Starting phenix.real_space_refine on Fri Mar 6 00:14:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nd3_12274/03_2026/7nd3_12274.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nd3_12274/03_2026/7nd3_12274.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nd3_12274/03_2026/7nd3_12274.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nd3_12274/03_2026/7nd3_12274.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nd3_12274/03_2026/7nd3_12274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nd3_12274/03_2026/7nd3_12274.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1524 atoms to isotropic. 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 111 5.16 5 C 15962 2.51 5 N 4109 2.21 5 O 4868 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25050 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 7628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7628 Classifications: {'peptide': 995} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 49, 'TRANS': 945} Chain breaks: 8 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 3, 'GLU:plan': 9, 'ARG:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 92 Chain: "B" Number of atoms: 7571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 989, 7571 Classifications: {'peptide': 989} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 49, 'TRANS': 939} Chain breaks: 9 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 5, 'ASN:plan1': 5, 'GLU:plan': 10, 'GLN:plan1': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 95 Chain: "C" Number of atoms: 7582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 991, 7582 Classifications: {'peptide': 991} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 49, 'TRANS': 941} Chain breaks: 7 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 4, 'ASP:plan': 8, 'GLN:plan1': 3, 'GLU:plan': 10, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 99 Chain: "H" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 833 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'TYR:plan': 2, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 34 Chain: "L" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 750 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TRP:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 3, 'ASN:plan1': 5, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 56 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 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: 6.40, per 1000 atoms: 0.26 Number of scatterers: 25050 At special positions: 0 Unit cell: (122.84, 135.29, 225.76, 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 111 16.00 O 4868 8.00 N 4109 7.00 C 15962 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 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 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 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 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B 717 " " NAG B1311 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C1134 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN C 717 " " NAG O 1 " - " ASN C 801 " " NAG P 1 " - " ASN C1098 " Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 1.1 seconds 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5968 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 49 sheets defined 26.3% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.973A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.203A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 760 through 783 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 852 through 856 removed outlier: 3.706A pdb=" N ASN A 856 " --> pdb=" O GLN A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.760A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 919 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: 3.555A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.719A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.458A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.009A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.194A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 853 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.627A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.364A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.742A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.630A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.016A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.673A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.230A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.590A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 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 966 removed outlier: 3.711A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.998A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.041A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.771A pdb=" N ILE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.718A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.630A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.270A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.263A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.790A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.219A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 715 removed outlier: 4.744A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.945A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB4, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.433A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 28 through 29 removed outlier: 5.971A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.489A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.633A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AB8, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.006A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 325 through 327 Processing sheet with id=AC1, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.239A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC5, first strand: chain 'B' and resid 565 through 566 removed outlier: 7.061A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.615A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AC9, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.896A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 31 removed outlier: 4.003A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.160A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.904A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AD7, first strand: chain 'C' and resid 309 through 319 removed outlier: 5.850A pdb=" N LYS C 310 " --> pdb=" O GLY C 601 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N GLY C 601 " --> pdb=" O LYS C 310 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE1, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.588A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.980A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 715 removed outlier: 4.119A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.837A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.198A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.513A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.095A pdb=" N TYR H 33 " --> pdb=" O ASP H 98 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N MET H 34 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.113A pdb=" N TYR H 108 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.895A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.596A pdb=" N LEU L 33 " --> pdb=" O PHE L 49 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N PHE L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 1100 hydrogen bonds defined for protein. 2958 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: 7.06 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7967 1.34 - 1.46: 6254 1.46 - 1.58: 11233 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 25592 Sorted by residual: bond pdb=" C1 NAG A1305 " pdb=" O5 NAG A1305 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.30e+00 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.12e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.75e+00 bond pdb=" C1 NAG C1307 " pdb=" O5 NAG C1307 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.70e+00 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.67e+00 ... (remaining 25587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 34555 2.45 - 4.90: 315 4.90 - 7.35: 11 7.35 - 9.80: 2 9.80 - 12.25: 1 Bond angle restraints: 34884 Sorted by residual: angle pdb=" CA LEU L 11 " pdb=" CB LEU L 11 " pdb=" CG LEU L 11 " ideal model delta sigma weight residual 116.30 128.55 -12.25 3.50e+00 8.16e-02 1.23e+01 angle pdb=" N ILE B 666 " pdb=" CA ILE B 666 " pdb=" C ILE B 666 " ideal model delta sigma weight residual 111.48 108.69 2.79 9.40e-01 1.13e+00 8.84e+00 angle pdb=" C ASN C 331 " pdb=" CA ASN C 331 " pdb=" CB ASN C 331 " ideal model delta sigma weight residual 111.30 115.88 -4.58 1.70e+00 3.46e-01 7.27e+00 angle pdb=" C PRO B 812 " pdb=" N SER B 813 " pdb=" CA SER B 813 " ideal model delta sigma weight residual 121.54 126.47 -4.93 1.91e+00 2.74e-01 6.66e+00 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 113.75 -3.05 1.22e+00 6.72e-01 6.27e+00 ... (remaining 34879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 14927 17.51 - 35.01: 655 35.01 - 52.52: 144 52.52 - 70.03: 48 70.03 - 87.53: 27 Dihedral angle restraints: 15801 sinusoidal: 6530 harmonic: 9271 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -158.99 72.99 1 1.00e+01 1.00e-02 6.79e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -158.16 72.16 1 1.00e+01 1.00e-02 6.66e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -158.04 72.04 1 1.00e+01 1.00e-02 6.64e+01 ... (remaining 15798 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3096 0.046 - 0.091: 749 0.091 - 0.137: 315 0.137 - 0.183: 15 0.183 - 0.229: 2 Chirality restraints: 4177 Sorted by residual: chirality pdb=" C1 NAG B1306 " pdb=" ND2 ASN B 603 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.06e-01 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.31e-01 ... (remaining 4174 not shown) Planarity restraints: 4477 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 122 " -0.013 2.00e-02 2.50e+03 2.52e-02 6.33e+00 pdb=" C ASN A 122 " 0.044 2.00e-02 2.50e+03 pdb=" O ASN A 122 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA A 123 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 122 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.73e+00 pdb=" C ASN B 122 " 0.041 2.00e-02 2.50e+03 pdb=" O ASN B 122 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA B 123 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 122 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.39e+00 pdb=" C ASN C 122 " -0.040 2.00e-02 2.50e+03 pdb=" O ASN C 122 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA C 123 " 0.013 2.00e-02 2.50e+03 ... (remaining 4474 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 703 2.71 - 3.26: 24584 3.26 - 3.80: 38975 3.80 - 4.35: 49446 4.35 - 4.90: 84944 Nonbonded interactions: 198652 Sorted by model distance: nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.159 3.040 nonbonded pdb=" OG1 THR B 33 " pdb=" O GLY B 219 " model vdw 2.219 3.040 nonbonded pdb=" O ALA B 475 " pdb=" ND2 ASN H 32 " model vdw 2.224 3.120 nonbonded pdb=" O GLU C 309 " pdb=" OH TYR C 313 " model vdw 2.244 3.040 nonbonded pdb=" OD2 ASP A 294 " pdb=" OG SER A 297 " model vdw 2.260 3.040 ... (remaining 198647 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 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 45 or (resid 46 and (name N or nam \ e CA or name C or name O or name CB )) or resid 47 through 52 or (resid 53 and ( \ name N or name CA or name C or name O or name CB )) or resid 54 through 66 or re \ sid 82 through 87 or (resid 88 and (name N or name CA or name C or name O or nam \ e CB )) or resid 89 through 95 or (resid 96 through 97 and (name N or name CA or \ name C or name O or name CB )) or resid 98 through 109 or (resid 110 and (name \ N or name CA or name C or name O or name CB )) or resid 111 or (resid 112 throug \ h 113 and (name N or name CA or name C or name O or name CB )) or resid 116 thro \ ugh 124 or (resid 125 and (name N or name CA or name C or name O or name CB )) o \ r resid 126 through 131 or (resid 132 and (name N or name CA or name C or name O \ or name CB )) or resid 133 or (resid 134 through 138 and (name N or name CA or \ name C or name O or name CB )) or resid 139 through 140 or resid 166 through 168 \ or (resid 169 and (name N or name CA or name C or name O or name CB )) or resid \ 170 through 171 or (resid 172 through 188 and (name N or name CA or name C or n \ ame O or name CB )) or resid 189 through 196 or resid 200 through 209 or (resid \ 210 and (name N or name CA or name C or name O or name CB )) or (resid 215 and ( \ name N or name CA or name C or name O or name CB )) or resid 216 through 217 or \ (resid 218 and (name N or name CA or name C or name O or name CB )) or resid 219 \ through 223 or (resid 224 and (name N or name CA or name C or name O or name CB \ )) or resid 225 through 263 or resid 265 through 308 or (resid 309 and (name N \ or name CA or name C or name O or name CB )) or resid 310 through 323 or (resid \ 324 and (name N or name CA or name C or name O or name CB )) or resid 325 throug \ h 332 or (resid 333 and (name N or name CA or name C or name O or name CB )) or \ resid 334 through 457 or (resid 458 and (name N or name CA or name C or name O o \ r name CB )) or resid 459 through 528 or (resid 529 and (name N or name CA or na \ me C or name O or name CB )) or resid 530 through 536 or (resid 537 and (name N \ or name CA or name C or name O or name CB )) or resid 538 through 747 or (resid \ 748 and (name N or name CA or name C or name O or name CB )) or resid 749 throug \ h 793 or (resid 794 and (name N or name CA or name C or name O or name CB )) or \ resid 795 or (resid 796 and (name N or name CA or name C or name O or name CB )) \ or resid 797 through 827 or (resid 854 through 855 and (name N or name CA or na \ me C or name O or name CB )) or resid 856 through 867 or (resid 868 and (name N \ or name CA or name C or name O or name CB )) or resid 869 through 939 or (resid \ 940 and (name N or name CA or name C or name O or name CB )) or resid 941 throug \ h 984 or (resid 985 and (name N or name CA or name C or name O or name CB )) or \ resid 986 through 987 or (resid 988 through 989 and (name N or name CA or name C \ or name O or name CB )) or resid 990 through 1141 or (resid 1142 and (name N or \ name CA or name C or name O or name CB )) or resid 1143 through 1144 or (resid \ 1145 through 1146 and (name N or name CA or name C or name O or name CB )) or re \ sid 1147 through 1308)) selection = (chain 'B' and (resid 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 45 or (resid 46 and (name N or nam \ e CA or name C or name O or name CB )) or resid 47 through 66 or resid 82 throug \ h 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) or re \ sid 89 through 109 or (resid 110 and (name N or name CA or name C or name O or n \ ame CB )) or resid 111 or (resid 112 through 113 and (name N or name CA or name \ C or name O or name CB )) or resid 116 through 128 or (resid 129 and (name N or \ name CA or name C or name O or name CB )) or resid 130 through 134 or (resid 135 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 39 through 140 or resid 166 through 190 or (resid 191 and (name N or name CA or \ name C or name O or name CB )) or resid 192 through 195 or (resid 196 and (name \ N or name CA or name C or name O or name CB )) or resid 200 through 205 or (resi \ d 206 and (name N or name CA or name C or name O or name CB )) or resid 207 thro \ ugh 236 or (resid 237 and (name N or name CA or name C or name O or name CB )) o \ r resid 238 through 241 or (resid 242 through 263 and (name N or name CA or name \ C or name O or name CB )) or resid 265 through 280 or (resid 281 and (name N or \ name CA or name C or name O or name CB )) or resid 282 through 297 or (resid 29 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 299 through \ 323 or (resid 324 and (name N or name CA or name C or name O or name CB )) or re \ sid 325 through 388 or (resid 389 and (name N or name CA or name C or name O or \ name CB )) or resid 390 through 457 or (resid 458 and (name N or name CA or name \ C or name O or name CB )) or resid 459 through 567 or (resid 568 and (name N or \ name CA or name C or name O or name CB )) or resid 569 through 570 or (resid 57 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 572 through \ 579 or (resid 580 and (name N or name CA or name C or name O or name CB )) or re \ sid 581 or (resid 582 through 583 and (name N or name CA or name C or name O or \ name CB )) or resid 584 through 613 or (resid 614 and (name N or name CA or name \ C or name O or name CB )) or resid 615 through 618 or (resid 619 and (name N or \ name CA or name C or name O or name CB )) or resid 620 through 676 or resid 690 \ through 744 or (resid 745 and (name N or name CA or name C or name O or name CB \ )) or resid 746 through 827 or (resid 854 through 855 and (name N or name CA or \ name C or name O or name CB )) or resid 856 through 867 or (resid 868 and (name \ N or name CA or name C or name O or name CB )) or resid 869 through 939 or (res \ id 940 and (name N or name CA or name C or name O or name CB )) or resid 941 thr \ ough 984 or (resid 985 and (name N or name CA or name C or name O or name CB )) \ or resid 986 through 987 or (resid 988 through 989 and (name N or name CA or nam \ e C or name O or name CB )) or resid 990 through 1143 or (resid 1144 through 114 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 1147 through \ 1308)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 through 113 or resid 116 through 134 or (resid 135 through 138 and (name N \ or name CA or name C or name O or name CB )) or resid 139 through 140 or resid 1 \ 66 through 172 or (resid 188 and (name N or name CA or name C or name O or name \ CB )) or resid 189 through 195 or (resid 196 and (name N or name CA or name C or \ name O or name CB )) or resid 200 through 205 or (resid 206 and (name N or name \ CA or name C or name O or name CB )) or resid 207 through 209 or (resid 210 and \ (name N or name CA or name C or name O or name CB )) or resid 215 through 217 o \ r (resid 218 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 19 through 223 or (resid 224 and (name N or name CA or name C or name O or name \ CB )) or resid 225 through 236 or (resid 237 and (name N or name CA or name C or \ name O or name CB )) or resid 238 through 297 or (resid 298 and (name N or name \ CA or name C or name O or name CB )) or resid 299 through 308 or (resid 309 and \ (name N or name CA or name C or name O or name CB )) or resid 310 through 332 o \ r (resid 333 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 34 through 388 or (resid 389 and (name N or name CA or name C or name O or name \ CB )) or resid 390 through 527 or (resid 528 through 529 and (name N or name CA \ or name C or name O or name CB )) or resid 530 through 536 or (resid 537 and (na \ me N or name CA or name C or name O or name CB )) or resid 538 through 553 or (r \ esid 554 and (name N or name CA or name C or name O or name CB )) or resid 555 t \ hrough 557 or (resid 558 and (name N or name CA or name C or name O or name CB ) \ ) or resid 559 through 567 or (resid 568 and (name N or name CA or name C or nam \ e O or name CB )) or resid 569 through 570 or (resid 571 and (name N or name CA \ or name C or name O or name CB )) or resid 572 through 579 or (resid 580 and (na \ me N or name CA or name C or name O or name CB )) or resid 581 or (resid 582 thr \ ough 583 and (name N or name CA or name C or name O or name CB )) or resid 584 t \ hrough 618 or (resid 619 and (name N or name CA or name C or name O or name CB ) \ ) or resid 620 through 645 or (resid 646 through 647 and (name N or name CA or n \ ame C or name O or name CB )) or resid 648 through 795 or (resid 796 and (name N \ or name CA or name C or name O or name CB )) or resid 797 through 1141 or (resi \ d 1142 and (name N or name CA or name C or name O or name CB )) or resid 1143 or \ (resid 1144 through 1146 and (name N or name CA or name C or name O or name CB \ )) or resid 1147 through 1308)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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 group one per residue 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: 12.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.130 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 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 : 0.003 0.040 25682 Z= 0.157 Angle : 0.572 12.253 35113 Z= 0.284 Chirality : 0.045 0.229 4177 Planarity : 0.004 0.038 4439 Dihedral : 11.383 87.534 9710 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.73 % Favored : 96.17 % Rotamer: Outliers : 0.64 % Allowed : 4.13 % Favored : 95.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.15), residues: 3134 helix: 1.07 (0.21), residues: 666 sheet: -0.40 (0.18), residues: 779 loop : -0.75 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 328 TYR 0.017 0.001 TYR A1067 PHE 0.013 0.001 PHE A 318 TRP 0.010 0.001 TRP A 104 HIS 0.002 0.000 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00324 (25592) covalent geometry : angle 0.55585 (34884) SS BOND : bond 0.00241 ( 41) SS BOND : angle 0.67403 ( 82) hydrogen bonds : bond 0.12572 ( 1095) hydrogen bonds : angle 6.93975 ( 2958) link_BETA1-4 : bond 0.00461 ( 11) link_BETA1-4 : angle 1.53647 ( 33) link_NAG-ASN : bond 0.00178 ( 38) link_NAG-ASN : angle 2.31025 ( 114) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 477 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.9038 (t) cc_final: 0.8794 (t) REVERT: A 97 LYS cc_start: 0.6297 (tttt) cc_final: 0.5442 (mmtp) REVERT: A 118 LEU cc_start: 0.9215 (tt) cc_final: 0.8685 (mt) REVERT: A 274 THR cc_start: 0.9118 (m) cc_final: 0.8766 (p) REVERT: A 303 LEU cc_start: 0.8362 (mt) cc_final: 0.8087 (tp) REVERT: A 316 SER cc_start: 0.7096 (m) cc_final: 0.6858 (t) REVERT: A 402 ILE cc_start: 0.8806 (pt) cc_final: 0.8190 (tt) REVERT: A 405 ASP cc_start: 0.8533 (m-30) cc_final: 0.8320 (m-30) REVERT: A 421 TYR cc_start: 0.8940 (m-10) cc_final: 0.8362 (m-10) REVERT: A 423 TYR cc_start: 0.7877 (t80) cc_final: 0.7446 (t80) REVERT: A 471 GLU cc_start: 0.9255 (tt0) cc_final: 0.9041 (tm-30) REVERT: A 497 PHE cc_start: 0.8168 (m-10) cc_final: 0.7348 (m-80) REVERT: A 543 PHE cc_start: 0.8746 (m-80) cc_final: 0.8098 (m-80) REVERT: A 559 PHE cc_start: 0.6603 (m-80) cc_final: 0.5552 (m-10) REVERT: A 560 LEU cc_start: 0.8840 (mt) cc_final: 0.8637 (mm) REVERT: A 979 ASP cc_start: 0.8840 (m-30) cc_final: 0.8618 (m-30) REVERT: B 56 LEU cc_start: 0.8654 (tp) cc_final: 0.8398 (tp) REVERT: B 65 PHE cc_start: 0.8748 (m-80) cc_final: 0.8341 (m-80) REVERT: B 201 PHE cc_start: 0.7776 (t80) cc_final: 0.7288 (t80) REVERT: B 223 LEU cc_start: 0.8665 (mt) cc_final: 0.8429 (mp) REVERT: B 269 TYR cc_start: 0.8160 (m-80) cc_final: 0.7458 (m-80) REVERT: B 342 PHE cc_start: 0.8946 (m-80) cc_final: 0.8720 (t80) REVERT: B 380 TYR cc_start: 0.9029 (m-80) cc_final: 0.8761 (m-80) REVERT: B 451 TYR cc_start: 0.7607 (m-80) cc_final: 0.7255 (m-80) REVERT: B 588 THR cc_start: 0.8669 (m) cc_final: 0.8432 (t) REVERT: B 699 LEU cc_start: 0.8282 (mt) cc_final: 0.8063 (mt) REVERT: C 200 TYR cc_start: 0.8763 (m-80) cc_final: 0.8101 (m-80) REVERT: C 202 LYS cc_start: 0.7609 (mmtt) cc_final: 0.7313 (mppt) REVERT: C 203 ILE cc_start: 0.8898 (mt) cc_final: 0.8575 (mp) REVERT: C 349 SER cc_start: 0.7766 (m) cc_final: 0.7551 (p) REVERT: C 365 TYR cc_start: 0.9082 (m-80) cc_final: 0.8856 (m-80) REVERT: C 388 ASN cc_start: 0.7929 (m110) cc_final: 0.7472 (m-40) REVERT: C 823 PHE cc_start: 0.8164 (m-80) cc_final: 0.7390 (m-10) REVERT: C 864 LEU cc_start: 0.8294 (tp) cc_final: 0.7706 (tt) REVERT: C 967 SER cc_start: 0.9070 (m) cc_final: 0.8699 (t) REVERT: C 1004 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8835 (tt) REVERT: C 1029 MET cc_start: 0.8803 (ttm) cc_final: 0.8580 (ttt) outliers start: 17 outliers final: 5 residues processed: 487 average time/residue: 0.1795 time to fit residues: 137.6280 Evaluate side-chains 253 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 247 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 15 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 30.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN A 641 ASN A 955 ASN B 207 HIS B1054 GLN C 52 GLN C 388 ASN C 460 ASN C 493 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.139264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.092302 restraints weight = 57708.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.093797 restraints weight = 33356.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.094900 restraints weight = 22436.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.095565 restraints weight = 19720.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.095660 restraints weight = 17194.063| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 25682 Z= 0.266 Angle : 0.671 12.666 35113 Z= 0.345 Chirality : 0.047 0.271 4177 Planarity : 0.004 0.050 4439 Dihedral : 6.304 58.677 4441 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.08 % Favored : 95.88 % Rotamer: Outliers : 2.35 % Allowed : 10.11 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.15), residues: 3134 helix: 1.38 (0.20), residues: 673 sheet: -0.27 (0.18), residues: 787 loop : -0.79 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 983 TYR 0.026 0.002 TYR C 495 PHE 0.031 0.002 PHE A 490 TRP 0.012 0.001 TRP B 436 HIS 0.008 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00614 (25592) covalent geometry : angle 0.66161 (34884) SS BOND : bond 0.00264 ( 41) SS BOND : angle 1.16442 ( 82) hydrogen bonds : bond 0.05039 ( 1095) hydrogen bonds : angle 5.90892 ( 2958) link_BETA1-4 : bond 0.00433 ( 11) link_BETA1-4 : angle 1.26128 ( 33) link_NAG-ASN : bond 0.00271 ( 38) link_NAG-ASN : angle 1.85671 ( 114) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 262 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8851 (t0) cc_final: 0.8634 (t0) REVERT: A 97 LYS cc_start: 0.6201 (tttt) cc_final: 0.5358 (mmpt) REVERT: A 274 THR cc_start: 0.9032 (m) cc_final: 0.8708 (p) REVERT: A 303 LEU cc_start: 0.8367 (mt) cc_final: 0.8055 (tp) REVERT: A 402 ILE cc_start: 0.8463 (pt) cc_final: 0.8247 (pt) REVERT: A 421 TYR cc_start: 0.8779 (m-10) cc_final: 0.8378 (m-10) REVERT: A 449 TYR cc_start: 0.8921 (m-80) cc_final: 0.8602 (m-10) REVERT: A 497 PHE cc_start: 0.8219 (m-10) cc_final: 0.7846 (m-80) REVERT: A 740 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.8005 (ttm) REVERT: A 878 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8883 (tt) REVERT: B 49 HIS cc_start: 0.8815 (t70) cc_final: 0.8495 (t-90) REVERT: B 56 LEU cc_start: 0.8876 (tp) cc_final: 0.8652 (tp) REVERT: B 201 PHE cc_start: 0.7833 (t80) cc_final: 0.7572 (t80) REVERT: B 273 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8435 (mmm-85) REVERT: B 380 TYR cc_start: 0.8871 (m-80) cc_final: 0.8470 (m-80) REVERT: B 451 TYR cc_start: 0.7770 (m-80) cc_final: 0.7415 (m-80) REVERT: C 200 TYR cc_start: 0.8658 (m-80) cc_final: 0.8243 (m-10) REVERT: C 380 TYR cc_start: 0.8229 (m-80) cc_final: 0.7827 (m-10) REVERT: C 408 ARG cc_start: 0.8491 (ttp80) cc_final: 0.7900 (tmm160) REVERT: C 699 LEU cc_start: 0.8768 (mp) cc_final: 0.8294 (mt) REVERT: C 1004 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8890 (tt) outliers start: 62 outliers final: 38 residues processed: 307 average time/residue: 0.1673 time to fit residues: 83.7491 Evaluate side-chains 250 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 208 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain H residue 11 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 234 optimal weight: 9.9990 chunk 157 optimal weight: 0.7980 chunk 241 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 158 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 255 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 95 optimal weight: 0.0470 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 ASN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.143044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.096752 restraints weight = 56736.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.097925 restraints weight = 33252.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.098788 restraints weight = 23649.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.099746 restraints weight = 19775.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.099816 restraints weight = 17823.417| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25682 Z= 0.124 Angle : 0.572 12.407 35113 Z= 0.294 Chirality : 0.044 0.183 4177 Planarity : 0.004 0.050 4439 Dihedral : 5.539 55.244 4437 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.90 % Favored : 97.06 % Rotamer: Outliers : 2.20 % Allowed : 12.05 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.15), residues: 3134 helix: 1.86 (0.21), residues: 690 sheet: -0.04 (0.18), residues: 782 loop : -0.64 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 408 TYR 0.024 0.001 TYR C1067 PHE 0.020 0.001 PHE A 490 TRP 0.009 0.001 TRP B 436 HIS 0.007 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00271 (25592) covalent geometry : angle 0.56207 (34884) SS BOND : bond 0.00195 ( 41) SS BOND : angle 1.40010 ( 82) hydrogen bonds : bond 0.04237 ( 1095) hydrogen bonds : angle 5.45528 ( 2958) link_BETA1-4 : bond 0.00410 ( 11) link_BETA1-4 : angle 1.11051 ( 33) link_NAG-ASN : bond 0.00195 ( 38) link_NAG-ASN : angle 1.55772 ( 114) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 243 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8732 (t0) cc_final: 0.8451 (t0) REVERT: A 97 LYS cc_start: 0.6187 (tttt) cc_final: 0.5368 (mmtm) REVERT: A 274 THR cc_start: 0.9123 (m) cc_final: 0.8739 (p) REVERT: A 276 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8335 (tt) REVERT: A 402 ILE cc_start: 0.8519 (pt) cc_final: 0.8228 (tt) REVERT: A 421 TYR cc_start: 0.8808 (m-10) cc_final: 0.8404 (m-10) REVERT: A 497 PHE cc_start: 0.8127 (m-10) cc_final: 0.7401 (m-80) REVERT: A 740 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7869 (ttm) REVERT: A 1029 MET cc_start: 0.9071 (tpp) cc_final: 0.8205 (ttt) REVERT: B 36 VAL cc_start: 0.9032 (t) cc_final: 0.8789 (p) REVERT: B 49 HIS cc_start: 0.8872 (t70) cc_final: 0.8503 (t-90) REVERT: B 56 LEU cc_start: 0.8919 (tp) cc_final: 0.8716 (tp) REVERT: B 201 PHE cc_start: 0.7856 (t80) cc_final: 0.7556 (t80) REVERT: B 223 LEU cc_start: 0.8633 (mp) cc_final: 0.8254 (mp) REVERT: B 273 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8549 (mmm-85) REVERT: B 380 TYR cc_start: 0.8687 (m-80) cc_final: 0.8401 (m-80) REVERT: B 451 TYR cc_start: 0.7453 (m-80) cc_final: 0.7180 (m-80) REVERT: B 517 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9097 (mm) REVERT: C 200 TYR cc_start: 0.8280 (m-80) cc_final: 0.8065 (m-10) REVERT: C 380 TYR cc_start: 0.8170 (m-80) cc_final: 0.7831 (m-10) REVERT: C 408 ARG cc_start: 0.8457 (ttp80) cc_final: 0.8048 (tmm160) REVERT: C 417 LYS cc_start: 0.8793 (mmmt) cc_final: 0.8317 (tptm) REVERT: C 699 LEU cc_start: 0.8620 (mp) cc_final: 0.8162 (mt) REVERT: C 967 SER cc_start: 0.8957 (m) cc_final: 0.8655 (t) REVERT: C 1004 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8832 (tt) REVERT: C 1067 TYR cc_start: 0.9131 (t80) cc_final: 0.8925 (t80) outliers start: 58 outliers final: 28 residues processed: 281 average time/residue: 0.1610 time to fit residues: 74.8960 Evaluate side-chains 240 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 207 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 599 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 858 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain H residue 11 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 182 optimal weight: 3.9990 chunk 267 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 296 optimal weight: 9.9990 chunk 263 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.136182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.086897 restraints weight = 59331.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.090142 restraints weight = 30422.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.092251 restraints weight = 20219.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.093622 restraints weight = 15655.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.094333 restraints weight = 13283.625| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25682 Z= 0.195 Angle : 0.595 11.105 35113 Z= 0.302 Chirality : 0.044 0.211 4177 Planarity : 0.004 0.052 4439 Dihedral : 5.160 52.590 4435 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.80 % Favored : 96.17 % Rotamer: Outliers : 2.84 % Allowed : 12.50 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.15), residues: 3134 helix: 1.82 (0.20), residues: 675 sheet: -0.03 (0.18), residues: 767 loop : -0.63 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 403 TYR 0.032 0.001 TYR C 369 PHE 0.024 0.002 PHE B 374 TRP 0.008 0.001 TRP B 436 HIS 0.006 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00445 (25592) covalent geometry : angle 0.58371 (34884) SS BOND : bond 0.00427 ( 41) SS BOND : angle 1.59935 ( 82) hydrogen bonds : bond 0.04417 ( 1095) hydrogen bonds : angle 5.44818 ( 2958) link_BETA1-4 : bond 0.00490 ( 11) link_BETA1-4 : angle 1.22271 ( 33) link_NAG-ASN : bond 0.00225 ( 38) link_NAG-ASN : angle 1.56138 ( 114) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 216 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8818 (t0) cc_final: 0.8528 (t0) REVERT: A 97 LYS cc_start: 0.6060 (tttt) cc_final: 0.5360 (mmtm) REVERT: A 274 THR cc_start: 0.9154 (m) cc_final: 0.8942 (m) REVERT: A 276 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8368 (tt) REVERT: A 421 TYR cc_start: 0.8772 (m-10) cc_final: 0.8432 (m-10) REVERT: A 585 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7677 (pp) REVERT: B 201 PHE cc_start: 0.7970 (t80) cc_final: 0.7508 (t80) REVERT: B 223 LEU cc_start: 0.8383 (mp) cc_final: 0.8131 (mp) REVERT: B 273 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8720 (mmm-85) REVERT: B 380 TYR cc_start: 0.9124 (m-80) cc_final: 0.8580 (m-80) REVERT: B 451 TYR cc_start: 0.8102 (m-80) cc_final: 0.7619 (m-80) REVERT: B 517 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9047 (mm) REVERT: C 201 PHE cc_start: 0.8076 (t80) cc_final: 0.7862 (t80) REVERT: C 380 TYR cc_start: 0.8237 (m-80) cc_final: 0.7839 (m-10) REVERT: C 417 LYS cc_start: 0.8911 (mmmt) cc_final: 0.8442 (tptp) REVERT: C 699 LEU cc_start: 0.8605 (mp) cc_final: 0.8153 (mt) REVERT: C 823 PHE cc_start: 0.7937 (m-10) cc_final: 0.7721 (m-10) REVERT: C 967 SER cc_start: 0.9060 (m) cc_final: 0.8766 (t) REVERT: C 1004 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8939 (tt) outliers start: 75 outliers final: 47 residues processed: 268 average time/residue: 0.1607 time to fit residues: 71.7417 Evaluate side-chains 245 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 193 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 711 SER 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 858 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1105 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 75 optimal weight: 0.8980 chunk 181 optimal weight: 0.7980 chunk 123 optimal weight: 20.0000 chunk 45 optimal weight: 3.9990 chunk 302 optimal weight: 50.0000 chunk 316 optimal weight: 50.0000 chunk 221 optimal weight: 0.7980 chunk 141 optimal weight: 0.0470 chunk 40 optimal weight: 4.9990 chunk 149 optimal weight: 0.4980 chunk 289 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN C1005 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.137808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.092981 restraints weight = 59250.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.095100 restraints weight = 33051.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.095252 restraints weight = 21382.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.096070 restraints weight = 21013.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.096198 restraints weight = 17572.694| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25682 Z= 0.116 Angle : 0.561 11.209 35113 Z= 0.284 Chirality : 0.044 0.195 4177 Planarity : 0.004 0.052 4439 Dihedral : 4.724 50.746 4433 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.81 % Favored : 97.16 % Rotamer: Outliers : 2.42 % Allowed : 13.56 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.15), residues: 3134 helix: 2.00 (0.21), residues: 669 sheet: 0.08 (0.18), residues: 764 loop : -0.50 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 403 TYR 0.025 0.001 TYR C 904 PHE 0.033 0.001 PHE A 497 TRP 0.012 0.001 TRP B 436 HIS 0.005 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00255 (25592) covalent geometry : angle 0.55085 (34884) SS BOND : bond 0.00181 ( 41) SS BOND : angle 1.55002 ( 82) hydrogen bonds : bond 0.03964 ( 1095) hydrogen bonds : angle 5.21949 ( 2958) link_BETA1-4 : bond 0.00428 ( 11) link_BETA1-4 : angle 1.08383 ( 33) link_NAG-ASN : bond 0.00194 ( 38) link_NAG-ASN : angle 1.37726 ( 114) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 222 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8923 (t0) cc_final: 0.8610 (t0) REVERT: A 97 LYS cc_start: 0.6191 (tttt) cc_final: 0.5342 (mmtm) REVERT: A 274 THR cc_start: 0.9177 (m) cc_final: 0.8755 (p) REVERT: A 276 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8394 (tt) REVERT: A 421 TYR cc_start: 0.8864 (m-10) cc_final: 0.8491 (m-10) REVERT: A 585 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7519 (pp) REVERT: B 36 VAL cc_start: 0.9126 (t) cc_final: 0.8832 (p) REVERT: B 201 PHE cc_start: 0.7979 (t80) cc_final: 0.7496 (t80) REVERT: B 223 LEU cc_start: 0.8642 (mp) cc_final: 0.8211 (mp) REVERT: B 269 TYR cc_start: 0.7413 (m-10) cc_final: 0.6945 (m-80) REVERT: B 273 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8667 (mmm-85) REVERT: B 380 TYR cc_start: 0.9034 (m-80) cc_final: 0.8557 (m-80) REVERT: B 451 TYR cc_start: 0.7402 (m-80) cc_final: 0.7109 (m-80) REVERT: B 517 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9057 (mm) REVERT: C 205 SER cc_start: 0.8968 (OUTLIER) cc_final: 0.8688 (p) REVERT: C 287 ASP cc_start: 0.8731 (t0) cc_final: 0.8516 (t0) REVERT: C 417 LYS cc_start: 0.8974 (mmmt) cc_final: 0.8634 (tptt) REVERT: C 967 SER cc_start: 0.9055 (m) cc_final: 0.8767 (t) REVERT: C 1004 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8920 (tt) outliers start: 64 outliers final: 30 residues processed: 265 average time/residue: 0.1501 time to fit residues: 67.7630 Evaluate side-chains 233 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 197 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1004 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 240 optimal weight: 9.9990 chunk 147 optimal weight: 7.9990 chunk 248 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 307 optimal weight: 50.0000 chunk 155 optimal weight: 4.9990 chunk 261 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN B 935 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN C1002 GLN ** H 32 ASN ** 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 = 0.4070 r_free = 0.4070 target = 0.136779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.087529 restraints weight = 59170.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.090728 restraints weight = 30763.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.092875 restraints weight = 20624.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.094208 restraints weight = 15973.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.094944 restraints weight = 13618.020| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 25682 Z= 0.229 Angle : 0.605 10.370 35113 Z= 0.310 Chirality : 0.044 0.194 4177 Planarity : 0.004 0.053 4439 Dihedral : 4.698 51.238 4433 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.18 % Favored : 95.79 % Rotamer: Outliers : 2.65 % Allowed : 14.05 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.15), residues: 3134 helix: 1.85 (0.20), residues: 665 sheet: -0.08 (0.18), residues: 794 loop : -0.57 (0.15), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 995 TYR 0.033 0.002 TYR C 369 PHE 0.038 0.002 PHE A 497 TRP 0.009 0.001 TRP B 436 HIS 0.006 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00524 (25592) covalent geometry : angle 0.59536 (34884) SS BOND : bond 0.00271 ( 41) SS BOND : angle 1.48388 ( 82) hydrogen bonds : bond 0.04498 ( 1095) hydrogen bonds : angle 5.39169 ( 2958) link_BETA1-4 : bond 0.00285 ( 11) link_BETA1-4 : angle 1.15541 ( 33) link_NAG-ASN : bond 0.00263 ( 38) link_NAG-ASN : angle 1.51160 ( 114) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 194 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8891 (t0) cc_final: 0.8616 (t0) REVERT: A 97 LYS cc_start: 0.6085 (tttt) cc_final: 0.5324 (mmtm) REVERT: A 276 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8353 (tt) REVERT: A 421 TYR cc_start: 0.8851 (m-10) cc_final: 0.8536 (m-10) REVERT: A 585 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7727 (pp) REVERT: A 1029 MET cc_start: 0.9157 (tpp) cc_final: 0.8306 (ttt) REVERT: B 201 PHE cc_start: 0.8062 (t80) cc_final: 0.7586 (t80) REVERT: B 223 LEU cc_start: 0.8498 (mp) cc_final: 0.8273 (mp) REVERT: B 269 TYR cc_start: 0.7356 (m-10) cc_final: 0.6967 (m-80) REVERT: B 273 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.8798 (mmm-85) REVERT: B 380 TYR cc_start: 0.8971 (m-80) cc_final: 0.8496 (m-80) REVERT: B 451 TYR cc_start: 0.8019 (m-80) cc_final: 0.7622 (m-80) REVERT: B 517 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.8996 (mm) REVERT: C 205 SER cc_start: 0.9030 (OUTLIER) cc_final: 0.8781 (p) REVERT: C 380 TYR cc_start: 0.8128 (m-80) cc_final: 0.7687 (m-10) REVERT: C 403 ARG cc_start: 0.7765 (ptt90) cc_final: 0.7253 (ptt180) REVERT: C 408 ARG cc_start: 0.8446 (ttp80) cc_final: 0.7956 (tmm160) REVERT: C 417 LYS cc_start: 0.8975 (mmmt) cc_final: 0.8521 (tptp) REVERT: C 1004 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8961 (tt) outliers start: 70 outliers final: 48 residues processed: 248 average time/residue: 0.1471 time to fit residues: 62.3068 Evaluate side-chains 236 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 182 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1004 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 246 optimal weight: 0.9990 chunk 70 optimal weight: 0.0010 chunk 264 optimal weight: 0.2980 chunk 85 optimal weight: 0.9990 chunk 238 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 81 optimal weight: 0.3980 chunk 248 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.139543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.091248 restraints weight = 58817.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.094577 restraints weight = 29968.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.096780 restraints weight = 19840.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.098127 restraints weight = 15283.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.098860 restraints weight = 12983.344| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25682 Z= 0.105 Angle : 0.549 11.106 35113 Z= 0.278 Chirality : 0.043 0.170 4177 Planarity : 0.004 0.054 4439 Dihedral : 4.367 50.034 4433 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.55 % Favored : 97.42 % Rotamer: Outliers : 2.01 % Allowed : 15.11 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.15), residues: 3134 helix: 2.11 (0.21), residues: 668 sheet: 0.07 (0.18), residues: 774 loop : -0.43 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 995 TYR 0.031 0.001 TYR A 495 PHE 0.020 0.001 PHE A 497 TRP 0.011 0.001 TRP B 436 HIS 0.004 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00225 (25592) covalent geometry : angle 0.54324 (34884) SS BOND : bond 0.00184 ( 41) SS BOND : angle 0.98417 ( 82) hydrogen bonds : bond 0.03863 ( 1095) hydrogen bonds : angle 5.06348 ( 2958) link_BETA1-4 : bond 0.00433 ( 11) link_BETA1-4 : angle 1.02836 ( 33) link_NAG-ASN : bond 0.00217 ( 38) link_NAG-ASN : angle 1.29497 ( 114) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 205 time to evaluate : 0.728 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: A 88 ASP cc_start: 0.8813 (t0) cc_final: 0.8533 (t0) REVERT: A 97 LYS cc_start: 0.6025 (tttt) cc_final: 0.5351 (mmtm) REVERT: A 276 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8312 (tt) REVERT: A 421 TYR cc_start: 0.8799 (m-10) cc_final: 0.8489 (m-10) REVERT: A 585 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7695 (pp) REVERT: A 1029 MET cc_start: 0.9063 (tpp) cc_final: 0.8397 (ttt) REVERT: B 201 PHE cc_start: 0.8006 (t80) cc_final: 0.7589 (t80) REVERT: B 269 TYR cc_start: 0.7249 (m-10) cc_final: 0.6914 (m-80) REVERT: B 380 TYR cc_start: 0.8973 (m-80) cc_final: 0.8462 (m-80) REVERT: B 517 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.8985 (mm) REVERT: C 205 SER cc_start: 0.8968 (OUTLIER) cc_final: 0.8682 (p) REVERT: C 269 TYR cc_start: 0.7868 (m-80) cc_final: 0.7529 (m-80) REVERT: C 408 ARG cc_start: 0.8439 (ttp80) cc_final: 0.7981 (tmm160) REVERT: C 417 LYS cc_start: 0.8945 (mmmt) cc_final: 0.8491 (tptp) REVERT: C 967 SER cc_start: 0.9079 (m) cc_final: 0.8774 (t) REVERT: C 984 LEU cc_start: 0.7938 (tp) cc_final: 0.7591 (tp) REVERT: C 1004 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8850 (tt) outliers start: 53 outliers final: 40 residues processed: 241 average time/residue: 0.1473 time to fit residues: 59.5711 Evaluate side-chains 230 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 185 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1004 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 57 optimal weight: 3.9990 chunk 209 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 303 optimal weight: 6.9990 chunk 207 optimal weight: 20.0000 chunk 3 optimal weight: 0.2980 chunk 81 optimal weight: 1.9990 chunk 312 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 308 optimal weight: 10.0000 chunk 236 optimal weight: 7.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.134224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.083862 restraints weight = 59076.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.086794 restraints weight = 31277.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.088755 restraints weight = 21218.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.089997 restraints weight = 16663.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.090770 restraints weight = 14345.489| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 25682 Z= 0.231 Angle : 0.617 10.516 35113 Z= 0.314 Chirality : 0.045 0.176 4177 Planarity : 0.004 0.054 4439 Dihedral : 4.522 51.963 4433 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.96 % Favored : 96.01 % Rotamer: Outliers : 2.39 % Allowed : 15.27 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.15), residues: 3134 helix: 1.94 (0.21), residues: 652 sheet: -0.08 (0.17), residues: 807 loop : -0.53 (0.15), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 995 TYR 0.032 0.002 TYR C1067 PHE 0.021 0.002 PHE A 515 TRP 0.007 0.001 TRP A1102 HIS 0.012 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00530 (25592) covalent geometry : angle 0.60991 (34884) SS BOND : bond 0.00262 ( 41) SS BOND : angle 1.07261 ( 82) hydrogen bonds : bond 0.04504 ( 1095) hydrogen bonds : angle 5.33173 ( 2958) link_BETA1-4 : bond 0.00281 ( 11) link_BETA1-4 : angle 1.15292 ( 33) link_NAG-ASN : bond 0.00271 ( 38) link_NAG-ASN : angle 1.47448 ( 114) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 183 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8956 (t0) cc_final: 0.8666 (t0) REVERT: A 97 LYS cc_start: 0.6040 (tttt) cc_final: 0.5316 (mmtm) REVERT: A 276 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8367 (tt) REVERT: A 421 TYR cc_start: 0.8792 (m-10) cc_final: 0.8526 (m-10) REVERT: A 585 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7833 (pp) REVERT: A 1029 MET cc_start: 0.9142 (tpp) cc_final: 0.8333 (ttt) REVERT: B 85 PRO cc_start: 0.8272 (Cg_exo) cc_final: 0.8012 (Cg_endo) REVERT: B 201 PHE cc_start: 0.8130 (t80) cc_final: 0.7653 (t80) REVERT: B 380 TYR cc_start: 0.9170 (m-80) cc_final: 0.8571 (m-80) REVERT: B 451 TYR cc_start: 0.8293 (m-80) cc_final: 0.7840 (m-80) REVERT: B 517 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9019 (mm) REVERT: B 702 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7976 (tm-30) REVERT: C 269 TYR cc_start: 0.7888 (m-80) cc_final: 0.7486 (m-80) REVERT: C 380 TYR cc_start: 0.8118 (m-80) cc_final: 0.7869 (m-10) REVERT: C 403 ARG cc_start: 0.7752 (ptt90) cc_final: 0.7291 (ptt180) REVERT: C 408 ARG cc_start: 0.8487 (ttp80) cc_final: 0.7981 (tmm160) REVERT: C 417 LYS cc_start: 0.8974 (mmmt) cc_final: 0.8514 (tptp) REVERT: C 984 LEU cc_start: 0.8114 (tp) cc_final: 0.7777 (tp) REVERT: C 1004 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8960 (tt) outliers start: 63 outliers final: 45 residues processed: 231 average time/residue: 0.1484 time to fit residues: 58.5178 Evaluate side-chains 225 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 175 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1008 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 54 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 156 optimal weight: 0.5980 chunk 81 optimal weight: 0.6980 chunk 125 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 292 optimal weight: 0.9980 chunk 242 optimal weight: 3.9990 chunk 289 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.138011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.089595 restraints weight = 59029.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.092804 restraints weight = 30768.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.094915 restraints weight = 20617.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.096157 restraints weight = 16020.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.097047 restraints weight = 13739.719| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25682 Z= 0.150 Angle : 0.579 10.591 35113 Z= 0.294 Chirality : 0.044 0.171 4177 Planarity : 0.004 0.055 4439 Dihedral : 4.375 50.999 4433 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.19 % Favored : 96.78 % Rotamer: Outliers : 2.08 % Allowed : 15.80 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.15), residues: 3134 helix: 2.09 (0.21), residues: 654 sheet: 0.01 (0.18), residues: 794 loop : -0.47 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 995 TYR 0.030 0.001 TYR C1067 PHE 0.024 0.001 PHE A 515 TRP 0.010 0.001 TRP C 104 HIS 0.013 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00341 (25592) covalent geometry : angle 0.57295 (34884) SS BOND : bond 0.00216 ( 41) SS BOND : angle 0.93380 ( 82) hydrogen bonds : bond 0.04089 ( 1095) hydrogen bonds : angle 5.15147 ( 2958) link_BETA1-4 : bond 0.00373 ( 11) link_BETA1-4 : angle 1.00380 ( 33) link_NAG-ASN : bond 0.00181 ( 38) link_NAG-ASN : angle 1.31604 ( 114) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 184 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8898 (t0) cc_final: 0.8592 (t0) REVERT: A 97 LYS cc_start: 0.6057 (tttt) cc_final: 0.5348 (mmtm) REVERT: A 276 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8362 (tt) REVERT: A 421 TYR cc_start: 0.8783 (m-10) cc_final: 0.8493 (m-10) REVERT: A 585 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7807 (pp) REVERT: A 1029 MET cc_start: 0.9090 (tpp) cc_final: 0.8434 (ttt) REVERT: B 201 PHE cc_start: 0.8114 (t80) cc_final: 0.7616 (t80) REVERT: B 223 LEU cc_start: 0.8257 (mm) cc_final: 0.7251 (mm) REVERT: B 269 TYR cc_start: 0.7155 (m-10) cc_final: 0.6828 (m-80) REVERT: B 380 TYR cc_start: 0.8990 (m-80) cc_final: 0.8528 (m-80) REVERT: B 451 TYR cc_start: 0.7946 (m-80) cc_final: 0.7558 (m-80) REVERT: B 517 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.8957 (mm) REVERT: C 269 TYR cc_start: 0.7891 (m-80) cc_final: 0.7523 (m-80) REVERT: C 408 ARG cc_start: 0.8457 (ttp80) cc_final: 0.7949 (tmm160) REVERT: C 417 LYS cc_start: 0.8961 (mmmt) cc_final: 0.8512 (tptp) REVERT: C 698 SER cc_start: 0.8712 (t) cc_final: 0.8496 (p) REVERT: C 984 LEU cc_start: 0.8091 (tp) cc_final: 0.7730 (tp) REVERT: C 990 GLU cc_start: 0.8279 (tm-30) cc_final: 0.8065 (tm-30) REVERT: C 1004 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8893 (tt) outliers start: 55 outliers final: 41 residues processed: 222 average time/residue: 0.1501 time to fit residues: 56.9024 Evaluate side-chains 226 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 181 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1004 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 156 optimal weight: 0.7980 chunk 303 optimal weight: 30.0000 chunk 312 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 244 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 46 optimal weight: 0.0770 chunk 231 optimal weight: 4.9990 chunk 222 optimal weight: 6.9990 chunk 145 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.135581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.085707 restraints weight = 59047.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.088786 restraints weight = 30958.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.090764 restraints weight = 20850.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.092067 restraints weight = 16253.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.092759 restraints weight = 13994.101| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25682 Z= 0.142 Angle : 0.573 13.962 35113 Z= 0.289 Chirality : 0.044 0.179 4177 Planarity : 0.004 0.056 4439 Dihedral : 4.271 51.276 4433 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.96 % Favored : 96.01 % Rotamer: Outliers : 1.86 % Allowed : 15.83 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.15), residues: 3134 helix: 2.16 (0.21), residues: 653 sheet: 0.04 (0.18), residues: 791 loop : -0.44 (0.15), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 466 TYR 0.032 0.001 TYR C 369 PHE 0.023 0.001 PHE A 515 TRP 0.011 0.001 TRP B 436 HIS 0.010 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00324 (25592) covalent geometry : angle 0.56740 (34884) SS BOND : bond 0.00196 ( 41) SS BOND : angle 0.89451 ( 82) hydrogen bonds : bond 0.04000 ( 1095) hydrogen bonds : angle 5.07356 ( 2958) link_BETA1-4 : bond 0.00322 ( 11) link_BETA1-4 : angle 1.02466 ( 33) link_NAG-ASN : bond 0.00193 ( 38) link_NAG-ASN : angle 1.31462 ( 114) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 183 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8946 (t0) cc_final: 0.8643 (t0) REVERT: A 97 LYS cc_start: 0.6006 (tttt) cc_final: 0.5372 (mmtm) REVERT: A 276 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8380 (tt) REVERT: A 421 TYR cc_start: 0.8743 (m-10) cc_final: 0.8470 (m-10) REVERT: A 585 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7819 (pp) REVERT: A 1029 MET cc_start: 0.9109 (tpp) cc_final: 0.8386 (ttt) REVERT: B 223 LEU cc_start: 0.8361 (mm) cc_final: 0.7481 (mm) REVERT: B 269 TYR cc_start: 0.7173 (m-10) cc_final: 0.6839 (m-80) REVERT: B 380 TYR cc_start: 0.9171 (m-80) cc_final: 0.8611 (m-80) REVERT: B 451 TYR cc_start: 0.8158 (m-80) cc_final: 0.7753 (m-80) REVERT: B 517 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9000 (mm) REVERT: C 269 TYR cc_start: 0.7864 (m-80) cc_final: 0.7515 (m-80) REVERT: C 408 ARG cc_start: 0.8516 (ttp80) cc_final: 0.7976 (tmm160) REVERT: C 417 LYS cc_start: 0.8948 (mmmt) cc_final: 0.8627 (tptt) REVERT: C 698 SER cc_start: 0.8696 (t) cc_final: 0.8479 (p) REVERT: C 984 LEU cc_start: 0.8079 (tp) cc_final: 0.7721 (tp) REVERT: C 1004 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8886 (tt) outliers start: 49 outliers final: 42 residues processed: 220 average time/residue: 0.1454 time to fit residues: 54.7872 Evaluate side-chains 225 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 179 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1004 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 187 optimal weight: 0.2980 chunk 237 optimal weight: 7.9990 chunk 303 optimal weight: 30.0000 chunk 246 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 152 optimal weight: 0.0770 chunk 149 optimal weight: 0.4980 chunk 1 optimal weight: 0.7980 chunk 258 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.136867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.087588 restraints weight = 59350.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.090714 restraints weight = 30762.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.092757 restraints weight = 20479.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.094104 restraints weight = 15926.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.095004 restraints weight = 13652.269| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25682 Z= 0.107 Angle : 0.556 12.689 35113 Z= 0.281 Chirality : 0.043 0.170 4177 Planarity : 0.004 0.056 4439 Dihedral : 4.097 51.246 4433 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.78 % Favored : 97.19 % Rotamer: Outliers : 1.67 % Allowed : 15.98 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.15), residues: 3134 helix: 2.28 (0.21), residues: 657 sheet: 0.05 (0.18), residues: 803 loop : -0.33 (0.16), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 995 TYR 0.023 0.001 TYR C1067 PHE 0.019 0.001 PHE C 374 TRP 0.013 0.001 TRP B 436 HIS 0.009 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00236 (25592) covalent geometry : angle 0.55038 (34884) SS BOND : bond 0.00206 ( 41) SS BOND : angle 0.90623 ( 82) hydrogen bonds : bond 0.03708 ( 1095) hydrogen bonds : angle 4.92837 ( 2958) link_BETA1-4 : bond 0.00382 ( 11) link_BETA1-4 : angle 0.98837 ( 33) link_NAG-ASN : bond 0.00182 ( 38) link_NAG-ASN : angle 1.23185 ( 114) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5103.76 seconds wall clock time: 88 minutes 46.59 seconds (5326.59 seconds total)