Starting phenix.real_space_refine on Fri Feb 6 17:04:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j6g_61170/02_2026/9j6g_61170.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j6g_61170/02_2026/9j6g_61170.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j6g_61170/02_2026/9j6g_61170.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j6g_61170/02_2026/9j6g_61170.map" model { file = "/net/cci-nas-00/data/ceres_data/9j6g_61170/02_2026/9j6g_61170.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j6g_61170/02_2026/9j6g_61170.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 131 5.16 5 C 16537 2.51 5 N 4259 2.21 5 O 5209 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26136 Number of models: 1 Model: "" Number of chains: 23 Chain: "B" Number of atoms: 8299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8299 Classifications: {'peptide': 1065} Link IDs: {'PTRANS': 50, 'TRANS': 1014} Chain breaks: 2 Chain: "A" Number of atoms: 8433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1084, 8433 Classifications: {'peptide': 1084} Link IDs: {'PTRANS': 51, 'TRANS': 1032} Chain breaks: 1 Chain: "C" Number of atoms: 8414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1082, 8414 Classifications: {'peptide': 1082} Link IDs: {'PTRANS': 51, 'TRANS': 1030} Chain breaks: 1 Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 5.83, per 1000 atoms: 0.22 Number of scatterers: 26136 At special positions: 0 Unit cell: (148.35, 150.42, 163.53, 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 131 16.00 O 5209 8.00 N 4259 7.00 C 16537 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 163 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 351 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 423 " distance=2.04 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 512 " distance=2.03 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 475 " distance=2.03 Simple disulfide: pdb=" SG CYS B 525 " - pdb=" SG CYS B 577 " distance=2.04 Simple disulfide: pdb=" SG CYS B 604 " - pdb=" SG CYS B 638 " distance=2.03 Simple disulfide: pdb=" SG CYS B 651 " - pdb=" SG CYS B 660 " distance=2.03 Simple disulfide: pdb=" SG CYS B 719 " - pdb=" SG CYS B 741 " distance=2.03 Simple disulfide: pdb=" SG CYS B 724 " - pdb=" SG CYS B 730 " distance=2.03 Simple disulfide: pdb=" SG CYS B1013 " - pdb=" SG CYS B1024 " distance=2.03 Simple disulfide: pdb=" SG CYS B1063 " - pdb=" SG CYS B1107 " distance=2.03 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 163 " distance=2.04 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 351 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 512 " distance=2.03 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 475 " distance=2.04 Simple disulfide: pdb=" SG CYS A 525 " - pdb=" SG CYS A 577 " distance=2.03 Simple disulfide: pdb=" SG CYS A 604 " - pdb=" SG CYS A 638 " distance=2.03 Simple disulfide: pdb=" SG CYS A 651 " - pdb=" SG CYS A 660 " distance=2.03 Simple disulfide: pdb=" SG CYS A 719 " - pdb=" SG CYS A 741 " distance=2.03 Simple disulfide: pdb=" SG CYS A 724 " - pdb=" SG CYS A 730 " distance=2.03 Simple disulfide: pdb=" SG CYS A1013 " - pdb=" SG CYS A1024 " distance=2.03 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 163 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 291 " distance=2.03 Simple disulfide: pdb=" SG CYS C 326 " - pdb=" SG CYS C 351 " distance=2.03 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 512 " distance=2.03 Simple disulfide: pdb=" SG CYS C 525 " - pdb=" SG CYS C 577 " distance=2.04 Simple disulfide: pdb=" SG CYS C 604 " - pdb=" SG CYS C 638 " distance=2.03 Simple disulfide: pdb=" SG CYS C 651 " - pdb=" SG CYS C 660 " distance=2.03 Simple disulfide: pdb=" SG CYS C 719 " - pdb=" SG CYS C 741 " distance=2.04 Simple disulfide: pdb=" SG CYS C 724 " - pdb=" SG CYS C 730 " distance=2.03 Simple disulfide: pdb=" SG CYS C1013 " - pdb=" SG CYS C1024 " distance=2.03 Simple disulfide: pdb=" SG CYS C1063 " - pdb=" SG CYS C1107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA K 3 " - " MAN K 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " BMA D 3 " - " BMA D 4 " " 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 I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " BMA P 3 " - " BMA P 4 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A1201 " - " ASN A 115 " " NAG A1202 " - " ASN A 125 " " NAG A1203 " - " ASN A 162 " " NAG A1204 " - " ASN A 207 " " NAG A1205 " - " ASN A 321 " " NAG A1206 " - " ASN A 333 " " NAG A1207 " - " ASN A 603 " " NAG A1208 " - " ASN A 690 " " NAG A1209 " - " ASN A1055 " " NAG A1210 " - " ASN A1079 " " NAG A1211 " - " ASN A 782 " " NAG B1201 " - " ASN B 24 " " NAG B1202 " - " ASN B 65 " " NAG B1203 " - " ASN B 115 " " NAG B1204 " - " ASN B 162 " " NAG B1205 " - " ASN B 207 " " NAG B1206 " - " ASN B 243 " " NAG B1207 " - " ASN B 333 " " NAG B1208 " - " ASN B 603 " " NAG B1209 " - " ASN B 690 " " NAG B1210 " - " ASN B1055 " " NAG B1211 " - " ASN B1079 " " NAG C1201 " - " ASN C 24 " " NAG C1202 " - " ASN C 65 " " NAG C1203 " - " ASN C 162 " " NAG C1204 " - " ASN C 207 " " NAG C1205 " - " ASN C 243 " " NAG C1206 " - " ASN C 272 " " NAG C1207 " - " ASN C 333 " " NAG C1208 " - " ASN C 603 " " NAG C1209 " - " ASN C 690 " " NAG C1210 " - " ASN C1079 " " NAG D 1 " - " ASN B 230 " " NAG E 1 " - " ASN B 272 " " NAG F 1 " - " ASN B 321 " " NAG G 1 " - " ASN B 360 " " NAG H 1 " - " ASN B 698 " " NAG I 1 " - " ASN B 782 " " NAG J 1 " - " ASN A 65 " " NAG K 1 " - " ASN A 230 " " NAG L 1 " - " ASN A 272 " " NAG M 1 " - " ASN A 360 " " NAG N 1 " - " ASN A 698 " " NAG O 1 " - " ASN C 115 " " NAG P 1 " - " ASN C 230 " " NAG Q 1 " - " ASN C 321 " " NAG R 1 " - " ASN C 360 " " NAG S 1 " - " ASN C 698 " " NAG T 1 " - " ASN C 782 " Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 1.1 seconds 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6042 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 49 sheets defined 23.7% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'B' and resid 284 through 293 removed outlier: 3.591A pdb=" N THR B 293 " --> pdb=" O LEU B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 360 removed outlier: 3.703A pdb=" N VAL B 357 " --> pdb=" O ASP B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 378 removed outlier: 3.744A pdb=" N LEU B 378 " --> pdb=" O PRO B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 401 removed outlier: 4.112A pdb=" N ARG B 399 " --> pdb=" O ASP B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 412 removed outlier: 3.650A pdb=" N TYR B 412 " --> pdb=" O VAL B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 611 Processing helix chain 'B' and resid 612 through 616 Processing helix chain 'B' and resid 718 through 724 Processing helix chain 'B' and resid 727 through 735 Processing helix chain 'B' and resid 736 through 738 No H-bonds generated for 'chain 'B' and resid 736 through 738' Processing helix chain 'B' and resid 739 through 764 removed outlier: 3.631A pdb=" N ASP B 756 " --> pdb=" O ALA B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 807 Processing helix chain 'B' and resid 830 through 838 removed outlier: 3.864A pdb=" N ASN B 837 " --> pdb=" O ALA B 833 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 865 Processing helix chain 'B' and resid 867 through 871 removed outlier: 3.624A pdb=" N ALA B 871 " --> pdb=" O THR B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 889 Processing helix chain 'B' and resid 894 through 900 removed outlier: 3.847A pdb=" N TYR B 898 " --> pdb=" O GLN B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 922 Processing helix chain 'B' and resid 926 through 946 removed outlier: 3.768A pdb=" N VAL B 932 " --> pdb=" O LYS B 928 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN B 936 " --> pdb=" O VAL B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 947 through 949 No H-bonds generated for 'chain 'B' and resid 947 through 949' Processing helix chain 'B' and resid 957 through 963 Processing helix chain 'B' and resid 966 through 1014 removed outlier: 4.323A pdb=" N VAL B 972 " --> pdb=" O PRO B 968 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG B 976 " --> pdb=" O VAL B 972 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU B 977 " --> pdb=" O GLN B 973 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B1014 " --> pdb=" O MET B1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 293 Processing helix chain 'A' and resid 356 through 361 removed outlier: 3.905A pdb=" N ASN A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 356 through 361' Processing helix chain 'A' and resid 374 through 380 removed outlier: 3.803A pdb=" N LEU A 378 " --> pdb=" O PRO A 375 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASN A 379 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP A 380 " --> pdb=" O LYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 401 Processing helix chain 'A' and resid 407 through 412 Processing helix chain 'A' and resid 606 through 611 removed outlier: 3.569A pdb=" N MET A 610 " --> pdb=" O ASP A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 622 removed outlier: 3.501A pdb=" N ARG A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL A 622 " --> pdb=" O HIS A 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 617 through 622' Processing helix chain 'A' and resid 718 through 724 Processing helix chain 'A' and resid 727 through 735 Processing helix chain 'A' and resid 736 through 738 No H-bonds generated for 'chain 'A' and resid 736 through 738' Processing helix chain 'A' and resid 739 through 764 removed outlier: 3.617A pdb=" N ASP A 756 " --> pdb=" O ALA A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 806 Processing helix chain 'A' and resid 830 through 836 removed outlier: 3.601A pdb=" N PHE A 836 " --> pdb=" O CYS A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 865 Processing helix chain 'A' and resid 867 through 871 removed outlier: 3.612A pdb=" N ALA A 871 " --> pdb=" O THR A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 890 removed outlier: 3.713A pdb=" N ILE A 890 " --> pdb=" O ARG A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 900 removed outlier: 3.673A pdb=" N TYR A 898 " --> pdb=" O GLN A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 922 Processing helix chain 'A' and resid 926 through 946 removed outlier: 3.863A pdb=" N VAL A 932 " --> pdb=" O LYS A 928 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN A 936 " --> pdb=" O VAL A 932 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 949 No H-bonds generated for 'chain 'A' and resid 947 through 949' Processing helix chain 'A' and resid 957 through 963 Processing helix chain 'A' and resid 966 through 1014 removed outlier: 4.206A pdb=" N VAL A 972 " --> pdb=" O PRO A 968 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ARG A 976 " --> pdb=" O VAL A 972 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU A 977 " --> pdb=" O GLN A 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 293 removed outlier: 3.576A pdb=" N THR C 293 " --> pdb=" O LEU C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 361 removed outlier: 3.693A pdb=" N TYR C 359 " --> pdb=" O TYR C 355 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN C 360 " --> pdb=" O SER C 356 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER C 361 " --> pdb=" O VAL C 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 355 through 361' Processing helix chain 'C' and resid 374 through 378 removed outlier: 3.908A pdb=" N LEU C 378 " --> pdb=" O PRO C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 399 removed outlier: 4.379A pdb=" N ARG C 399 " --> pdb=" O GLY C 395 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 395 through 399' Processing helix chain 'C' and resid 407 through 412 removed outlier: 3.619A pdb=" N TYR C 412 " --> pdb=" O VAL C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 611 Processing helix chain 'C' and resid 617 through 622 removed outlier: 3.508A pdb=" N ARG C 621 " --> pdb=" O ALA C 617 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL C 622 " --> pdb=" O HIS C 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 617 through 622' Processing helix chain 'C' and resid 718 through 725 Processing helix chain 'C' and resid 727 through 735 Processing helix chain 'C' and resid 736 through 738 No H-bonds generated for 'chain 'C' and resid 736 through 738' Processing helix chain 'C' and resid 739 through 764 removed outlier: 3.549A pdb=" N ASP C 756 " --> pdb=" O ALA C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 797 through 807 Processing helix chain 'C' and resid 831 through 836 Processing helix chain 'C' and resid 847 through 865 Processing helix chain 'C' and resid 867 through 871 Processing helix chain 'C' and resid 878 through 889 Processing helix chain 'C' and resid 894 through 900 Processing helix chain 'C' and resid 900 through 922 Processing helix chain 'C' and resid 926 through 946 removed outlier: 3.678A pdb=" N VAL C 932 " --> pdb=" O LYS C 928 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN C 936 " --> pdb=" O VAL C 932 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 940 " --> pdb=" O ASN C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 947 through 949 No H-bonds generated for 'chain 'C' and resid 947 through 949' Processing helix chain 'C' and resid 957 through 963 removed outlier: 3.627A pdb=" N ILE C 961 " --> pdb=" O VAL C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 1014 removed outlier: 4.520A pdb=" N VAL C 972 " --> pdb=" O PRO C 968 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG C 976 " --> pdb=" O VAL C 972 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU C 977 " --> pdb=" O GLN C 973 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 32 through 34 removed outlier: 8.222A pdb=" N ASN B 65 " --> pdb=" O HIS B 259 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N HIS B 259 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N HIS B 201 " --> pdb=" O PRO B 221 " (cutoff:3.500A) removed outlier: 9.635A pdb=" N TYR B 203 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N LEU B 219 " --> pdb=" O TYR B 203 " (cutoff:3.500A) removed outlier: 13.136A pdb=" N SER B 205 " --> pdb=" O SER B 217 " (cutoff:3.500A) removed outlier: 12.159A pdb=" N SER B 217 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ARG B 38 " --> pdb=" O SER B 217 " (cutoff:3.500A) removed outlier: 9.068A pdb=" N LEU B 219 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N PHE B 40 " --> pdb=" O LEU B 219 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 59 removed outlier: 4.612A pdb=" N ASP B 277 " --> pdb=" O ASP B 268 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 87 through 88 removed outlier: 3.589A pdb=" N ILE B 87 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE B 234 " --> pdb=" O ILE B 87 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 87 through 88 removed outlier: 3.589A pdb=" N ILE B 87 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE B 234 " --> pdb=" O ILE B 87 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY B 106 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N TRP B 107 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE B 129 " --> pdb=" O HIS B 169 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR B 165 " --> pdb=" O VAL B 133 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 301 through 304 Processing sheet with id=AA6, first strand: chain 'B' and resid 315 through 316 removed outlier: 3.557A pdb=" N VAL B 526 " --> pdb=" O GLY B 537 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY B 537 " --> pdb=" O VAL B 526 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 344 through 347 removed outlier: 3.896A pdb=" N GLY B 344 " --> pdb=" O TYR B 390 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR B 390 " --> pdb=" O GLY B 344 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 439 through 441 Processing sheet with id=AA9, first strand: chain 'B' and resid 460 through 461 Processing sheet with id=AB1, first strand: chain 'B' and resid 643 through 644 removed outlier: 6.469A pdb=" N ALA B 661 " --> pdb=" O PRO B 654 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 682 through 683 removed outlier: 6.493A pdb=" N GLU B 682 " --> pdb=" O ILE A 769 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 693 through 709 removed outlier: 6.762A pdb=" N ALA B 694 " --> pdb=" O ASN B1055 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN B1055 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N GLN B1053 " --> pdb=" O PRO B 696 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TYR B1048 " --> pdb=" O HIS B1029 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N HIS B1029 " --> pdb=" O TYR B1048 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 714 through 717 removed outlier: 4.424A pdb=" N LYS B 714 " --> pdb=" O LEU B 842 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 777 through 778 Processing sheet with id=AB6, first strand: chain 'B' and resid 1101 through 1106 removed outlier: 4.933A pdb=" N ALA B1068 " --> pdb=" O SER B1104 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1075 through 1078 Processing sheet with id=AB8, first strand: chain 'A' and resid 31 through 34 removed outlier: 4.239A pdb=" N ASP A 31 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N ASN A 65 " --> pdb=" O HIS A 259 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N HIS A 259 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N HIS A 201 " --> pdb=" O PRO A 221 " (cutoff:3.500A) removed outlier: 9.276A pdb=" N TYR A 203 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N LEU A 219 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N PHE A 40 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 54 through 59 Processing sheet with id=AC1, first strand: chain 'A' and resid 87 through 88 removed outlier: 3.535A pdb=" N ILE A 87 " --> pdb=" O PHE A 234 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY A 106 " --> pdb=" O ILE A 237 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 129 " --> pdb=" O HIS A 169 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 136 through 143 removed outlier: 6.622A pdb=" N ASN A 137 " --> pdb=" O THR A 158 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N CYS A 139 " --> pdb=" O VAL A 156 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL A 156 " --> pdb=" O CYS A 139 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 301 through 304 Processing sheet with id=AC4, first strand: chain 'A' and resid 315 through 316 Processing sheet with id=AC5, first strand: chain 'A' and resid 344 through 347 removed outlier: 3.702A pdb=" N GLY A 344 " --> pdb=" O TYR A 390 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR A 390 " --> pdb=" O GLY A 344 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 552 through 554 removed outlier: 6.656A pdb=" N GLY A 553 " --> pdb=" O ASP A 561 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 643 through 644 removed outlier: 6.212A pdb=" N ALA A 661 " --> pdb=" O PRO A 654 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 682 through 683 removed outlier: 7.047A pdb=" N GLU A 682 " --> pdb=" O ILE C 769 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'A' and resid 693 through 709 removed outlier: 6.717A pdb=" N ALA A 694 " --> pdb=" O ASN A1055 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN A1055 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLN A1053 " --> pdb=" O PRO A 696 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N TYR A1048 " --> pdb=" O HIS A1029 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N HIS A1029 " --> pdb=" O TYR A1048 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 693 through 709 removed outlier: 6.717A pdb=" N ALA A 694 " --> pdb=" O ASN A1055 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN A1055 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLN A1053 " --> pdb=" O PRO A 696 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR A1057 " --> pdb=" O MET A1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 714 through 717 removed outlier: 4.605A pdb=" N LYS A 714 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 777 through 778 Processing sheet with id=AD4, first strand: chain 'A' and resid 1101 through 1106 removed outlier: 5.058A pdb=" N ALA A1068 " --> pdb=" O SER A1104 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 31 through 34 removed outlier: 4.247A pdb=" N ASP C 31 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU C 99 " --> pdb=" O HIS C 184 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N HIS C 201 " --> pdb=" O PRO C 221 " (cutoff:3.500A) removed outlier: 9.571A pdb=" N TYR C 203 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 9.482A pdb=" N LEU C 219 " --> pdb=" O TYR C 203 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ARG C 38 " --> pdb=" O SER C 217 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N LEU C 219 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N PHE C 40 " --> pdb=" O LEU C 219 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 31 through 34 removed outlier: 4.247A pdb=" N ASP C 31 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR C 81 " --> pdb=" O LEU C 72 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 52 through 59 removed outlier: 3.837A pdb=" N VAL C 279 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP C 268 " --> pdb=" O ASP C 277 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASP C 277 " --> pdb=" O ASP C 268 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 87 through 88 removed outlier: 3.693A pdb=" N GLY C 106 " --> pdb=" O ILE C 237 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR C 165 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 136 through 138 removed outlier: 6.784A pdb=" N ASN C 137 " --> pdb=" O THR C 158 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 145 through 146 Processing sheet with id=AE2, first strand: chain 'C' and resid 301 through 304 Processing sheet with id=AE3, first strand: chain 'C' and resid 315 through 316 removed outlier: 3.656A pdb=" N VAL C 526 " --> pdb=" O GLY C 537 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY C 537 " --> pdb=" O VAL C 526 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE C 528 " --> pdb=" O GLY C 535 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 344 through 347 removed outlier: 4.040A pdb=" N GLY C 344 " --> pdb=" O TYR C 390 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR C 390 " --> pdb=" O GLY C 344 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 439 through 441 Processing sheet with id=AE6, first strand: chain 'C' and resid 460 through 461 removed outlier: 3.602A pdb=" N TYR C 476 " --> pdb=" O TYR C 460 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 552 through 553 removed outlier: 3.837A pdb=" N SER C 562 " --> pdb=" O GLY C 553 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 643 through 644 removed outlier: 6.093A pdb=" N THR C 643 " --> pdb=" O ALA C 675 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N THR C 677 " --> pdb=" O THR C 643 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ALA C 661 " --> pdb=" O PRO C 654 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 692 through 695 removed outlier: 4.516A pdb=" N THR C1057 " --> pdb=" O MET C1078 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA C1059 " --> pdb=" O PHE C1076 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N PHE C1076 " --> pdb=" O ALA C1059 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLN C1087 " --> pdb=" O SER C1092 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N SER C1092 " --> pdb=" O GLN C1087 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 699 through 709 removed outlier: 6.081A pdb=" N TYR C1048 " --> pdb=" O HIS C1029 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N HIS C1029 " --> pdb=" O TYR C1048 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 714 through 717 removed outlier: 4.502A pdb=" N LYS C 714 " --> pdb=" O LEU C 842 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 777 through 778 Processing sheet with id=AF4, first strand: chain 'C' and resid 1101 through 1106 removed outlier: 4.498A pdb=" N ALA C1068 " --> pdb=" O SER C1104 " (cutoff:3.500A) 960 hydrogen bonds defined for protein. 2637 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: 5.22 Time building geometry restraints manager: 2.83 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: 4882 1.33 - 1.45: 7226 1.45 - 1.58: 14434 1.58 - 1.70: 0 1.70 - 1.83: 176 Bond restraints: 26718 Sorted by residual: bond pdb=" N ILE C 322 " pdb=" CA ILE C 322 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.16e+00 bond pdb=" CA THR C 127 " pdb=" CB THR C 127 " ideal model delta sigma weight residual 1.524 1.562 -0.038 1.33e-02 5.65e+03 8.16e+00 bond pdb=" N ASN B 162 " pdb=" CA ASN B 162 " ideal model delta sigma weight residual 1.462 1.496 -0.034 1.20e-02 6.94e+03 7.83e+00 bond pdb=" N ASN C 162 " pdb=" CA ASN C 162 " ideal model delta sigma weight residual 1.463 1.501 -0.038 1.36e-02 5.41e+03 7.72e+00 bond pdb=" N ASN A1079 " pdb=" CA ASN A1079 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.10e-02 8.26e+03 7.44e+00 ... (remaining 26713 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 34916 1.88 - 3.77: 1272 3.77 - 5.65: 163 5.65 - 7.54: 25 7.54 - 9.42: 6 Bond angle restraints: 36382 Sorted by residual: angle pdb=" C ALA B 624 " pdb=" CA ALA B 624 " pdb=" CB ALA B 624 " ideal model delta sigma weight residual 117.23 109.91 7.32 1.36e+00 5.41e-01 2.90e+01 angle pdb=" C ASN A 603 " pdb=" CA ASN A 603 " pdb=" CB ASN A 603 " ideal model delta sigma weight residual 110.67 102.63 8.04 1.52e+00 4.33e-01 2.79e+01 angle pdb=" CA ASN A 125 " pdb=" CB ASN A 125 " pdb=" CG ASN A 125 " ideal model delta sigma weight residual 112.60 117.67 -5.07 1.00e+00 1.00e+00 2.57e+01 angle pdb=" CA ASN C 690 " pdb=" CB ASN C 690 " pdb=" CG ASN C 690 " ideal model delta sigma weight residual 112.60 117.66 -5.06 1.00e+00 1.00e+00 2.57e+01 angle pdb=" C ASN C 690 " pdb=" CA ASN C 690 " pdb=" CB ASN C 690 " ideal model delta sigma weight residual 110.85 118.97 -8.12 1.64e+00 3.72e-01 2.45e+01 ... (remaining 36377 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.60: 15900 22.60 - 45.20: 755 45.20 - 67.80: 91 67.80 - 90.39: 54 90.39 - 112.99: 19 Dihedral angle restraints: 16819 sinusoidal: 7403 harmonic: 9416 Sorted by residual: dihedral pdb=" CB CYS C 719 " pdb=" SG CYS C 719 " pdb=" SG CYS C 741 " pdb=" CB CYS C 741 " ideal model delta sinusoidal sigma weight residual -86.00 -42.03 -43.97 1 1.00e+01 1.00e-02 2.69e+01 dihedral pdb=" CA SER A 481 " pdb=" C SER A 481 " pdb=" N TYR A 482 " pdb=" CA TYR A 482 " ideal model delta harmonic sigma weight residual 180.00 155.66 24.34 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA ASN A 162 " pdb=" C ASN A 162 " pdb=" N CYS A 163 " pdb=" CA CYS A 163 " ideal model delta harmonic sigma weight residual -180.00 -155.73 -24.27 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 16816 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 4277 0.143 - 0.287: 55 0.287 - 0.430: 9 0.430 - 0.574: 5 0.574 - 0.717: 3 Chirality restraints: 4349 Sorted by residual: chirality pdb=" C1 BMA P 4 " pdb=" O4 BMA P 3 " pdb=" C2 BMA P 4 " pdb=" O5 BMA P 4 " both_signs ideal model delta sigma weight residual False -2.40 -1.68 -0.72 2.00e-02 2.50e+03 1.29e+03 chirality pdb=" C1 BMA P 3 " pdb=" O4 NAG P 2 " pdb=" C2 BMA P 3 " pdb=" O5 BMA P 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-02 2.50e+03 1.11e+03 chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-02 2.50e+03 2.92e+02 ... (remaining 4346 not shown) Planarity restraints: 4668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1210 " 0.353 2.00e-02 2.50e+03 3.04e-01 1.15e+03 pdb=" C7 NAG B1210 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG B1210 " 0.066 2.00e-02 2.50e+03 pdb=" N2 NAG B1210 " -0.535 2.00e-02 2.50e+03 pdb=" O7 NAG B1210 " 0.198 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1202 " -0.350 2.00e-02 2.50e+03 3.00e-01 1.12e+03 pdb=" C7 NAG B1202 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG B1202 " -0.156 2.00e-02 2.50e+03 pdb=" N2 NAG B1202 " 0.532 2.00e-02 2.50e+03 pdb=" O7 NAG B1202 " -0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 2 " -0.346 2.00e-02 2.50e+03 3.00e-01 1.12e+03 pdb=" C7 NAG T 2 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG T 2 " -0.109 2.00e-02 2.50e+03 pdb=" N2 NAG T 2 " 0.534 2.00e-02 2.50e+03 pdb=" O7 NAG T 2 " -0.159 2.00e-02 2.50e+03 ... (remaining 4665 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1880 2.74 - 3.28: 24993 3.28 - 3.82: 39627 3.82 - 4.36: 46968 4.36 - 4.90: 83246 Nonbonded interactions: 196714 Sorted by model distance: nonbonded pdb=" OG SER C 692 " pdb=" OD1 ASN C1055 " model vdw 2.198 3.040 nonbonded pdb=" O THR C 987 " pdb=" NE2 GLN C 991 " model vdw 2.200 3.120 nonbonded pdb=" OD1 ASN B 284 " pdb=" OG SER B 287 " model vdw 2.211 3.040 nonbonded pdb=" OE1 GLU C 73 " pdb=" N ALA C 250 " model vdw 2.218 3.120 nonbonded pdb=" O GLU A 650 " pdb=" OH TYR A 676 " model vdw 2.229 3.040 ... (remaining 196709 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 24 through 172 or resid 183 through 808 or resid 829 throu \ gh 1210)) selection = (chain 'B' and resid 24 through 1210) selection = (chain 'C' and (resid 24 through 172 or resid 183 through 1210)) } ncs_group { reference = (chain 'D' and resid 1 through 3) selection = (chain 'K' and resid 1 through 3) selection = (chain 'P' and resid 1 through 3) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 10.490 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: 0.030 Extract box with map and model: 0.690 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 22.820 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 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 : 0.005 0.061 26827 Z= 0.261 Angle : 0.823 13.388 36672 Z= 0.434 Chirality : 0.059 0.717 4349 Planarity : 0.024 0.304 4619 Dihedral : 13.837 112.992 10666 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.99 % Favored : 92.73 % Rotamer: Outliers : 0.21 % Allowed : 0.67 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.14), residues: 3217 helix: 0.90 (0.21), residues: 695 sheet: 0.45 (0.21), residues: 652 loop : -2.23 (0.13), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 318 TYR 0.022 0.002 TYR A 255 PHE 0.038 0.002 PHE C 887 TRP 0.019 0.001 TRP A 155 HIS 0.012 0.001 HIS C 128 Details of bonding type rmsd covalent geometry : bond 0.00479 (26718) covalent geometry : angle 0.77461 (36382) SS BOND : bond 0.00395 ( 37) SS BOND : angle 1.25557 ( 74) hydrogen bonds : bond 0.15384 ( 945) hydrogen bonds : angle 6.30975 ( 2637) link_ALPHA1-3 : bond 0.00331 ( 1) link_ALPHA1-3 : angle 0.88475 ( 3) link_BETA1-4 : bond 0.00520 ( 22) link_BETA1-4 : angle 2.81252 ( 66) link_NAG-ASN : bond 0.01009 ( 49) link_NAG-ASN : angle 4.01326 ( 147) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 250 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 255 average time/residue: 0.5525 time to fit residues: 165.2093 Evaluate side-chains 109 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 104 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain C residue 272 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 0.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 GLN ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 HIS B 743 GLN B 894 GLN B 903 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN A 618 HIS ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 941 ASN C 991 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.074519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.059728 restraints weight = 94796.607| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 3.88 r_work: 0.3155 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 26827 Z= 0.166 Angle : 0.704 11.041 36672 Z= 0.345 Chirality : 0.047 0.413 4349 Planarity : 0.005 0.060 4619 Dihedral : 8.870 98.334 4996 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.31 % Favored : 93.60 % Rotamer: Outliers : 1.49 % Allowed : 6.48 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.15), residues: 3217 helix: 1.24 (0.21), residues: 725 sheet: 0.32 (0.20), residues: 651 loop : -2.14 (0.13), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 746 TYR 0.020 0.001 TYR A1048 PHE 0.043 0.002 PHE A 123 TRP 0.010 0.001 TRP A 155 HIS 0.004 0.001 HIS C 169 Details of bonding type rmsd covalent geometry : bond 0.00377 (26718) covalent geometry : angle 0.65830 (36382) SS BOND : bond 0.00375 ( 37) SS BOND : angle 1.59255 ( 74) hydrogen bonds : bond 0.05390 ( 945) hydrogen bonds : angle 5.08684 ( 2637) link_ALPHA1-3 : bond 0.01273 ( 1) link_ALPHA1-3 : angle 1.65038 ( 3) link_BETA1-4 : bond 0.00908 ( 22) link_BETA1-4 : angle 2.79437 ( 66) link_NAG-ASN : bond 0.00557 ( 49) link_NAG-ASN : angle 3.38495 ( 147) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 107 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8767 (mttp) REVERT: A 472 GLN cc_start: 0.8547 (mm110) cc_final: 0.7533 (pp30) REVERT: A 503 GLU cc_start: 0.7678 (tp30) cc_final: 0.7473 (tp30) REVERT: A 1078 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8611 (tmt) REVERT: C 194 ASP cc_start: 0.9080 (OUTLIER) cc_final: 0.8872 (t70) REVERT: C 969 GLU cc_start: 0.8715 (tp30) cc_final: 0.8464 (tp30) outliers start: 42 outliers final: 18 residues processed: 138 average time/residue: 0.6230 time to fit residues: 101.3984 Evaluate side-chains 109 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 712 MET Chi-restraints excluded: chain B residue 903 GLN Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 1031 MET Chi-restraints excluded: chain B residue 1095 VAL Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 1078 MET Chi-restraints excluded: chain A residue 1102 PHE Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 272 ASN Chi-restraints excluded: chain C residue 600 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 239 optimal weight: 5.9990 chunk 275 optimal weight: 10.0000 chunk 157 optimal weight: 3.9990 chunk 259 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 269 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 224 optimal weight: 5.9990 chunk 314 optimal weight: 10.0000 chunk 190 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 GLN B 743 GLN A 201 HIS A 246 GLN ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.071116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.056253 restraints weight = 97597.196| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 3.89 r_work: 0.3076 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 26827 Z= 0.251 Angle : 0.741 11.254 36672 Z= 0.372 Chirality : 0.049 0.371 4349 Planarity : 0.005 0.059 4619 Dihedral : 7.370 85.063 4994 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.37 % Favored : 92.54 % Rotamer: Outliers : 2.30 % Allowed : 7.97 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.15), residues: 3217 helix: 1.20 (0.20), residues: 714 sheet: 0.24 (0.20), residues: 685 loop : -2.17 (0.13), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 746 TYR 0.021 0.002 TYR A1048 PHE 0.027 0.002 PHE C 337 TRP 0.013 0.002 TRP B 343 HIS 0.006 0.001 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00588 (26718) covalent geometry : angle 0.70408 (36382) SS BOND : bond 0.00608 ( 37) SS BOND : angle 1.74553 ( 74) hydrogen bonds : bond 0.06249 ( 945) hydrogen bonds : angle 5.16643 ( 2637) link_ALPHA1-3 : bond 0.01267 ( 1) link_ALPHA1-3 : angle 0.87263 ( 3) link_BETA1-4 : bond 0.00781 ( 22) link_BETA1-4 : angle 2.74072 ( 66) link_NAG-ASN : bond 0.00523 ( 49) link_NAG-ASN : angle 3.07958 ( 147) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 91 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8767 (mttp) REVERT: B 684 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7933 (tm-30) REVERT: A 472 GLN cc_start: 0.8560 (mm110) cc_final: 0.7479 (pp30) REVERT: A 473 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7238 (tp) REVERT: A 914 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8649 (mp10) REVERT: C 626 ASN cc_start: 0.7997 (m110) cc_final: 0.7625 (OUTLIER) REVERT: C 969 GLU cc_start: 0.8818 (tp30) cc_final: 0.8552 (tp30) outliers start: 65 outliers final: 24 residues processed: 143 average time/residue: 0.5722 time to fit residues: 98.5235 Evaluate side-chains 102 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 75 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 684 GLN Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 1095 VAL Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 914 GLN Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 272 ASN Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 600 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 237 optimal weight: 10.0000 chunk 257 optimal weight: 6.9990 chunk 186 optimal weight: 1.9990 chunk 114 optimal weight: 0.0020 chunk 203 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 201 optimal weight: 0.9980 chunk 141 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 GLN B 903 GLN B1017 GLN A 626 ASN ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.072895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.058123 restraints weight = 95722.210| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.89 r_work: 0.3118 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26827 Z= 0.126 Angle : 0.628 11.572 36672 Z= 0.311 Chirality : 0.045 0.355 4349 Planarity : 0.004 0.060 4619 Dihedral : 6.474 75.879 4994 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.69 % Favored : 94.22 % Rotamer: Outliers : 1.66 % Allowed : 10.06 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.15), residues: 3217 helix: 1.57 (0.21), residues: 707 sheet: 0.39 (0.20), residues: 656 loop : -2.02 (0.13), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 564 TYR 0.019 0.001 TYR C 898 PHE 0.029 0.001 PHE A1102 TRP 0.010 0.001 TRP A 427 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00277 (26718) covalent geometry : angle 0.59349 (36382) SS BOND : bond 0.00279 ( 37) SS BOND : angle 1.27278 ( 74) hydrogen bonds : bond 0.04801 ( 945) hydrogen bonds : angle 4.87046 ( 2637) link_ALPHA1-3 : bond 0.01140 ( 1) link_ALPHA1-3 : angle 1.34926 ( 3) link_BETA1-4 : bond 0.00734 ( 22) link_BETA1-4 : angle 2.47570 ( 66) link_NAG-ASN : bond 0.00472 ( 49) link_NAG-ASN : angle 2.77535 ( 147) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 84 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 881 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.7298 (mtm) REVERT: B 1078 MET cc_start: 0.8517 (tmm) cc_final: 0.8315 (tmm) REVERT: A 472 GLN cc_start: 0.8602 (mm110) cc_final: 0.7594 (pp30) REVERT: A 473 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7229 (tp) REVERT: A 982 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9174 (mm) REVERT: C 626 ASN cc_start: 0.8005 (m110) cc_final: 0.7635 (t0) REVERT: C 698 ASN cc_start: 0.7492 (t0) cc_final: 0.7204 (m-40) REVERT: C 969 GLU cc_start: 0.8843 (tp30) cc_final: 0.8571 (tp30) outliers start: 47 outliers final: 16 residues processed: 122 average time/residue: 0.6170 time to fit residues: 89.4096 Evaluate side-chains 93 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 881 MET Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 1095 VAL Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 272 ASN Chi-restraints excluded: chain C residue 958 LEU Chi-restraints excluded: chain C residue 1058 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 33 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 117 optimal weight: 8.9990 chunk 140 optimal weight: 7.9990 chunk 295 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 274 optimal weight: 10.0000 chunk 273 optimal weight: 4.9990 chunk 280 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 150 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 GLN B 903 GLN ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.070423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.055590 restraints weight = 97493.523| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 3.91 r_work: 0.3055 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 26827 Z= 0.259 Angle : 0.717 9.883 36672 Z= 0.361 Chirality : 0.048 0.353 4349 Planarity : 0.005 0.061 4619 Dihedral : 6.455 70.025 4994 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.77 % Favored : 92.14 % Rotamer: Outliers : 2.05 % Allowed : 10.77 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.15), residues: 3217 helix: 1.33 (0.20), residues: 716 sheet: 0.20 (0.20), residues: 684 loop : -2.09 (0.13), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 746 TYR 0.021 0.002 TYR C 898 PHE 0.033 0.002 PHE A1102 TRP 0.012 0.002 TRP B 343 HIS 0.006 0.001 HIS C1039 Details of bonding type rmsd covalent geometry : bond 0.00607 (26718) covalent geometry : angle 0.68204 (36382) SS BOND : bond 0.00489 ( 37) SS BOND : angle 1.51504 ( 74) hydrogen bonds : bond 0.06160 ( 945) hydrogen bonds : angle 5.10868 ( 2637) link_ALPHA1-3 : bond 0.01209 ( 1) link_ALPHA1-3 : angle 0.90185 ( 3) link_BETA1-4 : bond 0.00753 ( 22) link_BETA1-4 : angle 2.68612 ( 66) link_NAG-ASN : bond 0.00497 ( 49) link_NAG-ASN : angle 2.92087 ( 147) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 78 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8789 (mttp) REVERT: B 234 PHE cc_start: 0.7623 (OUTLIER) cc_final: 0.7399 (p90) REVERT: B 881 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.7357 (mtm) REVERT: A 472 GLN cc_start: 0.8551 (mm110) cc_final: 0.7454 (pp30) REVERT: A 473 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7222 (tp) REVERT: A 686 VAL cc_start: 0.9099 (OUTLIER) cc_final: 0.8733 (m) REVERT: A 982 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9181 (mm) REVERT: C 626 ASN cc_start: 0.7960 (m110) cc_final: 0.7623 (t0) REVERT: C 969 GLU cc_start: 0.8903 (tp30) cc_final: 0.8569 (tp30) outliers start: 58 outliers final: 24 residues processed: 127 average time/residue: 0.5939 time to fit residues: 90.4183 Evaluate side-chains 104 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 74 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 881 MET Chi-restraints excluded: chain B residue 903 GLN Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 1095 VAL Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 272 ASN Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 600 GLN Chi-restraints excluded: chain C residue 1058 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 296 optimal weight: 3.9990 chunk 304 optimal weight: 0.9980 chunk 200 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 254 optimal weight: 0.9990 chunk 177 optimal weight: 8.9990 chunk 273 optimal weight: 5.9990 chunk 292 optimal weight: 3.9990 chunk 100 optimal weight: 0.0040 chunk 19 optimal weight: 1.9990 chunk 228 optimal weight: 8.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 ASN ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 GLN B1116 ASN A 140 GLN ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 936 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.072461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.057749 restraints weight = 96162.374| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 3.89 r_work: 0.3110 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 26827 Z= 0.113 Angle : 0.605 10.575 36672 Z= 0.302 Chirality : 0.044 0.344 4349 Planarity : 0.004 0.063 4619 Dihedral : 5.976 69.215 4994 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.53 % Favored : 94.37 % Rotamer: Outliers : 1.81 % Allowed : 11.44 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.15), residues: 3217 helix: 1.70 (0.21), residues: 708 sheet: 0.33 (0.20), residues: 690 loop : -1.99 (0.13), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 746 TYR 0.022 0.001 TYR C 898 PHE 0.033 0.001 PHE A1102 TRP 0.010 0.001 TRP A 427 HIS 0.003 0.000 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00237 (26718) covalent geometry : angle 0.57150 (36382) SS BOND : bond 0.00262 ( 37) SS BOND : angle 1.12213 ( 74) hydrogen bonds : bond 0.04564 ( 945) hydrogen bonds : angle 4.78972 ( 2637) link_ALPHA1-3 : bond 0.00974 ( 1) link_ALPHA1-3 : angle 1.18196 ( 3) link_BETA1-4 : bond 0.00791 ( 22) link_BETA1-4 : angle 2.35111 ( 66) link_NAG-ASN : bond 0.00512 ( 49) link_NAG-ASN : angle 2.69289 ( 147) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 78 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 152 TYR cc_start: 0.8524 (t80) cc_final: 0.8122 (t80) REVERT: B 881 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.7296 (mtm) REVERT: A 143 MET cc_start: 0.8751 (mtm) cc_final: 0.7955 (mpt) REVERT: A 472 GLN cc_start: 0.8566 (mm110) cc_final: 0.7545 (pp30) REVERT: A 473 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7225 (tp) REVERT: A 686 VAL cc_start: 0.9057 (OUTLIER) cc_final: 0.8693 (m) REVERT: A 982 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9148 (mm) REVERT: C 122 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8304 (tt) REVERT: C 626 ASN cc_start: 0.7971 (m110) cc_final: 0.7567 (OUTLIER) REVERT: C 969 GLU cc_start: 0.8871 (tp30) cc_final: 0.8564 (tp30) outliers start: 51 outliers final: 23 residues processed: 124 average time/residue: 0.5497 time to fit residues: 82.5510 Evaluate side-chains 104 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 77 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 684 GLN Chi-restraints excluded: chain B residue 881 MET Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 1095 VAL Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 482 TYR Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 272 ASN Chi-restraints excluded: chain C residue 600 GLN Chi-restraints excluded: chain C residue 1058 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 60 optimal weight: 8.9990 chunk 265 optimal weight: 0.0980 chunk 307 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 255 optimal weight: 8.9990 chunk 197 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 282 optimal weight: 7.9990 chunk 294 optimal weight: 0.9990 chunk 208 optimal weight: 3.9990 chunk 284 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.072199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.057468 restraints weight = 96009.639| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 3.87 r_work: 0.3107 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26827 Z= 0.129 Angle : 0.600 9.744 36672 Z= 0.300 Chirality : 0.044 0.339 4349 Planarity : 0.004 0.061 4619 Dihedral : 5.780 67.014 4992 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.25 % Favored : 93.66 % Rotamer: Outliers : 1.77 % Allowed : 11.94 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.15), residues: 3217 helix: 1.72 (0.21), residues: 714 sheet: 0.27 (0.20), residues: 665 loop : -1.92 (0.13), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 746 TYR 0.020 0.001 TYR C 898 PHE 0.035 0.001 PHE A1102 TRP 0.009 0.001 TRP C 427 HIS 0.003 0.001 HIS C1039 Details of bonding type rmsd covalent geometry : bond 0.00291 (26718) covalent geometry : angle 0.56930 (36382) SS BOND : bond 0.00268 ( 37) SS BOND : angle 1.08188 ( 74) hydrogen bonds : bond 0.04620 ( 945) hydrogen bonds : angle 4.72034 ( 2637) link_ALPHA1-3 : bond 0.00893 ( 1) link_ALPHA1-3 : angle 1.13857 ( 3) link_BETA1-4 : bond 0.00688 ( 22) link_BETA1-4 : angle 2.30588 ( 66) link_NAG-ASN : bond 0.00407 ( 49) link_NAG-ASN : angle 2.59548 ( 147) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 83 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 152 TYR cc_start: 0.8515 (t80) cc_final: 0.8153 (t80) REVERT: B 881 MET cc_start: 0.7535 (OUTLIER) cc_final: 0.7299 (mtm) REVERT: A 472 GLN cc_start: 0.8572 (mm110) cc_final: 0.7542 (pp30) REVERT: A 473 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7216 (tp) REVERT: A 563 VAL cc_start: 0.9420 (t) cc_final: 0.9161 (m) REVERT: A 686 VAL cc_start: 0.9075 (OUTLIER) cc_final: 0.8719 (m) REVERT: A 982 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9154 (mm) REVERT: C 626 ASN cc_start: 0.7943 (m110) cc_final: 0.7645 (t0) REVERT: C 969 GLU cc_start: 0.8873 (tp30) cc_final: 0.8550 (tp30) outliers start: 50 outliers final: 25 residues processed: 127 average time/residue: 0.5487 time to fit residues: 84.0915 Evaluate side-chains 106 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 77 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 881 MET Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 1095 VAL Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 482 TYR Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 272 ASN Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 600 GLN Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 1058 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 72 optimal weight: 6.9990 chunk 192 optimal weight: 0.8980 chunk 199 optimal weight: 1.9990 chunk 176 optimal weight: 7.9990 chunk 196 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 321 optimal weight: 8.9990 chunk 154 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 GLN B 903 GLN ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.072084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.057363 restraints weight = 96376.487| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 3.88 r_work: 0.3101 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26827 Z= 0.142 Angle : 0.614 15.496 36672 Z= 0.306 Chirality : 0.045 0.337 4349 Planarity : 0.004 0.061 4619 Dihedral : 5.710 64.506 4992 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.00 % Favored : 93.91 % Rotamer: Outliers : 1.66 % Allowed : 12.15 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.15), residues: 3217 helix: 1.70 (0.20), residues: 721 sheet: 0.29 (0.20), residues: 674 loop : -1.93 (0.13), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 746 TYR 0.026 0.001 TYR C 898 PHE 0.036 0.001 PHE A1102 TRP 0.010 0.001 TRP A 427 HIS 0.003 0.001 HIS C1039 Details of bonding type rmsd covalent geometry : bond 0.00323 (26718) covalent geometry : angle 0.57947 (36382) SS BOND : bond 0.00286 ( 37) SS BOND : angle 1.06764 ( 74) hydrogen bonds : bond 0.04710 ( 945) hydrogen bonds : angle 4.72570 ( 2637) link_ALPHA1-3 : bond 0.00860 ( 1) link_ALPHA1-3 : angle 1.13516 ( 3) link_BETA1-4 : bond 0.00665 ( 22) link_BETA1-4 : angle 2.26888 ( 66) link_NAG-ASN : bond 0.00464 ( 49) link_NAG-ASN : angle 2.82382 ( 147) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 78 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 152 TYR cc_start: 0.8515 (t80) cc_final: 0.8193 (t80) REVERT: B 678 MET cc_start: 0.8999 (ttp) cc_final: 0.8754 (ptm) REVERT: B 881 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.7294 (mtm) REVERT: A 143 MET cc_start: 0.8747 (mtm) cc_final: 0.7995 (mpt) REVERT: A 472 GLN cc_start: 0.8558 (mm110) cc_final: 0.7531 (pp30) REVERT: A 473 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7182 (tp) REVERT: A 686 VAL cc_start: 0.9073 (OUTLIER) cc_final: 0.8710 (m) REVERT: A 982 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9162 (mm) REVERT: C 626 ASN cc_start: 0.7978 (m110) cc_final: 0.7574 (OUTLIER) REVERT: C 969 GLU cc_start: 0.8882 (tp30) cc_final: 0.8546 (tp30) outliers start: 47 outliers final: 27 residues processed: 117 average time/residue: 0.5537 time to fit residues: 78.6871 Evaluate side-chains 108 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 78 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 881 MET Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 954 ILE Chi-restraints excluded: chain B residue 1095 VAL Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 482 TYR Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 272 ASN Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 600 GLN Chi-restraints excluded: chain C residue 1058 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 147 optimal weight: 0.0010 chunk 210 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 240 optimal weight: 0.0370 chunk 0 optimal weight: 10.0000 chunk 154 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 203 optimal weight: 7.9990 chunk 291 optimal weight: 6.9990 chunk 237 optimal weight: 8.9990 overall best weight: 1.4070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 GLN ** B 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 ASN ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.072475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.057749 restraints weight = 95860.381| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 3.87 r_work: 0.3115 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26827 Z= 0.119 Angle : 0.597 11.986 36672 Z= 0.298 Chirality : 0.044 0.335 4349 Planarity : 0.004 0.061 4619 Dihedral : 5.495 61.810 4992 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.81 % Favored : 94.12 % Rotamer: Outliers : 1.31 % Allowed : 12.65 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.15), residues: 3217 helix: 1.76 (0.21), residues: 721 sheet: 0.30 (0.20), residues: 669 loop : -1.89 (0.13), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 746 TYR 0.026 0.001 TYR C 898 PHE 0.035 0.001 PHE A1102 TRP 0.009 0.001 TRP A 427 HIS 0.002 0.001 HIS C1039 Details of bonding type rmsd covalent geometry : bond 0.00263 (26718) covalent geometry : angle 0.56645 (36382) SS BOND : bond 0.00268 ( 37) SS BOND : angle 0.97057 ( 74) hydrogen bonds : bond 0.04392 ( 945) hydrogen bonds : angle 4.65432 ( 2637) link_ALPHA1-3 : bond 0.00778 ( 1) link_ALPHA1-3 : angle 1.19845 ( 3) link_BETA1-4 : bond 0.00624 ( 22) link_BETA1-4 : angle 2.16637 ( 66) link_NAG-ASN : bond 0.00435 ( 49) link_NAG-ASN : angle 2.60427 ( 147) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 82 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 152 TYR cc_start: 0.8524 (t80) cc_final: 0.8216 (t80) REVERT: B 678 MET cc_start: 0.8992 (ttp) cc_final: 0.8706 (ptm) REVERT: B 881 MET cc_start: 0.7517 (OUTLIER) cc_final: 0.7268 (mtm) REVERT: A 143 MET cc_start: 0.8657 (mtm) cc_final: 0.7874 (mpt) REVERT: A 472 GLN cc_start: 0.8553 (mm110) cc_final: 0.7533 (pp30) REVERT: A 473 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.7158 (tp) REVERT: A 503 GLU cc_start: 0.7763 (tp30) cc_final: 0.7485 (tp30) REVERT: A 563 VAL cc_start: 0.9413 (t) cc_final: 0.9135 (m) REVERT: A 686 VAL cc_start: 0.9072 (OUTLIER) cc_final: 0.8715 (m) REVERT: A 982 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9167 (mm) REVERT: C 626 ASN cc_start: 0.7943 (m110) cc_final: 0.7641 (t0) REVERT: C 969 GLU cc_start: 0.8874 (tp30) cc_final: 0.8599 (tp30) outliers start: 37 outliers final: 26 residues processed: 113 average time/residue: 0.5650 time to fit residues: 76.8112 Evaluate side-chains 109 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 79 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 684 GLN Chi-restraints excluded: chain B residue 881 MET Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 1095 VAL Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 482 TYR Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 600 GLN Chi-restraints excluded: chain C residue 1058 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 127 optimal weight: 0.8980 chunk 203 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 105 optimal weight: 20.0000 chunk 15 optimal weight: 6.9990 chunk 250 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 199 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 227 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 GLN B 903 GLN ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.072564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.057831 restraints weight = 95621.138| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 3.88 r_work: 0.3113 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26827 Z= 0.122 Angle : 0.598 14.627 36672 Z= 0.298 Chirality : 0.044 0.334 4349 Planarity : 0.004 0.063 4619 Dihedral : 5.423 60.451 4990 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.84 % Favored : 94.09 % Rotamer: Outliers : 1.35 % Allowed : 12.61 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.15), residues: 3217 helix: 1.80 (0.21), residues: 720 sheet: 0.27 (0.20), residues: 671 loop : -1.87 (0.14), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 746 TYR 0.026 0.001 TYR C 898 PHE 0.036 0.001 PHE A1102 TRP 0.009 0.001 TRP A 427 HIS 0.003 0.001 HIS B 259 Details of bonding type rmsd covalent geometry : bond 0.00272 (26718) covalent geometry : angle 0.56884 (36382) SS BOND : bond 0.00262 ( 37) SS BOND : angle 0.96446 ( 74) hydrogen bonds : bond 0.04396 ( 945) hydrogen bonds : angle 4.64390 ( 2637) link_ALPHA1-3 : bond 0.00765 ( 1) link_ALPHA1-3 : angle 1.18739 ( 3) link_BETA1-4 : bond 0.00603 ( 22) link_BETA1-4 : angle 2.15282 ( 66) link_NAG-ASN : bond 0.00420 ( 49) link_NAG-ASN : angle 2.56618 ( 147) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6434 Ramachandran restraints generated. 3217 Oldfield, 0 Emsley, 3217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 81 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 152 TYR cc_start: 0.8511 (t80) cc_final: 0.8195 (t80) REVERT: B 678 MET cc_start: 0.8996 (ttp) cc_final: 0.8724 (ptm) REVERT: B 881 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.7270 (mtm) REVERT: A 143 MET cc_start: 0.8663 (mtm) cc_final: 0.7900 (mpt) REVERT: A 472 GLN cc_start: 0.8551 (mm110) cc_final: 0.7533 (pp30) REVERT: A 473 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7158 (tp) REVERT: A 503 GLU cc_start: 0.7753 (tp30) cc_final: 0.7473 (tp30) REVERT: A 563 VAL cc_start: 0.9412 (t) cc_final: 0.9129 (m) REVERT: A 686 VAL cc_start: 0.9066 (OUTLIER) cc_final: 0.8711 (m) REVERT: A 982 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9149 (mm) REVERT: C 122 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8316 (tt) REVERT: C 626 ASN cc_start: 0.7953 (m110) cc_final: 0.7570 (OUTLIER) REVERT: C 969 GLU cc_start: 0.8872 (tp30) cc_final: 0.8585 (tp30) outliers start: 38 outliers final: 28 residues processed: 114 average time/residue: 0.5455 time to fit residues: 74.7053 Evaluate side-chains 111 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 79 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 881 MET Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 1031 MET Chi-restraints excluded: chain B residue 1095 VAL Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 482 TYR Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 600 GLN Chi-restraints excluded: chain C residue 1058 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 315 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 199 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 232 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 317 optimal weight: 2.9990 chunk 165 optimal weight: 0.2980 chunk 45 optimal weight: 4.9990 chunk 188 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 HIS ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 GLN ** B 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.073430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.058748 restraints weight = 95205.319| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 3.88 r_work: 0.3137 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 26827 Z= 0.103 Angle : 0.580 11.086 36672 Z= 0.290 Chirality : 0.044 0.333 4349 Planarity : 0.004 0.061 4619 Dihedral : 5.240 58.108 4990 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.50 % Favored : 94.47 % Rotamer: Outliers : 1.28 % Allowed : 12.82 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.15), residues: 3217 helix: 1.89 (0.21), residues: 713 sheet: 0.24 (0.20), residues: 681 loop : -1.81 (0.14), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 105 TYR 0.024 0.001 TYR C 898 PHE 0.035 0.001 PHE A1102 TRP 0.009 0.001 TRP A 427 HIS 0.004 0.000 HIS B 259 Details of bonding type rmsd covalent geometry : bond 0.00219 (26718) covalent geometry : angle 0.55351 (36382) SS BOND : bond 0.00227 ( 37) SS BOND : angle 0.82782 ( 74) hydrogen bonds : bond 0.03973 ( 945) hydrogen bonds : angle 4.52877 ( 2637) link_ALPHA1-3 : bond 0.00681 ( 1) link_ALPHA1-3 : angle 1.27118 ( 3) link_BETA1-4 : bond 0.00613 ( 22) link_BETA1-4 : angle 2.04699 ( 66) link_NAG-ASN : bond 0.00438 ( 49) link_NAG-ASN : angle 2.41247 ( 147) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6911.51 seconds wall clock time: 119 minutes 14.71 seconds (7154.71 seconds total)