Starting phenix.real_space_refine on Mon Jun 23 14:55:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hhy_34807/06_2025/8hhy_34807.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hhy_34807/06_2025/8hhy_34807.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hhy_34807/06_2025/8hhy_34807.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hhy_34807/06_2025/8hhy_34807.map" model { file = "/net/cci-nas-00/data/ceres_data/8hhy_34807/06_2025/8hhy_34807.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hhy_34807/06_2025/8hhy_34807.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.077 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 123 5.16 5 C 17431 2.51 5 N 4528 2.21 5 O 5338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27420 Number of models: 1 Model: "" Number of chains: 16 Chain: "F" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 955 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "W" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "G" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 675 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 82} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "I" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 753 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 92} Chain breaks: 1 Chain: "H" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 819 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 4, 'TRANS': 113} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 82 Chain: "L" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 660 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 86} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 7454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 957, 7454 Classifications: {'peptide': 957} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 45, 'TRANS': 911} Chain breaks: 10 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 7574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7574 Classifications: {'peptide': 971} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 46, 'TRANS': 924} Chain breaks: 9 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 7264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 934, 7264 Classifications: {'peptide': 934} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 44, 'TRANS': 889} Chain breaks: 9 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 16.76, per 1000 atoms: 0.61 Number of scatterers: 27420 At special positions: 0 Unit cell: (157.7, 158.53, 182.6, 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 123 16.00 O 5338 8.00 N 4528 7.00 C 17431 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS W 23 " - pdb=" SG CYS W 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 709 " " NAG A1304 " - " ASN A1074 " " NAG A1305 " - " ASN A 122 " " NAG A1306 " - " ASN A1134 " " NAG A1307 " - " ASN A1098 " " NAG A1308 " - " ASN A 717 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B 122 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B1098 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B 717 " " NAG C1301 " - " ASN C 616 " " NAG C1302 " - " ASN C 709 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 122 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C1098 " " NAG C1307 " - " ASN C1134 " " NAG C1308 " - " ASN C 801 " " NAG D 1 " - " ASN A 801 " " NAG E 1 " - " ASN B 331 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN C 717 " Time building additional restraints: 6.72 Conformation dependent library (CDL) restraints added in 3.7 seconds 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6496 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 62 sheets defined 22.2% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.82 Creating SS restraints... Processing helix chain 'F' and resid 28 through 30 No H-bonds generated for 'chain 'F' and resid 28 through 30' Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'W' and resid 79 through 83 removed outlier: 4.079A pdb=" N ILE W 83 " --> pdb=" O PRO W 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.872A pdb=" N ILE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.045A pdb=" N ILE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.847A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 416 through 423 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 755 Processing helix chain 'A' and resid 759 through 782 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.644A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.765A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.593A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.003A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.024A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 3.873A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.504A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 747 through 756 Processing helix chain 'B' and resid 759 through 782 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 941 removed outlier: 7.115A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.552A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.830A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.672A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.595A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.754A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.807A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.926A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG C 905 " --> pdb=" O GLN C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 940 removed outlier: 4.267A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 977 through 984 removed outlier: 3.508A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.546A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.564A pdb=" N TRP F 33 " --> pdb=" O GLY F 99 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE F 34 " --> pdb=" O ARG F 50 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ARG F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N MET F 48 " --> pdb=" O TRP F 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 18 through 23 removed outlier: 3.602A pdb=" N THR F 78 " --> pdb=" O ASP F 73 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP F 73 " --> pdb=" O THR F 78 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR F 80 " --> pdb=" O SER F 71 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER F 71 " --> pdb=" O TYR F 80 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLN F 82 " --> pdb=" O THR F 69 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR F 69 " --> pdb=" O GLN F 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'W' and resid 48 through 49 removed outlier: 3.947A pdb=" N TYR W 49 " --> pdb=" O ASN W 53 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN W 53 " --> pdb=" O TYR W 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'W' and resid 66 through 67 removed outlier: 3.748A pdb=" N SER W 67 " --> pdb=" O ASP W 70 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP W 70 " --> pdb=" O SER W 67 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'W' and resid 89 through 91 removed outlier: 4.651A pdb=" N GLN W 90 " --> pdb=" O THR W 97 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N THR W 97 " --> pdb=" O GLN W 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 32 through 34 removed outlier: 5.995A pdb=" N TRP G 33 " --> pdb=" O GLY G 99 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY G 99 " --> pdb=" O TRP G 33 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 37 through 38 Processing sheet with id=AA8, first strand: chain 'G' and resid 49 through 52 removed outlier: 3.738A pdb=" N ARG G 50 " --> pdb=" O ASN G 59 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN G 59 " --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR G 57 " --> pdb=" O ASP G 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 68 through 73 removed outlier: 4.151A pdb=" N THR G 69 " --> pdb=" O GLN G 82 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLN G 82 " --> pdb=" O THR G 69 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 36 through 37 removed outlier: 4.424A pdb=" N GLN I 37 " --> pdb=" O LYS I 45 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS I 45 " --> pdb=" O GLN I 37 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'I' and resid 48 through 49 removed outlier: 4.168A pdb=" N TYR I 49 " --> pdb=" O ASN I 53 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN I 53 " --> pdb=" O TYR I 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'I' and resid 90 through 91 removed outlier: 4.604A pdb=" N GLN I 90 " --> pdb=" O THR I 97 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR I 97 " --> pdb=" O GLN I 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'H' and resid 46 through 51 removed outlier: 4.145A pdb=" N MET H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 46 through 51 removed outlier: 4.145A pdb=" N MET H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 6 through 7 Processing sheet with id=AB7, first strand: chain 'L' and resid 36 through 38 Processing sheet with id=AB8, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.538A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.675A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 65 through 66 removed outlier: 3.530A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'A' and resid 120 through 121 Processing sheet with id=AC4, first strand: chain 'A' and resid 190 through 191 removed outlier: 6.777A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 311 through 318 removed outlier: 5.384A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.614A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.673A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 654 through 656 removed outlier: 5.550A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 711 through 712 Processing sheet with id=AD1, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.914A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 3.549A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id=AD5, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.716A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.701A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AD8, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.584A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.584A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.344A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.950A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 376 through 380 Processing sheet with id=AE4, first strand: chain 'B' and resid 654 through 656 removed outlier: 5.287A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AE6, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.901A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 718 through 728 Processing sheet with id=AE8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE9, first strand: chain 'B' and resid 1094 through 1097 removed outlier: 4.756A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.552A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 50 through 52 removed outlier: 7.878A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 65 through 66 Processing sheet with id=AF4, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AF5, first strand: chain 'C' and resid 101 through 103 Processing sheet with id=AF6, first strand: chain 'C' and resid 118 through 121 Processing sheet with id=AF7, first strand: chain 'C' and resid 190 through 191 removed outlier: 6.723A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 311 through 313 Processing sheet with id=AF9, first strand: chain 'C' and resid 318 through 319 removed outlier: 3.605A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AG2, first strand: chain 'C' and resid 354 through 357 removed outlier: 4.981A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 565 through 566 removed outlier: 4.115A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.365A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AG6, first strand: chain 'C' and resid 718 through 727 Processing sheet with id=AG7, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AG8, first strand: chain 'C' and resid 1094 through 1096 removed outlier: 3.699A pdb=" N VAL C1096 " --> pdb=" O PHE C1103 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE C1103 " --> pdb=" O VAL C1096 " (cutoff:3.500A) 870 hydrogen bonds defined for protein. 2358 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: 12.28 Time building geometry restraints manager: 7.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8766 1.35 - 1.47: 7212 1.47 - 1.60: 11871 1.60 - 1.73: 1 1.73 - 1.85: 159 Bond restraints: 28009 Sorted by residual: bond pdb=" CG PRO B 272 " pdb=" CD PRO B 272 " ideal model delta sigma weight residual 1.503 1.367 0.136 3.40e-02 8.65e+02 1.60e+01 bond pdb=" N SER L 30 " pdb=" CA SER L 30 " ideal model delta sigma weight residual 1.457 1.504 -0.046 1.29e-02 6.01e+03 1.28e+01 bond pdb=" CB PRO B 272 " pdb=" CG PRO B 272 " ideal model delta sigma weight residual 1.492 1.639 -0.147 5.00e-02 4.00e+02 8.65e+00 bond pdb=" C1 NAG C1305 " pdb=" O5 NAG C1305 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.82e+00 bond pdb=" C MET H 40 " pdb=" N PRO H 41 " ideal model delta sigma weight residual 1.332 1.359 -0.027 1.12e-02 7.97e+03 5.66e+00 ... (remaining 28004 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 37782 2.88 - 5.76: 266 5.76 - 8.64: 28 8.64 - 11.52: 6 11.52 - 14.40: 2 Bond angle restraints: 38084 Sorted by residual: angle pdb=" N PRO B 272 " pdb=" CD PRO B 272 " pdb=" CG PRO B 272 " ideal model delta sigma weight residual 103.20 92.64 10.56 1.50e+00 4.44e-01 4.96e+01 angle pdb=" CA PRO B 272 " pdb=" N PRO B 272 " pdb=" CD PRO B 272 " ideal model delta sigma weight residual 112.00 102.66 9.34 1.40e+00 5.10e-01 4.45e+01 angle pdb=" CG1 ILE L 29 " pdb=" CB ILE L 29 " pdb=" CG2 ILE L 29 " ideal model delta sigma weight residual 110.70 125.10 -14.40 3.00e+00 1.11e-01 2.30e+01 angle pdb=" C ILE L 29 " pdb=" N SER L 30 " pdb=" CA SER L 30 " ideal model delta sigma weight residual 121.54 130.38 -8.84 1.91e+00 2.74e-01 2.14e+01 angle pdb=" N PRO C1090 " pdb=" CD PRO C1090 " pdb=" CG PRO C1090 " ideal model delta sigma weight residual 103.20 96.50 6.70 1.50e+00 4.44e-01 1.99e+01 ... (remaining 38079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.84: 15947 21.84 - 43.69: 922 43.69 - 65.53: 138 65.53 - 87.37: 61 87.37 - 109.21: 7 Dihedral angle restraints: 17075 sinusoidal: 6978 harmonic: 10097 Sorted by residual: dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 169.36 -76.36 1 1.00e+01 1.00e-02 7.34e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 167.77 -74.77 1 1.00e+01 1.00e-02 7.08e+01 dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual 93.00 165.71 -72.71 1 1.00e+01 1.00e-02 6.75e+01 ... (remaining 17072 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 4402 0.148 - 0.295: 18 0.295 - 0.443: 0 0.443 - 0.591: 0 0.591 - 0.738: 2 Chirality restraints: 4422 Sorted by residual: chirality pdb=" CB ILE L 29 " pdb=" CA ILE L 29 " pdb=" CG1 ILE L 29 " pdb=" CG2 ILE L 29 " both_signs ideal model delta sigma weight residual False 2.64 1.91 0.74 2.00e-01 2.50e+01 1.36e+01 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 616 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 9.77e+00 chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 2.03e+00 ... (remaining 4419 not shown) Planarity restraints: 4900 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 616 " -0.000 2.00e-02 2.50e+03 3.70e-02 1.71e+01 pdb=" CG ASN B 616 " -0.043 2.00e-02 2.50e+03 pdb=" OD1 ASN B 616 " 0.044 2.00e-02 2.50e+03 pdb=" ND2 ASN B 616 " -0.040 2.00e-02 2.50e+03 pdb=" C1 NAG B1302 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA H 9 " -0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C ALA H 9 " 0.067 2.00e-02 2.50e+03 pdb=" O ALA H 9 " -0.025 2.00e-02 2.50e+03 pdb=" N GLU H 10 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C1078 " 0.063 5.00e-02 4.00e+02 9.60e-02 1.47e+01 pdb=" N PRO C1079 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO C1079 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO C1079 " 0.051 5.00e-02 4.00e+02 ... (remaining 4897 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 386 2.64 - 3.20: 24988 3.20 - 3.77: 41071 3.77 - 4.33: 57633 4.33 - 4.90: 92203 Nonbonded interactions: 216281 Sorted by model distance: nonbonded pdb=" O PHE B 106 " pdb=" OG SER B 116 " model vdw 2.074 3.040 nonbonded pdb=" OE2 GLU B 819 " pdb=" OG SER B1055 " model vdw 2.082 3.040 nonbonded pdb=" OE2 GLU C 819 " pdb=" OG SER C1055 " model vdw 2.111 3.040 nonbonded pdb=" O ALA B 879 " pdb=" OG1 THR B 883 " model vdw 2.128 3.040 nonbonded pdb=" NZ LYS B1028 " pdb=" O PHE B1042 " model vdw 2.129 3.120 ... (remaining 216276 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 141 or (resid 142 and (name N or name CA or nam \ e C or name O or name CB )) or resid 166 through 442 or resid 502 through 1120 o \ r (resid 1121 and (name N or name CA or name C or name O or name CB )) or resid \ 1122 through 1145 or resid 1301 through 1308)) selection = (chain 'B' and (resid 27 through 68 or resid 80 through 96 or (resid 97 and (nam \ e N or name CA or name C or name O or name CB )) or resid 98 through 142 or resi \ d 166 through 209 or resid 216 through 243 or resid 263 through 442 or resid 502 \ through 1145 or resid 1301 through 1308)) selection = (chain 'C' and (resid 27 through 96 or (resid 97 and (name N or name CA or name \ C or name O or name CB )) or resid 98 through 141 or (resid 142 and (name N or n \ ame CA or name C or name O or name CB )) or resid 166 through 209 or resid 216 t \ hrough 1120 or (resid 1121 and (name N or name CA or name C or name O or name CB \ )) or resid 1122 through 1145 or resid 1301 through 1308)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'J' selection = chain 'K' } ncs_group { reference = (chain 'F' and (resid 3 through 10 or (resid 11 through 13 and (name N or name C \ A or name C or name O or name CB )) or resid 14 through 15 or (resid 16 and (nam \ e N or name CA or name C or name O or name CB )) or resid 17 through 24 or (resi \ d 25 and (name N or name CA or name C or name O or name CB )) or resid 26 or (re \ sid 27 through 28 and (name N or name CA or name C or name O or name CB )) or re \ sid 29 through 31 or (resid 32 through 33 and (name N or name CA or name C or na \ me O or name CB )) or resid 34 through 54 or (resid 55 through 60 and (name N or \ name CA or name C or name O or name CB )) or resid 61 through 64 or (resid 65 a \ nd (name N or name CA or name C or name O or name CB )) or resid 66 through 72 o \ r (resid 73 through 77 and (name N or name CA or name C or name O or name CB )) \ or resid 78 through 99 or (resid 100 through 106 and (name N or name CA or name \ C or name O or name CB )) or resid 107 or (resid 108 and (name N or name CA or n \ ame C or name O or name CB )) or resid 109 through 120)) selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 8 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 26 or (resid 27 through \ 28 and (name N or name CA or name C or name O or name CB )) or resid 29 through \ 31 or (resid 32 and (name N or name CA or name C or name O or name CB )) or res \ id 33 through 91 or (resid 92 and (name N or name CA or name C or name O or name \ CB )))) selection = (chain 'L' and (resid 2 through 8 or resid 15 through 92)) selection = (chain 'W' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 8 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 26 or (resid 27 through \ 28 and (name N or name CA or name C or name O or name CB )) or resid 29 through \ 31 or (resid 32 and (name N or name CA or name C or name O or name CB )) or res \ id 33 through 91 or (resid 92 and (name N or name CA or name C or name O or name \ CB )))) } 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: 3.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.110 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 64.310 Find NCS groups from input model: 1.670 Set up NCS constraints: 0.170 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:14.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5282 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.147 28083 Z= 0.189 Angle : 0.732 17.070 38264 Z= 0.380 Chirality : 0.049 0.738 4422 Planarity : 0.005 0.096 4872 Dihedral : 14.260 109.215 10453 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.64 % Favored : 94.28 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.14), residues: 3407 helix: -0.80 (0.19), residues: 653 sheet: -1.22 (0.21), residues: 655 loop : -1.47 (0.13), residues: 2099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 886 HIS 0.021 0.001 HIS B1048 PHE 0.035 0.001 PHE C 906 TYR 0.022 0.001 TYR A 873 ARG 0.007 0.000 ARG B 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00701 ( 28) link_NAG-ASN : angle 4.53390 ( 84) link_BETA1-4 : bond 0.00379 ( 4) link_BETA1-4 : angle 0.86019 ( 12) hydrogen bonds : bond 0.20824 ( 855) hydrogen bonds : angle 9.60943 ( 2358) SS BOND : bond 0.00243 ( 42) SS BOND : angle 2.30302 ( 84) covalent geometry : bond 0.00403 (28009) covalent geometry : angle 0.69377 (38084) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 2.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 4 MET cc_start: 0.0484 (mtm) cc_final: 0.0270 (tmt) REVERT: A 902 MET cc_start: 0.5852 (tpt) cc_final: 0.5516 (mmm) REVERT: C 912 THR cc_start: 0.5915 (t) cc_final: 0.5590 (m) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 1.0062 time to fit residues: 314.3651 Evaluate side-chains 168 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 2.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 290 optimal weight: 3.9990 chunk 260 optimal weight: 9.9990 chunk 144 optimal weight: 1.9990 chunk 89 optimal weight: 20.0000 chunk 175 optimal weight: 0.9980 chunk 139 optimal weight: 6.9990 chunk 269 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 163 optimal weight: 10.0000 chunk 200 optimal weight: 0.9990 chunk 312 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 27 GLN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 501 ASN B 762 GLN ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5037 r_free = 0.5037 target = 0.266707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.241374 restraints weight = 36484.726| |-----------------------------------------------------------------------------| r_work (start): 0.4826 rms_B_bonded: 1.62 r_work: 0.4557 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work (final): 0.4557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6298 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 28083 Z= 0.254 Angle : 0.749 13.871 38264 Z= 0.381 Chirality : 0.048 0.283 4422 Planarity : 0.005 0.063 4872 Dihedral : 8.409 94.631 4388 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.61 % Favored : 94.34 % Rotamer: Outliers : 1.68 % Allowed : 8.26 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.14), residues: 3407 helix: -0.73 (0.19), residues: 661 sheet: -1.38 (0.20), residues: 682 loop : -1.53 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 886 HIS 0.006 0.001 HIS B1048 PHE 0.033 0.002 PHE C 906 TYR 0.028 0.002 TYR C1067 ARG 0.006 0.000 ARG C1091 Details of bonding type rmsd link_NAG-ASN : bond 0.00638 ( 28) link_NAG-ASN : angle 3.87170 ( 84) link_BETA1-4 : bond 0.00265 ( 4) link_BETA1-4 : angle 1.75439 ( 12) hydrogen bonds : bond 0.06696 ( 855) hydrogen bonds : angle 7.80426 ( 2358) SS BOND : bond 0.00330 ( 42) SS BOND : angle 1.98133 ( 84) covalent geometry : bond 0.00575 (28009) covalent geometry : angle 0.72190 (38084) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 182 time to evaluate : 2.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 4 MET cc_start: 0.0044 (ptt) cc_final: -0.1605 (mpt) REVERT: G 40 MET cc_start: 0.2084 (pmm) cc_final: 0.0970 (ptt) REVERT: L 4 MET cc_start: 0.0538 (mtm) cc_final: -0.0918 (tpt) REVERT: A 1001 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7847 (tt) REVERT: B 902 MET cc_start: 0.5726 (tpt) cc_final: 0.5503 (mmp) REVERT: B 1001 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.8029 (tt) REVERT: B 1091 ARG cc_start: 0.7305 (mmt-90) cc_final: 0.6012 (mpp-170) REVERT: C 861 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7306 (pt) outliers start: 50 outliers final: 26 residues processed: 215 average time/residue: 1.0086 time to fit residues: 269.2105 Evaluate side-chains 187 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 2.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 63 SER Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 959 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 225 optimal weight: 0.6980 chunk 66 optimal weight: 20.0000 chunk 196 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 339 optimal weight: 0.7980 chunk 169 optimal weight: 6.9990 chunk 321 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 343 optimal weight: 0.0970 chunk 301 optimal weight: 0.3980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 34 ASN W 89 GLN A 804 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN A1002 GLN A1023 ASN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 762 GLN ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5055 r_free = 0.5055 target = 0.269860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4848 r_free = 0.4848 target = 0.242669 restraints weight = 36732.545| |-----------------------------------------------------------------------------| r_work (start): 0.4847 rms_B_bonded: 1.92 r_work: 0.4567 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.4567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6194 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28083 Z= 0.142 Angle : 0.623 13.089 38264 Z= 0.315 Chirality : 0.045 0.273 4422 Planarity : 0.004 0.068 4872 Dihedral : 7.579 86.575 4388 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.61 % Favored : 95.33 % Rotamer: Outliers : 2.01 % Allowed : 11.21 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.14), residues: 3407 helix: -0.26 (0.20), residues: 658 sheet: -1.21 (0.20), residues: 664 loop : -1.43 (0.13), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 886 HIS 0.004 0.001 HIS C1058 PHE 0.020 0.001 PHE C 906 TYR 0.019 0.001 TYR B 91 ARG 0.005 0.000 ARG A1000 Details of bonding type rmsd link_NAG-ASN : bond 0.00700 ( 28) link_NAG-ASN : angle 3.50484 ( 84) link_BETA1-4 : bond 0.00233 ( 4) link_BETA1-4 : angle 1.89006 ( 12) hydrogen bonds : bond 0.05565 ( 855) hydrogen bonds : angle 7.05723 ( 2358) SS BOND : bond 0.00292 ( 42) SS BOND : angle 1.50673 ( 84) covalent geometry : bond 0.00301 (28009) covalent geometry : angle 0.59729 (38084) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 208 time to evaluate : 2.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 4 MET cc_start: -0.0124 (ptt) cc_final: -0.1693 (mpt) REVERT: G 40 MET cc_start: 0.1948 (pmm) cc_final: 0.0958 (ptt) REVERT: A 567 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.5437 (mpp80) REVERT: A 740 MET cc_start: 0.5823 (OUTLIER) cc_final: 0.5064 (mtp) REVERT: A 902 MET cc_start: 0.6070 (tpt) cc_final: 0.5330 (tmm) REVERT: A 1001 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7608 (tt) REVERT: B 275 PHE cc_start: 0.6175 (OUTLIER) cc_final: 0.5696 (t80) REVERT: B 1001 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7916 (tt) REVERT: C 215 ASP cc_start: 0.5309 (m-30) cc_final: 0.5066 (m-30) REVERT: C 926 GLN cc_start: 0.5948 (tm130) cc_final: 0.5637 (tm130) outliers start: 60 outliers final: 23 residues processed: 251 average time/residue: 0.9114 time to fit residues: 287.4816 Evaluate side-chains 196 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 2.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain W residue 63 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 51 optimal weight: 9.9990 chunk 86 optimal weight: 30.0000 chunk 297 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 283 optimal weight: 8.9990 chunk 335 optimal weight: 0.7980 chunk 202 optimal weight: 4.9990 chunk 164 optimal weight: 20.0000 chunk 267 optimal weight: 8.9990 chunk 234 optimal weight: 5.9990 chunk 239 optimal weight: 0.9980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 6 GLN A 901 GLN A1002 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS A1113 GLN B 762 GLN B 919 ASN B 978 ASN B1002 GLN B1058 HIS ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5037 r_free = 0.5037 target = 0.266736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.240303 restraints weight = 36635.779| |-----------------------------------------------------------------------------| r_work (start): 0.4814 rms_B_bonded: 1.76 r_work: 0.4518 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.4409 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.4409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6534 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 28083 Z= 0.226 Angle : 0.704 13.980 38264 Z= 0.354 Chirality : 0.047 0.253 4422 Planarity : 0.005 0.065 4872 Dihedral : 7.397 79.931 4388 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.75 % Favored : 94.19 % Rotamer: Outliers : 3.05 % Allowed : 12.92 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.14), residues: 3407 helix: -0.38 (0.20), residues: 659 sheet: -1.31 (0.20), residues: 665 loop : -1.50 (0.13), residues: 2083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 886 HIS 0.004 0.001 HIS C 207 PHE 0.030 0.002 PHE B 168 TYR 0.025 0.002 TYR C1067 ARG 0.004 0.000 ARG C 815 Details of bonding type rmsd link_NAG-ASN : bond 0.00552 ( 28) link_NAG-ASN : angle 3.51694 ( 84) link_BETA1-4 : bond 0.00355 ( 4) link_BETA1-4 : angle 2.10377 ( 12) hydrogen bonds : bond 0.06118 ( 855) hydrogen bonds : angle 7.15524 ( 2358) SS BOND : bond 0.00324 ( 42) SS BOND : angle 1.63255 ( 84) covalent geometry : bond 0.00506 (28009) covalent geometry : angle 0.68046 (38084) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 170 time to evaluate : 2.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 4 MET cc_start: 0.0061 (ptt) cc_final: -0.1636 (mpt) REVERT: L 4 MET cc_start: -0.0207 (mmm) cc_final: -0.1090 (tmt) REVERT: A 567 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.5715 (mpp80) REVERT: A 740 MET cc_start: 0.6086 (OUTLIER) cc_final: 0.5189 (mtp) REVERT: A 984 LEU cc_start: 0.3230 (OUTLIER) cc_final: 0.2066 (mp) REVERT: A 1001 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7849 (tt) REVERT: B 275 PHE cc_start: 0.6361 (OUTLIER) cc_final: 0.6160 (m-80) REVERT: B 978 ASN cc_start: 0.7095 (OUTLIER) cc_final: 0.6886 (t160) REVERT: B 1001 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8141 (tt) REVERT: B 1106 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7481 (pt0) outliers start: 91 outliers final: 41 residues processed: 239 average time/residue: 0.9536 time to fit residues: 286.7064 Evaluate side-chains 205 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 156 time to evaluate : 2.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain W residue 63 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 180 optimal weight: 0.0030 chunk 336 optimal weight: 0.5980 chunk 42 optimal weight: 7.9990 chunk 39 optimal weight: 50.0000 chunk 11 optimal weight: 30.0000 chunk 61 optimal weight: 5.9990 chunk 16 optimal weight: 30.0000 chunk 219 optimal weight: 2.9990 chunk 205 optimal weight: 6.9990 chunk 225 optimal weight: 0.8980 chunk 315 optimal weight: 3.9990 overall best weight: 1.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 919 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5044 r_free = 0.5044 target = 0.267302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.238939 restraints weight = 36326.355| |-----------------------------------------------------------------------------| r_work (start): 0.4802 rms_B_bonded: 1.86 r_work: 0.4513 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work (final): 0.4513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6381 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 28083 Z= 0.205 Angle : 0.679 11.422 38264 Z= 0.342 Chirality : 0.046 0.267 4422 Planarity : 0.004 0.063 4872 Dihedral : 7.121 72.768 4388 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.49 % Favored : 94.45 % Rotamer: Outliers : 3.12 % Allowed : 13.66 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.14), residues: 3407 helix: -0.36 (0.20), residues: 658 sheet: -1.35 (0.20), residues: 647 loop : -1.46 (0.13), residues: 2102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 886 HIS 0.005 0.001 HIS C 207 PHE 0.027 0.002 PHE B 168 TYR 0.024 0.002 TYR C1067 ARG 0.004 0.000 ARG C1091 Details of bonding type rmsd link_NAG-ASN : bond 0.00532 ( 28) link_NAG-ASN : angle 3.44880 ( 84) link_BETA1-4 : bond 0.00331 ( 4) link_BETA1-4 : angle 2.28561 ( 12) hydrogen bonds : bond 0.05962 ( 855) hydrogen bonds : angle 7.03947 ( 2358) SS BOND : bond 0.00288 ( 42) SS BOND : angle 1.78294 ( 84) covalent geometry : bond 0.00458 (28009) covalent geometry : angle 0.65457 (38084) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 172 time to evaluate : 3.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 4 MET cc_start: -0.0110 (ptt) cc_final: -0.1643 (mpt) REVERT: H 93 MET cc_start: 0.0606 (mtt) cc_final: -0.1643 (tmm) REVERT: L 4 MET cc_start: -0.0017 (mmm) cc_final: -0.0949 (tmt) REVERT: A 34 ARG cc_start: 0.6460 (OUTLIER) cc_final: 0.5385 (mpt180) REVERT: A 567 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.5694 (mpp80) REVERT: A 740 MET cc_start: 0.6010 (OUTLIER) cc_final: 0.5040 (mtp) REVERT: A 878 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7100 (tt) REVERT: A 984 LEU cc_start: 0.3170 (OUTLIER) cc_final: 0.2045 (mp) REVERT: A 1001 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7787 (tt) REVERT: C 273 ARG cc_start: 0.6925 (tpp80) cc_final: 0.6421 (ttp80) REVERT: C 926 GLN cc_start: 0.6186 (tm130) cc_final: 0.5878 (tm130) outliers start: 93 outliers final: 44 residues processed: 242 average time/residue: 0.9316 time to fit residues: 283.1527 Evaluate side-chains 205 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 155 time to evaluate : 2.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain W residue 63 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 138 optimal weight: 7.9990 chunk 320 optimal weight: 0.6980 chunk 235 optimal weight: 0.1980 chunk 205 optimal weight: 6.9990 chunk 166 optimal weight: 1.9990 chunk 284 optimal weight: 9.9990 chunk 136 optimal weight: 4.9990 chunk 167 optimal weight: 0.0040 chunk 213 optimal weight: 0.7980 chunk 171 optimal weight: 10.0000 chunk 159 optimal weight: 1.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN A1002 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS B 317 ASN B 762 GLN B 919 ASN B1058 HIS ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5043 r_free = 0.5043 target = 0.268501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.240420 restraints weight = 36708.058| |-----------------------------------------------------------------------------| r_work (start): 0.4812 rms_B_bonded: 1.89 r_work: 0.4596 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.4596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6141 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28083 Z= 0.146 Angle : 0.619 11.006 38264 Z= 0.311 Chirality : 0.045 0.251 4422 Planarity : 0.004 0.065 4872 Dihedral : 6.729 66.536 4388 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.99 % Favored : 94.95 % Rotamer: Outliers : 2.95 % Allowed : 14.87 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.14), residues: 3407 helix: -0.14 (0.20), residues: 659 sheet: -1.33 (0.20), residues: 655 loop : -1.38 (0.13), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 886 HIS 0.004 0.001 HIS B1058 PHE 0.025 0.001 PHE B 168 TYR 0.020 0.001 TYR C1067 ARG 0.003 0.000 ARG A1000 Details of bonding type rmsd link_NAG-ASN : bond 0.00479 ( 28) link_NAG-ASN : angle 3.20031 ( 84) link_BETA1-4 : bond 0.00279 ( 4) link_BETA1-4 : angle 2.23702 ( 12) hydrogen bonds : bond 0.05406 ( 855) hydrogen bonds : angle 6.72269 ( 2358) SS BOND : bond 0.00254 ( 42) SS BOND : angle 1.48299 ( 84) covalent geometry : bond 0.00323 (28009) covalent geometry : angle 0.59679 (38084) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 187 time to evaluate : 2.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 4 MET cc_start: -0.0010 (ptt) cc_final: -0.1553 (mpt) REVERT: H 93 MET cc_start: 0.0702 (mtt) cc_final: -0.1518 (tmm) REVERT: L 4 MET cc_start: -0.0228 (mmm) cc_final: -0.1001 (tmt) REVERT: A 34 ARG cc_start: 0.6410 (OUTLIER) cc_final: 0.5345 (mpt180) REVERT: A 567 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.5699 (mpp80) REVERT: A 740 MET cc_start: 0.5965 (OUTLIER) cc_final: 0.5029 (mtp) REVERT: A 878 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7128 (tt) REVERT: A 984 LEU cc_start: 0.3021 (OUTLIER) cc_final: 0.2111 (mp) REVERT: A 1001 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7703 (tt) REVERT: B 858 LEU cc_start: 0.6217 (OUTLIER) cc_final: 0.5973 (pt) outliers start: 88 outliers final: 43 residues processed: 257 average time/residue: 0.8613 time to fit residues: 282.9826 Evaluate side-chains 212 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 162 time to evaluate : 2.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain W residue 63 SER Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 184 optimal weight: 20.0000 chunk 73 optimal weight: 0.9990 chunk 48 optimal weight: 50.0000 chunk 110 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 74 optimal weight: 0.2980 chunk 266 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 269 optimal weight: 0.9980 chunk 154 optimal weight: 9.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN A1002 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN B 196 ASN B 762 GLN B 919 ASN B 978 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5036 r_free = 0.5036 target = 0.267680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.238884 restraints weight = 36702.214| |-----------------------------------------------------------------------------| r_work (start): 0.4797 rms_B_bonded: 1.99 r_work: 0.4586 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.4586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6167 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 28083 Z= 0.171 Angle : 0.653 24.022 38264 Z= 0.324 Chirality : 0.047 0.699 4422 Planarity : 0.004 0.063 4872 Dihedral : 6.747 62.984 4388 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.25 % Favored : 94.72 % Rotamer: Outliers : 3.22 % Allowed : 15.13 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.14), residues: 3407 helix: -0.15 (0.20), residues: 659 sheet: -1.31 (0.20), residues: 650 loop : -1.37 (0.13), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 886 HIS 0.004 0.001 HIS C 207 PHE 0.025 0.002 PHE C 927 TYR 0.024 0.001 TYR C1067 ARG 0.003 0.000 ARG C 815 Details of bonding type rmsd link_NAG-ASN : bond 0.00465 ( 28) link_NAG-ASN : angle 4.31957 ( 84) link_BETA1-4 : bond 0.00304 ( 4) link_BETA1-4 : angle 2.27464 ( 12) hydrogen bonds : bond 0.05519 ( 855) hydrogen bonds : angle 6.70548 ( 2358) SS BOND : bond 0.00274 ( 42) SS BOND : angle 1.46504 ( 84) covalent geometry : bond 0.00385 (28009) covalent geometry : angle 0.61717 (38084) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 173 time to evaluate : 3.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 4 MET cc_start: -0.0007 (ptt) cc_final: -0.1534 (mpt) REVERT: H 93 MET cc_start: 0.0428 (mtt) cc_final: -0.1669 (tmm) REVERT: L 4 MET cc_start: -0.0133 (mmm) cc_final: -0.0902 (tmt) REVERT: A 34 ARG cc_start: 0.6424 (OUTLIER) cc_final: 0.5351 (mpt180) REVERT: A 567 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.5677 (mpp80) REVERT: A 740 MET cc_start: 0.5994 (OUTLIER) cc_final: 0.5035 (mtp) REVERT: A 878 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7117 (tt) REVERT: A 984 LEU cc_start: 0.2948 (OUTLIER) cc_final: 0.2028 (mp) REVERT: A 1001 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7733 (tt) REVERT: B 196 ASN cc_start: 0.6709 (OUTLIER) cc_final: 0.5236 (t0) REVERT: B 858 LEU cc_start: 0.6303 (OUTLIER) cc_final: 0.6054 (pt) REVERT: B 1058 HIS cc_start: 0.6332 (OUTLIER) cc_final: 0.5938 (m-70) REVERT: C 865 LEU cc_start: 0.6340 (OUTLIER) cc_final: 0.6108 (mp) outliers start: 96 outliers final: 51 residues processed: 250 average time/residue: 0.8554 time to fit residues: 273.1999 Evaluate side-chains 220 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 159 time to evaluate : 2.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain W residue 63 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 240 optimal weight: 0.4980 chunk 32 optimal weight: 30.0000 chunk 41 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 296 optimal weight: 0.7980 chunk 175 optimal weight: 0.8980 chunk 120 optimal weight: 0.5980 chunk 235 optimal weight: 0.8980 chunk 306 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN A1002 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS B 196 ASN B 762 GLN B 919 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5047 r_free = 0.5047 target = 0.268939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.241544 restraints weight = 36567.188| |-----------------------------------------------------------------------------| r_work (start): 0.4821 rms_B_bonded: 1.89 r_work: 0.4600 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.4600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6154 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 28083 Z= 0.146 Angle : 0.637 19.845 38264 Z= 0.316 Chirality : 0.046 0.539 4422 Planarity : 0.004 0.063 4872 Dihedral : 6.538 59.891 4388 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.02 % Favored : 94.95 % Rotamer: Outliers : 2.72 % Allowed : 16.04 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.14), residues: 3407 helix: -0.07 (0.20), residues: 653 sheet: -1.24 (0.20), residues: 650 loop : -1.34 (0.13), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 886 HIS 0.007 0.001 HIS B1058 PHE 0.030 0.001 PHE C 927 TYR 0.021 0.001 TYR C1067 ARG 0.003 0.000 ARG A1000 Details of bonding type rmsd link_NAG-ASN : bond 0.00514 ( 28) link_NAG-ASN : angle 4.05305 ( 84) link_BETA1-4 : bond 0.00289 ( 4) link_BETA1-4 : angle 2.31317 ( 12) hydrogen bonds : bond 0.05329 ( 855) hydrogen bonds : angle 6.57249 ( 2358) SS BOND : bond 0.00250 ( 42) SS BOND : angle 1.58916 ( 84) covalent geometry : bond 0.00326 (28009) covalent geometry : angle 0.60335 (38084) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 174 time to evaluate : 2.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 4 MET cc_start: -0.0062 (ptt) cc_final: -0.1577 (mpt) REVERT: H 45 LEU cc_start: 0.1235 (OUTLIER) cc_final: 0.0532 (pt) REVERT: H 93 MET cc_start: 0.0506 (mtt) cc_final: -0.1554 (tmm) REVERT: L 4 MET cc_start: -0.0230 (mmm) cc_final: -0.0998 (tmt) REVERT: A 34 ARG cc_start: 0.6393 (OUTLIER) cc_final: 0.5343 (mpt180) REVERT: A 141 LEU cc_start: -0.0301 (OUTLIER) cc_final: -0.0739 (pp) REVERT: A 567 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.5679 (mpp80) REVERT: A 740 MET cc_start: 0.5967 (OUTLIER) cc_final: 0.5606 (mtp) REVERT: A 878 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7160 (tt) REVERT: A 984 LEU cc_start: 0.3141 (OUTLIER) cc_final: 0.2212 (mp) REVERT: A 1001 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7681 (tt) REVERT: B 129 LYS cc_start: 0.5279 (mmpt) cc_final: 0.4673 (ptmt) REVERT: B 858 LEU cc_start: 0.6264 (OUTLIER) cc_final: 0.6012 (pt) REVERT: C 926 GLN cc_start: 0.6234 (tm130) cc_final: 0.5914 (tm130) outliers start: 81 outliers final: 47 residues processed: 240 average time/residue: 0.8433 time to fit residues: 257.2531 Evaluate side-chains 221 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 165 time to evaluate : 2.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain W residue 63 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 177 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 85 optimal weight: 8.9990 chunk 219 optimal weight: 3.9990 chunk 24 optimal weight: 20.0000 chunk 3 optimal weight: 50.0000 chunk 323 optimal weight: 0.5980 chunk 152 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 242 optimal weight: 0.6980 chunk 340 optimal weight: 4.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN A1002 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS A1113 GLN B 317 ASN B 675 GLN B 762 GLN B 919 ASN B 978 ASN B1010 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5033 r_free = 0.5033 target = 0.266185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.238046 restraints weight = 36197.252| |-----------------------------------------------------------------------------| r_work (start): 0.4803 rms_B_bonded: 1.86 r_work: 0.4522 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work (final): 0.4522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6375 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 28083 Z= 0.241 Angle : 0.729 16.400 38264 Z= 0.366 Chirality : 0.048 0.456 4422 Planarity : 0.005 0.058 4872 Dihedral : 6.701 59.444 4388 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.08 % Favored : 93.89 % Rotamer: Outliers : 2.99 % Allowed : 16.21 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.14), residues: 3407 helix: -0.38 (0.20), residues: 652 sheet: -1.35 (0.20), residues: 645 loop : -1.42 (0.13), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1102 HIS 0.009 0.001 HIS B1058 PHE 0.041 0.002 PHE C 927 TYR 0.026 0.002 TYR C1067 ARG 0.004 0.000 ARG C1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00544 ( 28) link_NAG-ASN : angle 3.88947 ( 84) link_BETA1-4 : bond 0.00362 ( 4) link_BETA1-4 : angle 2.35739 ( 12) hydrogen bonds : bond 0.06148 ( 855) hydrogen bonds : angle 6.90546 ( 2358) SS BOND : bond 0.00296 ( 42) SS BOND : angle 1.77926 ( 84) covalent geometry : bond 0.00547 (28009) covalent geometry : angle 0.70148 (38084) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 170 time to evaluate : 2.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 48 MET cc_start: 0.4824 (OUTLIER) cc_final: 0.3182 (pmm) REVERT: W 4 MET cc_start: -0.0158 (ptt) cc_final: -0.1596 (mpt) REVERT: G 40 MET cc_start: 0.2251 (pmm) cc_final: 0.1295 (ptp) REVERT: H 45 LEU cc_start: 0.1096 (OUTLIER) cc_final: 0.0290 (pt) REVERT: H 93 MET cc_start: 0.0607 (mtt) cc_final: -0.1419 (tmm) REVERT: L 4 MET cc_start: -0.0068 (mmm) cc_final: -0.0972 (tmt) REVERT: A 34 ARG cc_start: 0.6436 (OUTLIER) cc_final: 0.5470 (mpt180) REVERT: A 567 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.5768 (mpp80) REVERT: A 740 MET cc_start: 0.6154 (OUTLIER) cc_final: 0.5765 (mtp) REVERT: A 811 LYS cc_start: 0.4388 (tmtt) cc_final: 0.3894 (ttpm) REVERT: A 878 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7256 (tt) REVERT: A 1001 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7884 (tt) REVERT: B 858 LEU cc_start: 0.6479 (OUTLIER) cc_final: 0.6202 (pt) REVERT: B 922 LEU cc_start: 0.6701 (mp) cc_final: 0.6467 (mt) REVERT: B 1106 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7415 (pt0) REVERT: C 926 GLN cc_start: 0.6284 (tm130) cc_final: 0.5906 (tm130) outliers start: 89 outliers final: 53 residues processed: 240 average time/residue: 0.9974 time to fit residues: 300.4301 Evaluate side-chains 221 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 159 time to evaluate : 2.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain W residue 63 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 135 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 180 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 chunk 304 optimal weight: 0.7980 chunk 136 optimal weight: 0.8980 chunk 143 optimal weight: 0.8980 chunk 317 optimal weight: 1.9990 chunk 56 optimal weight: 0.0980 chunk 119 optimal weight: 2.9990 chunk 308 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN A 901 GLN A1002 GLN A1058 HIS A1113 GLN B 762 GLN B 919 ASN B 978 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5053 r_free = 0.5053 target = 0.268821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4831 r_free = 0.4831 target = 0.239758 restraints weight = 36265.700| |-----------------------------------------------------------------------------| r_work (start): 0.4816 rms_B_bonded: 1.99 r_work: 0.4533 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.4533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6341 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 28083 Z= 0.160 Angle : 0.660 15.466 38264 Z= 0.330 Chirality : 0.046 0.476 4422 Planarity : 0.004 0.059 4872 Dihedral : 6.426 59.479 4388 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.70 % Favored : 95.27 % Rotamer: Outliers : 2.62 % Allowed : 16.91 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.14), residues: 3407 helix: -0.23 (0.20), residues: 650 sheet: -1.33 (0.20), residues: 633 loop : -1.37 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 886 HIS 0.004 0.001 HIS B1058 PHE 0.029 0.001 PHE C 927 TYR 0.026 0.001 TYR C1067 ARG 0.003 0.000 ARG A1000 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 28) link_NAG-ASN : angle 3.79985 ( 84) link_BETA1-4 : bond 0.00250 ( 4) link_BETA1-4 : angle 2.32517 ( 12) hydrogen bonds : bond 0.05601 ( 855) hydrogen bonds : angle 6.66129 ( 2358) SS BOND : bond 0.00259 ( 42) SS BOND : angle 1.59787 ( 84) covalent geometry : bond 0.00358 (28009) covalent geometry : angle 0.63163 (38084) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 170 time to evaluate : 2.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 48 MET cc_start: 0.4889 (OUTLIER) cc_final: 0.3163 (pmm) REVERT: W 4 MET cc_start: -0.0133 (ptt) cc_final: -0.1590 (mpt) REVERT: G 40 MET cc_start: 0.2528 (pmm) cc_final: 0.1321 (ptp) REVERT: H 45 LEU cc_start: 0.1079 (OUTLIER) cc_final: 0.0191 (pt) REVERT: H 93 MET cc_start: 0.0508 (mtt) cc_final: -0.1464 (tmm) REVERT: L 4 MET cc_start: -0.0079 (mmm) cc_final: -0.0971 (tmt) REVERT: A 34 ARG cc_start: 0.6466 (OUTLIER) cc_final: 0.5359 (mpt180) REVERT: A 141 LEU cc_start: -0.0559 (OUTLIER) cc_final: -0.1004 (pp) REVERT: A 567 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.5701 (mpp80) REVERT: A 740 MET cc_start: 0.6024 (OUTLIER) cc_final: 0.5676 (mtp) REVERT: A 878 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7103 (tt) REVERT: A 1001 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7765 (tt) REVERT: B 858 LEU cc_start: 0.6335 (OUTLIER) cc_final: 0.5948 (pt) REVERT: B 1058 HIS cc_start: 0.6627 (OUTLIER) cc_final: 0.6342 (m-70) REVERT: C 740 MET cc_start: 0.6284 (OUTLIER) cc_final: 0.5477 (mtp) outliers start: 78 outliers final: 51 residues processed: 230 average time/residue: 0.8840 time to fit residues: 258.4603 Evaluate side-chains 224 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 162 time to evaluate : 3.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain W residue 63 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 128 optimal weight: 0.8980 chunk 32 optimal weight: 20.0000 chunk 166 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 172 optimal weight: 8.9990 chunk 135 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 279 optimal weight: 0.4980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS B 762 GLN B 919 ASN B 978 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 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 = 0.5050 r_free = 0.5050 target = 0.268064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4823 r_free = 0.4823 target = 0.238522 restraints weight = 36324.142| |-----------------------------------------------------------------------------| r_work (start): 0.4804 rms_B_bonded: 1.97 r_work: 0.4518 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.4518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6370 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 28083 Z= 0.190 Angle : 0.675 14.866 38264 Z= 0.338 Chirality : 0.047 0.466 4422 Planarity : 0.004 0.058 4872 Dihedral : 6.398 59.100 4388 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.38 % Allowed : 17.28 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.14), residues: 3407 helix: -0.26 (0.20), residues: 651 sheet: -1.35 (0.20), residues: 648 loop : -1.35 (0.13), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 886 HIS 0.007 0.001 HIS B1058 PHE 0.034 0.002 PHE C 927 TYR 0.029 0.002 TYR C1067 ARG 0.003 0.000 ARG C1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00518 ( 28) link_NAG-ASN : angle 3.70995 ( 84) link_BETA1-4 : bond 0.00274 ( 4) link_BETA1-4 : angle 2.34845 ( 12) hydrogen bonds : bond 0.05719 ( 855) hydrogen bonds : angle 6.69085 ( 2358) SS BOND : bond 0.00270 ( 42) SS BOND : angle 1.59172 ( 84) covalent geometry : bond 0.00428 (28009) covalent geometry : angle 0.64815 (38084) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18426.88 seconds wall clock time: 319 minutes 18.02 seconds (19158.02 seconds total)