Starting phenix.real_space_refine on Mon Jul 6 01:02:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yr2_34043/07_2026/7yr2_34043.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yr2_34043/07_2026/7yr2_34043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yr2_34043/07_2026/7yr2_34043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yr2_34043/07_2026/7yr2_34043.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7yr2_34043/07_2026/7yr2_34043.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yr2_34043/07_2026/7yr2_34043.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yr2_34043/07_2026/7yr2_34043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yr2_34043/07_2026/7yr2_34043.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 S 140 5.16 5 Cl 1 4.86 5 C 20008 2.51 5 N 5142 2.21 5 O 6200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31492 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "D" Number of atoms: 8535 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1097, 8530 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 58, 'TRANS': 1038} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'ARG:plan': 4, 'TYR:plan': 1, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 42 Conformer: "B" Number of residues, atoms: 1097, 8530 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 58, 'TRANS': 1038} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'ARG:plan': 4, 'TYR:plan': 1, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 8729 Chain: "E" Number of atoms: 8540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8540 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 58, 'TRANS': 1038} Chain breaks: 2 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'ARG:plan': 4, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 8536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8536 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 58, 'TRANS': 1038} Chain breaks: 2 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 58 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen chiralities: 15 Chain: "E" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen chiralities: 15 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG D 78 " occ=0.51 ... (8 atoms not shown) pdb=" CB BARG D 78 " occ=0.49 Time building chain proxies: 7.55, per 1000 atoms: 0.24 Number of scatterers: 31492 At special positions: 0 Unit cell: (156, 173.68, 237.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Cl 1 17.00 S 140 16.00 O 6200 8.00 N 5142 7.00 C 20008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.02 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " 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 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 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 B 1 " - " NAG B 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " NAG-ASN " NAG A 903 " - " ASN A 546 " " NAG A 904 " - " ASN A 90 " " NAG A 905 " - " ASN A 322 " " NAG A 906 " - " ASN A 53 " " NAG B 1 " - " ASN D 717 " " NAG C1301 " - " ASN C 61 " " NAG C1311 " - " ASN C 616 " " NAG C1313 " - " ASN C 709 " " NAG C1315 " - " ASN C1134 " " NAG D1301 " - " ASN D 61 " " NAG D1302 " - " ASN D 74 " " NAG D1303 " - " ASN D 122 " " NAG D1304 " - " ASN D 149 " " NAG D1305 " - " ASN D 165 " " NAG D1306 " - " ASN D 234 " " NAG D1307 " - " ASN D 282 " " NAG D1308 " - " ASN D 331 " " NAG D1310 " - " ASN D 603 " " NAG D1311 " - " ASN D 616 " " NAG D1312 " - " ASN D 657 " " NAG D1313 " - " ASN D 709 " " NAG E1301 " - " ASN E 61 " " NAG E1302 " - " ASN E 74 " " NAG E1303 " - " ASN E 122 " " NAG E1304 " - " ASN E 149 " " NAG E1305 " - " ASN E 165 " " NAG E1306 " - " ASN E 234 " " NAG E1307 " - " ASN E 282 " " NAG E1308 " - " ASN E 331 " " NAG E1309 " - " ASN E 343 " " NAG E1310 " - " ASN E 603 " " NAG E1311 " - " ASN E 616 " " NAG E1312 " - " ASN E 657 " " NAG E1313 " - " ASN E 709 " " NAG E1314 " - " ASN E1098 " " NAG E1315 " - " ASN E1134 " " NAG F 1 " - " ASN D 801 " " NAG G 1 " - " ASN D1074 " " NAG H 1 " - " ASN E 717 " " NAG I 1 " - " ASN E 801 " " NAG J 1 " - " ASN E1074 " " NAG K 1 " - " ASN C 717 " " NAG L 1 " - " ASN C 801 " " NAG M 1 " - " ASN C1074 " Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7294 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 53 sheets defined 27.6% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 4.270A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 92 through 101 removed outlier: 3.799A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.841A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 104 through 108' Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 146 through 155 removed outlier: 3.576A pdb=" N ASN A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.692A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 218 through 252 removed outlier: 3.701A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 301 Processing helix chain 'A' and resid 303 through 318 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.744A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 384 Processing helix chain 'A' and resid 399 through 413 Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 446 Processing helix chain 'A' and resid 448 through 466 removed outlier: 4.391A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.119A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.542A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 4.487A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 574 " --> pdb=" O LEU A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix Processing helix chain 'D' and resid 294 through 303 Processing helix chain 'D' and resid 337 through 343 removed outlier: 4.052A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 371 Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 737 through 742 Processing helix chain 'D' and resid 746 through 754 removed outlier: 3.808A pdb=" N LEU D 752 " --> pdb=" O GLU D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 760 through 783 removed outlier: 3.513A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE D 782 " --> pdb=" O THR D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 826 Processing helix chain 'D' and resid 869 through 884 removed outlier: 3.624A pdb=" N THR D 883 " --> pdb=" O ALA D 879 " (cutoff:3.500A) Processing helix chain 'D' and resid 886 through 890 Processing helix chain 'D' and resid 897 through 908 Processing helix chain 'D' and resid 913 through 918 Processing helix chain 'D' and resid 919 through 941 removed outlier: 4.555A pdb=" N GLN D 935 " --> pdb=" O ILE D 931 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP D 936 " --> pdb=" O GLY D 932 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR D 941 " --> pdb=" O SER D 937 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.610A pdb=" N GLN D 965 " --> pdb=" O THR D 961 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 983 Processing helix chain 'D' and resid 985 through 1033 removed outlier: 4.336A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG D 995 " --> pdb=" O VAL D 991 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU D 996 " --> pdb=" O GLN D 992 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN D1002 " --> pdb=" O THR D 998 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 303 removed outlier: 3.533A pdb=" N LEU E 303 " --> pdb=" O THR E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.499A pdb=" N SER E 408 " --> pdb=" O ASN E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 removed outlier: 3.558A pdb=" N TYR E 421 " --> pdb=" O ASN E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 737 through 742 Processing helix chain 'E' and resid 746 through 755 Processing helix chain 'E' and resid 759 through 783 removed outlier: 3.668A pdb=" N LEU E 763 " --> pdb=" O PHE E 759 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR E 778 " --> pdb=" O GLN E 774 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN E 779 " --> pdb=" O ASP E 775 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 826 Processing helix chain 'E' and resid 851 through 855 removed outlier: 3.569A pdb=" N PHE E 855 " --> pdb=" O ALA E 852 " (cutoff:3.500A) Processing helix chain 'E' and resid 869 through 884 Processing helix chain 'E' and resid 886 through 890 Processing helix chain 'E' and resid 897 through 908 Processing helix chain 'E' and resid 912 through 941 removed outlier: 4.401A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS E 921 " --> pdb=" O TYR E 917 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU E 922 " --> pdb=" O GLU E 918 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN E 935 " --> pdb=" O ILE E 931 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP E 936 " --> pdb=" O GLY E 932 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR E 941 " --> pdb=" O SER E 937 " (cutoff:3.500A) Processing helix chain 'E' and resid 945 through 965 removed outlier: 3.552A pdb=" N ASN E 955 " --> pdb=" O VAL E 951 " (cutoff:3.500A) Processing helix chain 'E' and resid 976 through 984 Processing helix chain 'E' and resid 985 through 1032 removed outlier: 4.541A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 366 through 371 removed outlier: 3.668A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.718A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.765A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.604A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 850 through 854 Processing helix chain 'C' and resid 869 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.512A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.637A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 941 removed outlier: 6.998A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.526A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 981 removed outlier: 3.775A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.096A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.945A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA3, first strand: chain 'D' and resid 26 through 30 removed outlier: 4.346A pdb=" N TYR D 265 " --> pdb=" O PHE D 65 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 42 through 43 removed outlier: 3.848A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 50 through 55 removed outlier: 3.747A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 84 through 85 Processing sheet with id=AA7, first strand: chain 'D' and resid 311 through 318 removed outlier: 7.565A pdb=" N VAL D 595 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ASN D 317 " --> pdb=" O GLY D 593 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLY D 593 " --> pdb=" O ASN D 317 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 325 through 326 removed outlier: 3.620A pdb=" N ASN D 542 " --> pdb=" O ILE D 326 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL D 539 " --> pdb=" O GLY D 550 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 356 through 358 Processing sheet with id=AB1, first strand: chain 'D' and resid 361 through 362 removed outlier: 6.632A pdb=" N CYS D 361 " --> pdb=" O CYS D 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 452 through 454 removed outlier: 4.042A pdb=" N TYR D 453 " --> pdb=" O GLN D 493 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 575 through 577 Processing sheet with id=AB4, first strand: chain 'D' and resid 654 through 655 removed outlier: 5.642A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER D 691 " --> pdb=" O GLN D 675 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 702 through 704 Processing sheet with id=AB6, first strand: chain 'D' and resid 711 through 715 removed outlier: 3.550A pdb=" N LYS D1073 " --> pdb=" O ILE D 714 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 718 through 728 removed outlier: 7.324A pdb=" N GLY D1059 " --> pdb=" O SER D1055 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N SER D1055 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL D1061 " --> pdb=" O PRO D1053 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU D1063 " --> pdb=" O SER D1051 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N SER D1051 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL D1065 " --> pdb=" O LEU D1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 733 through 735 removed outlier: 4.395A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 787 through 788 Processing sheet with id=AC1, first strand: chain 'D' and resid 1088 through 1090 Processing sheet with id=AC2, first strand: chain 'E' and resid 28 through 30 removed outlier: 3.528A pdb=" N THR E 63 " --> pdb=" O VAL E 267 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL E 267 " --> pdb=" O THR E 63 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR E 91 " --> pdb=" O GLY E 268 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR E 208 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR E 204 " --> pdb=" O VAL E 193 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 50 through 55 removed outlier: 4.240A pdb=" N ASP E 287 " --> pdb=" O LYS E 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 168 through 169 removed outlier: 3.821A pdb=" N PHE E 168 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE E 106 " --> pdb=" O LEU E 117 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 311 through 319 removed outlier: 7.093A pdb=" N VAL E 595 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASN E 317 " --> pdb=" O GLY E 593 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLY E 593 " --> pdb=" O ASN E 317 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 325 through 326 Processing sheet with id=AC7, first strand: chain 'E' and resid 354 through 358 removed outlier: 4.167A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.352A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'E' and resid 565 through 566 removed outlier: 7.099A pdb=" N PHE E 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'E' and resid 654 through 655 removed outlier: 5.732A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 702 through 704 removed outlier: 3.736A pdb=" N LYS C 790 " --> pdb=" O ASN E 703 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 711 through 715 Processing sheet with id=AD5, first strand: chain 'E' and resid 718 through 727 removed outlier: 7.073A pdb=" N GLY E1059 " --> pdb=" O SER E1055 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N SER E1055 " --> pdb=" O GLY E1059 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL E1061 " --> pdb=" O PRO E1053 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU E1063 " --> pdb=" O SER E1051 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER E1051 " --> pdb=" O LEU E1063 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL E1065 " --> pdb=" O LEU E1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 733 through 735 removed outlier: 4.377A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 1081 through 1082 Processing sheet with id=AD8, first strand: chain 'E' and resid 1094 through 1097 Processing sheet with id=AD9, first strand: chain 'C' and resid 26 through 30 removed outlier: 3.509A pdb=" N SER C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.806A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 168 through 169 removed outlier: 3.943A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C 130 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 201 through 202 removed outlier: 3.781A pdb=" N LEU C 229 " --> pdb=" O PHE C 201 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.323A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 324 through 326 removed outlier: 7.692A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.043A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.366A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.763A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 659 through 660 removed outlier: 4.489A pdb=" N TYR C 660 " --> pdb=" O THR C 696 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 674 through 675 Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AF4, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.012A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF6, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AF7, first strand: chain 'C' and resid 1089 through 1090 Processing sheet with id=AF8, first strand: chain 'C' and resid 1094 through 1097 1073 hydrogen bonds defined for protein. 2991 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.90 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.89 - 1.08: 1 1.08 - 1.27: 5101 1.27 - 1.46: 12806 1.46 - 1.65: 14076 1.65 - 1.85: 189 Bond restraints: 32173 Sorted by residual: bond pdb=" CG PRO A 321 " pdb=" CD PRO A 321 " ideal model delta sigma weight residual 1.503 0.890 0.613 3.40e-02 8.65e+02 3.25e+02 bond pdb=" N PRO A 321 " pdb=" CD PRO A 321 " ideal model delta sigma weight residual 1.473 1.606 -0.133 1.40e-02 5.10e+03 9.02e+01 bond pdb=" CB PRO A 321 " pdb=" CG PRO A 321 " ideal model delta sigma weight residual 1.492 1.846 -0.354 5.00e-02 4.00e+02 5.00e+01 bond pdb=" N PRO A 321 " pdb=" CA PRO A 321 " ideal model delta sigma weight residual 1.466 1.404 0.063 1.17e-02 7.31e+03 2.86e+01 bond pdb=" C1 NAG E1303 " pdb=" O5 NAG E1303 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.19e+01 ... (remaining 32168 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.86: 43738 4.86 - 9.72: 60 9.72 - 14.57: 4 14.57 - 19.43: 1 19.43 - 24.29: 2 Bond angle restraints: 43805 Sorted by residual: angle pdb=" N PRO A 321 " pdb=" CD PRO A 321 " pdb=" CG PRO A 321 " ideal model delta sigma weight residual 103.20 78.91 24.29 1.50e+00 4.44e-01 2.62e+02 angle pdb=" CA PRO A 321 " pdb=" N PRO A 321 " pdb=" CD PRO A 321 " ideal model delta sigma weight residual 112.00 94.34 17.66 1.40e+00 5.10e-01 1.59e+02 angle pdb=" N ASN D 331 " pdb=" CA ASN D 331 " pdb=" C ASN D 331 " ideal model delta sigma weight residual 111.71 97.76 13.95 1.15e+00 7.56e-01 1.47e+02 angle pdb=" CA PRO A 321 " pdb=" CB PRO A 321 " pdb=" CG PRO A 321 " ideal model delta sigma weight residual 104.50 84.26 20.24 1.90e+00 2.77e-01 1.14e+02 angle pdb=" N PRO D 330 " pdb=" CA PRO D 330 " pdb=" C PRO D 330 " ideal model delta sigma weight residual 112.47 125.47 -13.00 2.06e+00 2.36e-01 3.98e+01 ... (remaining 43800 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 16771 17.98 - 35.95: 1467 35.95 - 53.93: 263 53.93 - 71.90: 53 71.90 - 89.88: 39 Dihedral angle restraints: 18593 sinusoidal: 7244 harmonic: 11349 Sorted by residual: dihedral pdb=" CB CYS D 738 " pdb=" SG CYS D 738 " pdb=" SG CYS D 760 " pdb=" CB CYS D 760 " ideal model delta sinusoidal sigma weight residual 93.00 -178.79 -88.21 1 1.00e+01 1.00e-02 9.30e+01 dihedral pdb=" CB CYS E 662 " pdb=" SG CYS E 662 " pdb=" SG CYS E 671 " pdb=" CB CYS E 671 " ideal model delta sinusoidal sigma weight residual -86.00 -2.86 -83.14 1 1.00e+01 1.00e-02 8.45e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual 93.00 21.16 71.84 1 1.00e+01 1.00e-02 6.61e+01 ... (remaining 18590 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 4699 0.090 - 0.181: 363 0.181 - 0.271: 8 0.271 - 0.362: 4 0.362 - 0.452: 5 Chirality restraints: 5079 Sorted by residual: chirality pdb=" C1 NAG D1301 " pdb=" ND2 ASN D 61 " pdb=" C2 NAG D1301 " pdb=" O5 NAG D1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.12e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN E 801 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.00e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN D 801 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.52e+00 ... (remaining 5076 not shown) Planarity restraints: 5639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 320 " -0.112 5.00e-02 4.00e+02 1.52e-01 3.68e+01 pdb=" N PRO A 321 " 0.261 5.00e-02 4.00e+02 pdb=" CA PRO A 321 " -0.078 5.00e-02 4.00e+02 pdb=" CD PRO A 321 " -0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 328 " 0.025 2.00e-02 2.50e+03 5.01e-02 2.51e+01 pdb=" C ARG D 328 " -0.087 2.00e-02 2.50e+03 pdb=" O ARG D 328 " 0.033 2.00e-02 2.50e+03 pdb=" N PHE D 329 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 122 " 0.006 2.00e-02 2.50e+03 3.23e-02 1.30e+01 pdb=" CG ASN D 122 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN D 122 " 0.038 2.00e-02 2.50e+03 pdb=" ND2 ASN D 122 " -0.033 2.00e-02 2.50e+03 pdb=" C1 NAG D1303 " 0.030 2.00e-02 2.50e+03 ... (remaining 5636 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 580 2.66 - 3.22: 29861 3.22 - 3.78: 47600 3.78 - 4.34: 64075 4.34 - 4.90: 105860 Nonbonded interactions: 247976 Sorted by model distance: nonbonded pdb=" OD2 ASP D 737 " pdb=" ND2 ASN C 317 " model vdw 2.101 3.120 nonbonded pdb=" O THR D 393 " pdb=" OG1 THR D 523 " model vdw 2.153 3.040 nonbonded pdb=" OD1 ASN C 122 " pdb=" N ALA C 123 " model vdw 2.156 3.120 nonbonded pdb=" OG SER D 116 " pdb=" O CYS D 131 " model vdw 2.161 3.040 nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 901 " model vdw 2.168 2.230 ... (remaining 247971 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 'B' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } ncs_group { reference = (chain 'C' and (resid 25 through 77 or resid 79 through 189 or (resid 190 and (n \ ame N or name CA or name C or name O or name CB )) or resid 191 through 194 or ( \ resid 195 and (name N or name CA or name C or name O or name CB )) or resid 196 \ through 327 or (resid 328 through 329 and (name N or name CA or name C or name O \ or name CB )) or resid 330 through 1315)) selection = (chain 'D' and (resid 25 through 77 or resid 79 through 95 or (resid 96 and (nam \ e N or name CA or name C or name O or name CB )) or resid 97 through 189 or (res \ id 190 and (name N or name CA or name C or name O or name CB )) or resid 191 thr \ ough 346 or (resid 347 through 348 and (name N or name CA or name C or name O or \ name CB )) or resid 349 through 1315)) selection = (chain 'E' and (resid 25 through 77 or resid 79 through 95 or (resid 96 and (nam \ e N or name CA or name C or name O or name CB )) or resid 97 through 194 or (res \ id 195 and (name N or name CA or name C or name O or name CB )) or resid 196 thr \ ough 327 or (resid 328 through 329 and (name N or name CA or name C or name O or \ name CB )) or resid 330 through 346 or (resid 347 through 348 and (name N or na \ me CA or name C or name O or name CB )) or resid 349 through 1315)) } 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=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.050 Process input model: 32.600 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.080 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.613 32267 Z= 0.217 Angle : 0.714 24.290 44042 Z= 0.374 Chirality : 0.048 0.452 5079 Planarity : 0.005 0.152 5595 Dihedral : 14.231 89.880 11182 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.03 % Favored : 92.79 % Rotamer: Outliers : 0.03 % Allowed : 0.30 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % 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: -1.35 (0.13), residues: 3871 helix: 0.83 (0.17), residues: 1008 sheet: -0.60 (0.20), residues: 592 loop : -1.87 (0.12), residues: 2271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1107 TYR 0.032 0.001 TYR C 495 PHE 0.019 0.001 PHE C 490 TRP 0.041 0.002 TRP A 271 HIS 0.008 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.22 (32173) covalent geometry : angle 0.68665 / 0.37 (43805) SS BOND : bond 0.00290 / 0.17 ( 39) SS BOND : angle 1.34334 / 0.93 ( 78) hydrogen bonds : bond 0.16894 / 11.23 ( 1073) hydrogen bonds : angle 7.20685 / 5.15 ( 2991) metal coordination : bond 0.00017 / 0.01 ( 2) link_BETA1-4 : bond 0.00551 / 0.33 ( 9) link_BETA1-4 : angle 3.29716 / 2.08 ( 27) link_NAG-ASN : bond 0.00736 / 0.56 ( 44) link_NAG-ASN : angle 3.23239 / 2.26 ( 132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 321 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.4352 (ppp) cc_final: 0.2022 (ttt) REVERT: A 249 MET cc_start: 0.1329 (tmm) cc_final: 0.0828 (tmm) REVERT: A 360 MET cc_start: -0.1243 (tpt) cc_final: -0.2029 (ptt) REVERT: A 480 MET cc_start: 0.0779 (mtt) cc_final: 0.0453 (mtt) REVERT: D 578 ASP cc_start: 0.5818 (t0) cc_final: 0.5539 (t0) REVERT: D 950 ASP cc_start: 0.7306 (m-30) cc_final: 0.6965 (m-30) REVERT: E 389 ASP cc_start: 0.7465 (p0) cc_final: 0.7254 (p0) REVERT: E 867 ASP cc_start: 0.7597 (m-30) cc_final: 0.7117 (m-30) REVERT: C 574 ASP cc_start: 0.8257 (t70) cc_final: 0.7493 (t0) REVERT: C 950 ASP cc_start: 0.7682 (m-30) cc_final: 0.7399 (m-30) outliers start: 1 outliers final: 0 residues processed: 321 average time/residue: 0.1539 time to fit residues: 85.1687 Evaluate side-chains 226 residues out of total 3400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.0670 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 0.0670 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN A 154 ASN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 542 ASN D 607 GLN E 450 ASN ** E 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 949 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.200323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.136690 restraints weight = 51206.529| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 3.57 r_work: 0.3542 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3545 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3545 r_free = 0.3545 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3545 r_free = 0.3545 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3545 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32267 Z= 0.119 Angle : 0.622 14.383 44042 Z= 0.310 Chirality : 0.045 0.244 5079 Planarity : 0.004 0.059 5595 Dihedral : 4.321 29.706 4173 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.26 % Favored : 92.68 % Rotamer: Outliers : 0.92 % Allowed : 6.34 % Favored : 92.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.13), residues: 3871 helix: 0.98 (0.17), residues: 1010 sheet: -0.67 (0.20), residues: 583 loop : -1.68 (0.13), residues: 2278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 161 TYR 0.023 0.001 TYR C 495 PHE 0.031 0.001 PHE D 541 TRP 0.031 0.002 TRP A 271 HIS 0.008 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (32173) covalent geometry : angle 0.59512 / 0.30 (43805) SS BOND : bond 0.00257 / 0.15 ( 39) SS BOND : angle 1.21438 / 0.86 ( 78) hydrogen bonds : bond 0.04179 / 2.77 ( 1073) hydrogen bonds : angle 5.74441 / 4.08 ( 2991) metal coordination : bond 0.00124 / 0.06 ( 2) link_BETA1-4 : bond 0.00769 / 0.47 ( 9) link_BETA1-4 : angle 2.87655 / 1.79 ( 27) link_NAG-ASN : bond 0.00465 / 0.32 ( 44) link_NAG-ASN : angle 2.98361 / 2.05 ( 132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 279 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.4122 (ppp) cc_final: 0.2985 (ttt) REVERT: A 323 MET cc_start: -0.1631 (mmm) cc_final: -0.2358 (mtm) REVERT: A 360 MET cc_start: -0.0705 (tpt) cc_final: -0.1383 (ptt) REVERT: D 206 LYS cc_start: 0.6531 (pttm) cc_final: 0.5978 (mtmt) REVERT: D 737 ASP cc_start: 0.8282 (m-30) cc_final: 0.8081 (t70) REVERT: D 902 MET cc_start: 0.8817 (tpp) cc_final: 0.8541 (mmt) REVERT: E 389 ASP cc_start: 0.7921 (p0) cc_final: 0.7659 (p0) REVERT: E 585 LEU cc_start: 0.8319 (pp) cc_final: 0.8083 (pp) REVERT: E 723 THR cc_start: 0.9045 (t) cc_final: 0.8770 (p) REVERT: C 26 GLN cc_start: 0.7735 (tm-30) cc_final: 0.7070 (tm-30) REVERT: C 462 LYS cc_start: 0.8496 (mttp) cc_final: 0.8282 (mmmt) REVERT: C 574 ASP cc_start: 0.8507 (t70) cc_final: 0.7696 (t0) REVERT: C 950 ASP cc_start: 0.8414 (m-30) cc_final: 0.8104 (m-30) outliers start: 31 outliers final: 15 residues processed: 303 average time/residue: 0.1744 time to fit residues: 91.0005 Evaluate side-chains 252 residues out of total 3400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 237 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 660 TYR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 20 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 114 optimal weight: 0.0770 chunk 195 optimal weight: 0.8980 chunk 188 optimal weight: 8.9990 chunk 168 optimal weight: 20.0000 chunk 26 optimal weight: 8.9990 chunk 211 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 299 optimal weight: 0.2980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 ASN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 321 GLN D 542 ASN D 607 GLN ** E 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN C 394 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.200348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.136335 restraints weight = 51193.160| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 3.61 r_work: 0.3536 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3542 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3542 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 32267 Z= 0.113 Angle : 0.592 17.062 44042 Z= 0.291 Chirality : 0.047 0.985 5079 Planarity : 0.004 0.058 5595 Dihedral : 4.182 27.335 4173 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.83 % Favored : 93.15 % Rotamer: Outliers : 1.42 % Allowed : 8.48 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.13), residues: 3871 helix: 1.14 (0.17), residues: 1005 sheet: -0.54 (0.20), residues: 590 loop : -1.70 (0.13), residues: 2276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 161 TYR 0.021 0.001 TYR C 265 PHE 0.017 0.001 PHE D 541 TRP 0.035 0.001 TRP A 271 HIS 0.008 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (32173) covalent geometry : angle 0.56758 / 0.29 (43805) SS BOND : bond 0.00220 / 0.15 ( 39) SS BOND : angle 1.19654 / 0.86 ( 78) hydrogen bonds : bond 0.03725 / 2.46 ( 1073) hydrogen bonds : angle 5.27929 / 3.76 ( 2991) metal coordination : bond 0.00314 / 0.15 ( 2) link_BETA1-4 : bond 0.00640 / 0.40 ( 9) link_BETA1-4 : angle 2.47302 / 1.55 ( 27) link_NAG-ASN : bond 0.00554 / 0.41 ( 44) link_NAG-ASN : angle 2.83965 / 1.89 ( 132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 264 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.4204 (ppp) cc_final: 0.3209 (ttt) REVERT: A 360 MET cc_start: -0.0743 (tpt) cc_final: -0.1472 (ptt) REVERT: D 542 ASN cc_start: 0.6991 (t0) cc_final: 0.6369 (t0) REVERT: D 902 MET cc_start: 0.8834 (tpp) cc_final: 0.8504 (mmt) REVERT: E 389 ASP cc_start: 0.7984 (p0) cc_final: 0.7713 (p0) REVERT: E 420 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.8073 (t0) REVERT: E 451 TYR cc_start: 0.4526 (m-10) cc_final: 0.4152 (m-10) REVERT: E 585 LEU cc_start: 0.8308 (pp) cc_final: 0.8059 (pp) REVERT: C 26 GLN cc_start: 0.7731 (tm-30) cc_final: 0.7341 (tm-30) REVERT: C 950 ASP cc_start: 0.8394 (m-30) cc_final: 0.8082 (m-30) outliers start: 48 outliers final: 28 residues processed: 297 average time/residue: 0.1676 time to fit residues: 86.0898 Evaluate side-chains 262 residues out of total 3400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 233 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 420 ASP Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain E residue 660 TYR Chi-restraints excluded: chain E residue 666 ILE Chi-restraints excluded: chain E residue 1109 PHE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 123 optimal weight: 0.9980 chunk 179 optimal weight: 20.0000 chunk 265 optimal weight: 6.9990 chunk 12 optimal weight: 20.0000 chunk 30 optimal weight: 7.9990 chunk 48 optimal weight: 8.9990 chunk 186 optimal weight: 0.7980 chunk 278 optimal weight: 0.9990 chunk 312 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 332 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 GLN D 607 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 658 ASN E1005 GLN C 183 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.197864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.132585 restraints weight = 50710.033| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 3.69 r_work: 0.3475 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3484 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3484 r_free = 0.3484 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3484 r_free = 0.3484 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3484 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 32267 Z= 0.157 Angle : 0.604 10.477 44042 Z= 0.298 Chirality : 0.045 0.544 5079 Planarity : 0.004 0.060 5595 Dihedral : 4.282 26.848 4173 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.52 % Favored : 92.43 % Rotamer: Outliers : 1.72 % Allowed : 10.20 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.13), residues: 3871 helix: 1.10 (0.17), residues: 1010 sheet: -0.66 (0.20), residues: 589 loop : -1.72 (0.13), residues: 2272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 905 TYR 0.023 0.001 TYR C 265 PHE 0.035 0.001 PHE C 855 TRP 0.032 0.002 TRP A 271 HIS 0.008 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (32173) covalent geometry : angle 0.58339 / 0.29 (43805) SS BOND : bond 0.00286 / 0.20 ( 39) SS BOND : angle 1.36657 / 0.99 ( 78) hydrogen bonds : bond 0.03681 / 2.43 ( 1073) hydrogen bonds : angle 5.15719 / 3.67 ( 2991) metal coordination : bond 0.00401 / 0.20 ( 2) link_BETA1-4 : bond 0.00619 / 0.40 ( 9) link_BETA1-4 : angle 2.34623 / 1.47 ( 27) link_NAG-ASN : bond 0.00424 / 0.30 ( 44) link_NAG-ASN : angle 2.56759 / 1.67 ( 132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 244 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.3923 (ppp) cc_final: 0.2725 (ttt) REVERT: A 323 MET cc_start: -0.1145 (mmm) cc_final: -0.1544 (mtm) REVERT: A 360 MET cc_start: -0.1099 (tpt) cc_final: -0.1977 (ptp) REVERT: D 206 LYS cc_start: 0.6731 (OUTLIER) cc_final: 0.6500 (ptpt) REVERT: D 542 ASN cc_start: 0.7042 (t0) cc_final: 0.6449 (t0) REVERT: D 902 MET cc_start: 0.8895 (tpp) cc_final: 0.8496 (mmt) REVERT: E 389 ASP cc_start: 0.8127 (p0) cc_final: 0.7816 (p0) REVERT: E 451 TYR cc_start: 0.4710 (m-10) cc_final: 0.4289 (m-10) REVERT: E 737 ASP cc_start: 0.8344 (t0) cc_final: 0.8043 (t0) REVERT: C 26 GLN cc_start: 0.7708 (tm-30) cc_final: 0.7265 (tm-30) REVERT: C 394 ASN cc_start: 0.8830 (t0) cc_final: 0.8515 (t0) REVERT: C 462 LYS cc_start: 0.8485 (mmmt) cc_final: 0.8168 (mttp) REVERT: C 867 ASP cc_start: 0.8311 (t0) cc_final: 0.8018 (t0) REVERT: C 950 ASP cc_start: 0.8459 (m-30) cc_final: 0.8137 (m-30) outliers start: 58 outliers final: 40 residues processed: 283 average time/residue: 0.1723 time to fit residues: 82.6520 Evaluate side-chains 264 residues out of total 3400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 223 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 1122 VAL Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 660 TYR Chi-restraints excluded: chain E residue 666 ILE Chi-restraints excluded: chain E residue 869 MET Chi-restraints excluded: chain E residue 1005 GLN Chi-restraints excluded: chain E residue 1097 SER Chi-restraints excluded: chain E residue 1109 PHE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 244 optimal weight: 1.9990 chunk 291 optimal weight: 6.9990 chunk 210 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 118 optimal weight: 7.9990 chunk 225 optimal weight: 0.9990 chunk 347 optimal weight: 2.9990 chunk 220 optimal weight: 9.9990 chunk 293 optimal weight: 5.9990 chunk 370 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 GLN D 506 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 657 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.194548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.126555 restraints weight = 50565.375| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 3.59 r_work: 0.3431 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3437 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 32267 Z= 0.222 Angle : 0.664 9.675 44042 Z= 0.330 Chirality : 0.046 0.280 5079 Planarity : 0.005 0.060 5595 Dihedral : 4.595 28.848 4173 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 1.99 % Allowed : 11.62 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.13), residues: 3871 helix: 0.87 (0.16), residues: 1022 sheet: -0.82 (0.20), residues: 593 loop : -1.81 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 273 TYR 0.029 0.002 TYR C 265 PHE 0.027 0.002 PHE D 855 TRP 0.033 0.002 TRP A 271 HIS 0.008 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.22 (32173) covalent geometry : angle 0.64472 / 0.33 (43805) SS BOND : bond 0.00344 / 0.24 ( 39) SS BOND : angle 1.60469 / 1.16 ( 78) hydrogen bonds : bond 0.03908 / 2.59 ( 1073) hydrogen bonds : angle 5.26419 / 3.75 ( 2991) metal coordination : bond 0.00286 / 0.14 ( 2) link_BETA1-4 : bond 0.00634 / 0.40 ( 9) link_BETA1-4 : angle 2.53539 / 1.58 ( 27) link_NAG-ASN : bond 0.00448 / 0.31 ( 44) link_NAG-ASN : angle 2.51045 / 1.63 ( 132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 236 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.3832 (ppp) cc_final: 0.3103 (ttt) REVERT: A 323 MET cc_start: -0.1523 (mmm) cc_final: -0.1949 (mtm) REVERT: A 360 MET cc_start: -0.1574 (tpt) cc_final: -0.1979 (ptp) REVERT: D 52 GLN cc_start: 0.8565 (tt0) cc_final: 0.8266 (tm-30) REVERT: D 125 ASN cc_start: 0.6876 (t0) cc_final: 0.6620 (t0) REVERT: D 158 ARG cc_start: 0.8330 (ttm170) cc_final: 0.6830 (tpt90) REVERT: D 542 ASN cc_start: 0.7191 (t0) cc_final: 0.6554 (t0) REVERT: E 389 ASP cc_start: 0.8147 (p0) cc_final: 0.7767 (p0) REVERT: E 1005 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8222 (mt0) REVERT: C 26 GLN cc_start: 0.7909 (tm-30) cc_final: 0.7468 (tm-30) REVERT: C 233 ILE cc_start: 0.7162 (OUTLIER) cc_final: 0.6910 (pt) REVERT: C 740 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8506 (ttt) REVERT: C 950 ASP cc_start: 0.8483 (m-30) cc_final: 0.8139 (m-30) outliers start: 67 outliers final: 52 residues processed: 282 average time/residue: 0.1658 time to fit residues: 80.2885 Evaluate side-chains 274 residues out of total 3400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 219 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 1097 SER Chi-restraints excluded: chain D residue 1122 VAL Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 374 PHE Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain E residue 632 THR Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 660 TYR Chi-restraints excluded: chain E residue 666 ILE Chi-restraints excluded: chain E residue 826 VAL Chi-restraints excluded: chain E residue 869 MET Chi-restraints excluded: chain E residue 1005 GLN Chi-restraints excluded: chain E residue 1097 SER Chi-restraints excluded: chain E residue 1109 PHE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 381 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 210 optimal weight: 0.9980 chunk 99 optimal weight: 0.4980 chunk 371 optimal weight: 0.9990 chunk 282 optimal weight: 0.8980 chunk 253 optimal weight: 0.5980 chunk 364 optimal weight: 0.7980 chunk 174 optimal weight: 0.9990 chunk 340 optimal weight: 4.9990 chunk 6 optimal weight: 0.0770 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 506 GLN D 607 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 926 GLN E1005 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.198182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.130806 restraints weight = 50345.526| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 3.41 r_work: 0.3497 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 32267 Z= 0.112 Angle : 0.588 13.201 44042 Z= 0.290 Chirality : 0.044 0.257 5079 Planarity : 0.004 0.061 5595 Dihedral : 4.277 27.119 4173 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.70 % Favored : 92.27 % Rotamer: Outliers : 1.78 % Allowed : 12.54 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.13), residues: 3871 helix: 1.20 (0.17), residues: 1010 sheet: -0.62 (0.20), residues: 585 loop : -1.76 (0.13), residues: 2276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 273 TYR 0.022 0.001 TYR C 265 PHE 0.025 0.001 PHE C 133 TRP 0.027 0.001 TRP A 271 HIS 0.006 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (32173) covalent geometry : angle 0.56714 / 0.29 (43805) SS BOND : bond 0.00251 / 0.16 ( 39) SS BOND : angle 1.15533 / 0.84 ( 78) hydrogen bonds : bond 0.03410 / 2.25 ( 1073) hydrogen bonds : angle 5.04423 / 3.61 ( 2991) metal coordination : bond 0.00037 / 0.02 ( 2) link_BETA1-4 : bond 0.00622 / 0.39 ( 9) link_BETA1-4 : angle 2.42092 / 1.52 ( 27) link_NAG-ASN : bond 0.00477 / 0.34 ( 44) link_NAG-ASN : angle 2.57343 / 1.78 ( 132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 242 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.3833 (ppp) cc_final: 0.2938 (ttt) REVERT: A 323 MET cc_start: -0.1304 (mmm) cc_final: -0.1664 (mtm) REVERT: A 360 MET cc_start: -0.1842 (tpt) cc_final: -0.2447 (ptp) REVERT: D 92 PHE cc_start: 0.7095 (OUTLIER) cc_final: 0.6827 (t80) REVERT: D 125 ASN cc_start: 0.7337 (t0) cc_final: 0.6997 (t0) REVERT: D 190 ARG cc_start: 0.6002 (ttt90) cc_final: 0.5547 (ttm-80) REVERT: D 542 ASN cc_start: 0.7286 (t0) cc_final: 0.6715 (t0) REVERT: D 902 MET cc_start: 0.8809 (tpp) cc_final: 0.8486 (mmt) REVERT: E 41 LYS cc_start: 0.7910 (tptm) cc_final: 0.7242 (tptm) REVERT: E 389 ASP cc_start: 0.8124 (p0) cc_final: 0.7783 (p0) REVERT: E 409 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8463 (tt0) REVERT: E 1005 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8217 (mm-40) REVERT: C 26 GLN cc_start: 0.7665 (tm-30) cc_final: 0.7089 (tm-30) REVERT: C 462 LYS cc_start: 0.8568 (mmmt) cc_final: 0.8095 (mttp) REVERT: C 950 ASP cc_start: 0.8410 (m-30) cc_final: 0.8077 (m-30) outliers start: 60 outliers final: 37 residues processed: 289 average time/residue: 0.1677 time to fit residues: 82.6937 Evaluate side-chains 261 residues out of total 3400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 221 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 92 PHE Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 1097 SER Chi-restraints excluded: chain D residue 1122 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 409 GLN Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain E residue 632 THR Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 660 TYR Chi-restraints excluded: chain E residue 1005 GLN Chi-restraints excluded: chain E residue 1097 SER Chi-restraints excluded: chain E residue 1109 PHE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 211 optimal weight: 3.9990 chunk 197 optimal weight: 8.9990 chunk 259 optimal weight: 0.5980 chunk 372 optimal weight: 3.9990 chunk 128 optimal weight: 0.4980 chunk 350 optimal weight: 0.6980 chunk 305 optimal weight: 0.9990 chunk 47 optimal weight: 20.0000 chunk 357 optimal weight: 3.9990 chunk 318 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 506 GLN D 607 GLN D 955 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 GLN ** E 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.197263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.130034 restraints weight = 50629.356| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 3.43 r_work: 0.3489 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3496 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3496 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 32267 Z= 0.125 Angle : 0.587 10.329 44042 Z= 0.289 Chirality : 0.045 0.501 5079 Planarity : 0.004 0.062 5595 Dihedral : 4.235 27.172 4173 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.70 % Favored : 92.27 % Rotamer: Outliers : 2.02 % Allowed : 12.63 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.13), residues: 3871 helix: 1.27 (0.17), residues: 1004 sheet: -0.60 (0.20), residues: 601 loop : -1.72 (0.13), residues: 2266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 273 TYR 0.021 0.001 TYR C 265 PHE 0.024 0.001 PHE C 133 TRP 0.025 0.001 TRP E 64 HIS 0.006 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (32173) covalent geometry : angle 0.56665 / 0.28 (43805) SS BOND : bond 0.00271 / 0.18 ( 39) SS BOND : angle 1.22168 / 0.89 ( 78) hydrogen bonds : bond 0.03409 / 2.23 ( 1073) hydrogen bonds : angle 4.94899 / 3.54 ( 2991) metal coordination : bond 0.00067 / 0.03 ( 2) link_BETA1-4 : bond 0.00611 / 0.38 ( 9) link_BETA1-4 : angle 2.28201 / 1.43 ( 27) link_NAG-ASN : bond 0.00311 / 0.20 ( 44) link_NAG-ASN : angle 2.53997 / 1.72 ( 132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 235 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.3746 (ppp) cc_final: 0.2953 (ttt) REVERT: A 323 MET cc_start: -0.1486 (mmm) cc_final: -0.1855 (mtm) REVERT: A 360 MET cc_start: -0.1973 (tpt) cc_final: -0.2591 (ptp) REVERT: D 92 PHE cc_start: 0.7259 (OUTLIER) cc_final: 0.6880 (t80) REVERT: D 158 ARG cc_start: 0.8313 (ttm170) cc_final: 0.6754 (tmt-80) REVERT: D 190 ARG cc_start: 0.6096 (ttt90) cc_final: 0.5653 (ttm-80) REVERT: D 542 ASN cc_start: 0.7196 (t0) cc_final: 0.6611 (t0) REVERT: E 389 ASP cc_start: 0.8097 (p0) cc_final: 0.7728 (p0) REVERT: E 409 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8505 (tt0) REVERT: E 1005 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8322 (mm-40) REVERT: C 26 GLN cc_start: 0.7688 (tm-30) cc_final: 0.7151 (tm-30) REVERT: C 950 ASP cc_start: 0.8416 (m-30) cc_final: 0.8069 (m-30) outliers start: 68 outliers final: 49 residues processed: 288 average time/residue: 0.1785 time to fit residues: 87.7472 Evaluate side-chains 277 residues out of total 3400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 225 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 92 PHE Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 1122 VAL Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 409 GLN Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain E residue 632 THR Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 660 TYR Chi-restraints excluded: chain E residue 931 ILE Chi-restraints excluded: chain E residue 1005 GLN Chi-restraints excluded: chain E residue 1097 SER Chi-restraints excluded: chain E residue 1109 PHE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 285 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 250 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 257 optimal weight: 0.9990 chunk 197 optimal weight: 6.9990 chunk 195 optimal weight: 0.9980 chunk 188 optimal weight: 7.9990 chunk 304 optimal weight: 0.8980 chunk 344 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1005 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.196744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.129279 restraints weight = 50310.074| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 3.56 r_work: 0.3471 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3477 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 32267 Z= 0.133 Angle : 0.586 10.464 44042 Z= 0.290 Chirality : 0.044 0.256 5079 Planarity : 0.004 0.062 5595 Dihedral : 4.228 27.107 4173 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.63 % Favored : 92.35 % Rotamer: Outliers : 1.78 % Allowed : 12.95 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.13), residues: 3871 helix: 1.30 (0.17), residues: 1004 sheet: -0.64 (0.20), residues: 610 loop : -1.72 (0.13), residues: 2257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E1107 TYR 0.023 0.001 TYR C 265 PHE 0.022 0.001 PHE C 133 TRP 0.024 0.001 TRP E 64 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (32173) covalent geometry : angle 0.56961 / 0.29 (43805) SS BOND : bond 0.00413 / 0.27 ( 39) SS BOND : angle 1.23262 / 0.89 ( 78) hydrogen bonds : bond 0.03400 / 2.23 ( 1073) hydrogen bonds : angle 4.92998 / 3.53 ( 2991) metal coordination : bond 0.00104 / 0.05 ( 2) link_BETA1-4 : bond 0.00565 / 0.35 ( 9) link_BETA1-4 : angle 2.23455 / 1.40 ( 27) link_NAG-ASN : bond 0.00313 / 0.21 ( 44) link_NAG-ASN : angle 2.26356 / 1.47 ( 132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 245 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.3747 (ppp) cc_final: 0.2858 (mtt) REVERT: A 323 MET cc_start: -0.1241 (mmm) cc_final: -0.1683 (mtm) REVERT: A 360 MET cc_start: -0.2329 (tpt) cc_final: -0.3074 (ptp) REVERT: D 158 ARG cc_start: 0.8296 (ttm170) cc_final: 0.6822 (tmt-80) REVERT: D 190 ARG cc_start: 0.6211 (ttt90) cc_final: 0.5868 (ttm-80) REVERT: D 542 ASN cc_start: 0.7288 (t0) cc_final: 0.6706 (t0) REVERT: E 41 LYS cc_start: 0.7874 (tptm) cc_final: 0.7155 (tptm) REVERT: E 389 ASP cc_start: 0.8214 (p0) cc_final: 0.7838 (p0) REVERT: E 409 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8488 (tt0) REVERT: E 462 LYS cc_start: 0.8461 (mmmm) cc_final: 0.7777 (mtpt) REVERT: E 740 MET cc_start: 0.8824 (tpp) cc_final: 0.8595 (tpp) REVERT: C 26 GLN cc_start: 0.7708 (tm-30) cc_final: 0.7353 (tm-30) REVERT: C 105 ILE cc_start: 0.7852 (OUTLIER) cc_final: 0.7167 (pt) REVERT: C 462 LYS cc_start: 0.8520 (mmmt) cc_final: 0.8055 (mttp) REVERT: C 950 ASP cc_start: 0.8410 (m-30) cc_final: 0.8055 (m-30) outliers start: 60 outliers final: 52 residues processed: 293 average time/residue: 0.1767 time to fit residues: 87.6755 Evaluate side-chains 290 residues out of total 3400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 236 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 1122 VAL Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 409 GLN Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain E residue 632 THR Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 660 TYR Chi-restraints excluded: chain E residue 931 ILE Chi-restraints excluded: chain E residue 1005 GLN Chi-restraints excluded: chain E residue 1097 SER Chi-restraints excluded: chain E residue 1107 ARG Chi-restraints excluded: chain E residue 1109 PHE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 467 ASP Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 336 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 157 optimal weight: 0.0370 chunk 180 optimal weight: 2.9990 chunk 145 optimal weight: 0.6980 chunk 319 optimal weight: 0.7980 chunk 102 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 379 optimal weight: 0.9980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 GLN E1005 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.197518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.130188 restraints weight = 50446.060| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 3.56 r_work: 0.3484 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3492 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3492 r_free = 0.3492 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3492 r_free = 0.3492 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3492 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32267 Z= 0.111 Angle : 0.576 10.753 44042 Z= 0.285 Chirality : 0.044 0.256 5079 Planarity : 0.004 0.063 5595 Dihedral : 4.162 26.882 4173 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.37 % Favored : 92.61 % Rotamer: Outliers : 1.66 % Allowed : 13.31 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.13), residues: 3871 helix: 1.36 (0.17), residues: 1003 sheet: -0.62 (0.20), residues: 612 loop : -1.71 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E1107 TYR 0.021 0.001 TYR C 265 PHE 0.024 0.001 PHE C 133 TRP 0.020 0.001 TRP E 64 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (32173) covalent geometry : angle 0.56033 / 0.28 (43805) SS BOND : bond 0.00238 / 0.16 ( 39) SS BOND : angle 1.14113 / 0.82 ( 78) hydrogen bonds : bond 0.03299 / 2.16 ( 1073) hydrogen bonds : angle 4.88019 / 3.50 ( 2991) metal coordination : bond 0.00106 / 0.05 ( 2) link_BETA1-4 : bond 0.00582 / 0.36 ( 9) link_BETA1-4 : angle 2.19128 / 1.37 ( 27) link_NAG-ASN : bond 0.00326 / 0.22 ( 44) link_NAG-ASN : angle 2.20965 / 1.44 ( 132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 242 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.3736 (ppp) cc_final: 0.2848 (mtt) REVERT: A 323 MET cc_start: -0.1217 (mmm) cc_final: -0.1464 (mtm) REVERT: A 360 MET cc_start: -0.2742 (tpt) cc_final: -0.3496 (ptp) REVERT: D 158 ARG cc_start: 0.8337 (ttm170) cc_final: 0.6788 (tmt-80) REVERT: D 190 ARG cc_start: 0.6058 (ttt90) cc_final: 0.5693 (mtp85) REVERT: D 542 ASN cc_start: 0.7151 (t0) cc_final: 0.6934 (t0) REVERT: E 41 LYS cc_start: 0.7841 (tptm) cc_final: 0.7141 (tptm) REVERT: E 389 ASP cc_start: 0.8173 (p0) cc_final: 0.7794 (p0) REVERT: E 409 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8456 (tt0) REVERT: E 462 LYS cc_start: 0.8465 (mmmm) cc_final: 0.7788 (mtpt) REVERT: C 26 GLN cc_start: 0.7651 (tm-30) cc_final: 0.7293 (tm-30) REVERT: C 105 ILE cc_start: 0.7866 (OUTLIER) cc_final: 0.7161 (pt) REVERT: C 462 LYS cc_start: 0.8488 (mmmt) cc_final: 0.8060 (mttp) REVERT: C 950 ASP cc_start: 0.8393 (m-30) cc_final: 0.8044 (m-30) outliers start: 56 outliers final: 47 residues processed: 286 average time/residue: 0.1845 time to fit residues: 89.5534 Evaluate side-chains 280 residues out of total 3400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 231 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 1122 VAL Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 409 GLN Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain E residue 632 THR Chi-restraints excluded: chain E residue 660 TYR Chi-restraints excluded: chain E residue 931 ILE Chi-restraints excluded: chain E residue 1005 GLN Chi-restraints excluded: chain E residue 1097 SER Chi-restraints excluded: chain E residue 1109 PHE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 40 optimal weight: 3.9990 chunk 321 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 276 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 274 optimal weight: 1.9990 chunk 341 optimal weight: 0.5980 chunk 328 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 GLN E1005 GLN C 185 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.194730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.127077 restraints weight = 50121.943| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 3.54 r_work: 0.3441 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3447 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3447 r_free = 0.3447 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3447 r_free = 0.3447 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3447 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 32267 Z= 0.176 Angle : 0.621 10.790 44042 Z= 0.307 Chirality : 0.045 0.256 5079 Planarity : 0.004 0.063 5595 Dihedral : 4.351 27.608 4173 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.35 % Favored : 91.62 % Rotamer: Outliers : 1.69 % Allowed : 13.54 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.13), residues: 3871 helix: 1.24 (0.17), residues: 1003 sheet: -0.73 (0.20), residues: 616 loop : -1.75 (0.13), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 273 TYR 0.024 0.001 TYR E 451 PHE 0.028 0.002 PHE C 133 TRP 0.022 0.002 TRP E 64 HIS 0.006 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (32173) covalent geometry : angle 0.60475 / 0.30 (43805) SS BOND : bond 0.00310 / 0.21 ( 39) SS BOND : angle 1.40904 / 1.01 ( 78) hydrogen bonds : bond 0.03529 / 2.32 ( 1073) hydrogen bonds : angle 4.95696 / 3.54 ( 2991) metal coordination : bond 0.00093 / 0.04 ( 2) link_BETA1-4 : bond 0.00545 / 0.35 ( 9) link_BETA1-4 : angle 2.20136 / 1.37 ( 27) link_NAG-ASN : bond 0.00344 / 0.23 ( 44) link_NAG-ASN : angle 2.26719 / 1.48 ( 132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 241 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.3737 (ppp) cc_final: 0.2881 (mtt) REVERT: A 323 MET cc_start: -0.1298 (mmm) cc_final: -0.1555 (mtm) REVERT: A 360 MET cc_start: -0.2948 (tpt) cc_final: -0.3369 (ptp) REVERT: D 158 ARG cc_start: 0.8297 (ttm170) cc_final: 0.6831 (tpt90) REVERT: D 190 ARG cc_start: 0.6581 (ttt90) cc_final: 0.6183 (ttm-80) REVERT: D 542 ASN cc_start: 0.7421 (t0) cc_final: 0.6867 (t0) REVERT: E 41 LYS cc_start: 0.7954 (tptm) cc_final: 0.7210 (tptm) REVERT: E 389 ASP cc_start: 0.8227 (p0) cc_final: 0.7819 (p0) REVERT: E 409 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8522 (tt0) REVERT: E 462 LYS cc_start: 0.8503 (mmmm) cc_final: 0.7849 (mtpt) REVERT: E 1005 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8189 (mt0) REVERT: C 26 GLN cc_start: 0.7702 (tm-30) cc_final: 0.7367 (tm-30) REVERT: C 950 ASP cc_start: 0.8390 (m-30) cc_final: 0.8045 (m-30) outliers start: 57 outliers final: 49 residues processed: 287 average time/residue: 0.1731 time to fit residues: 84.0339 Evaluate side-chains 278 residues out of total 3400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 227 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 1097 SER Chi-restraints excluded: chain D residue 1122 VAL Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 409 GLN Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain E residue 632 THR Chi-restraints excluded: chain E residue 660 TYR Chi-restraints excluded: chain E residue 931 ILE Chi-restraints excluded: chain E residue 1005 GLN Chi-restraints excluded: chain E residue 1097 SER Chi-restraints excluded: chain E residue 1109 PHE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 265 optimal weight: 1.9990 chunk 235 optimal weight: 2.9990 chunk 257 optimal weight: 0.8980 chunk 203 optimal weight: 2.9990 chunk 333 optimal weight: 5.9990 chunk 24 optimal weight: 30.0000 chunk 359 optimal weight: 0.8980 chunk 51 optimal weight: 20.0000 chunk 344 optimal weight: 0.9980 chunk 251 optimal weight: 0.9980 chunk 353 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 505 HIS E1005 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.196011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.128680 restraints weight = 50375.084| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 3.55 r_work: 0.3463 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3470 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3470 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32267 Z= 0.123 Angle : 0.594 11.507 44042 Z= 0.294 Chirality : 0.044 0.256 5079 Planarity : 0.004 0.063 5595 Dihedral : 4.266 27.097 4173 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.42 % Favored : 92.55 % Rotamer: Outliers : 1.63 % Allowed : 13.69 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.13), residues: 3871 helix: 1.31 (0.17), residues: 1008 sheet: -0.62 (0.20), residues: 613 loop : -1.74 (0.13), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 273 TYR 0.024 0.001 TYR C 265 PHE 0.025 0.001 PHE D 543 TRP 0.019 0.001 TRP A 48 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (32173) covalent geometry : angle 0.57865 / 0.29 (43805) SS BOND : bond 0.00254 / 0.17 ( 39) SS BOND : angle 1.17584 / 0.85 ( 78) hydrogen bonds : bond 0.03328 / 2.18 ( 1073) hydrogen bonds : angle 4.89332 / 3.51 ( 2991) metal coordination : bond 0.00036 / 0.02 ( 2) link_BETA1-4 : bond 0.00565 / 0.35 ( 9) link_BETA1-4 : angle 2.21178 / 1.38 ( 27) link_NAG-ASN : bond 0.00317 / 0.21 ( 44) link_NAG-ASN : angle 2.21030 / 1.45 ( 132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10861.08 seconds wall clock time: 185 minutes 40.13 seconds (11140.13 seconds total)