Starting phenix.real_space_refine on Sun Jul 5 04:16:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7u6r_26378/07_2026/7u6r_26378.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u6r_26378/07_2026/7u6r_26378.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7u6r_26378/07_2026/7u6r_26378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u6r_26378/07_2026/7u6r_26378.map" model { file = "/net/cci-nas-00/data/ceres_data/7u6r_26378/07_2026/7u6r_26378.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u6r_26378/07_2026/7u6r_26378.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7u6r_26378/07_2026/7u6r_26378.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7u6r_26378/07_2026/7u6r_26378.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.191 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 138 5.16 5 C 16434 2.51 5 N 4215 2.21 5 O 4774 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 210 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25561 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8282 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PTRANS': 51, 'TRANS': 1045} Chain breaks: 11 Unresolved non-hydrogen bonds: 288 Unresolved non-hydrogen angles: 357 Unresolved non-hydrogen dihedrals: 233 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 10, 'GLU:plan': 13, 'ARG:plan': 1, 'GLN:plan1': 5} Unresolved non-hydrogen planarities: 146 Chain: "B" Number of atoms: 8283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8283 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 134} Link IDs: {'PTRANS': 51, 'TRANS': 1045} Chain breaks: 11 Unresolved non-hydrogen bonds: 287 Unresolved non-hydrogen angles: 356 Unresolved non-hydrogen dihedrals: 232 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 10, 'GLU:plan': 13, 'ARG:plan': 1, 'GLN:plan1': 5} Unresolved non-hydrogen planarities: 146 Chain: "C" Number of atoms: 8282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8282 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PTRANS': 51, 'TRANS': 1045} Chain breaks: 11 Unresolved non-hydrogen bonds: 288 Unresolved non-hydrogen angles: 357 Unresolved non-hydrogen dihedrals: 233 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 10, 'GLU:plan': 13, 'ARG:plan': 1, 'GLN:plan1': 5} Unresolved non-hydrogen planarities: 146 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 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 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 chiralities: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 5.67, per 1000 atoms: 0.22 Number of scatterers: 25561 At special positions: 0 Unit cell: (131.25, 132.3, 155.4, 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 138 16.00 O 4774 8.00 N 4215 7.00 C 16434 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 33 " - pdb=" SG CYS A 199 " distance=2.02 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 241 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 353 " distance=2.02 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 411 " distance=2.02 Simple disulfide: pdb=" SG CYS A 429 " - pdb=" SG CYS A 482 " distance=2.03 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 583 " distance=2.29 Simple disulfide: pdb=" SG CYS A 506 " - pdb=" SG CYS A 527 " distance=2.03 Simple disulfide: pdb=" SG CYS A 602 " - pdb=" SG CYS A 651 " distance=2.02 Simple disulfide: pdb=" SG CYS A 619 " - pdb=" SG CYS A 647 " distance=2.03 Simple disulfide: pdb=" SG CYS A 676 " - pdb=" SG CYS A 711 " distance=2.05 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 734 " distance=2.02 Simple disulfide: pdb=" SG CYS A 798 " - pdb=" SG CYS A 820 " distance=2.14 Simple disulfide: pdb=" SG CYS A 803 " - pdb=" SG CYS A 809 " distance=2.16 Simple disulfide: pdb=" SG CYS A 904 " - pdb=" SG CYS A 917 " distance=2.10 Simple disulfide: pdb=" SG CYS A1098 " - pdb=" SG CYS A1109 " distance=2.02 Simple disulfide: pdb=" SG CYS A1148 " - pdb=" SG CYS A1156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 33 " - pdb=" SG CYS B 199 " distance=2.02 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 241 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 353 " distance=2.02 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 411 " distance=2.02 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 482 " distance=2.03 Simple disulfide: pdb=" SG CYS B 441 " - pdb=" SG CYS B 583 " distance=2.29 Simple disulfide: pdb=" SG CYS B 506 " - pdb=" SG CYS B 527 " distance=2.03 Simple disulfide: pdb=" SG CYS B 602 " - pdb=" SG CYS B 651 " distance=2.02 Simple disulfide: pdb=" SG CYS B 619 " - pdb=" SG CYS B 647 " distance=2.03 Simple disulfide: pdb=" SG CYS B 676 " - pdb=" SG CYS B 711 " distance=2.05 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 734 " distance=2.02 Simple disulfide: pdb=" SG CYS B 798 " - pdb=" SG CYS B 820 " distance=2.14 Simple disulfide: pdb=" SG CYS B 803 " - pdb=" SG CYS B 809 " distance=2.16 Simple disulfide: pdb=" SG CYS B 904 " - pdb=" SG CYS B 917 " distance=2.10 Simple disulfide: pdb=" SG CYS B1098 " - pdb=" SG CYS B1109 " distance=2.02 Simple disulfide: pdb=" SG CYS B1148 " - pdb=" SG CYS B1156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 33 " - pdb=" SG CYS C 199 " distance=2.02 Simple disulfide: pdb=" SG CYS C 189 " - pdb=" SG CYS C 241 " distance=2.03 Simple disulfide: pdb=" SG CYS C 343 " - pdb=" SG CYS C 353 " distance=2.02 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 411 " distance=2.02 Simple disulfide: pdb=" SG CYS C 429 " - pdb=" SG CYS C 482 " distance=2.03 Simple disulfide: pdb=" SG CYS C 441 " - pdb=" SG CYS C 583 " distance=2.29 Simple disulfide: pdb=" SG CYS C 506 " - pdb=" SG CYS C 527 " distance=2.03 Simple disulfide: pdb=" SG CYS C 602 " - pdb=" SG CYS C 651 " distance=2.02 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 647 " distance=2.03 Simple disulfide: pdb=" SG CYS C 676 " - pdb=" SG CYS C 711 " distance=2.05 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 734 " distance=2.02 Simple disulfide: pdb=" SG CYS C 798 " - pdb=" SG CYS C 820 " distance=2.14 Simple disulfide: pdb=" SG CYS C 803 " - pdb=" SG CYS C 809 " distance=2.16 Simple disulfide: pdb=" SG CYS C 904 " - pdb=" SG CYS C 917 " distance=2.10 Simple disulfide: pdb=" SG CYS C1098 " - pdb=" SG CYS C1109 " distance=2.02 Simple disulfide: pdb=" SG CYS C1148 " - pdb=" SG CYS C1156 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG 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-ASN " NAG A1401 " - " ASN A 70 " " NAG A1402 " - " ASN A 108 " " NAG A1403 " - " ASN A 158 " " NAG A1404 " - " ASN A 862 " " NAG A1405 " - " ASN A 388 " " NAG A1406 " - " ASN A 594 " " NAG A1407 " - " ASN A1167 " " NAG A1408 " - " ASN A 240 " " NAG A1409 " - " ASN A 248 " " NAG A1410 " - " ASN A 777 " " NAG A1411 " - " ASN A1205 " " NAG A1412 " - " ASN A 719 " " NAG A1413 " - " ASN A 489 " " NAG B1401 " - " ASN B 70 " " NAG B1402 " - " ASN B 108 " " NAG B1403 " - " ASN B 158 " " NAG B1404 " - " ASN B 862 " " NAG B1405 " - " ASN B 388 " " NAG B1406 " - " ASN B 594 " " NAG B1407 " - " ASN B1167 " " NAG B1408 " - " ASN B 240 " " NAG B1409 " - " ASN B 248 " " NAG B1410 " - " ASN B 777 " " NAG B1411 " - " ASN B1205 " " NAG B1412 " - " ASN B 719 " " NAG B1413 " - " ASN B 489 " " NAG C1401 " - " ASN C 70 " " NAG C1402 " - " ASN C 108 " " NAG C1403 " - " ASN C 158 " " NAG C1404 " - " ASN C 862 " " NAG C1405 " - " ASN C 388 " " NAG C1406 " - " ASN C 594 " " NAG C1407 " - " ASN C1167 " " NAG C1408 " - " ASN C 240 " " NAG C1409 " - " ASN C 248 " " NAG C1410 " - " ASN C 777 " " NAG C1411 " - " ASN C1205 " " NAG C1412 " - " ASN C 719 " " NAG C1413 " - " ASN C 489 " " NAG D 1 " - " ASN A 414 " " NAG E 1 " - " ASN A 170 " " NAG F 1 " - " ASN B 414 " " NAG G 1 " - " ASN B 170 " " NAG H 1 " - " ASN C 414 " " NAG I 1 " - " ASN C 170 " Time building additional restraints: 2.28 Conformation dependent library (CDL) restraints added in 1.0 seconds 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6126 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 48 sheets defined 28.7% alpha, 30.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 40 through 44 Processing helix chain 'A' and resid 53 through 57 Processing helix chain 'A' and resid 108 through 112 Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'A' and resid 346 through 356 Processing helix chain 'A' and resid 389 through 394 removed outlier: 3.956A pdb=" N PHE A 393 " --> pdb=" O PHE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 420 removed outlier: 3.690A pdb=" N LEU A 418 " --> pdb=" O ASN A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 438 Processing helix chain 'A' and resid 453 through 457 Processing helix chain 'A' and resid 466 through 471 Processing helix chain 'A' and resid 489 through 493 Processing helix chain 'A' and resid 524 through 533 removed outlier: 3.608A pdb=" N ASN A 533 " --> pdb=" O THR A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 561 Processing helix chain 'A' and resid 595 through 599 Processing helix chain 'A' and resid 676 through 682 removed outlier: 4.293A pdb=" N SER A 680 " --> pdb=" O CYS A 676 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N THR A 681 " --> pdb=" O GLN A 677 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET A 682 " --> pdb=" O HIS A 678 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 676 through 682' Processing helix chain 'A' and resid 683 through 686 Processing helix chain 'A' and resid 687 through 694 Processing helix chain 'A' and resid 797 through 804 Processing helix chain 'A' and resid 806 through 813 Processing helix chain 'A' and resid 814 through 817 Processing helix chain 'A' and resid 818 through 846 removed outlier: 3.546A pdb=" N SER A 844 " --> pdb=" O ASN A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 890 Processing helix chain 'A' and resid 899 through 904 removed outlier: 3.945A pdb=" N ASP A 903 " --> pdb=" O GLN A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 918 Processing helix chain 'A' and resid 918 through 923 Processing helix chain 'A' and resid 932 through 945 Processing helix chain 'A' and resid 963 through 974 Processing helix chain 'A' and resid 978 through 985 Processing helix chain 'A' and resid 985 through 999 Processing helix chain 'A' and resid 1000 through 1003 Processing helix chain 'A' and resid 1008 through 1032 removed outlier: 3.620A pdb=" N VAL A1014 " --> pdb=" O ALA A1010 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A1028 " --> pdb=" O ALA A1024 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU A1032 " --> pdb=" O LEU A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1048 Processing helix chain 'A' and resid 1051 through 1098 removed outlier: 3.806A pdb=" N GLU A1056 " --> pdb=" O VAL A1052 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 44 Processing helix chain 'B' and resid 53 through 57 Processing helix chain 'B' and resid 108 through 112 Processing helix chain 'B' and resid 228 through 233 Processing helix chain 'B' and resid 346 through 356 Processing helix chain 'B' and resid 389 through 394 removed outlier: 3.956A pdb=" N PHE B 393 " --> pdb=" O PHE B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 420 removed outlier: 3.690A pdb=" N LEU B 418 " --> pdb=" O ASN B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 438 Processing helix chain 'B' and resid 453 through 457 Processing helix chain 'B' and resid 466 through 471 Processing helix chain 'B' and resid 489 through 493 Processing helix chain 'B' and resid 524 through 533 removed outlier: 3.608A pdb=" N ASN B 533 " --> pdb=" O THR B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 561 Processing helix chain 'B' and resid 595 through 599 Processing helix chain 'B' and resid 676 through 682 removed outlier: 4.293A pdb=" N SER B 680 " --> pdb=" O CYS B 676 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N THR B 681 " --> pdb=" O GLN B 677 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET B 682 " --> pdb=" O HIS B 678 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 676 through 682' Processing helix chain 'B' and resid 683 through 686 Processing helix chain 'B' and resid 687 through 694 Processing helix chain 'B' and resid 797 through 804 Processing helix chain 'B' and resid 806 through 813 Processing helix chain 'B' and resid 814 through 817 Processing helix chain 'B' and resid 818 through 846 removed outlier: 3.546A pdb=" N SER B 844 " --> pdb=" O ASN B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 880 through 890 Processing helix chain 'B' and resid 899 through 904 removed outlier: 3.946A pdb=" N ASP B 903 " --> pdb=" O GLN B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 918 Processing helix chain 'B' and resid 918 through 923 Processing helix chain 'B' and resid 932 through 945 Processing helix chain 'B' and resid 963 through 974 Processing helix chain 'B' and resid 978 through 985 Processing helix chain 'B' and resid 985 through 999 Processing helix chain 'B' and resid 1000 through 1003 Processing helix chain 'B' and resid 1008 through 1032 removed outlier: 3.620A pdb=" N VAL B1014 " --> pdb=" O ALA B1010 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B1028 " --> pdb=" O ALA B1024 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU B1032 " --> pdb=" O LEU B1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 1042 through 1048 Processing helix chain 'B' and resid 1051 through 1098 removed outlier: 3.805A pdb=" N GLU B1056 " --> pdb=" O VAL B1052 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 44 Processing helix chain 'C' and resid 53 through 57 Processing helix chain 'C' and resid 108 through 112 Processing helix chain 'C' and resid 228 through 233 Processing helix chain 'C' and resid 346 through 356 Processing helix chain 'C' and resid 389 through 394 removed outlier: 3.956A pdb=" N PHE C 393 " --> pdb=" O PHE C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 420 removed outlier: 3.690A pdb=" N LEU C 418 " --> pdb=" O ASN C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 438 Processing helix chain 'C' and resid 453 through 457 Processing helix chain 'C' and resid 466 through 471 Processing helix chain 'C' and resid 489 through 493 Processing helix chain 'C' and resid 524 through 533 removed outlier: 3.608A pdb=" N ASN C 533 " --> pdb=" O THR C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 561 Processing helix chain 'C' and resid 595 through 599 Processing helix chain 'C' and resid 676 through 682 removed outlier: 4.293A pdb=" N SER C 680 " --> pdb=" O CYS C 676 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N THR C 681 " --> pdb=" O GLN C 677 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET C 682 " --> pdb=" O HIS C 678 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 676 through 682' Processing helix chain 'C' and resid 683 through 686 Processing helix chain 'C' and resid 687 through 694 Processing helix chain 'C' and resid 797 through 804 Processing helix chain 'C' and resid 806 through 813 Processing helix chain 'C' and resid 814 through 817 Processing helix chain 'C' and resid 818 through 846 removed outlier: 3.546A pdb=" N SER C 844 " --> pdb=" O ASN C 840 " (cutoff:3.500A) Processing helix chain 'C' and resid 880 through 890 Processing helix chain 'C' and resid 899 through 904 removed outlier: 3.946A pdb=" N ASP C 903 " --> pdb=" O GLN C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 918 Processing helix chain 'C' and resid 918 through 923 Processing helix chain 'C' and resid 932 through 945 Processing helix chain 'C' and resid 963 through 974 Processing helix chain 'C' and resid 978 through 985 Processing helix chain 'C' and resid 985 through 999 Processing helix chain 'C' and resid 1000 through 1003 Processing helix chain 'C' and resid 1008 through 1032 removed outlier: 3.620A pdb=" N VAL C1014 " --> pdb=" O ALA C1010 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C1028 " --> pdb=" O ALA C1024 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU C1032 " --> pdb=" O LEU C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1042 through 1048 Processing helix chain 'C' and resid 1051 through 1098 removed outlier: 3.805A pdb=" N GLU C1056 " --> pdb=" O VAL C1052 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 38 removed outlier: 6.315A pdb=" N ASP A 37 " --> pdb=" O ILE A 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 79 removed outlier: 3.746A pdb=" N GLN A 339 " --> pdb=" O ASN A 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 91 removed outlier: 6.063A pdb=" N THR A 271 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N LEU A 284 " --> pdb=" O THR A 271 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 114 through 115 removed outlier: 6.506A pdb=" N PHE A 184 " --> pdb=" O GLU A 245 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLU A 245 " --> pdb=" O PHE A 184 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL A 186 " --> pdb=" O TYR A 243 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N TYR A 243 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N TYR A 188 " --> pdb=" O CYS A 241 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N CYS A 241 " --> pdb=" O TYR A 188 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 156 through 158 Processing sheet with id=AA6, first strand: chain 'A' and resid 363 through 366 Processing sheet with id=AA7, first strand: chain 'A' and resid 377 through 380 removed outlier: 4.721A pdb=" N ILE A 636 " --> pdb=" O VAL A 648 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY A 637 " --> pdb=" O VAL A 628 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 404 through 408 removed outlier: 3.875A pdb=" N SER A 444 " --> pdb=" O LYS A 574 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N SER A 481 " --> pdb=" O CYS A 429 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N CYS A 429 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ARG A 483 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE A 427 " --> pdb=" O ARG A 483 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N HIS A 485 " --> pdb=" O ASP A 425 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 411 through 413 Processing sheet with id=AB1, first strand: chain 'A' and resid 513 through 514 removed outlier: 6.442A pdb=" N SER A 553 " --> pdb=" O THR A 504 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N CYS A 506 " --> pdb=" O ARG A 551 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ARG A 551 " --> pdb=" O CYS A 506 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N TYR A 508 " --> pdb=" O PRO A 549 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 715 through 722 removed outlier: 6.756A pdb=" N HIS A 716 " --> pdb=" O LEU A 751 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N SER A 753 " --> pdb=" O HIS A 716 " (cutoff:3.500A) removed outlier: 9.978A pdb=" N THR A 718 " --> pdb=" O SER A 753 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU A 733 " --> pdb=" O LEU A 729 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 760 through 761 removed outlier: 5.757A pdb=" N LEU A 760 " --> pdb=" O THR C 850 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 1113 through 1122 removed outlier: 5.908A pdb=" N HIS A1114 " --> pdb=" O TYR A1133 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N TYR A1133 " --> pdb=" O HIS A1114 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N VAL A1142 " --> pdb=" O LYS A1166 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N PHE A1164 " --> pdb=" O ALA A1144 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N GLY A1180 " --> pdb=" O ALA A1185 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ALA A1185 " --> pdb=" O GLY A1180 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1113 through 1122 removed outlier: 5.908A pdb=" N HIS A1114 " --> pdb=" O TYR A1133 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N TYR A1133 " --> pdb=" O HIS A1114 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER A1136 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASN A 777 " --> pdb=" O SER A1136 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N HIS A1138 " --> pdb=" O PRO A 775 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLU A1140 " --> pdb=" O SER A 773 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N SER A 773 " --> pdb=" O GLU A1140 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL A1142 " --> pdb=" O LYS A 771 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LYS A 771 " --> pdb=" O VAL A1142 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 794 through 796 Processing sheet with id=AB7, first strand: chain 'A' and resid 849 through 850 Processing sheet with id=AB8, first strand: chain 'A' and resid 959 through 960 removed outlier: 6.744A pdb=" N LYS B 771 " --> pdb=" O VAL B1142 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL B1142 " --> pdb=" O LYS B 771 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N SER B 773 " --> pdb=" O GLU B1140 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLU B1140 " --> pdb=" O SER B 773 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N HIS B1138 " --> pdb=" O PRO B 775 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASN B 777 " --> pdb=" O SER B1136 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B1136 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N TYR B1133 " --> pdb=" O HIS B1114 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N HIS B1114 " --> pdb=" O TYR B1133 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 959 through 960 removed outlier: 6.744A pdb=" N LYS B 771 " --> pdb=" O VAL B1142 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL B1142 " --> pdb=" O LYS B 771 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N SER B 773 " --> pdb=" O GLU B1140 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLU B1140 " --> pdb=" O SER B 773 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N HIS B1138 " --> pdb=" O PRO B 775 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASN B 777 " --> pdb=" O SER B1136 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B1136 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N VAL B1142 " --> pdb=" O LYS B1166 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N PHE B1164 " --> pdb=" O ALA B1144 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N GLY B1180 " --> pdb=" O ALA B1185 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ALA B1185 " --> pdb=" O GLY B1180 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1194 through 1197 removed outlier: 4.219A pdb=" N CYS A1156 " --> pdb=" O VAL A1197 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ASN A1155 " --> pdb=" O ASP A1149 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 37 through 38 removed outlier: 6.314A pdb=" N ASP B 37 " --> pdb=" O ILE B 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 72 through 79 removed outlier: 3.746A pdb=" N GLN B 339 " --> pdb=" O ASN B 330 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 87 through 91 removed outlier: 6.064A pdb=" N THR B 271 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LEU B 284 " --> pdb=" O THR B 271 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 114 through 115 removed outlier: 6.506A pdb=" N PHE B 184 " --> pdb=" O GLU B 245 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLU B 245 " --> pdb=" O PHE B 184 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL B 186 " --> pdb=" O TYR B 243 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TYR B 243 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N TYR B 188 " --> pdb=" O CYS B 241 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N CYS B 241 " --> pdb=" O TYR B 188 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AC7, first strand: chain 'B' and resid 363 through 366 Processing sheet with id=AC8, first strand: chain 'B' and resid 377 through 380 removed outlier: 4.722A pdb=" N ILE B 636 " --> pdb=" O VAL B 648 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY B 637 " --> pdb=" O VAL B 628 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 404 through 408 removed outlier: 3.874A pdb=" N SER B 444 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N SER B 481 " --> pdb=" O CYS B 429 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N CYS B 429 " --> pdb=" O SER B 481 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ARG B 483 " --> pdb=" O PHE B 427 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE B 427 " --> pdb=" O ARG B 483 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N HIS B 485 " --> pdb=" O ASP B 425 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 411 through 413 Processing sheet with id=AD2, first strand: chain 'B' and resid 513 through 514 removed outlier: 6.442A pdb=" N SER B 553 " --> pdb=" O THR B 504 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N CYS B 506 " --> pdb=" O ARG B 551 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ARG B 551 " --> pdb=" O CYS B 506 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N TYR B 508 " --> pdb=" O PRO B 549 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 715 through 722 removed outlier: 6.756A pdb=" N HIS B 716 " --> pdb=" O LEU B 751 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N SER B 753 " --> pdb=" O HIS B 716 " (cutoff:3.500A) removed outlier: 9.978A pdb=" N THR B 718 " --> pdb=" O SER B 753 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU B 733 " --> pdb=" O LEU B 729 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 794 through 796 Processing sheet with id=AD5, first strand: chain 'B' and resid 849 through 850 Processing sheet with id=AD6, first strand: chain 'B' and resid 959 through 960 removed outlier: 6.744A pdb=" N LYS C 771 " --> pdb=" O VAL C1142 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL C1142 " --> pdb=" O LYS C 771 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N SER C 773 " --> pdb=" O GLU C1140 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLU C1140 " --> pdb=" O SER C 773 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N HIS C1138 " --> pdb=" O PRO C 775 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASN C 777 " --> pdb=" O SER C1136 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER C1136 " --> pdb=" O ASN C 777 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N TYR C1133 " --> pdb=" O HIS C1114 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N HIS C1114 " --> pdb=" O TYR C1133 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 959 through 960 removed outlier: 6.744A pdb=" N LYS C 771 " --> pdb=" O VAL C1142 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL C1142 " --> pdb=" O LYS C 771 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N SER C 773 " --> pdb=" O GLU C1140 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLU C1140 " --> pdb=" O SER C 773 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N HIS C1138 " --> pdb=" O PRO C 775 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASN C 777 " --> pdb=" O SER C1136 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER C1136 " --> pdb=" O ASN C 777 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N VAL C1142 " --> pdb=" O LYS C1166 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N PHE C1164 " --> pdb=" O ALA C1144 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N GLY C1180 " --> pdb=" O ALA C1185 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ALA C1185 " --> pdb=" O GLY C1180 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1194 through 1197 removed outlier: 4.219A pdb=" N CYS B1156 " --> pdb=" O VAL B1197 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ASN B1155 " --> pdb=" O ASP B1149 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 37 through 38 removed outlier: 6.314A pdb=" N ASP C 37 " --> pdb=" O ILE C 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 72 through 79 removed outlier: 3.746A pdb=" N GLN C 339 " --> pdb=" O ASN C 330 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 87 through 91 removed outlier: 6.063A pdb=" N THR C 271 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LEU C 284 " --> pdb=" O THR C 271 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 114 through 115 removed outlier: 6.506A pdb=" N PHE C 184 " --> pdb=" O GLU C 245 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLU C 245 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL C 186 " --> pdb=" O TYR C 243 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TYR C 243 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N TYR C 188 " --> pdb=" O CYS C 241 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N CYS C 241 " --> pdb=" O TYR C 188 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 156 through 158 Processing sheet with id=AE5, first strand: chain 'C' and resid 363 through 366 Processing sheet with id=AE6, first strand: chain 'C' and resid 377 through 380 removed outlier: 4.722A pdb=" N ILE C 636 " --> pdb=" O VAL C 648 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY C 637 " --> pdb=" O VAL C 628 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 404 through 408 removed outlier: 3.875A pdb=" N SER C 444 " --> pdb=" O LYS C 574 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N SER C 481 " --> pdb=" O CYS C 429 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N CYS C 429 " --> pdb=" O SER C 481 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ARG C 483 " --> pdb=" O PHE C 427 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE C 427 " --> pdb=" O ARG C 483 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N HIS C 485 " --> pdb=" O ASP C 425 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 411 through 413 Processing sheet with id=AE9, first strand: chain 'C' and resid 513 through 514 removed outlier: 6.443A pdb=" N SER C 553 " --> pdb=" O THR C 504 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N CYS C 506 " --> pdb=" O ARG C 551 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ARG C 551 " --> pdb=" O CYS C 506 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N TYR C 508 " --> pdb=" O PRO C 549 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 715 through 722 removed outlier: 6.757A pdb=" N HIS C 716 " --> pdb=" O LEU C 751 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N SER C 753 " --> pdb=" O HIS C 716 " (cutoff:3.500A) removed outlier: 9.979A pdb=" N THR C 718 " --> pdb=" O SER C 753 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU C 733 " --> pdb=" O LEU C 729 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 794 through 796 Processing sheet with id=AF3, first strand: chain 'C' and resid 1194 through 1197 removed outlier: 4.219A pdb=" N CYS C1156 " --> pdb=" O VAL C1197 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ASN C1155 " --> pdb=" O ASP C1149 " (cutoff:3.500A) 1099 hydrogen bonds defined for protein. 2955 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: 6.62 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.27: 4104 1.27 - 1.42: 7015 1.42 - 1.57: 14783 1.57 - 1.72: 73 1.72 - 1.87: 180 Bond restraints: 26155 Sorted by residual: bond pdb=" C LYS C 487 " pdb=" O LYS C 487 " ideal model delta sigma weight residual 1.236 1.116 0.119 1.22e-02 6.72e+03 9.59e+01 bond pdb=" C LYS B 487 " pdb=" O LYS B 487 " ideal model delta sigma weight residual 1.236 1.117 0.119 1.22e-02 6.72e+03 9.53e+01 bond pdb=" C LYS A 487 " pdb=" O LYS A 487 " ideal model delta sigma weight residual 1.236 1.117 0.119 1.22e-02 6.72e+03 9.52e+01 bond pdb=" C LYS C1013 " pdb=" O LYS C1013 " ideal model delta sigma weight residual 1.236 1.123 0.114 1.24e-02 6.50e+03 8.43e+01 bond pdb=" C LYS B1013 " pdb=" O LYS B1013 " ideal model delta sigma weight residual 1.236 1.123 0.114 1.24e-02 6.50e+03 8.38e+01 ... (remaining 26150 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 34168 3.41 - 6.83: 1380 6.83 - 10.24: 129 10.24 - 13.66: 21 13.66 - 17.07: 12 Bond angle restraints: 35710 Sorted by residual: angle pdb=" C ARG A 588 " pdb=" CA ARG A 588 " pdb=" CB ARG A 588 " ideal model delta sigma weight residual 109.60 124.44 -14.84 1.51e+00 4.39e-01 9.66e+01 angle pdb=" C ARG C 588 " pdb=" CA ARG C 588 " pdb=" CB ARG C 588 " ideal model delta sigma weight residual 109.60 124.42 -14.82 1.51e+00 4.39e-01 9.63e+01 angle pdb=" C ARG B 588 " pdb=" CA ARG B 588 " pdb=" CB ARG B 588 " ideal model delta sigma weight residual 109.60 124.41 -14.81 1.51e+00 4.39e-01 9.62e+01 angle pdb=" N VAL B 249 " pdb=" CA VAL B 249 " pdb=" C VAL B 249 " ideal model delta sigma weight residual 111.67 103.22 8.45 9.50e-01 1.11e+00 7.92e+01 angle pdb=" N VAL A 249 " pdb=" CA VAL A 249 " pdb=" C VAL A 249 " ideal model delta sigma weight residual 111.67 103.22 8.45 9.50e-01 1.11e+00 7.92e+01 ... (remaining 35705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 14070 16.75 - 33.51: 596 33.51 - 50.26: 146 50.26 - 67.02: 93 67.02 - 83.77: 27 Dihedral angle restraints: 14932 sinusoidal: 5332 harmonic: 9600 Sorted by residual: dihedral pdb=" CD ARG C 913 " pdb=" NE ARG C 913 " pdb=" CZ ARG C 913 " pdb=" NH1 ARG C 913 " ideal model delta sinusoidal sigma weight residual 0.00 64.47 -64.47 1 1.00e+01 1.00e-02 5.46e+01 dihedral pdb=" CD ARG A 913 " pdb=" NE ARG A 913 " pdb=" CZ ARG A 913 " pdb=" NH1 ARG A 913 " ideal model delta sinusoidal sigma weight residual 0.00 64.44 -64.44 1 1.00e+01 1.00e-02 5.46e+01 dihedral pdb=" CD ARG B 913 " pdb=" NE ARG B 913 " pdb=" CZ ARG B 913 " pdb=" NH1 ARG B 913 " ideal model delta sinusoidal sigma weight residual 0.00 64.44 -64.44 1 1.00e+01 1.00e-02 5.46e+01 ... (remaining 14929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 3644 0.131 - 0.262: 419 0.262 - 0.393: 97 0.393 - 0.525: 10 0.525 - 0.656: 3 Chirality restraints: 4173 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.65e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.63e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.62e+01 ... (remaining 4170 not shown) Planarity restraints: 4629 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1410 " -0.139 2.00e-02 2.50e+03 1.14e-01 1.63e+02 pdb=" C7 NAG B1410 " 0.040 2.00e-02 2.50e+03 pdb=" C8 NAG B1410 " -0.104 2.00e-02 2.50e+03 pdb=" N2 NAG B1410 " 0.182 2.00e-02 2.50e+03 pdb=" O7 NAG B1410 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1410 " 0.139 2.00e-02 2.50e+03 1.14e-01 1.63e+02 pdb=" C7 NAG C1410 " -0.039 2.00e-02 2.50e+03 pdb=" C8 NAG C1410 " 0.104 2.00e-02 2.50e+03 pdb=" N2 NAG C1410 " -0.182 2.00e-02 2.50e+03 pdb=" O7 NAG C1410 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1410 " 0.138 2.00e-02 2.50e+03 1.14e-01 1.63e+02 pdb=" C7 NAG A1410 " -0.039 2.00e-02 2.50e+03 pdb=" C8 NAG A1410 " 0.104 2.00e-02 2.50e+03 pdb=" N2 NAG A1410 " -0.182 2.00e-02 2.50e+03 pdb=" O7 NAG A1410 " -0.021 2.00e-02 2.50e+03 ... (remaining 4626 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 9914 2.89 - 3.39: 22956 3.39 - 3.90: 45052 3.90 - 4.40: 52925 4.40 - 4.90: 85516 Nonbonded interactions: 216363 Sorted by model distance: nonbonded pdb=" NE ARG A1105 " pdb=" OE2 GLU C1097 " model vdw 2.390 3.120 nonbonded pdb=" OE2 GLU B1097 " pdb=" NE ARG C1105 " model vdw 2.390 3.120 nonbonded pdb=" OE2 GLU A1097 " pdb=" NE ARG B1105 " model vdw 2.390 3.120 nonbonded pdb=" O LYS B 145 " pdb=" CB LYS B 145 " model vdw 2.428 2.752 nonbonded pdb=" O LYS A 145 " pdb=" CB LYS A 145 " model vdw 2.428 2.752 ... (remaining 216358 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 33 through 365 or (resid 366 and (name N or name CA or nam \ e C or name O or name CB )) or resid 367 through 1413)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 4.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 26.110 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 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 : 0.016 0.259 26254 Z= 0.899 Angle : 1.630 20.986 35959 Z= 1.077 Chirality : 0.098 0.656 4173 Planarity : 0.020 0.453 4584 Dihedral : 12.038 83.770 8662 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.58 % Favored : 98.23 % Rotamer: Outliers : 1.61 % Allowed : 1.36 % Favored : 97.03 % Cbeta Deviations : 1.53 % 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: 0.53 (0.14), residues: 3219 helix: -0.21 (0.17), residues: 735 sheet: 1.20 (0.19), residues: 615 loop : 0.44 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 588 TYR 0.042 0.006 TYR A 109 PHE 0.025 0.004 PHE C 184 TRP 0.016 0.003 TRP B1176 HIS 0.005 0.001 HIS C1114 Details of bonding type rmsd/Z covalent geometry : bond 0.01503 / 0.88 (26155) covalent geometry : angle 1.59503 / 1.07 (35710) SS BOND : bond 0.08019 / 3.65 ( 48) SS BOND : angle 3.37388 / 2.74 ( 96) hydrogen bonds : bond 0.17368 / 11.41 ( 1067) hydrogen bonds : angle 7.71449 / 5.31 ( 2955) link_BETA1-4 : bond 0.06357 / 3.37 ( 6) link_BETA1-4 : angle 3.79116 / 2.27 ( 18) link_NAG-ASN : bond 0.05517 / 3.44 ( 45) link_NAG-ASN : angle 4.97874 / 3.27 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 339 time to evaluate : 1.045 Fit side-chains revert: symmetry clash REVERT: A 395 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7412 (mp0) REVERT: A 401 MET cc_start: 0.8424 (ptm) cc_final: 0.8115 (ptm) REVERT: A 931 MET cc_start: 0.8526 (mtt) cc_final: 0.8192 (mtm) REVERT: B 391 ASP cc_start: 0.6522 (t70) cc_final: 0.6151 (t0) REVERT: B 395 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6822 (mt-10) REVERT: B 631 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7725 (mmtp) REVERT: B 691 ARG cc_start: 0.7966 (ttt180) cc_final: 0.7616 (ttm110) REVERT: B 822 LYS cc_start: 0.7944 (mttt) cc_final: 0.7385 (pttt) REVERT: B 931 MET cc_start: 0.8546 (mtt) cc_final: 0.8176 (mtt) REVERT: C 395 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6837 (mt-10) outliers start: 39 outliers final: 11 residues processed: 378 average time/residue: 0.6748 time to fit residues: 294.8483 Evaluate side-chains 222 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 207 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 588 ARG Chi-restraints excluded: chain A residue 631 LYS Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1140 GLU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 631 LYS Chi-restraints excluded: chain B residue 888 ASP Chi-restraints excluded: chain B residue 1013 LYS Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 888 ASP Chi-restraints excluded: chain C residue 1013 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 GLN A 192 GLN A 991 ASN A1089 GLN A1114 HIS A1121 ASN B 35 GLN B 192 GLN B 324 GLN B 423 GLN B 991 ASN B1089 GLN B1114 HIS C 35 GLN C 185 GLN C 280 ASN C1076 GLN C1114 HIS C1137 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.135175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.113007 restraints weight = 28228.773| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.74 r_work: 0.3306 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26254 Z= 0.155 Angle : 0.645 10.211 35959 Z= 0.337 Chirality : 0.045 0.213 4173 Planarity : 0.004 0.035 4584 Dihedral : 6.374 66.068 3621 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.65 % Allowed : 5.60 % Favored : 92.75 % 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: 0.94 (0.15), residues: 3219 helix: 1.29 (0.19), residues: 756 sheet: 0.75 (0.19), residues: 654 loop : 0.41 (0.15), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 913 TYR 0.015 0.001 TYR C 365 PHE 0.021 0.002 PHE B 842 TRP 0.012 0.002 TRP B 449 HIS 0.004 0.001 HIS C 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (26155) covalent geometry : angle 0.61841 / 0.33 (35710) SS BOND : bond 0.00446 / 0.27 ( 48) SS BOND : angle 1.54814 / 1.09 ( 96) hydrogen bonds : bond 0.05577 / 3.69 ( 1067) hydrogen bonds : angle 6.02336 / 4.16 ( 2955) link_BETA1-4 : bond 0.00360 / 0.21 ( 6) link_BETA1-4 : angle 1.46361 / 1.03 ( 18) link_NAG-ASN : bond 0.00805 / 0.35 ( 45) link_NAG-ASN : angle 2.76161 / 1.82 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 249 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7075 (OUTLIER) cc_final: 0.6742 (tp40) REVERT: A 395 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7489 (mp0) REVERT: A 448 ASP cc_start: 0.9052 (m-30) cc_final: 0.8750 (m-30) REVERT: A 818 GLN cc_start: 0.7465 (mm-40) cc_final: 0.6976 (mt0) REVERT: A 931 MET cc_start: 0.8942 (mtt) cc_final: 0.8647 (mtm) REVERT: A 1000 MET cc_start: 0.7309 (mtp) cc_final: 0.6995 (mmm) REVERT: A 1031 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7943 (mm-30) REVERT: A 1056 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7847 (tt0) REVERT: B 184 PHE cc_start: 0.7823 (m-80) cc_final: 0.7469 (m-80) REVERT: B 391 ASP cc_start: 0.8087 (t70) cc_final: 0.7712 (t0) REVERT: B 395 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7660 (mt-10) REVERT: B 539 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.7882 (mp10) REVERT: B 588 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7277 (mtt180) REVERT: B 691 ARG cc_start: 0.8347 (ttt180) cc_final: 0.7397 (ttm110) REVERT: B 822 LYS cc_start: 0.8525 (mttt) cc_final: 0.7502 (pttt) REVERT: B 840 ASN cc_start: 0.8545 (OUTLIER) cc_final: 0.8120 (m-40) REVERT: B 846 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8016 (ttmm) REVERT: B 898 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8375 (ttt) REVERT: B 931 MET cc_start: 0.8896 (mtt) cc_final: 0.8693 (mtt) REVERT: B 1193 ASN cc_start: 0.7690 (m-40) cc_final: 0.7433 (m110) REVERT: B 1195 ARG cc_start: 0.8402 (ptp90) cc_final: 0.8177 (ptt-90) REVERT: C 395 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7574 (mt-10) REVERT: C 539 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7728 (mp10) REVERT: C 562 LYS cc_start: 0.8126 (mmtm) cc_final: 0.7757 (mttp) REVERT: C 740 THR cc_start: 0.8259 (p) cc_final: 0.7927 (t) REVERT: C 815 GLN cc_start: 0.7262 (mt0) cc_final: 0.6601 (mp10) REVERT: C 905 MET cc_start: 0.6806 (OUTLIER) cc_final: 0.6562 (mtp) REVERT: C 1195 ARG cc_start: 0.8335 (ptp90) cc_final: 0.8091 (ptt-90) outliers start: 40 outliers final: 10 residues processed: 275 average time/residue: 0.6654 time to fit residues: 211.9844 Evaluate side-chains 227 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain A residue 986 GLN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain A residue 1140 GLU Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 539 GLN Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 846 LYS Chi-restraints excluded: chain B residue 888 ASP Chi-restraints excluded: chain B residue 898 MET Chi-restraints excluded: chain B residue 1104 THR Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 539 GLN Chi-restraints excluded: chain C residue 888 ASP Chi-restraints excluded: chain C residue 905 MET Chi-restraints excluded: chain C residue 1104 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 198 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 247 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 179 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 297 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 GLN A1076 GLN A1077 GLN A1089 GLN B 35 GLN B 324 GLN B1023 GLN B1076 GLN B1077 GLN C 35 GLN C 324 GLN C 423 GLN C1137 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.128851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.106245 restraints weight = 28439.933| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.75 r_work: 0.3213 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 26254 Z= 0.245 Angle : 0.679 9.693 35959 Z= 0.351 Chirality : 0.048 0.183 4173 Planarity : 0.005 0.051 4584 Dihedral : 6.055 59.625 3595 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.51 % Allowed : 6.14 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.64 (0.14), residues: 3219 helix: 1.17 (0.19), residues: 774 sheet: 0.36 (0.18), residues: 696 loop : 0.24 (0.15), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 522 TYR 0.017 0.002 TYR A 198 PHE 0.020 0.002 PHE B 842 TRP 0.018 0.002 TRP B 449 HIS 0.018 0.001 HIS B 678 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.25 (26155) covalent geometry : angle 0.65867 / 0.35 (35710) SS BOND : bond 0.00664 / 0.43 ( 48) SS BOND : angle 1.85375 / 1.37 ( 96) hydrogen bonds : bond 0.05731 / 3.81 ( 1067) hydrogen bonds : angle 5.80857 / 4.02 ( 2955) link_BETA1-4 : bond 0.00353 / 0.19 ( 6) link_BETA1-4 : angle 1.33959 / 0.87 ( 18) link_NAG-ASN : bond 0.00565 / 0.31 ( 45) link_NAG-ASN : angle 2.29020 / 1.58 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 202 time to evaluate : 0.980 Fit side-chains REVERT: A 246 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7404 (mp0) REVERT: A 394 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7985 (mtp-110) REVERT: A 395 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7609 (mp0) REVERT: A 678 HIS cc_start: 0.7347 (t-90) cc_final: 0.6874 (t-90) REVERT: A 833 ARG cc_start: 0.8111 (mtp180) cc_final: 0.7225 (mtm-85) REVERT: A 840 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.7917 (m110) REVERT: A 931 MET cc_start: 0.9013 (mtt) cc_final: 0.8678 (mtm) REVERT: A 1000 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.7311 (mmm) REVERT: A 1031 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8015 (mm-30) REVERT: A 1137 GLN cc_start: 0.8396 (tt0) cc_final: 0.7790 (mt0) REVERT: B 184 PHE cc_start: 0.7754 (m-80) cc_final: 0.7434 (m-80) REVERT: B 360 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.8191 (mtm) REVERT: B 386 ASP cc_start: 0.8631 (m-30) cc_final: 0.8416 (m-30) REVERT: B 539 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.7953 (mp10) REVERT: B 588 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7793 (mtt180) REVERT: B 822 LYS cc_start: 0.8643 (mttt) cc_final: 0.7609 (pttt) REVERT: B 840 ASN cc_start: 0.8675 (OUTLIER) cc_final: 0.8212 (m-40) REVERT: B 846 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7993 (ttpp) REVERT: B 883 GLU cc_start: 0.8326 (tt0) cc_final: 0.8099 (tt0) REVERT: B 931 MET cc_start: 0.8943 (mtt) cc_final: 0.8676 (mtt) REVERT: B 1137 GLN cc_start: 0.8375 (tt0) cc_final: 0.7788 (mt0) REVERT: B 1195 ARG cc_start: 0.8605 (ptp90) cc_final: 0.8295 (ptt90) REVERT: C 198 TYR cc_start: 0.7706 (m-80) cc_final: 0.7342 (m-10) REVERT: C 395 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7264 (mp0) REVERT: C 525 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.7433 (mp10) REVERT: C 539 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7825 (mp10) REVERT: C 562 LYS cc_start: 0.8332 (mmtm) cc_final: 0.7852 (mttp) REVERT: C 815 GLN cc_start: 0.7382 (mt0) cc_final: 0.6670 (mp10) REVERT: C 905 MET cc_start: 0.6610 (OUTLIER) cc_final: 0.6395 (mtp) outliers start: 61 outliers final: 19 residues processed: 241 average time/residue: 0.6983 time to fit residues: 194.0310 Evaluate side-chains 224 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 191 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 394 ARG Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain A residue 1000 MET Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain A residue 1140 GLU Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 539 GLN Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 846 LYS Chi-restraints excluded: chain B residue 888 ASP Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 394 ARG Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 525 GLN Chi-restraints excluded: chain C residue 539 GLN Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 888 ASP Chi-restraints excluded: chain C residue 905 MET Chi-restraints excluded: chain C residue 986 GLN Chi-restraints excluded: chain C residue 1104 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 58 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 281 optimal weight: 0.0670 chunk 152 optimal weight: 0.8980 chunk 153 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 299 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 chunk 286 optimal weight: 0.9990 chunk 259 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1012 GLN B 35 GLN B 171 HIS B 324 GLN B1012 GLN B1023 GLN B1121 ASN C 35 GLN C 678 HIS C1012 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.132252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.110280 restraints weight = 29214.255| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.73 r_work: 0.3244 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26254 Z= 0.119 Angle : 0.541 9.245 35959 Z= 0.283 Chirality : 0.043 0.193 4173 Planarity : 0.004 0.037 4584 Dihedral : 5.585 59.203 3595 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.65 % Allowed : 7.87 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.76 (0.14), residues: 3219 helix: 1.58 (0.19), residues: 756 sheet: 0.35 (0.18), residues: 684 loop : 0.20 (0.15), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1195 TYR 0.013 0.001 TYR C1133 PHE 0.020 0.001 PHE B 842 TRP 0.015 0.001 TRP B 449 HIS 0.013 0.001 HIS B 678 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (26155) covalent geometry : angle 0.52436 / 0.28 (35710) SS BOND : bond 0.00411 / 0.28 ( 48) SS BOND : angle 1.46235 / 1.03 ( 96) hydrogen bonds : bond 0.04478 / 2.99 ( 1067) hydrogen bonds : angle 5.52119 / 3.82 ( 2955) link_BETA1-4 : bond 0.00320 / 0.18 ( 6) link_BETA1-4 : angle 1.20623 / 0.83 ( 18) link_NAG-ASN : bond 0.00258 / 0.16 ( 45) link_NAG-ASN : angle 1.89906 / 1.29 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 210 time to evaluate : 0.762 Fit side-chains REVERT: A 394 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.8024 (mtp-110) REVERT: A 395 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7644 (mp0) REVERT: A 426 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8288 (tt0) REVERT: A 448 ASP cc_start: 0.9110 (m-30) cc_final: 0.8845 (m-30) REVERT: A 818 GLN cc_start: 0.7221 (mm-40) cc_final: 0.6735 (mt0) REVERT: A 840 ASN cc_start: 0.8284 (OUTLIER) cc_final: 0.7807 (m110) REVERT: A 931 MET cc_start: 0.8974 (mtt) cc_final: 0.8654 (mtm) REVERT: A 1000 MET cc_start: 0.7460 (mtp) cc_final: 0.7114 (mmm) REVERT: A 1031 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7971 (mm-30) REVERT: A 1137 GLN cc_start: 0.8312 (tt0) cc_final: 0.7747 (mt0) REVERT: B 184 PHE cc_start: 0.7742 (m-80) cc_final: 0.7417 (m-80) REVERT: B 386 ASP cc_start: 0.8598 (m-30) cc_final: 0.8393 (m-30) REVERT: B 562 LYS cc_start: 0.8473 (ptpt) cc_final: 0.7835 (mmtm) REVERT: B 630 ASP cc_start: 0.8181 (p0) cc_final: 0.7794 (p0) REVERT: B 631 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7984 (mmtp) REVERT: B 682 MET cc_start: 0.7964 (mtp) cc_final: 0.7587 (mtm) REVERT: B 818 GLN cc_start: 0.7458 (mm-40) cc_final: 0.6787 (mm-40) REVERT: B 822 LYS cc_start: 0.8518 (mttt) cc_final: 0.7500 (pttt) REVERT: B 840 ASN cc_start: 0.8567 (OUTLIER) cc_final: 0.8071 (m-40) REVERT: B 883 GLU cc_start: 0.8050 (tt0) cc_final: 0.7821 (tt0) REVERT: B 931 MET cc_start: 0.8877 (mtt) cc_final: 0.8650 (mtt) REVERT: B 1137 GLN cc_start: 0.8255 (tt0) cc_final: 0.7649 (mt0) REVERT: B 1195 ARG cc_start: 0.8519 (ptp90) cc_final: 0.8194 (ptt90) REVERT: C 198 TYR cc_start: 0.7678 (m-80) cc_final: 0.7435 (m-10) REVERT: C 395 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: C 562 LYS cc_start: 0.8309 (mmtm) cc_final: 0.7842 (mttp) REVERT: C 815 GLN cc_start: 0.7249 (mt0) cc_final: 0.6476 (mp10) REVERT: C 905 MET cc_start: 0.6539 (OUTLIER) cc_final: 0.6319 (mtp) REVERT: C 1137 GLN cc_start: 0.8297 (tt0) cc_final: 0.7963 (mt0) outliers start: 40 outliers final: 9 residues processed: 230 average time/residue: 0.7096 time to fit residues: 187.6402 Evaluate side-chains 214 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 196 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 ARG Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain A residue 986 GLN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1140 GLU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 631 LYS Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 888 ASP Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 888 ASP Chi-restraints excluded: chain C residue 905 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 46 optimal weight: 5.9990 chunk 319 optimal weight: 5.9990 chunk 201 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 229 optimal weight: 6.9990 chunk 49 optimal weight: 0.5980 chunk 255 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 313 optimal weight: 5.9990 chunk 200 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 HIS A1193 ASN B 35 GLN B1023 GLN B1076 GLN C 35 GLN ** C 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.130733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.108685 restraints weight = 29254.642| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.73 r_work: 0.3216 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 26254 Z= 0.152 Angle : 0.562 11.775 35959 Z= 0.292 Chirality : 0.044 0.249 4173 Planarity : 0.004 0.038 4584 Dihedral : 5.469 59.208 3591 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.89 % Allowed : 8.57 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.74 (0.14), residues: 3219 helix: 1.60 (0.19), residues: 759 sheet: 0.33 (0.18), residues: 690 loop : 0.16 (0.15), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 522 TYR 0.014 0.001 TYR C1133 PHE 0.021 0.001 PHE B 842 TRP 0.017 0.001 TRP B 449 HIS 0.013 0.001 HIS C 678 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (26155) covalent geometry : angle 0.54326 / 0.29 (35710) SS BOND : bond 0.00494 / 0.30 ( 48) SS BOND : angle 1.75261 / 1.20 ( 96) hydrogen bonds : bond 0.04675 / 3.12 ( 1067) hydrogen bonds : angle 5.48940 / 3.80 ( 2955) link_BETA1-4 : bond 0.00325 / 0.17 ( 6) link_BETA1-4 : angle 1.15570 / 0.76 ( 18) link_NAG-ASN : bond 0.00332 / 0.19 ( 45) link_NAG-ASN : angle 1.89316 / 1.30 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 200 time to evaluate : 0.842 Fit side-chains REVERT: A 190 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8370 (mp) REVERT: A 246 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7332 (mp0) REVERT: A 394 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.8067 (mtp-110) REVERT: A 426 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8276 (tt0) REVERT: A 448 ASP cc_start: 0.9134 (m-30) cc_final: 0.8867 (m-30) REVERT: A 840 ASN cc_start: 0.8309 (OUTLIER) cc_final: 0.7823 (m110) REVERT: A 931 MET cc_start: 0.8958 (mtt) cc_final: 0.8647 (mtm) REVERT: A 1031 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8006 (mm-30) REVERT: A 1137 GLN cc_start: 0.8290 (tt0) cc_final: 0.7775 (mt0) REVERT: B 184 PHE cc_start: 0.7753 (m-80) cc_final: 0.7443 (m-80) REVERT: B 386 ASP cc_start: 0.8644 (m-30) cc_final: 0.8439 (m-30) REVERT: B 539 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8102 (mp10) REVERT: B 562 LYS cc_start: 0.8508 (ptpt) cc_final: 0.7854 (mmtm) REVERT: B 630 ASP cc_start: 0.8177 (p0) cc_final: 0.7857 (p0) REVERT: B 822 LYS cc_start: 0.8587 (mttt) cc_final: 0.7534 (pttt) REVERT: B 840 ASN cc_start: 0.8587 (OUTLIER) cc_final: 0.8096 (m-40) REVERT: B 931 MET cc_start: 0.8904 (mtt) cc_final: 0.8665 (mtt) REVERT: B 1137 GLN cc_start: 0.8241 (tt0) cc_final: 0.7664 (mt0) REVERT: B 1195 ARG cc_start: 0.8527 (ptp90) cc_final: 0.8205 (ptt90) REVERT: C 147 TYR cc_start: 0.8151 (OUTLIER) cc_final: 0.7877 (m-80) REVERT: C 198 TYR cc_start: 0.7720 (m-80) cc_final: 0.7420 (m-10) REVERT: C 234 LYS cc_start: 0.7315 (mtpt) cc_final: 0.7096 (mtmt) REVERT: C 539 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.8085 (mp10) REVERT: C 562 LYS cc_start: 0.8354 (mmtm) cc_final: 0.7814 (mttp) REVERT: C 815 GLN cc_start: 0.7287 (mt0) cc_final: 0.6518 (mp10) REVERT: C 857 PHE cc_start: 0.6525 (t80) cc_final: 0.6295 (t80) REVERT: C 1137 GLN cc_start: 0.8380 (tt0) cc_final: 0.7966 (mt0) outliers start: 46 outliers final: 17 residues processed: 227 average time/residue: 0.6976 time to fit residues: 181.6841 Evaluate side-chains 221 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 195 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 394 ARG Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain A residue 986 GLN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain A residue 1140 GLU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 539 GLN Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 888 ASP Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 539 GLN Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 888 ASP Chi-restraints excluded: chain C residue 905 MET Chi-restraints excluded: chain C residue 986 GLN Chi-restraints excluded: chain C residue 1104 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 14 optimal weight: 0.5980 chunk 261 optimal weight: 1.9990 chunk 32 optimal weight: 0.0020 chunk 117 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 197 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 278 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 35 GLN B1023 GLN C 35 GLN C 678 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.132317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.110447 restraints weight = 29286.724| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.73 r_work: 0.3241 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 26254 Z= 0.120 Angle : 0.528 11.727 35959 Z= 0.275 Chirality : 0.043 0.194 4173 Planarity : 0.004 0.038 4584 Dihedral : 5.031 59.953 3585 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.48 % Allowed : 9.43 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.73 (0.14), residues: 3219 helix: 1.64 (0.19), residues: 771 sheet: 0.26 (0.18), residues: 693 loop : 0.15 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1195 TYR 0.014 0.001 TYR C1133 PHE 0.017 0.001 PHE A 842 TRP 0.016 0.001 TRP B 449 HIS 0.012 0.001 HIS C 678 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (26155) covalent geometry : angle 0.50988 / 0.27 (35710) SS BOND : bond 0.00453 / 0.26 ( 48) SS BOND : angle 1.72340 / 1.13 ( 96) hydrogen bonds : bond 0.04270 / 2.85 ( 1067) hydrogen bonds : angle 5.36796 / 3.72 ( 2955) link_BETA1-4 : bond 0.00318 / 0.17 ( 6) link_BETA1-4 : angle 1.15209 / 0.78 ( 18) link_NAG-ASN : bond 0.00260 / 0.15 ( 45) link_NAG-ASN : angle 1.75143 / 1.20 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 201 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: A 246 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7309 (mp0) REVERT: A 394 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.8036 (mtp-110) REVERT: A 426 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8270 (tt0) REVERT: A 448 ASP cc_start: 0.9087 (m-30) cc_final: 0.8795 (m-30) REVERT: A 818 GLN cc_start: 0.7360 (mm-40) cc_final: 0.6833 (mt0) REVERT: A 840 ASN cc_start: 0.8255 (OUTLIER) cc_final: 0.7798 (m110) REVERT: A 931 MET cc_start: 0.8957 (mtt) cc_final: 0.8662 (mtm) REVERT: A 1000 MET cc_start: 0.7618 (mtp) cc_final: 0.7346 (mmm) REVERT: A 1031 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7983 (mm-30) REVERT: A 1137 GLN cc_start: 0.8265 (tt0) cc_final: 0.7771 (mt0) REVERT: A 1205 ASN cc_start: 0.8681 (m-40) cc_final: 0.8471 (m-40) REVERT: B 539 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8069 (mp10) REVERT: B 562 LYS cc_start: 0.8476 (ptpt) cc_final: 0.7867 (mmtm) REVERT: B 588 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7554 (mtt180) REVERT: B 630 ASP cc_start: 0.8165 (p0) cc_final: 0.7858 (p0) REVERT: B 682 MET cc_start: 0.8012 (mtp) cc_final: 0.7428 (mtm) REVERT: B 822 LYS cc_start: 0.8616 (mttt) cc_final: 0.7589 (pttt) REVERT: B 840 ASN cc_start: 0.8548 (OUTLIER) cc_final: 0.8072 (m-40) REVERT: B 905 MET cc_start: 0.6637 (mtp) cc_final: 0.6353 (mtp) REVERT: B 931 MET cc_start: 0.8867 (mtt) cc_final: 0.8613 (mtt) REVERT: B 1137 GLN cc_start: 0.8263 (tt0) cc_final: 0.7720 (mt0) REVERT: B 1195 ARG cc_start: 0.8465 (ptp90) cc_final: 0.8148 (ptt90) REVERT: C 147 TYR cc_start: 0.8134 (OUTLIER) cc_final: 0.7882 (m-80) REVERT: C 198 TYR cc_start: 0.7701 (m-80) cc_final: 0.7459 (m-10) REVERT: C 202 ASN cc_start: 0.7439 (t0) cc_final: 0.7098 (t160) REVERT: C 234 LYS cc_start: 0.7276 (mtpt) cc_final: 0.7073 (mtmt) REVERT: C 539 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.8015 (mp10) REVERT: C 562 LYS cc_start: 0.8341 (mmtm) cc_final: 0.7771 (mttp) REVERT: C 815 GLN cc_start: 0.7466 (mt0) cc_final: 0.6715 (mp10) REVERT: C 857 PHE cc_start: 0.6553 (t80) cc_final: 0.6318 (t80) REVERT: C 1000 MET cc_start: 0.7802 (mtp) cc_final: 0.7372 (mmm) REVERT: C 1137 GLN cc_start: 0.8323 (tt0) cc_final: 0.7961 (mt0) outliers start: 36 outliers final: 11 residues processed: 220 average time/residue: 0.6867 time to fit residues: 174.0769 Evaluate side-chains 209 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 ARG Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 676 CYS Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1140 GLU Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 539 GLN Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 631 LYS Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 888 ASP Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 539 GLN Chi-restraints excluded: chain C residue 888 ASP Chi-restraints excluded: chain C residue 905 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 94 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 74 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 276 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 HIS B 35 GLN B 185 GLN B1023 GLN ** B1076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1193 ASN C 35 GLN ** C 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1193 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.128786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.107034 restraints weight = 29525.922| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.71 r_work: 0.3200 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 26254 Z= 0.214 Angle : 0.625 13.299 35959 Z= 0.321 Chirality : 0.046 0.242 4173 Planarity : 0.004 0.040 4584 Dihedral : 5.231 57.566 3580 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.85 % Allowed : 9.43 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.63 (0.14), residues: 3219 helix: 1.50 (0.19), residues: 759 sheet: 0.18 (0.18), residues: 684 loop : 0.14 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 522 TYR 0.017 0.002 TYR B 500 PHE 0.021 0.002 PHE A 842 TRP 0.017 0.002 TRP B 449 HIS 0.016 0.002 HIS C 678 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.21 (26155) covalent geometry : angle 0.60373 / 0.31 (35710) SS BOND : bond 0.00668 / 0.41 ( 48) SS BOND : angle 2.12812 / 1.43 ( 96) hydrogen bonds : bond 0.05142 / 3.44 ( 1067) hydrogen bonds : angle 5.60967 / 3.88 ( 2955) link_BETA1-4 : bond 0.00321 / 0.17 ( 6) link_BETA1-4 : angle 1.31704 / 0.85 ( 18) link_NAG-ASN : bond 0.00397 / 0.25 ( 45) link_NAG-ASN : angle 2.01077 / 1.39 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 193 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 246 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7433 (mp0) REVERT: A 394 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.8026 (mtp-110) REVERT: A 395 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7833 (mp0) REVERT: A 448 ASP cc_start: 0.9131 (m-30) cc_final: 0.8902 (m-30) REVERT: A 818 GLN cc_start: 0.7390 (mm-40) cc_final: 0.6942 (mt0) REVERT: A 840 ASN cc_start: 0.8381 (OUTLIER) cc_final: 0.7898 (m110) REVERT: A 931 MET cc_start: 0.9003 (mtt) cc_final: 0.8679 (mtm) REVERT: A 1000 MET cc_start: 0.7688 (mtp) cc_final: 0.7465 (mmm) REVERT: A 1031 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8012 (mm-30) REVERT: A 1137 GLN cc_start: 0.8319 (tt0) cc_final: 0.7827 (mt0) REVERT: A 1205 ASN cc_start: 0.8696 (m-40) cc_final: 0.8475 (m-40) REVERT: B 147 TYR cc_start: 0.8177 (OUTLIER) cc_final: 0.7958 (t80) REVERT: B 184 PHE cc_start: 0.7775 (m-80) cc_final: 0.7446 (m-80) REVERT: B 518 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8095 (mttp) REVERT: B 562 LYS cc_start: 0.8572 (ptpt) cc_final: 0.7942 (mmtm) REVERT: B 588 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7772 (mtt180) REVERT: B 682 MET cc_start: 0.8255 (mtp) cc_final: 0.7574 (mtm) REVERT: B 822 LYS cc_start: 0.8634 (mttt) cc_final: 0.7592 (pttt) REVERT: B 840 ASN cc_start: 0.8654 (OUTLIER) cc_final: 0.8172 (m-40) REVERT: B 905 MET cc_start: 0.6686 (mtp) cc_final: 0.6418 (mtp) REVERT: B 931 MET cc_start: 0.8968 (mtt) cc_final: 0.8726 (mtt) REVERT: B 1137 GLN cc_start: 0.8337 (tt0) cc_final: 0.7762 (mt0) REVERT: C 234 LYS cc_start: 0.7392 (mtpt) cc_final: 0.7183 (mtmt) REVERT: C 518 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.7906 (mttt) REVERT: C 539 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7787 (mp10) REVERT: C 815 GLN cc_start: 0.7635 (mt0) cc_final: 0.6866 (mp10) REVERT: C 857 PHE cc_start: 0.6622 (t80) cc_final: 0.6376 (t80) REVERT: C 1000 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7238 (mmm) REVERT: C 1137 GLN cc_start: 0.8349 (tt0) cc_final: 0.7980 (mt0) outliers start: 45 outliers final: 20 residues processed: 217 average time/residue: 0.6903 time to fit residues: 172.6085 Evaluate side-chains 221 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 ARG Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 676 CYS Chi-restraints excluded: chain A residue 711 CYS Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain A residue 1140 GLU Chi-restraints excluded: chain B residue 147 TYR Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 518 LYS Chi-restraints excluded: chain B residue 539 GLN Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 631 LYS Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 888 ASP Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 394 ARG Chi-restraints excluded: chain C residue 518 LYS Chi-restraints excluded: chain C residue 539 GLN Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 888 ASP Chi-restraints excluded: chain C residue 905 MET Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 1000 MET Chi-restraints excluded: chain C residue 1104 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 227 optimal weight: 3.9990 chunk 230 optimal weight: 0.7980 chunk 293 optimal weight: 0.2980 chunk 118 optimal weight: 3.9990 chunk 312 optimal weight: 1.9990 chunk 61 optimal weight: 0.2980 chunk 6 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 314 optimal weight: 0.8980 chunk 144 optimal weight: 0.7980 chunk 203 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 GLN ** B1076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.131759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.110197 restraints weight = 29434.531| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.71 r_work: 0.3233 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 26254 Z= 0.119 Angle : 0.534 12.076 35959 Z= 0.278 Chirality : 0.043 0.200 4173 Planarity : 0.004 0.039 4584 Dihedral : 4.876 58.578 3580 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.15 % Allowed : 10.42 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.70 (0.15), residues: 3219 helix: 1.66 (0.19), residues: 771 sheet: 0.11 (0.18), residues: 684 loop : 0.17 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1195 TYR 0.013 0.001 TYR C1133 PHE 0.018 0.001 PHE C 184 TRP 0.019 0.001 TRP B 449 HIS 0.013 0.001 HIS C 678 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (26155) covalent geometry : angle 0.51542 / 0.27 (35710) SS BOND : bond 0.00444 / 0.27 ( 48) SS BOND : angle 1.78061 / 1.13 ( 96) hydrogen bonds : bond 0.04256 / 2.84 ( 1067) hydrogen bonds : angle 5.41899 / 3.76 ( 2955) link_BETA1-4 : bond 0.00321 / 0.18 ( 6) link_BETA1-4 : angle 1.21968 / 0.84 ( 18) link_NAG-ASN : bond 0.00279 / 0.18 ( 45) link_NAG-ASN : angle 1.76576 / 1.21 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 197 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 TYR cc_start: 0.7992 (m-80) cc_final: 0.7757 (m-80) REVERT: A 246 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7376 (mp0) REVERT: A 394 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.8010 (mtp-110) REVERT: A 448 ASP cc_start: 0.9067 (m-30) cc_final: 0.8734 (m-30) REVERT: A 818 GLN cc_start: 0.7302 (mm-40) cc_final: 0.6845 (mt0) REVERT: A 840 ASN cc_start: 0.8312 (OUTLIER) cc_final: 0.7854 (m110) REVERT: A 931 MET cc_start: 0.8953 (mtt) cc_final: 0.8672 (mtm) REVERT: A 1000 MET cc_start: 0.7649 (mtp) cc_final: 0.7340 (mmm) REVERT: A 1031 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7972 (mm-30) REVERT: A 1137 GLN cc_start: 0.8311 (tt0) cc_final: 0.7812 (mt0) REVERT: A 1205 ASN cc_start: 0.8680 (m-40) cc_final: 0.8449 (m-40) REVERT: B 518 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.8064 (mttp) REVERT: B 562 LYS cc_start: 0.8583 (ptpt) cc_final: 0.7944 (mmtm) REVERT: B 588 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7488 (mtt180) REVERT: B 682 MET cc_start: 0.7838 (mtp) cc_final: 0.7137 (mtm) REVERT: B 822 LYS cc_start: 0.8591 (mttt) cc_final: 0.7594 (pttt) REVERT: B 840 ASN cc_start: 0.8567 (OUTLIER) cc_final: 0.8087 (m-40) REVERT: B 931 MET cc_start: 0.8883 (mtt) cc_final: 0.8607 (mtt) REVERT: B 1137 GLN cc_start: 0.8292 (tt0) cc_final: 0.7778 (mt0) REVERT: B 1193 ASN cc_start: 0.8054 (m-40) cc_final: 0.7834 (m110) REVERT: C 147 TYR cc_start: 0.8052 (m-80) cc_final: 0.7506 (t80) REVERT: C 539 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.8042 (mp10) REVERT: C 562 LYS cc_start: 0.8406 (mmtm) cc_final: 0.7785 (mttp) REVERT: C 815 GLN cc_start: 0.7431 (mt0) cc_final: 0.7180 (mt0) REVERT: C 857 PHE cc_start: 0.6611 (t80) cc_final: 0.6407 (t80) REVERT: C 913 ARG cc_start: 0.6565 (OUTLIER) cc_final: 0.5771 (mmp-170) REVERT: C 1000 MET cc_start: 0.7802 (mtp) cc_final: 0.7246 (mmm) REVERT: C 1031 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7749 (mm-30) REVERT: C 1137 GLN cc_start: 0.8316 (tt0) cc_final: 0.7946 (mt0) outliers start: 28 outliers final: 15 residues processed: 211 average time/residue: 0.6693 time to fit residues: 162.6159 Evaluate side-chains 215 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 192 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 ARG Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 676 CYS Chi-restraints excluded: chain A residue 711 CYS Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain A residue 1140 GLU Chi-restraints excluded: chain B residue 518 LYS Chi-restraints excluded: chain B residue 539 GLN Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 631 LYS Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 888 ASP Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 539 GLN Chi-restraints excluded: chain C residue 888 ASP Chi-restraints excluded: chain C residue 905 MET Chi-restraints excluded: chain C residue 913 ARG Chi-restraints excluded: chain C residue 1104 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 273 optimal weight: 4.9990 chunk 282 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 179 optimal weight: 0.1980 chunk 30 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 323 optimal weight: 1.9990 chunk 246 optimal weight: 1.9990 chunk 180 optimal weight: 0.7980 chunk 107 optimal weight: 0.0270 chunk 156 optimal weight: 3.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 GLN ** B1076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1193 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.132912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.111487 restraints weight = 29449.561| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.71 r_work: 0.3264 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 26254 Z= 0.109 Angle : 0.513 10.663 35959 Z= 0.267 Chirality : 0.042 0.205 4173 Planarity : 0.004 0.038 4584 Dihedral : 4.712 59.689 3580 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.24 % Allowed : 10.58 % Favored : 88.18 % 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: 0.81 (0.15), residues: 3219 helix: 1.82 (0.19), residues: 771 sheet: 0.17 (0.18), residues: 684 loop : 0.21 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1195 TYR 0.014 0.001 TYR C1133 PHE 0.019 0.001 PHE C 184 TRP 0.019 0.001 TRP B 449 HIS 0.014 0.001 HIS C 678 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (26155) covalent geometry : angle 0.49624 / 0.26 (35710) SS BOND : bond 0.00438 / 0.26 ( 48) SS BOND : angle 1.70258 / 1.06 ( 96) hydrogen bonds : bond 0.04039 / 2.69 ( 1067) hydrogen bonds : angle 5.29774 / 3.68 ( 2955) link_BETA1-4 : bond 0.00346 / 0.19 ( 6) link_BETA1-4 : angle 1.13197 / 0.77 ( 18) link_NAG-ASN : bond 0.00229 / 0.13 ( 45) link_NAG-ASN : angle 1.65548 / 1.13 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 TYR cc_start: 0.7943 (m-80) cc_final: 0.7690 (m-80) REVERT: A 246 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7368 (mp0) REVERT: A 394 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.8008 (mtp-110) REVERT: A 448 ASP cc_start: 0.8981 (m-30) cc_final: 0.8626 (m-30) REVERT: A 818 GLN cc_start: 0.7288 (mm-40) cc_final: 0.6804 (mt0) REVERT: A 905 MET cc_start: 0.6572 (mtp) cc_final: 0.6252 (mtp) REVERT: A 931 MET cc_start: 0.8925 (mtt) cc_final: 0.8666 (mtm) REVERT: A 1000 MET cc_start: 0.7627 (mtp) cc_final: 0.7312 (mmm) REVERT: A 1031 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7947 (mm-30) REVERT: A 1137 GLN cc_start: 0.8297 (tt0) cc_final: 0.7840 (mt0) REVERT: A 1205 ASN cc_start: 0.8676 (m-40) cc_final: 0.8446 (m-40) REVERT: B 426 GLU cc_start: 0.8688 (tp30) cc_final: 0.8486 (tt0) REVERT: B 562 LYS cc_start: 0.8483 (ptpt) cc_final: 0.7929 (mmtm) REVERT: B 682 MET cc_start: 0.7648 (mtp) cc_final: 0.7147 (mtm) REVERT: B 822 LYS cc_start: 0.8569 (mttt) cc_final: 0.7585 (pttt) REVERT: B 840 ASN cc_start: 0.8510 (OUTLIER) cc_final: 0.8035 (m-40) REVERT: B 931 MET cc_start: 0.8790 (mtt) cc_final: 0.8505 (mtm) REVERT: B 1137 GLN cc_start: 0.8296 (tt0) cc_final: 0.7790 (mt0) REVERT: B 1193 ASN cc_start: 0.7898 (m-40) cc_final: 0.7659 (m110) REVERT: C 147 TYR cc_start: 0.8026 (OUTLIER) cc_final: 0.7619 (t80) REVERT: C 539 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.8050 (mp10) REVERT: C 562 LYS cc_start: 0.8387 (mmtm) cc_final: 0.7794 (mttp) REVERT: C 815 GLN cc_start: 0.7389 (mt0) cc_final: 0.7150 (mt0) REVERT: C 905 MET cc_start: 0.6609 (OUTLIER) cc_final: 0.6243 (mtp) REVERT: C 913 ARG cc_start: 0.6575 (OUTLIER) cc_final: 0.5723 (mmp-170) REVERT: C 1000 MET cc_start: 0.7796 (mtp) cc_final: 0.7212 (mmm) REVERT: C 1031 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7749 (mm-30) REVERT: C 1137 GLN cc_start: 0.8257 (tt0) cc_final: 0.7936 (mt0) outliers start: 30 outliers final: 13 residues processed: 212 average time/residue: 0.6457 time to fit residues: 158.0412 Evaluate side-chains 207 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 187 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 ARG Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 676 CYS Chi-restraints excluded: chain A residue 711 CYS Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain A residue 1140 GLU Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 631 LYS Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 888 ASP Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 539 GLN Chi-restraints excluded: chain C residue 905 MET Chi-restraints excluded: chain C residue 913 ARG Chi-restraints excluded: chain C residue 1104 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 166 optimal weight: 3.9990 chunk 316 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 214 optimal weight: 10.0000 chunk 104 optimal weight: 0.9980 chunk 185 optimal weight: 4.9990 chunk 57 optimal weight: 0.0270 chunk 182 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 overall best weight: 1.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 GLN ** A 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 GLN ** B1076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1161 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.128817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.107137 restraints weight = 29459.030| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.71 r_work: 0.3188 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 26254 Z= 0.216 Angle : 0.627 16.918 35959 Z= 0.322 Chirality : 0.046 0.329 4173 Planarity : 0.004 0.040 4584 Dihedral : 5.092 56.138 3578 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.07 % Allowed : 10.91 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.62 (0.14), residues: 3219 helix: 1.53 (0.19), residues: 765 sheet: 0.06 (0.18), residues: 696 loop : 0.17 (0.15), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1195 TYR 0.020 0.002 TYR C 198 PHE 0.019 0.002 PHE A 842 TRP 0.014 0.002 TRP B 449 HIS 0.013 0.002 HIS C 678 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.22 (26155) covalent geometry : angle 0.60679 / 0.32 (35710) SS BOND : bond 0.00672 / 0.45 ( 48) SS BOND : angle 2.19632 / 1.45 ( 96) hydrogen bonds : bond 0.05079 / 3.40 ( 1067) hydrogen bonds : angle 5.55207 / 3.85 ( 2955) link_BETA1-4 : bond 0.00327 / 0.18 ( 6) link_BETA1-4 : angle 1.30860 / 0.85 ( 18) link_NAG-ASN : bond 0.00357 / 0.22 ( 45) link_NAG-ASN : angle 1.92768 / 1.34 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 TYR cc_start: 0.8092 (m-80) cc_final: 0.7772 (m-80) REVERT: A 246 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7490 (mp0) REVERT: A 394 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7997 (mtp-110) REVERT: A 395 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7845 (mp0) REVERT: A 448 ASP cc_start: 0.9094 (m-30) cc_final: 0.8759 (m-30) REVERT: A 818 GLN cc_start: 0.7383 (mm-40) cc_final: 0.6876 (mt0) REVERT: A 840 ASN cc_start: 0.8404 (OUTLIER) cc_final: 0.7940 (m110) REVERT: A 931 MET cc_start: 0.8993 (mtt) cc_final: 0.8667 (mtm) REVERT: A 1000 MET cc_start: 0.7689 (mtp) cc_final: 0.7354 (mmm) REVERT: A 1031 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8010 (mm-30) REVERT: A 1137 GLN cc_start: 0.8382 (tt0) cc_final: 0.7901 (mt0) REVERT: A 1205 ASN cc_start: 0.8663 (m-40) cc_final: 0.8423 (m-40) REVERT: B 147 TYR cc_start: 0.8050 (t80) cc_final: 0.7836 (t80) REVERT: B 184 PHE cc_start: 0.7706 (m-80) cc_final: 0.7400 (m-80) REVERT: B 562 LYS cc_start: 0.8559 (ptpt) cc_final: 0.7945 (mmtm) REVERT: B 682 MET cc_start: 0.8028 (mtp) cc_final: 0.7413 (mtm) REVERT: B 822 LYS cc_start: 0.8624 (mttt) cc_final: 0.7583 (pttt) REVERT: B 840 ASN cc_start: 0.8646 (OUTLIER) cc_final: 0.8157 (m-40) REVERT: B 931 MET cc_start: 0.8973 (mtt) cc_final: 0.8719 (mtt) REVERT: B 1137 GLN cc_start: 0.8322 (tt0) cc_final: 0.7810 (mt0) REVERT: C 147 TYR cc_start: 0.8163 (m-80) cc_final: 0.7746 (t80) REVERT: C 234 LYS cc_start: 0.7341 (mtpt) cc_final: 0.7135 (mtmt) REVERT: C 539 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7732 (mp10) REVERT: C 815 GLN cc_start: 0.7531 (mt0) cc_final: 0.6790 (mp10) REVERT: C 840 ASN cc_start: 0.8486 (OUTLIER) cc_final: 0.8047 (m-40) REVERT: C 1000 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7288 (mmm) REVERT: C 1031 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7743 (mm-30) REVERT: C 1137 GLN cc_start: 0.8303 (tt0) cc_final: 0.8012 (mt0) outliers start: 26 outliers final: 13 residues processed: 201 average time/residue: 0.6711 time to fit residues: 156.5857 Evaluate side-chains 204 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 ARG Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 676 CYS Chi-restraints excluded: chain A residue 711 CYS Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain A residue 1140 GLU Chi-restraints excluded: chain B residue 631 LYS Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 888 ASP Chi-restraints excluded: chain C residue 539 GLN Chi-restraints excluded: chain C residue 840 ASN Chi-restraints excluded: chain C residue 905 MET Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 1000 MET Chi-restraints excluded: chain C residue 1104 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 206 optimal weight: 4.9990 chunk 292 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 268 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 116 optimal weight: 0.5980 chunk 208 optimal weight: 7.9990 chunk 152 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1161 ASN B 35 GLN ** B1076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1161 ASN C 339 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.127999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.106396 restraints weight = 29395.702| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.70 r_work: 0.3187 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 26254 Z= 0.246 Angle : 0.660 15.800 35959 Z= 0.338 Chirality : 0.047 0.311 4173 Planarity : 0.005 0.045 4584 Dihedral : 5.275 56.406 3578 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.28 % Allowed : 10.96 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.14), residues: 3219 helix: 1.33 (0.19), residues: 762 sheet: 0.07 (0.18), residues: 690 loop : -0.04 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1195 TYR 0.029 0.002 TYR C 198 PHE 0.020 0.002 PHE A 842 TRP 0.014 0.002 TRP B 449 HIS 0.012 0.002 HIS B 678 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.25 (26155) covalent geometry : angle 0.63758 / 0.33 (35710) SS BOND : bond 0.00703 / 0.46 ( 48) SS BOND : angle 2.35711 / 1.59 ( 96) hydrogen bonds : bond 0.05301 / 3.55 ( 1067) hydrogen bonds : angle 5.65562 / 3.92 ( 2955) link_BETA1-4 : bond 0.00289 / 0.16 ( 6) link_BETA1-4 : angle 1.46564 / 0.95 ( 18) link_NAG-ASN : bond 0.00383 / 0.24 ( 45) link_NAG-ASN : angle 2.09946 / 1.46 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8426.33 seconds wall clock time: 144 minutes 47.17 seconds (8687.17 seconds total)