20.0000 chunk 115 optimal weight: 0.9990 chunk 158 optimal weight: 0.4980 chunk 128 optimal weight: 0.9980 chunk 224 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 613 GLN A 935 GLN A1101 HIS B 613 GLN B1002 GLN B1119 ASN C 564 GLN C1002 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.191973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.126310 restraints weight = 27551.716| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.19 r_work: 0.3235 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26130 Z= 0.156 Angle : 0.633 8.357 35655 Z= 0.324 Chirality : 0.046 0.205 4155 Planarity : 0.004 0.045 4497 Dihedral : 6.351 45.949 4491 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.99 % Allowed : 9.50 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.14), residues: 3108 helix: 2.52 (0.19), residues: 705 sheet: 0.82 (0.20), residues: 618 loop : -0.29 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 64 HIS 0.003 0.001 HIS A1058 PHE 0.015 0.002 PHE B 898 TYR 0.021 0.002 TYR A1067 ARG 0.007 0.001 ARG A 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00880 ( 30) link_NAG-ASN : angle 2.17378 ( 90) link_BETA1-4 : bond 0.01003 ( 21) link_BETA1-4 : angle 3.29296 ( 63) hydrogen bonds : bond 0.04925 ( 1055) hydrogen bonds : angle 6.00076 ( 3075) SS BOND : bond 0.00298 ( 39) SS BOND : angle 1.29662 ( 78) link_NAG-THR : bond 0.00812 ( 3) link_NAG-THR : angle 3.61480 ( 6) covalent geometry : bond 0.00353 (26037) covalent geometry : angle 0.60538 (35418) *********************** 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 345 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 290 time to evaluate : 2.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 SER cc_start: 0.7343 (t) cc_final: 0.6736 (p) REVERT: A 534 VAL cc_start: 0.8348 (m) cc_final: 0.8023 (p) REVERT: A 540 ASN cc_start: 0.8361 (m-40) cc_final: 0.8134 (m110) REVERT: A 554 LYS cc_start: 0.7685 (tttp) cc_final: 0.7467 (ptmm) REVERT: A 558 LYS cc_start: 0.7651 (mmtt) cc_final: 0.7131 (mmtp) REVERT: A 646 ARG cc_start: 0.8481 (mmm-85) cc_final: 0.8132 (mpp80) REVERT: A 654 GLU cc_start: 0.7745 (tt0) cc_final: 0.7471 (tm-30) REVERT: A 779 GLN cc_start: 0.8206 (tp40) cc_final: 0.7758 (tm-30) REVERT: A 878 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8375 (tp) REVERT: A 888 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.7263 (t80) REVERT: A 955 ASN cc_start: 0.8303 (m-40) cc_final: 0.8094 (m110) REVERT: A 964 LYS cc_start: 0.7982 (tptt) cc_final: 0.7615 (mtmt) REVERT: A 1002 GLN cc_start: 0.8235 (tt0) cc_final: 0.7593 (tp-100) REVERT: A 1010 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7153 (mp10) REVERT: A 1045 LYS cc_start: 0.8326 (mmmt) cc_final: 0.7759 (ttpt) REVERT: A 1073 LYS cc_start: 0.8380 (tttt) cc_final: 0.8123 (ttmt) REVERT: B 88 ASP cc_start: 0.7726 (m-30) cc_final: 0.7378 (m-30) REVERT: B 282 ASN cc_start: 0.7327 (m-40) cc_final: 0.7011 (t0) REVERT: B 399 SER cc_start: 0.7414 (t) cc_final: 0.6795 (p) REVERT: B 534 VAL cc_start: 0.8278 (m) cc_final: 0.7981 (p) REVERT: B 646 ARG cc_start: 0.8517 (mmm-85) cc_final: 0.8217 (mpp80) REVERT: B 654 GLU cc_start: 0.7783 (tt0) cc_final: 0.7502 (tm-30) REVERT: B 779 GLN cc_start: 0.8145 (tp40) cc_final: 0.7650 (tm-30) REVERT: B 888 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.6940 (t80) REVERT: B 964 LYS cc_start: 0.7979 (tptt) cc_final: 0.7599 (mttt) REVERT: B 1002 GLN cc_start: 0.8155 (tt0) cc_final: 0.7497 (tp-100) REVERT: B 1005 GLN cc_start: 0.8608 (mt0) cc_final: 0.8386 (mt0) REVERT: B 1010 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7084 (mp10) REVERT: B 1045 LYS cc_start: 0.8350 (mmmt) cc_final: 0.7803 (ttpt) REVERT: B 1073 LYS cc_start: 0.8373 (tttt) cc_final: 0.8097 (ttmt) REVERT: B 1125 ASN cc_start: 0.8287 (m-40) cc_final: 0.7982 (p0) REVERT: C 59 PHE cc_start: 0.8874 (m-80) cc_final: 0.8627 (m-80) REVERT: C 319 ARG cc_start: 0.8200 (mtp-110) cc_final: 0.7804 (ttm-80) REVERT: C 378 LYS cc_start: 0.7492 (pttt) cc_final: 0.7275 (pttt) REVERT: C 399 SER cc_start: 0.7410 (t) cc_final: 0.6899 (p) REVERT: C 513 LEU cc_start: 0.8040 (mt) cc_final: 0.7802 (mt) REVERT: C 534 VAL cc_start: 0.8322 (m) cc_final: 0.8013 (p) REVERT: C 558 LYS cc_start: 0.7702 (mmtt) cc_final: 0.7469 (mmtp) REVERT: C 654 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7630 (tt0) REVERT: C 675 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7481 (mt0) REVERT: C 779 GLN cc_start: 0.8179 (tp40) cc_final: 0.7731 (tm-30) REVERT: C 888 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.7396 (t80) REVERT: C 964 LYS cc_start: 0.7929 (tptt) cc_final: 0.7537 (mttt) REVERT: C 1002 GLN cc_start: 0.8165 (tt0) cc_final: 0.7548 (tp40) REVERT: C 1005 GLN cc_start: 0.8663 (mt0) cc_final: 0.8435 (mt0) REVERT: C 1010 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7187 (mp10) REVERT: C 1045 LYS cc_start: 0.8341 (mmmt) cc_final: 0.7809 (ttpt) REVERT: C 1073 LYS cc_start: 0.8335 (tttt) cc_final: 0.8018 (ttmt) REVERT: C 1101 HIS cc_start: 0.8381 (m90) cc_final: 0.8106 (m-70) REVERT: C 1125 ASN cc_start: 0.8262 (m-40) cc_final: 0.8000 (p0) outliers start: 55 outliers final: 33 residues processed: 325 average time/residue: 1.1150 time to fit residues: 433.0944 Evaluate side-chains 314 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 272 time to evaluate : 2.732 ------------------------------------------------------------------------------- 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 305 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 878 LEU 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 227 VAL Chi-restraints excluded: chain B residue 307 THR 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 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 888 PHE 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 189 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 307 THR 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 553 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 888 PHE 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 151 optimal weight: 3.9990 chunk 168 optimal weight: 0.8980 chunk 280 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 193 optimal weight: 3.9990 chunk 294 optimal weight: 0.9980 chunk 292 optimal weight: 0.9980 chunk 239 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 279 optimal weight: 0.5980 chunk 125 optimal weight: 5.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A1101 HIS B1101 HIS C 321 GLN C 544 ASN C1002 GLN C1119 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.189477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.117217 restraints weight = 27703.715| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.10 r_work: 0.3161 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26130 Z= 0.179 Angle : 0.617 8.253 35655 Z= 0.317 Chirality : 0.046 0.210 4155 Planarity : 0.004 0.061 4497 Dihedral : 5.562 43.697 4491 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.42 % Allowed : 9.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.15), residues: 3108 helix: 2.45 (0.19), residues: 705 sheet: 0.55 (0.19), residues: 651 loop : -0.40 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 64 HIS 0.005 0.001 HIS A1058 PHE 0.019 0.002 PHE C 238 TYR 0.028 0.002 TYR A 170 ARG 0.008 0.001 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00475 ( 30) link_NAG-ASN : angle 2.13434 ( 90) link_BETA1-4 : bond 0.00990 ( 21) link_BETA1-4 : angle 3.08784 ( 63) hydrogen bonds : bond 0.04998 ( 1055) hydrogen bonds : angle 5.93723 ( 3075) SS BOND : bond 0.00276 ( 39) SS BOND : angle 1.06115 ( 78) link_NAG-THR : bond 0.00725 ( 3) link_NAG-THR : angle 2.97552 ( 6) covalent geometry : bond 0.00422 (26037) covalent geometry : angle 0.59244 (35418) *********************** 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 355 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 288 time to evaluate : 3.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 ASN cc_start: 0.7295 (m-40) cc_final: 0.7030 (t0) REVERT: A 359 SER cc_start: 0.7974 (p) cc_final: 0.7719 (t) REVERT: A 399 SER cc_start: 0.7365 (t) cc_final: 0.6856 (p) REVERT: A 534 VAL cc_start: 0.8374 (m) cc_final: 0.8093 (p) REVERT: A 554 LYS cc_start: 0.7781 (tttp) cc_final: 0.7520 (ptmm) REVERT: A 646 ARG cc_start: 0.8543 (mmm-85) cc_final: 0.8260 (mpp80) REVERT: A 654 GLU cc_start: 0.7790 (tt0) cc_final: 0.7495 (tm-30) REVERT: A 779 GLN cc_start: 0.8258 (tp40) cc_final: 0.7771 (tm-30) REVERT: A 888 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.7571 (t80) REVERT: A 955 ASN cc_start: 0.8295 (m-40) cc_final: 0.8087 (m110) REVERT: A 964 LYS cc_start: 0.8007 (tptt) cc_final: 0.7609 (mtmt) REVERT: A 1002 GLN cc_start: 0.8233 (tt0) cc_final: 0.7614 (tp-100) REVERT: A 1010 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7177 (mp10) REVERT: A 1045 LYS cc_start: 0.8346 (mmmt) cc_final: 0.7736 (ttpt) REVERT: A 1073 LYS cc_start: 0.8393 (tttt) cc_final: 0.8125 (ttmt) REVERT: B 88 ASP cc_start: 0.7588 (m-30) cc_final: 0.7366 (m-30) REVERT: B 282 ASN cc_start: 0.7414 (m-40) cc_final: 0.7023 (t0) REVERT: B 399 SER cc_start: 0.7356 (t) cc_final: 0.6792 (p) REVERT: B 534 VAL cc_start: 0.8365 (m) cc_final: 0.8079 (p) REVERT: B 569 ILE cc_start: 0.8555 (tp) cc_final: 0.8340 (tp) REVERT: B 646 ARG cc_start: 0.8549 (mmm-85) cc_final: 0.8230 (mpp80) REVERT: B 654 GLU cc_start: 0.7828 (tt0) cc_final: 0.7458 (tm-30) REVERT: B 779 GLN cc_start: 0.8179 (tp40) cc_final: 0.7736 (tm-30) REVERT: B 888 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.7220 (t80) REVERT: B 955 ASN cc_start: 0.8233 (m-40) cc_final: 0.8019 (m110) REVERT: B 964 LYS cc_start: 0.8085 (tptt) cc_final: 0.7720 (mttt) REVERT: B 1002 GLN cc_start: 0.8180 (tt0) cc_final: 0.7449 (tp-100) REVERT: B 1010 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7188 (mp10) REVERT: B 1045 LYS cc_start: 0.8369 (mmmt) cc_final: 0.7807 (ttpt) REVERT: B 1073 LYS cc_start: 0.8417 (tttt) cc_final: 0.8152 (ttmt) REVERT: B 1125 ASN cc_start: 0.8318 (m-40) cc_final: 0.7978 (p0) REVERT: C 319 ARG cc_start: 0.8119 (mtp-110) cc_final: 0.7601 (ttm-80) REVERT: C 399 SER cc_start: 0.7509 (t) cc_final: 0.6966 (p) REVERT: C 534 VAL cc_start: 0.8324 (m) cc_final: 0.8014 (p) REVERT: C 558 LYS cc_start: 0.7739 (mmtt) cc_final: 0.7272 (mmtp) REVERT: C 646 ARG cc_start: 0.8360 (mmm-85) cc_final: 0.8130 (mpp80) REVERT: C 654 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7623 (tt0) REVERT: C 675 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7535 (mt0) REVERT: C 779 GLN cc_start: 0.8221 (tp40) cc_final: 0.7745 (tm-30) REVERT: C 964 LYS cc_start: 0.7984 (tptt) cc_final: 0.7560 (mttt) REVERT: C 1002 GLN cc_start: 0.8218 (tt0) cc_final: 0.7611 (tp40) REVERT: C 1010 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7150 (mp10) REVERT: C 1045 LYS cc_start: 0.8356 (mmmt) cc_final: 0.7826 (ttpt) REVERT: C 1073 LYS cc_start: 0.8331 (tttt) cc_final: 0.8020 (ttmt) REVERT: C 1101 HIS cc_start: 0.8560 (m90) cc_final: 0.8265 (m-70) REVERT: C 1125 ASN cc_start: 0.8221 (m-40) cc_final: 0.7967 (p0) outliers start: 67 outliers final: 46 residues processed: 329 average time/residue: 1.5238 time to fit residues: 604.4939 Evaluate side-chains 318 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 265 time to evaluate : 2.622 ------------------------------------------------------------------------------- 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 305 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 325 SER 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 878 LEU 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 305 SER Chi-restraints excluded: chain B residue 307 THR 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 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 900 MET 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 189 LEU 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 356 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 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 787 GLN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 888 PHE 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 206 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 95 optimal weight: 0.4980 chunk 273 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 261 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 286 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 307 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS A1119 ASN B 87 ASN B 556 ASN B1002 GLN B1005 GLN B1101 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.190884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.119215 restraints weight = 27607.347| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.10 r_work: 0.3205 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26130 Z= 0.125 Angle : 0.571 8.131 35655 Z= 0.290 Chirality : 0.045 0.271 4155 Planarity : 0.004 0.066 4497 Dihedral : 5.206 43.559 4491 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.09 % Allowed : 10.91 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.15), residues: 3108 helix: 2.65 (0.19), residues: 705 sheet: 0.39 (0.18), residues: 681 loop : -0.40 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 64 HIS 0.002 0.001 HIS C1058 PHE 0.014 0.001 PHE C 565 TYR 0.019 0.001 TYR A1067 ARG 0.007 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00644 ( 30) link_NAG-ASN : angle 2.07736 ( 90) link_BETA1-4 : bond 0.00934 ( 21) link_BETA1-4 : angle 2.87345 ( 63) hydrogen bonds : bond 0.04381 ( 1055) hydrogen bonds : angle 5.72078 ( 3075) SS BOND : bond 0.00168 ( 39) SS BOND : angle 0.90134 ( 78) link_NAG-THR : bond 0.00611 ( 3) link_NAG-THR : angle 2.60213 ( 6) covalent geometry : bond 0.00278 (26037) covalent geometry : angle 0.54780 (35418) *********************** 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 346 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 288 time to evaluate : 2.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.6762 (mmp-170) REVERT: A 358 ILE cc_start: 0.7741 (OUTLIER) cc_final: 0.7191 (mp) REVERT: A 359 SER cc_start: 0.8058 (p) cc_final: 0.7705 (t) REVERT: A 399 SER cc_start: 0.7414 (t) cc_final: 0.6918 (p) REVERT: A 534 VAL cc_start: 0.8289 (m) cc_final: 0.8032 (p) REVERT: A 554 LYS cc_start: 0.7757 (tttp) cc_final: 0.7511 (ptmm) REVERT: A 646 ARG cc_start: 0.8563 (mmm-85) cc_final: 0.8202 (mpp80) REVERT: A 654 GLU cc_start: 0.7805 (tt0) cc_final: 0.7534 (tm-30) REVERT: A 779 GLN cc_start: 0.8175 (tp40) cc_final: 0.7732 (tm-30) REVERT: A 888 PHE cc_start: 0.8502 (OUTLIER) cc_final: 0.7319 (t80) REVERT: A 955 ASN cc_start: 0.8266 (m-40) cc_final: 0.8050 (m110) REVERT: A 964 LYS cc_start: 0.7968 (tptt) cc_final: 0.7629 (mttt) REVERT: A 1002 GLN cc_start: 0.8228 (tt0) cc_final: 0.7667 (tp-100) REVERT: A 1010 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.7149 (mp10) REVERT: A 1045 LYS cc_start: 0.8365 (mmmt) cc_final: 0.7804 (ttpt) REVERT: A 1073 LYS cc_start: 0.8383 (tttt) cc_final: 0.8143 (ttmt) REVERT: B 88 ASP cc_start: 0.7577 (m-30) cc_final: 0.7352 (m-30) REVERT: B 281 GLU cc_start: 0.7980 (mp0) cc_final: 0.7715 (pm20) REVERT: B 399 SER cc_start: 0.7356 (t) cc_final: 0.6806 (p) REVERT: B 534 VAL cc_start: 0.8366 (m) cc_final: 0.8083 (p) REVERT: B 646 ARG cc_start: 0.8553 (mmm-85) cc_final: 0.8253 (mpp80) REVERT: B 654 GLU cc_start: 0.7841 (tt0) cc_final: 0.7496 (tm-30) REVERT: B 779 GLN cc_start: 0.8163 (tp40) cc_final: 0.7668 (tm-30) REVERT: B 888 PHE cc_start: 0.8397 (OUTLIER) cc_final: 0.7140 (t80) REVERT: B 955 ASN cc_start: 0.8211 (m-40) cc_final: 0.7977 (m-40) REVERT: B 964 LYS cc_start: 0.7979 (tptt) cc_final: 0.7601 (mttt) REVERT: B 1002 GLN cc_start: 0.8213 (tt0) cc_final: 0.7498 (tp40) REVERT: B 1010 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.7114 (mp10) REVERT: B 1045 LYS cc_start: 0.8378 (mmmt) cc_final: 0.7878 (ttpt) REVERT: B 1073 LYS cc_start: 0.8421 (tttt) cc_final: 0.8178 (ttmt) REVERT: B 1125 ASN cc_start: 0.8348 (m-40) cc_final: 0.8011 (p0) REVERT: C 319 ARG cc_start: 0.8063 (mtp-110) cc_final: 0.7651 (ttm-80) REVERT: C 399 SER cc_start: 0.7446 (t) cc_final: 0.6931 (p) REVERT: C 534 VAL cc_start: 0.8304 (m) cc_final: 0.8012 (p) REVERT: C 558 LYS cc_start: 0.7736 (mmtt) cc_final: 0.7467 (mmtp) REVERT: C 646 ARG cc_start: 0.8400 (mmm-85) cc_final: 0.8152 (mpp80) REVERT: C 654 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7636 (tt0) REVERT: C 779 GLN cc_start: 0.8203 (tp40) cc_final: 0.7738 (tm-30) REVERT: C 888 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.7656 (t80) REVERT: C 964 LYS cc_start: 0.7953 (tptt) cc_final: 0.7563 (mttt) REVERT: C 1002 GLN cc_start: 0.8237 (tt0) cc_final: 0.7657 (tp40) REVERT: C 1010 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.7178 (mp10) REVERT: C 1045 LYS cc_start: 0.8368 (mmmt) cc_final: 0.7878 (ttpt) REVERT: C 1073 LYS cc_start: 0.8316 (tttt) cc_final: 0.8028 (ttmt) REVERT: C 1101 HIS cc_start: 0.8581 (m90) cc_final: 0.8292 (m-70) REVERT: C 1125 ASN cc_start: 0.8241 (m-40) cc_final: 0.8014 (p0) outliers start: 58 outliers final: 36 residues processed: 330 average time/residue: 1.0734 time to fit residues: 425.1903 Evaluate side-chains 311 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 266 time to evaluate : 3.081 ------------------------------------------------------------------------------- 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 205 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 358 ILE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 916 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 305 SER 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 576 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 189 LEU 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 356 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 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 878 LEU Chi-restraints excluded: chain C residue 888 PHE 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 293 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 33 optimal weight: 0.0980 chunk 246 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 206 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 309 optimal weight: 0.8980 chunk 199 optimal weight: 0.5980 chunk 296 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS B 339 HIS ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4079 r_free = 0.4079 target = 0.189269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.117222 restraints weight = 27459.600| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.09 r_work: 0.3176 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26130 Z= 0.159 Angle : 0.581 8.100 35655 Z= 0.297 Chirality : 0.046 0.347 4155 Planarity : 0.004 0.067 4497 Dihedral : 5.138 43.636 4491 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.96 % Allowed : 10.55 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.15), residues: 3108 helix: 2.58 (0.19), residues: 705 sheet: 0.37 (0.18), residues: 696 loop : -0.48 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 64 HIS 0.004 0.001 HIS A1058 PHE 0.020 0.002 PHE B 238 TYR 0.028 0.002 TYR C 170 ARG 0.007 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00599 ( 30) link_NAG-ASN : angle 2.07260 ( 90) link_BETA1-4 : bond 0.00945 ( 21) link_BETA1-4 : angle 2.80973 ( 63) hydrogen bonds : bond 0.04659 ( 1055) hydrogen bonds : angle 5.73858 ( 3075) SS BOND : bond 0.00327 ( 39) SS BOND : angle 1.14492 ( 78) link_NAG-THR : bond 0.00636 ( 3) link_NAG-THR : angle 2.40985 ( 6) covalent geometry : bond 0.00372 (26037) covalent geometry : angle 0.55718 (35418) *********************** 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 348 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 266 time to evaluate : 2.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 ASN cc_start: 0.7361 (m-40) cc_final: 0.7041 (t0) REVERT: A 328 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.6752 (mmp-170) REVERT: A 358 ILE cc_start: 0.7665 (OUTLIER) cc_final: 0.7121 (mp) REVERT: A 399 SER cc_start: 0.7414 (t) cc_final: 0.6933 (p) REVERT: A 534 VAL cc_start: 0.8328 (m) cc_final: 0.8068 (p) REVERT: A 554 LYS cc_start: 0.7779 (tttp) cc_final: 0.7531 (ptmm) REVERT: A 646 ARG cc_start: 0.8544 (mmm-85) cc_final: 0.8194 (mpp80) REVERT: A 654 GLU cc_start: 0.7786 (tt0) cc_final: 0.7490 (tm-30) REVERT: A 779 GLN cc_start: 0.8197 (tp40) cc_final: 0.7700 (tm-30) REVERT: A 888 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.7234 (t80) REVERT: A 964 LYS cc_start: 0.7993 (tptt) cc_final: 0.7607 (mttt) REVERT: A 1002 GLN cc_start: 0.8198 (tt0) cc_final: 0.7598 (tp-100) REVERT: A 1010 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7132 (mp10) REVERT: A 1045 LYS cc_start: 0.8381 (mmmt) cc_final: 0.7792 (ttpt) REVERT: A 1073 LYS cc_start: 0.8367 (tttt) cc_final: 0.8101 (ttmt) REVERT: B 88 ASP cc_start: 0.7589 (m-30) cc_final: 0.7361 (m-30) REVERT: B 281 GLU cc_start: 0.7964 (mp0) cc_final: 0.7650 (pm20) REVERT: B 399 SER cc_start: 0.7382 (t) cc_final: 0.6875 (p) REVERT: B 534 VAL cc_start: 0.8349 (m) cc_final: 0.8074 (p) REVERT: B 569 ILE cc_start: 0.8572 (tp) cc_final: 0.8338 (tp) REVERT: B 646 ARG cc_start: 0.8548 (mmm-85) cc_final: 0.8244 (mpp80) REVERT: B 654 GLU cc_start: 0.7834 (tt0) cc_final: 0.7412 (tm-30) REVERT: B 779 GLN cc_start: 0.8142 (tp40) cc_final: 0.7617 (tm-30) REVERT: B 888 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.7124 (t80) REVERT: B 921 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8360 (tttp) REVERT: B 955 ASN cc_start: 0.8173 (m-40) cc_final: 0.7940 (m110) REVERT: B 964 LYS cc_start: 0.8056 (tptt) cc_final: 0.7682 (mttt) REVERT: B 1002 GLN cc_start: 0.8169 (tt0) cc_final: 0.7487 (tp-100) REVERT: B 1010 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7074 (mp10) REVERT: B 1045 LYS cc_start: 0.8367 (mmmt) cc_final: 0.7862 (ttpt) REVERT: B 1073 LYS cc_start: 0.8391 (tttt) cc_final: 0.8115 (ttmt) REVERT: B 1125 ASN cc_start: 0.8333 (m-40) cc_final: 0.8014 (p0) REVERT: C 319 ARG cc_start: 0.7983 (mtp-110) cc_final: 0.7656 (ttm-80) REVERT: C 399 SER cc_start: 0.7321 (t) cc_final: 0.6853 (p) REVERT: C 534 VAL cc_start: 0.8336 (m) cc_final: 0.8042 (p) REVERT: C 558 LYS cc_start: 0.7718 (mmtt) cc_final: 0.7354 (mmtp) REVERT: C 654 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7632 (tt0) REVERT: C 779 GLN cc_start: 0.8208 (tp40) cc_final: 0.7709 (tm-30) REVERT: C 888 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.7735 (t80) REVERT: C 964 LYS cc_start: 0.7997 (tptt) cc_final: 0.7565 (mttt) REVERT: C 1002 GLN cc_start: 0.8199 (tt0) cc_final: 0.7605 (tp40) REVERT: C 1010 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7138 (mp10) REVERT: C 1045 LYS cc_start: 0.8378 (mmmt) cc_final: 0.7854 (ttpt) REVERT: C 1073 LYS cc_start: 0.8301 (tttt) cc_final: 0.7973 (ttmt) REVERT: C 1125 ASN cc_start: 0.8224 (m-40) cc_final: 0.7980 (p0) outliers start: 82 outliers final: 51 residues processed: 325 average time/residue: 1.1245 time to fit residues: 440.1285 Evaluate side-chains 315 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 254 time to evaluate : 2.934 ------------------------------------------------------------------------------- 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 205 SER 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 358 ILE 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 888 PHE Chi-restraints excluded: chain A residue 916 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 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 888 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 189 LEU 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 356 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 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 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 888 PHE 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 158 optimal weight: 4.9990 chunk 224 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 150 optimal weight: 0.9990 chunk 217 optimal weight: 1.9990 chunk 284 optimal weight: 5.9990 chunk 202 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A1101 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B1005 GLN B1101 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.185963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.118061 restraints weight = 27454.088| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.42 r_work: 0.3099 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 26130 Z= 0.249 Angle : 0.669 9.440 35655 Z= 0.342 Chirality : 0.049 0.344 4155 Planarity : 0.005 0.070 4497 Dihedral : 5.698 46.039 4491 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.00 % Allowed : 10.69 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.15), residues: 3108 helix: 2.28 (0.19), residues: 702 sheet: 0.25 (0.18), residues: 681 loop : -0.65 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 64 HIS 0.008 0.001 HIS A1058 PHE 0.021 0.002 PHE C 898 TYR 0.023 0.002 TYR B1067 ARG 0.007 0.001 ARG A 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00586 ( 30) link_NAG-ASN : angle 2.17935 ( 90) link_BETA1-4 : bond 0.00976 ( 21) link_BETA1-4 : angle 2.91417 ( 63) hydrogen bonds : bond 0.05601 ( 1055) hydrogen bonds : angle 6.06336 ( 3075) SS BOND : bond 0.00438 ( 39) SS BOND : angle 1.41506 ( 78) link_NAG-THR : bond 0.00740 ( 3) link_NAG-THR : angle 2.42383 ( 6) covalent geometry : bond 0.00604 (26037) covalent geometry : angle 0.64689 (35418) *********************** 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 345 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 262 time to evaluate : 2.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7099 (mmp-170) REVERT: A 399 SER cc_start: 0.7325 (t) cc_final: 0.6854 (p) REVERT: A 534 VAL cc_start: 0.8478 (m) cc_final: 0.8207 (p) REVERT: A 554 LYS cc_start: 0.7921 (tttp) cc_final: 0.7691 (ptmm) REVERT: A 646 ARG cc_start: 0.8550 (mmm-85) cc_final: 0.8243 (mpp80) REVERT: A 654 GLU cc_start: 0.7931 (tt0) cc_final: 0.7530 (tm-30) REVERT: A 779 GLN cc_start: 0.8288 (tp40) cc_final: 0.7816 (tm-30) REVERT: A 955 ASN cc_start: 0.8289 (m-40) cc_final: 0.8049 (m110) REVERT: A 964 LYS cc_start: 0.8084 (tptt) cc_final: 0.7725 (mtmt) REVERT: A 1002 GLN cc_start: 0.8238 (tt0) cc_final: 0.7612 (tp-100) REVERT: A 1010 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7193 (mp10) REVERT: A 1045 LYS cc_start: 0.8381 (mmmt) cc_final: 0.7769 (ttpt) REVERT: A 1073 LYS cc_start: 0.8368 (tttt) cc_final: 0.8077 (ttmt) REVERT: B 88 ASP cc_start: 0.7634 (m-30) cc_final: 0.7430 (m-30) REVERT: B 238 PHE cc_start: 0.7037 (OUTLIER) cc_final: 0.6213 (p90) REVERT: B 281 GLU cc_start: 0.7960 (mp0) cc_final: 0.7663 (pm20) REVERT: B 399 SER cc_start: 0.7368 (t) cc_final: 0.6874 (p) REVERT: B 534 VAL cc_start: 0.8408 (m) cc_final: 0.8144 (p) REVERT: B 646 ARG cc_start: 0.8605 (mmm-85) cc_final: 0.8294 (mpp80) REVERT: B 654 GLU cc_start: 0.7866 (tt0) cc_final: 0.7329 (tm-30) REVERT: B 779 GLN cc_start: 0.8242 (tp40) cc_final: 0.7783 (tm-30) REVERT: B 921 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8418 (tttp) REVERT: B 955 ASN cc_start: 0.8268 (m-40) cc_final: 0.8033 (m110) REVERT: B 964 LYS cc_start: 0.8187 (tptt) cc_final: 0.7858 (mttt) REVERT: B 1002 GLN cc_start: 0.8226 (tt0) cc_final: 0.7530 (tp-100) REVERT: B 1010 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7212 (mp10) REVERT: B 1045 LYS cc_start: 0.8376 (mmmt) cc_final: 0.7824 (ttpt) REVERT: B 1073 LYS cc_start: 0.8440 (tttt) cc_final: 0.8158 (ttmt) REVERT: B 1125 ASN cc_start: 0.8410 (m-40) cc_final: 0.8089 (p0) REVERT: C 319 ARG cc_start: 0.8050 (mtp-110) cc_final: 0.7713 (ttm-80) REVERT: C 399 SER cc_start: 0.7314 (t) cc_final: 0.6890 (p) REVERT: C 534 VAL cc_start: 0.8467 (m) cc_final: 0.8164 (p) REVERT: C 654 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7724 (tt0) REVERT: C 779 GLN cc_start: 0.8287 (tp40) cc_final: 0.7808 (tm-30) REVERT: C 964 LYS cc_start: 0.8093 (tptt) cc_final: 0.7689 (mttt) REVERT: C 1002 GLN cc_start: 0.8242 (tt0) cc_final: 0.7612 (tp40) REVERT: C 1010 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.7198 (mp10) REVERT: C 1045 LYS cc_start: 0.8377 (mmmt) cc_final: 0.7815 (ttpt) REVERT: C 1073 LYS cc_start: 0.8369 (tttt) cc_final: 0.8024 (ttmt) REVERT: C 1125 ASN cc_start: 0.8304 (m-40) cc_final: 0.8042 (p0) outliers start: 83 outliers final: 52 residues processed: 323 average time/residue: 1.0996 time to fit residues: 425.4269 Evaluate side-chains 307 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 248 time to evaluate : 2.756 ------------------------------------------------------------------------------- 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 205 SER 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 205 SER Chi-restraints excluded: chain B residue 238 PHE 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 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 921 LYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 205 SER 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 430 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 794 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 45 optimal weight: 2.9990 chunk 201 optimal weight: 0.9990 chunk 153 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 264 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 chunk 253 optimal weight: 10.0000 chunk 30 optimal weight: 0.2980 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS A1119 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1119 ASN C1119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.187384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.115600 restraints weight = 27414.942| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.08 r_work: 0.3141 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26130 Z= 0.167 Angle : 0.601 8.690 35655 Z= 0.306 Chirality : 0.046 0.366 4155 Planarity : 0.004 0.054 4497 Dihedral : 5.515 45.848 4491 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.31 % Allowed : 12.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.15), residues: 3108 helix: 2.40 (0.19), residues: 705 sheet: 0.13 (0.18), residues: 678 loop : -0.58 (0.15), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 64 HIS 0.004 0.001 HIS A1058 PHE 0.019 0.002 PHE B 238 TYR 0.026 0.002 TYR C 170 ARG 0.009 0.001 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00924 ( 30) link_NAG-ASN : angle 2.23885 ( 90) link_BETA1-4 : bond 0.00963 ( 21) link_BETA1-4 : angle 2.80631 ( 63) hydrogen bonds : bond 0.04804 ( 1055) hydrogen bonds : angle 5.83088 ( 3075) SS BOND : bond 0.00281 ( 39) SS BOND : angle 1.25925 ( 78) link_NAG-THR : bond 0.00602 ( 3) link_NAG-THR : angle 2.32027 ( 6) covalent geometry : bond 0.00392 (26037) covalent geometry : angle 0.57621 (35418) *********************** 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 322 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 258 time to evaluate : 2.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.6986 (mmp-170) REVERT: A 399 SER cc_start: 0.7198 (t) cc_final: 0.6732 (p) REVERT: A 534 VAL cc_start: 0.8442 (m) cc_final: 0.8180 (p) REVERT: A 646 ARG cc_start: 0.8508 (mmm-85) cc_final: 0.8198 (mpp80) REVERT: A 654 GLU cc_start: 0.7871 (tt0) cc_final: 0.7416 (tm-30) REVERT: A 779 GLN cc_start: 0.8207 (tp40) cc_final: 0.7704 (tm-30) REVERT: A 964 LYS cc_start: 0.7963 (tptt) cc_final: 0.7607 (mtmt) REVERT: A 1002 GLN cc_start: 0.8196 (tt0) cc_final: 0.7570 (tp-100) REVERT: A 1010 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7113 (mp10) REVERT: A 1045 LYS cc_start: 0.8400 (mmmt) cc_final: 0.8023 (mppt) REVERT: A 1073 LYS cc_start: 0.8335 (tttt) cc_final: 0.8050 (ttmt) REVERT: A 1128 VAL cc_start: 0.8735 (OUTLIER) cc_final: 0.8440 (t) REVERT: B 88 ASP cc_start: 0.7534 (m-30) cc_final: 0.7305 (m-30) REVERT: B 205 SER cc_start: 0.8809 (OUTLIER) cc_final: 0.8586 (t) REVERT: B 238 PHE cc_start: 0.6926 (OUTLIER) cc_final: 0.6056 (p90) REVERT: B 281 GLU cc_start: 0.7893 (mp0) cc_final: 0.7631 (pm20) REVERT: B 399 SER cc_start: 0.7241 (t) cc_final: 0.6754 (p) REVERT: B 534 VAL cc_start: 0.8406 (m) cc_final: 0.8156 (p) REVERT: B 569 ILE cc_start: 0.8626 (tp) cc_final: 0.8420 (tp) REVERT: B 646 ARG cc_start: 0.8556 (mmm-85) cc_final: 0.8246 (mpp80) REVERT: B 654 GLU cc_start: 0.7796 (tt0) cc_final: 0.7310 (tm-30) REVERT: B 779 GLN cc_start: 0.8114 (tp40) cc_final: 0.7633 (tm-30) REVERT: B 921 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8354 (tttp) REVERT: B 955 ASN cc_start: 0.8208 (m-40) cc_final: 0.7961 (m-40) REVERT: B 964 LYS cc_start: 0.8100 (tptt) cc_final: 0.7759 (mttt) REVERT: B 1002 GLN cc_start: 0.8128 (tt0) cc_final: 0.7461 (tp-100) REVERT: B 1010 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7047 (mp10) REVERT: B 1045 LYS cc_start: 0.8377 (mmmt) cc_final: 0.8023 (mppt) REVERT: B 1073 LYS cc_start: 0.8386 (tttt) cc_final: 0.8100 (ttmt) REVERT: B 1125 ASN cc_start: 0.8342 (m-40) cc_final: 0.8022 (p0) REVERT: C 52 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8148 (tt0) REVERT: C 319 ARG cc_start: 0.8027 (mtp-110) cc_final: 0.7620 (ttm-80) REVERT: C 399 SER cc_start: 0.7226 (t) cc_final: 0.6788 (p) REVERT: C 512 VAL cc_start: 0.8243 (t) cc_final: 0.8001 (m) REVERT: C 534 VAL cc_start: 0.8424 (m) cc_final: 0.8134 (p) REVERT: C 654 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7653 (tt0) REVERT: C 779 GLN cc_start: 0.8234 (tp40) cc_final: 0.7735 (tm-30) REVERT: C 964 LYS cc_start: 0.8011 (tptt) cc_final: 0.7601 (mttt) REVERT: C 1002 GLN cc_start: 0.8191 (tt0) cc_final: 0.7586 (tp40) REVERT: C 1010 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7095 (mp10) REVERT: C 1045 LYS cc_start: 0.8370 (mmmt) cc_final: 0.7829 (ttpt) REVERT: C 1073 LYS cc_start: 0.8323 (tttt) cc_final: 0.7973 (ttmt) REVERT: C 1125 ASN cc_start: 0.8258 (m-40) cc_final: 0.7987 (p0) outliers start: 64 outliers final: 48 residues processed: 307 average time/residue: 1.1785 time to fit residues: 429.6614 Evaluate side-chains 304 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 246 time to evaluate : 2.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 94 SER 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 238 PHE 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 480 CYS Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 524 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 921 LYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 94 SER 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 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 430 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 196 optimal weight: 1.9990 chunk 220 optimal weight: 5.9990 chunk 292 optimal weight: 0.7980 chunk 289 optimal weight: 0.7980 chunk 223 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 229 optimal weight: 1.9990 chunk 280 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS A1119 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1101 HIS B1119 ASN C 339 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.188633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.117917 restraints weight = 27576.228| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.99 r_work: 0.3159 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3400 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= 0.136 Angle : 0.566 8.888 35655 Z= 0.288 Chirality : 0.045 0.422 4155 Planarity : 0.004 0.049 4497 Dihedral : 5.184 44.206 4491 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.20 % Allowed : 12.46 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.15), residues: 3108 helix: 2.57 (0.19), residues: 705 sheet: 0.18 (0.18), residues: 693 loop : -0.57 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 633 HIS 0.003 0.001 HIS A1058 PHE 0.019 0.001 PHE A 238 TYR 0.027 0.001 TYR B 170 ARG 0.008 0.001 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00694 ( 30) link_NAG-ASN : angle 2.14607 ( 90) link_BETA1-4 : bond 0.00870 ( 21) link_BETA1-4 : angle 2.64594 ( 63) hydrogen bonds : bond 0.04405 ( 1055) hydrogen bonds : angle 5.65838 ( 3075) SS BOND : bond 0.00215 ( 39) SS BOND : angle 1.10871 ( 78) link_NAG-THR : bond 0.00519 ( 3) link_NAG-THR : angle 2.10578 ( 6) covalent geometry : bond 0.00311 (26037) covalent geometry : angle 0.54328 (35418) *********************** 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 328 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 267 time to evaluate : 2.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ARG cc_start: 0.7961 (ttm-80) cc_final: 0.7733 (ttm-80) REVERT: A 321 GLN cc_start: 0.8332 (mm110) cc_final: 0.8121 (mm110) REVERT: A 328 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.6702 (mmp-170) REVERT: A 399 SER cc_start: 0.7124 (t) cc_final: 0.6654 (p) REVERT: A 534 VAL cc_start: 0.8407 (m) cc_final: 0.8144 (p) REVERT: A 646 ARG cc_start: 0.8454 (mmm-85) cc_final: 0.8144 (mpp80) REVERT: A 654 GLU cc_start: 0.7874 (tt0) cc_final: 0.7431 (tm-30) REVERT: A 779 GLN cc_start: 0.8109 (tp40) cc_final: 0.7585 (tm-30) REVERT: A 964 LYS cc_start: 0.7906 (tptt) cc_final: 0.7523 (mtmt) REVERT: A 1002 GLN cc_start: 0.8139 (tt0) cc_final: 0.7473 (tp40) REVERT: A 1010 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7086 (mp10) REVERT: A 1045 LYS cc_start: 0.8407 (mmmt) cc_final: 0.8022 (mppt) REVERT: A 1073 LYS cc_start: 0.8298 (tttt) cc_final: 0.8001 (ttmt) REVERT: B 88 ASP cc_start: 0.7516 (m-30) cc_final: 0.7264 (m-30) REVERT: B 238 PHE cc_start: 0.6803 (OUTLIER) cc_final: 0.5822 (p90) REVERT: B 281 GLU cc_start: 0.7887 (mp0) cc_final: 0.7664 (pm20) REVERT: B 399 SER cc_start: 0.7143 (t) cc_final: 0.6633 (p) REVERT: B 534 VAL cc_start: 0.8351 (m) cc_final: 0.8093 (p) REVERT: B 646 ARG cc_start: 0.8496 (mmm-85) cc_final: 0.8208 (mpp80) REVERT: B 654 GLU cc_start: 0.7771 (tt0) cc_final: 0.7309 (tm-30) REVERT: B 779 GLN cc_start: 0.8045 (tp40) cc_final: 0.7500 (tm-30) REVERT: B 921 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8281 (tttp) REVERT: B 955 ASN cc_start: 0.8171 (m-40) cc_final: 0.7911 (m-40) REVERT: B 964 LYS cc_start: 0.8009 (tptt) cc_final: 0.7592 (mttt) REVERT: B 1002 GLN cc_start: 0.8062 (tt0) cc_final: 0.7418 (tp-100) REVERT: B 1010 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7010 (mp10) REVERT: B 1045 LYS cc_start: 0.8374 (mmmt) cc_final: 0.8013 (mppt) REVERT: B 1073 LYS cc_start: 0.8370 (tttt) cc_final: 0.8071 (ttmt) REVERT: B 1125 ASN cc_start: 0.8344 (m-40) cc_final: 0.7998 (p0) REVERT: C 52 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.8055 (tt0) REVERT: C 153 MET cc_start: 0.0530 (ptm) cc_final: 0.0021 (tpt) REVERT: C 319 ARG cc_start: 0.7959 (mtp-110) cc_final: 0.7588 (ttm-80) REVERT: C 399 SER cc_start: 0.7102 (t) cc_final: 0.6628 (p) REVERT: C 512 VAL cc_start: 0.8154 (t) cc_final: 0.7928 (m) REVERT: C 534 VAL cc_start: 0.8365 (m) cc_final: 0.8093 (p) REVERT: C 654 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7634 (tt0) REVERT: C 779 GLN cc_start: 0.8124 (tp40) cc_final: 0.7594 (tm-30) REVERT: C 964 LYS cc_start: 0.7915 (tptt) cc_final: 0.7464 (mttt) REVERT: C 1002 GLN cc_start: 0.8099 (tt0) cc_final: 0.7468 (tp40) REVERT: C 1010 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7050 (mp10) REVERT: C 1045 LYS cc_start: 0.8364 (mmmt) cc_final: 0.7830 (ttpt) REVERT: C 1073 LYS cc_start: 0.8263 (tttt) cc_final: 0.7898 (ttmt) REVERT: C 1125 ASN cc_start: 0.8215 (m-40) cc_final: 0.7960 (p0) outliers start: 61 outliers final: 47 residues processed: 309 average time/residue: 1.0850 time to fit residues: 403.1985 Evaluate side-chains 310 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 255 time to evaluate : 2.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 286 THR 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 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 94 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 238 PHE 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 480 CYS Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 524 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 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 94 SER 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 325 SER 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 430 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 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 278 optimal weight: 0.9980 chunk 277 optimal weight: 1.9990 chunk 306 optimal weight: 0.8980 chunk 244 optimal weight: 4.9990 chunk 242 optimal weight: 0.9980 chunk 155 optimal weight: 0.5980 chunk 189 optimal weight: 0.4980 chunk 299 optimal weight: 2.9990 chunk 313 optimal weight: 6.9990 chunk 84 optimal weight: 0.6980 chunk 196 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1101 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4075 r_free = 0.4075 target = 0.189236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.122911 restraints weight = 27473.586| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.18 r_work: 0.3180 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26130 Z= 0.125 Angle : 0.552 8.109 35655 Z= 0.281 Chirality : 0.045 0.382 4155 Planarity : 0.004 0.065 4497 Dihedral : 5.038 43.323 4491 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.99 % Allowed : 12.93 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.15), residues: 3108 helix: 2.66 (0.19), residues: 705 sheet: 0.13 (0.18), residues: 672 loop : -0.58 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 886 HIS 0.003 0.001 HIS A1058 PHE 0.018 0.001 PHE B 238 TYR 0.031 0.001 TYR A 170 ARG 0.009 0.001 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00638 ( 30) link_NAG-ASN : angle 2.12251 ( 90) link_BETA1-4 : bond 0.00895 ( 21) link_BETA1-4 : angle 2.57993 ( 63) hydrogen bonds : bond 0.04253 ( 1055) hydrogen bonds : angle 5.55733 ( 3075) SS BOND : bond 0.00195 ( 39) SS BOND : angle 1.04364 ( 78) link_NAG-THR : bond 0.00474 ( 3) link_NAG-THR : angle 2.04278 ( 6) covalent geometry : bond 0.00282 (26037) covalent geometry : angle 0.52906 (35418) ********************** 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 319 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 264 time to evaluate : 2.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.6842 (mtt90) cc_final: 0.6384 (ttm110) REVERT: A 205 SER cc_start: 0.8811 (OUTLIER) cc_final: 0.8611 (t) REVERT: A 328 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.6682 (mmp-170) REVERT: A 399 SER cc_start: 0.7139 (t) cc_final: 0.6676 (p) REVERT: A 534 VAL cc_start: 0.8419 (m) cc_final: 0.8157 (p) REVERT: A 646 ARG cc_start: 0.8482 (mmm-85) cc_final: 0.8174 (mpp80) REVERT: A 654 GLU cc_start: 0.7903 (tt0) cc_final: 0.7470 (tm-30) REVERT: A 779 GLN cc_start: 0.8138 (tp40) cc_final: 0.7594 (tm-30) REVERT: A 964 LYS cc_start: 0.7923 (tptt) cc_final: 0.7541 (mtmt) REVERT: A 1002 GLN cc_start: 0.8152 (tt0) cc_final: 0.7490 (tp40) REVERT: A 1010 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7105 (mp10) REVERT: A 1045 LYS cc_start: 0.8419 (mmmt) cc_final: 0.8042 (mppt) REVERT: A 1073 LYS cc_start: 0.8309 (tttt) cc_final: 0.8026 (ttmt) REVERT: A 1128 VAL cc_start: 0.8764 (OUTLIER) cc_final: 0.8423 (t) REVERT: B 88 ASP cc_start: 0.7475 (m-30) cc_final: 0.7251 (m-30) REVERT: B 281 GLU cc_start: 0.7880 (mp0) cc_final: 0.7636 (pm20) REVERT: B 399 SER cc_start: 0.7064 (t) cc_final: 0.6524 (p) REVERT: B 534 VAL cc_start: 0.8382 (m) cc_final: 0.8125 (p) REVERT: B 646 ARG cc_start: 0.8523 (mmm-85) cc_final: 0.8240 (mpp80) REVERT: B 654 GLU cc_start: 0.7788 (tt0) cc_final: 0.7334 (tm-30) REVERT: B 779 GLN cc_start: 0.8078 (tp40) cc_final: 0.7515 (tm-30) REVERT: B 921 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8302 (tttp) REVERT: B 955 ASN cc_start: 0.8146 (m-40) cc_final: 0.7875 (m-40) REVERT: B 964 LYS cc_start: 0.8001 (tptt) cc_final: 0.7575 (mttt) REVERT: B 1002 GLN cc_start: 0.8149 (tt0) cc_final: 0.7486 (tp-100) REVERT: B 1010 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7020 (mp10) REVERT: B 1045 LYS cc_start: 0.8381 (mmmt) cc_final: 0.7845 (ttpt) REVERT: B 1073 LYS cc_start: 0.8386 (tttt) cc_final: 0.8088 (ttmt) REVERT: B 1125 ASN cc_start: 0.8346 (m-40) cc_final: 0.7977 (p0) REVERT: C 319 ARG cc_start: 0.7917 (mtp-110) cc_final: 0.7609 (ttm-80) REVERT: C 399 SER cc_start: 0.7104 (t) cc_final: 0.6632 (p) REVERT: C 512 VAL cc_start: 0.8203 (t) cc_final: 0.7983 (m) REVERT: C 534 VAL cc_start: 0.8388 (m) cc_final: 0.8098 (p) REVERT: C 654 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7643 (tt0) REVERT: C 779 GLN cc_start: 0.8142 (tp40) cc_final: 0.7601 (tm-30) REVERT: C 964 LYS cc_start: 0.7949 (tptt) cc_final: 0.7487 (mttt) REVERT: C 1002 GLN cc_start: 0.8089 (tt0) cc_final: 0.7481 (tp40) REVERT: C 1010 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.7098 (mp10) REVERT: C 1045 LYS cc_start: 0.8382 (mmmt) cc_final: 0.7850 (ttpt) REVERT: C 1073 LYS cc_start: 0.8298 (tttt) cc_final: 0.7938 (ttmt) REVERT: C 1125 ASN cc_start: 0.8218 (m-40) cc_final: 0.7929 (p0) outliers start: 55 outliers final: 43 residues processed: 300 average time/residue: 1.0886 time to fit residues: 392.1653 Evaluate side-chains 303 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 252 time to evaluate : 2.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 286 THR 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 480 CYS Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 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 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 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 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 94 SER 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 325 SER 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 430 THR Chi-restraints excluded: chain C residue 480 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 35 optimal weight: 0.9990 chunk 144 optimal weight: 10.0000 chunk 308 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 218 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 224 optimal weight: 7.9990 chunk 201 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 311 optimal weight: 3.9990 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 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1101 HIS A1119 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1101 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.185329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.118860 restraints weight = 27458.072| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.19 r_work: 0.3114 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 26130 Z= 0.289 Angle : 0.670 9.423 35655 Z= 0.342 Chirality : 0.051 0.378 4155 Planarity : 0.005 0.109 4497 Dihedral : 5.733 46.241 4491 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.38 % Allowed : 12.68 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.15), residues: 3108 helix: 2.20 (0.19), residues: 705 sheet: 0.07 (0.18), residues: 696 loop : -0.72 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 64 HIS 0.008 0.002 HIS A1058 PHE 0.022 0.002 PHE C 541 TYR 0.022 0.002 TYR B1067 ARG 0.010 0.001 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00691 ( 30) link_NAG-ASN : angle 2.30567 ( 90) link_BETA1-4 : bond 0.00956 ( 21) link_BETA1-4 : angle 2.81775 ( 63) hydrogen bonds : bond 0.05651 ( 1055) hydrogen bonds : angle 6.00512 ( 3075) SS BOND : bond 0.00475 ( 39) SS BOND : angle 1.33481 ( 78) link_NAG-THR : bond 0.00765 ( 3) link_NAG-THR : angle 2.25035 ( 6) covalent geometry : bond 0.00707 (26037) covalent geometry : angle 0.64760 (35418) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22647.30 seconds wall clock time: 393 minutes 31.63 seconds (23611.63 seconds total)