Starting phenix.real_space_refine on Fri Mar 6 07:59:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sc1_25008/03_2026/7sc1_25008.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sc1_25008/03_2026/7sc1_25008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sc1_25008/03_2026/7sc1_25008.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sc1_25008/03_2026/7sc1_25008.map" model { file = "/net/cci-nas-00/data/ceres_data/7sc1_25008/03_2026/7sc1_25008.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sc1_25008/03_2026/7sc1_25008.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 18711 2.51 5 N 4851 2.21 5 O 5727 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29415 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7896 Classifications: {'peptide': 1011} Link IDs: {'PTRANS': 54, 'TRANS': 956} Chain breaks: 7 Chain: "H" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 890 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "L" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 809 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "B" Number of atoms: 7896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7896 Classifications: {'peptide': 1011} Link IDs: {'PTRANS': 54, 'TRANS': 956} Chain breaks: 7 Chain: "M" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 890 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "N" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 809 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "C" Number of atoms: 7896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7896 Classifications: {'peptide': 1011} Link IDs: {'PTRANS': 54, 'TRANS': 956} Chain breaks: 7 Chain: "P" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 890 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "Q" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 809 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "A" 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 dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "B" 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 dihedrals: 45 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 dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Time building chain proxies: 6.55, per 1000 atoms: 0.22 Number of scatterers: 29415 At special positions: 0 Unit cell: (142.272, 143.936, 212.992, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 126 16.00 O 5727 8.00 N 4851 7.00 C 18711 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " 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 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=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 603 " " NAG A1309 " - " ASN A 616 " " NAG A1310 " - " ASN A 657 " " NAG A1311 " - " ASN A 709 " " NAG A1312 " - " ASN A 717 " " NAG A1313 " - " ASN A1074 " " NAG A1314 " - " ASN A1098 " " NAG A1315 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 603 " " NAG B1309 " - " ASN B 616 " " NAG B1310 " - " ASN B 657 " " NAG B1311 " - " ASN B 709 " " NAG B1312 " - " ASN B 717 " " NAG B1313 " - " ASN B1074 " " NAG B1314 " - " ASN B1098 " " NAG B1315 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 603 " " NAG C1309 " - " ASN C 616 " " NAG C1310 " - " ASN C 657 " " NAG C1311 " - " ASN C 709 " " NAG C1312 " - " ASN C 717 " " NAG C1313 " - " ASN C1074 " " NAG C1314 " - " ASN C1098 " " NAG C1315 " - " ASN C1134 " Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 1.3 seconds 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6888 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 64 sheets defined 21.7% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 371 Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.395A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.948A pdb=" N ASN A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.642A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.359A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.215A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.102A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.800A pdb=" N ASN H 32 " --> pdb=" O VAL H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.755A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 371 Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.387A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.960A pdb=" N ASN B 422 " --> pdb=" O ILE B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.596A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.643A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.341A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.329A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.097A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.747A pdb=" N ASN M 32 " --> pdb=" O VAL M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 75 No H-bonds generated for 'chain 'M' and resid 73 through 75' Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.736A pdb=" N THR M 87 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 364 through 371 Processing helix chain 'C' and resid 383 through 388 removed outlier: 4.381A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.921A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.637A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.327A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 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 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.221A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.137A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 32 removed outlier: 3.871A pdb=" N ASN P 32 " --> pdb=" O VAL P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 73 through 75 No H-bonds generated for 'chain 'P' and resid 73 through 75' Processing helix chain 'P' and resid 83 through 87 removed outlier: 3.737A pdb=" N THR P 87 " --> pdb=" O ALA P 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.738A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.206A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.611A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.860A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.849A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.565A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.592A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.852A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.833A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.038A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 734 removed outlier: 4.346A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC2, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.588A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 58 through 59 removed outlier: 5.463A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR H 90 " --> pdb=" O THR H 107 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 6 through 7 removed outlier: 4.054A pdb=" N THR L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.866A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.668A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC8, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.164A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.172A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 141 through 142 removed outlier: 5.682A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.864A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.578A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.590A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 512 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.862A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.086A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD9, first strand: chain 'B' and resid 718 through 728 Processing sheet with id=AE1, first strand: chain 'B' and resid 718 through 728 Processing sheet with id=AE2, first strand: chain 'B' and resid 733 through 734 removed outlier: 4.309A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE5, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.590A pdb=" N GLN M 3 " --> pdb=" O SER M 25 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 58 through 59 removed outlier: 5.466A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA M 88 " --> pdb=" O VAL M 109 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR M 90 " --> pdb=" O THR M 107 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR M 107 " --> pdb=" O TYR M 90 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 6 through 7 removed outlier: 4.061A pdb=" N THR N 22 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.860A pdb=" N GLU N 105 " --> pdb=" O LEU N 11 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR N 102 " --> pdb=" O TYR N 86 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.716A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.149A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.625A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.869A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.832A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.522A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.585A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C 512 " --> pdb=" O ASP C 398 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.870A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.066A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AG2, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.799A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 718 through 728 Processing sheet with id=AG4, first strand: chain 'C' and resid 733 through 734 removed outlier: 4.331A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AG6, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AG7, first strand: chain 'P' and resid 3 through 7 removed outlier: 3.586A pdb=" N GLN P 3 " --> pdb=" O SER P 25 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'P' and resid 58 through 59 removed outlier: 5.467A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA P 88 " --> pdb=" O VAL P 109 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR P 90 " --> pdb=" O THR P 107 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR P 107 " --> pdb=" O TYR P 90 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Q' and resid 6 through 7 removed outlier: 4.045A pdb=" N THR Q 22 " --> pdb=" O SER Q 7 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Q' and resid 10 through 13 removed outlier: 3.874A pdb=" N GLU Q 105 " --> pdb=" O LEU Q 11 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR Q 102 " --> pdb=" O TYR Q 86 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) 1083 hydrogen bonds defined for protein. 3012 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.61 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9361 1.34 - 1.46: 6074 1.46 - 1.58: 14469 1.58 - 1.70: 0 1.70 - 1.81: 159 Bond restraints: 30063 Sorted by residual: bond pdb=" C1 NAG A1305 " pdb=" O5 NAG A1305 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C1 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C1 NAG C1305 " pdb=" O5 NAG C1305 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C LEU C 223 " pdb=" N GLU C 224 " ideal model delta sigma weight residual 1.331 1.381 -0.050 2.07e-02 2.33e+03 5.91e+00 bond pdb=" CB ASN B 777 " pdb=" CG ASN B 777 " ideal model delta sigma weight residual 1.516 1.457 0.059 2.50e-02 1.60e+03 5.58e+00 ... (remaining 30058 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 39820 1.75 - 3.51: 934 3.51 - 5.26: 111 5.26 - 7.01: 18 7.01 - 8.76: 7 Bond angle restraints: 40890 Sorted by residual: angle pdb=" N GLY C 857 " pdb=" CA GLY C 857 " pdb=" C GLY C 857 " ideal model delta sigma weight residual 114.48 109.15 5.33 1.19e+00 7.06e-01 2.00e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 114.75 -4.05 1.22e+00 6.72e-01 1.10e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 114.64 -3.94 1.22e+00 6.72e-01 1.04e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 114.17 -3.47 1.22e+00 6.72e-01 8.11e+00 angle pdb=" CB MET P 34 " pdb=" CG MET P 34 " pdb=" SD MET P 34 " ideal model delta sigma weight residual 112.70 120.99 -8.29 3.00e+00 1.11e-01 7.64e+00 ... (remaining 40885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.65: 17289 24.65 - 49.30: 870 49.30 - 73.94: 147 73.94 - 98.59: 44 98.59 - 123.24: 109 Dihedral angle restraints: 18459 sinusoidal: 7731 harmonic: 10728 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -165.85 79.85 1 1.00e+01 1.00e-02 7.91e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -165.66 79.66 1 1.00e+01 1.00e-02 7.88e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual -86.00 -157.70 71.70 1 1.00e+01 1.00e-02 6.58e+01 ... (remaining 18456 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 4386 0.090 - 0.180: 371 0.180 - 0.270: 13 0.270 - 0.360: 0 0.360 - 0.450: 3 Chirality restraints: 4773 Sorted by residual: chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.07e+00 chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.92e+00 chirality pdb=" C1 NAG C1304 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG C1304 " pdb=" O5 NAG C1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.87e+00 ... (remaining 4770 not shown) Planarity restraints: 5271 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 526 " 0.036 5.00e-02 4.00e+02 5.37e-02 4.62e+00 pdb=" N PRO B 527 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 527 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 527 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 84 " -0.032 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO A 85 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 85 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 85 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR C 881 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.37e+00 pdb=" C THR C 881 " 0.032 2.00e-02 2.50e+03 pdb=" O THR C 881 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE C 882 " -0.011 2.00e-02 2.50e+03 ... (remaining 5268 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1260 2.72 - 3.26: 29537 3.26 - 3.81: 47622 3.81 - 4.35: 57909 4.35 - 4.90: 100555 Nonbonded interactions: 236883 Sorted by model distance: nonbonded pdb=" O GLU A 661 " pdb=" OH TYR A 695 " model vdw 2.169 3.040 nonbonded pdb=" OG SER N 9 " pdb=" O GLY N 101 " model vdw 2.184 3.040 nonbonded pdb=" OG SER Q 9 " pdb=" O GLY Q 101 " model vdw 2.185 3.040 nonbonded pdb=" OG SER L 9 " pdb=" O GLY L 101 " model vdw 2.188 3.040 nonbonded pdb=" O GLU B 661 " pdb=" OH TYR B 695 " model vdw 2.193 3.040 ... (remaining 236878 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'P' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 28.720 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 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 : 0.006 0.077 30147 Z= 0.255 Angle : 0.676 12.137 41103 Z= 0.337 Chirality : 0.048 0.450 4773 Planarity : 0.004 0.054 5226 Dihedral : 18.119 123.238 11454 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.06 % Allowed : 0.28 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.13), residues: 3645 helix: 1.29 (0.19), residues: 693 sheet: -0.52 (0.17), residues: 960 loop : -0.85 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1039 TYR 0.023 0.001 TYR C 873 PHE 0.032 0.002 PHE A 906 TRP 0.024 0.002 TRP A 64 HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00598 (30063) covalent geometry : angle 0.63386 (40890) SS BOND : bond 0.00315 ( 39) SS BOND : angle 1.59694 ( 78) hydrogen bonds : bond 0.19977 ( 1049) hydrogen bonds : angle 8.91451 ( 3012) link_NAG-ASN : bond 0.00696 ( 45) link_NAG-ASN : angle 3.98961 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 194 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 GLN cc_start: 0.6895 (tp-100) cc_final: 0.6170 (tp40) REVERT: A 987 PRO cc_start: 0.7980 (Cg_exo) cc_final: 0.7748 (Cg_endo) REVERT: B 917 TYR cc_start: 0.8118 (m-10) cc_final: 0.7827 (m-10) REVERT: C 104 TRP cc_start: 0.7660 (m-90) cc_final: 0.7245 (m-90) REVERT: C 239 GLN cc_start: 0.6732 (tp-100) cc_final: 0.6062 (tp40) REVERT: P 34 MET cc_start: 0.1282 (mmm) cc_final: 0.1073 (mmm) outliers start: 2 outliers final: 1 residues processed: 194 average time/residue: 0.1670 time to fit residues: 55.3955 Evaluate side-chains 151 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 675 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 6.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 935 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 81 ASN B 690 GLN B 774 GLN B 804 GLN B 935 GLN N 37 GLN C 52 GLN C 239 GLN ** C 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C1106 GLN Q 37 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.222369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.126439 restraints weight = 39689.782| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 3.61 r_work: 0.3341 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.0812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 30147 Z= 0.184 Angle : 0.655 11.741 41103 Z= 0.317 Chirality : 0.049 0.430 4773 Planarity : 0.004 0.047 5226 Dihedral : 15.228 110.696 4920 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.37 % Allowed : 5.82 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.13), residues: 3645 helix: 1.46 (0.19), residues: 690 sheet: -0.55 (0.16), residues: 1005 loop : -0.91 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1039 TYR 0.027 0.001 TYR A1067 PHE 0.020 0.002 PHE B1121 TRP 0.024 0.002 TRP A 64 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00435 (30063) covalent geometry : angle 0.61586 (40890) SS BOND : bond 0.00264 ( 39) SS BOND : angle 1.23999 ( 78) hydrogen bonds : bond 0.04484 ( 1049) hydrogen bonds : angle 6.24249 ( 3012) link_NAG-ASN : bond 0.00733 ( 45) link_NAG-ASN : angle 3.85481 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 163 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 987 PRO cc_start: 0.8183 (Cg_exo) cc_final: 0.7941 (Cg_endo) REVERT: A 1135 ASN cc_start: 0.8098 (t0) cc_final: 0.7831 (t0) REVERT: C 663 ASP cc_start: 0.8713 (m-30) cc_final: 0.8452 (m-30) REVERT: C 675 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7377 (pp30) REVERT: C 987 PRO cc_start: 0.8165 (Cg_exo) cc_final: 0.7831 (Cg_endo) outliers start: 12 outliers final: 9 residues processed: 174 average time/residue: 0.1677 time to fit residues: 50.5698 Evaluate side-chains 148 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 68 optimal weight: 0.0670 chunk 134 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 289 optimal weight: 0.6980 chunk 191 optimal weight: 0.0570 chunk 273 optimal weight: 4.9990 chunk 352 optimal weight: 30.0000 chunk 96 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 282 optimal weight: 50.0000 chunk 235 optimal weight: 3.9990 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 762 GLN A1088 HIS H 39 GLN B1088 HIS M 39 GLN C 388 ASN C 675 GLN ** C 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C1088 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.224795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.127914 restraints weight = 40030.800| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 3.75 r_work: 0.3405 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 30147 Z= 0.121 Angle : 0.586 11.543 41103 Z= 0.281 Chirality : 0.046 0.413 4773 Planarity : 0.004 0.048 5226 Dihedral : 11.448 110.623 4920 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.65 % Allowed : 8.28 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.13), residues: 3645 helix: 1.77 (0.19), residues: 687 sheet: -0.51 (0.15), residues: 1062 loop : -0.85 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 190 TYR 0.020 0.001 TYR A1067 PHE 0.014 0.001 PHE A 192 TRP 0.017 0.001 TRP A 64 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00276 (30063) covalent geometry : angle 0.54918 (40890) SS BOND : bond 0.00425 ( 39) SS BOND : angle 1.12102 ( 78) hydrogen bonds : bond 0.03815 ( 1049) hydrogen bonds : angle 5.54090 ( 3012) link_NAG-ASN : bond 0.00730 ( 45) link_NAG-ASN : angle 3.54064 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 987 PRO cc_start: 0.8043 (Cg_exo) cc_final: 0.7785 (Cg_endo) REVERT: A 1135 ASN cc_start: 0.8065 (t0) cc_final: 0.7786 (t0) REVERT: B 190 ARG cc_start: 0.5478 (mtm180) cc_final: 0.5025 (mtt180) REVERT: B 1111 GLU cc_start: 0.8583 (tp30) cc_final: 0.8309 (tt0) REVERT: C 63 THR cc_start: 0.6990 (m) cc_final: 0.6743 (m) REVERT: C 663 ASP cc_start: 0.8663 (m-30) cc_final: 0.8392 (m-30) REVERT: C 934 ILE cc_start: 0.7972 (mm) cc_final: 0.7758 (mm) REVERT: C 987 PRO cc_start: 0.8169 (Cg_exo) cc_final: 0.7846 (Cg_endo) outliers start: 21 outliers final: 10 residues processed: 176 average time/residue: 0.1591 time to fit residues: 49.2110 Evaluate side-chains 146 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 149 optimal weight: 20.0000 chunk 290 optimal weight: 5.9990 chunk 33 optimal weight: 50.0000 chunk 323 optimal weight: 4.9990 chunk 196 optimal weight: 0.6980 chunk 313 optimal weight: 0.5980 chunk 349 optimal weight: 40.0000 chunk 110 optimal weight: 50.0000 chunk 150 optimal weight: 9.9990 chunk 332 optimal weight: 0.6980 chunk 47 optimal weight: 0.1980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN P 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.223137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.125683 restraints weight = 39493.494| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 3.16 r_work: 0.3355 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 30147 Z= 0.157 Angle : 0.595 11.351 41103 Z= 0.285 Chirality : 0.046 0.407 4773 Planarity : 0.004 0.048 5226 Dihedral : 9.869 109.535 4917 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.84 % Allowed : 9.31 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.13), residues: 3645 helix: 1.72 (0.19), residues: 687 sheet: -0.48 (0.16), residues: 1038 loop : -0.84 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1039 TYR 0.020 0.001 TYR A1067 PHE 0.020 0.001 PHE C 192 TRP 0.018 0.001 TRP A 64 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00376 (30063) covalent geometry : angle 0.55569 (40890) SS BOND : bond 0.00163 ( 39) SS BOND : angle 1.07514 ( 78) hydrogen bonds : bond 0.03740 ( 1049) hydrogen bonds : angle 5.36388 ( 3012) link_NAG-ASN : bond 0.00682 ( 45) link_NAG-ASN : angle 3.67060 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 556 ASN cc_start: 0.8697 (t0) cc_final: 0.8427 (t0) REVERT: A 987 PRO cc_start: 0.8099 (Cg_exo) cc_final: 0.7823 (Cg_endo) REVERT: A 1135 ASN cc_start: 0.8251 (t0) cc_final: 0.7922 (t0) REVERT: B 190 ARG cc_start: 0.5656 (mtm180) cc_final: 0.5208 (mtt180) REVERT: B 563 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8175 (tt0) REVERT: B 1111 GLU cc_start: 0.8845 (tp30) cc_final: 0.8546 (tt0) REVERT: C 63 THR cc_start: 0.7357 (m) cc_final: 0.7076 (m) REVERT: C 556 ASN cc_start: 0.8732 (t0) cc_final: 0.8470 (t0) REVERT: C 902 MET cc_start: 0.8380 (tpp) cc_final: 0.8130 (mmt) REVERT: C 934 ILE cc_start: 0.8256 (mm) cc_final: 0.8009 (mm) REVERT: C 987 PRO cc_start: 0.8182 (Cg_exo) cc_final: 0.7860 (Cg_endo) REVERT: C 1050 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8503 (mtp) outliers start: 27 outliers final: 16 residues processed: 175 average time/residue: 0.1676 time to fit residues: 51.3596 Evaluate side-chains 159 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain M residue 100 MET Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 178 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 179 optimal weight: 0.3980 chunk 202 optimal weight: 0.0970 chunk 152 optimal weight: 30.0000 chunk 304 optimal weight: 0.0020 chunk 48 optimal weight: 4.9990 chunk 357 optimal weight: 30.0000 chunk 229 optimal weight: 6.9990 chunk 317 optimal weight: 1.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.228876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.132504 restraints weight = 41132.875| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 4.82 r_work: 0.3368 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 30147 Z= 0.109 Angle : 0.559 11.072 41103 Z= 0.266 Chirality : 0.045 0.397 4773 Planarity : 0.004 0.048 5226 Dihedral : 9.256 107.670 4917 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.96 % Allowed : 10.58 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.13), residues: 3645 helix: 1.84 (0.19), residues: 693 sheet: -0.42 (0.15), residues: 1059 loop : -0.77 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1039 TYR 0.019 0.001 TYR B1067 PHE 0.020 0.001 PHE C 192 TRP 0.015 0.001 TRP A 64 HIS 0.003 0.000 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00249 (30063) covalent geometry : angle 0.52075 (40890) SS BOND : bond 0.00241 ( 39) SS BOND : angle 1.08731 ( 78) hydrogen bonds : bond 0.03398 ( 1049) hydrogen bonds : angle 5.09486 ( 3012) link_NAG-ASN : bond 0.00645 ( 45) link_NAG-ASN : angle 3.51741 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 556 ASN cc_start: 0.8601 (t0) cc_final: 0.8348 (t0) REVERT: A 987 PRO cc_start: 0.8015 (Cg_exo) cc_final: 0.7780 (Cg_endo) REVERT: A 1031 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7838 (mt-10) REVERT: A 1111 GLU cc_start: 0.8705 (tp30) cc_final: 0.8335 (tt0) REVERT: A 1135 ASN cc_start: 0.8111 (t0) cc_final: 0.7814 (t0) REVERT: B 63 THR cc_start: 0.7255 (m) cc_final: 0.6917 (m) REVERT: B 190 ARG cc_start: 0.5345 (mtm180) cc_final: 0.4944 (mtt180) REVERT: B 563 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.8131 (tt0) REVERT: B 663 ASP cc_start: 0.8488 (m-30) cc_final: 0.8188 (m-30) REVERT: B 1111 GLU cc_start: 0.8676 (tp30) cc_final: 0.8375 (tt0) REVERT: M 100 MET cc_start: 0.0878 (OUTLIER) cc_final: -0.0413 (tpt) REVERT: C 556 ASN cc_start: 0.8621 (t0) cc_final: 0.8384 (t0) REVERT: C 663 ASP cc_start: 0.8676 (m-30) cc_final: 0.8321 (m-30) REVERT: C 902 MET cc_start: 0.8313 (tpp) cc_final: 0.8085 (mmt) REVERT: C 934 ILE cc_start: 0.7903 (mm) cc_final: 0.7617 (mm) REVERT: C 987 PRO cc_start: 0.8149 (Cg_exo) cc_final: 0.7808 (Cg_endo) REVERT: C 1050 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8457 (mtp) REVERT: P 100 MET cc_start: 0.0414 (ptm) cc_final: -0.0689 (tpp) outliers start: 31 outliers final: 18 residues processed: 185 average time/residue: 0.1637 time to fit residues: 53.1506 Evaluate side-chains 166 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain M residue 100 MET Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 242 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 226 optimal weight: 50.0000 chunk 220 optimal weight: 3.9990 chunk 20 optimal weight: 0.0370 chunk 10 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 334 optimal weight: 3.9990 chunk 327 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 overall best weight: 1.3660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN C 81 ASN C 239 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.223339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.125090 restraints weight = 39540.831| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 3.05 r_work: 0.3374 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30147 Z= 0.148 Angle : 0.576 10.843 41103 Z= 0.274 Chirality : 0.045 0.396 4773 Planarity : 0.004 0.048 5226 Dihedral : 8.930 105.339 4917 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.37 % Allowed : 11.02 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.13), residues: 3645 helix: 1.84 (0.19), residues: 687 sheet: -0.38 (0.16), residues: 1056 loop : -0.79 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 983 TYR 0.019 0.001 TYR A1067 PHE 0.017 0.001 PHE B1121 TRP 0.018 0.001 TRP A 64 HIS 0.002 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00352 (30063) covalent geometry : angle 0.53741 (40890) SS BOND : bond 0.00170 ( 39) SS BOND : angle 0.99266 ( 78) hydrogen bonds : bond 0.03502 ( 1049) hydrogen bonds : angle 5.09481 ( 3012) link_NAG-ASN : bond 0.00612 ( 45) link_NAG-ASN : angle 3.59924 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 154 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 556 ASN cc_start: 0.8721 (t0) cc_final: 0.8458 (t0) REVERT: A 1031 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8244 (mt-10) REVERT: A 1111 GLU cc_start: 0.8926 (tp30) cc_final: 0.8522 (tt0) REVERT: A 1135 ASN cc_start: 0.8284 (t0) cc_final: 0.7945 (t0) REVERT: B 63 THR cc_start: 0.7345 (m) cc_final: 0.6960 (m) REVERT: B 190 ARG cc_start: 0.5419 (mtm180) cc_final: 0.4976 (mtt180) REVERT: B 563 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8149 (tt0) REVERT: B 590 CYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7342 (m) REVERT: B 987 PRO cc_start: 0.8224 (Cg_exo) cc_final: 0.7960 (Cg_endo) REVERT: B 1111 GLU cc_start: 0.8899 (tp30) cc_final: 0.8554 (tt0) REVERT: M 100 MET cc_start: 0.1106 (OUTLIER) cc_final: -0.0037 (tpt) REVERT: C 556 ASN cc_start: 0.8722 (t0) cc_final: 0.8454 (t0) REVERT: C 643 PHE cc_start: 0.8351 (t80) cc_final: 0.7688 (t80) REVERT: C 661 GLU cc_start: 0.8474 (mt-10) cc_final: 0.7969 (mp0) REVERT: C 934 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7819 (mm) REVERT: C 1050 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8670 (mtp) REVERT: P 100 MET cc_start: 0.0483 (ptm) cc_final: -0.0665 (tpp) outliers start: 44 outliers final: 25 residues processed: 189 average time/residue: 0.1613 time to fit residues: 53.3946 Evaluate side-chains 168 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain M residue 100 MET Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 243 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 365 optimal weight: 8.9990 chunk 230 optimal weight: 9.9990 chunk 236 optimal weight: 10.0000 chunk 158 optimal weight: 50.0000 chunk 253 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 364 optimal weight: 7.9990 chunk 191 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.211943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.120970 restraints weight = 39470.525| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.82 r_work: 0.3257 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.117 30147 Z= 0.444 Angle : 0.790 11.565 41103 Z= 0.390 Chirality : 0.054 0.379 4773 Planarity : 0.005 0.052 5226 Dihedral : 9.353 107.191 4917 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.56 % Allowed : 11.64 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.13), residues: 3645 helix: 0.92 (0.19), residues: 693 sheet: -0.76 (0.16), residues: 1035 loop : -0.98 (0.13), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1039 TYR 0.032 0.002 TYR A1067 PHE 0.034 0.003 PHE C 238 TRP 0.027 0.002 TRP A 64 HIS 0.005 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.01079 (30063) covalent geometry : angle 0.75028 (40890) SS BOND : bond 0.00622 ( 39) SS BOND : angle 1.30931 ( 78) hydrogen bonds : bond 0.04881 ( 1049) hydrogen bonds : angle 5.80107 ( 3012) link_NAG-ASN : bond 0.00806 ( 45) link_NAG-ASN : angle 4.29911 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 159 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 190 ARG cc_start: 0.5769 (mtm180) cc_final: 0.5233 (mtt180) REVERT: B 563 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8265 (tt0) REVERT: B 987 PRO cc_start: 0.8333 (Cg_exo) cc_final: 0.8044 (Cg_endo) REVERT: B 1138 TYR cc_start: 0.7658 (t80) cc_final: 0.7353 (t80) REVERT: M 100 MET cc_start: 0.0897 (OUTLIER) cc_final: 0.0424 (ptm) REVERT: C 556 ASN cc_start: 0.8771 (t0) cc_final: 0.8494 (t0) REVERT: C 661 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8102 (mp0) REVERT: C 663 ASP cc_start: 0.8951 (m-30) cc_final: 0.8679 (m-30) REVERT: P 100 MET cc_start: 0.0213 (ptm) cc_final: -0.0914 (tpp) outliers start: 50 outliers final: 29 residues processed: 196 average time/residue: 0.1765 time to fit residues: 59.2351 Evaluate side-chains 173 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain M residue 100 MET Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1105 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 84 optimal weight: 3.9990 chunk 176 optimal weight: 0.7980 chunk 309 optimal weight: 0.9990 chunk 326 optimal weight: 0.9990 chunk 305 optimal weight: 0.9980 chunk 263 optimal weight: 0.9980 chunk 217 optimal weight: 0.6980 chunk 365 optimal weight: 40.0000 chunk 208 optimal weight: 0.7980 chunk 268 optimal weight: 7.9990 chunk 129 optimal weight: 0.0870 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.222320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.125702 restraints weight = 39444.396| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 3.38 r_work: 0.3379 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 30147 Z= 0.123 Angle : 0.593 11.428 41103 Z= 0.286 Chirality : 0.045 0.385 4773 Planarity : 0.004 0.049 5226 Dihedral : 8.897 104.892 4917 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.15 % Allowed : 12.51 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.13), residues: 3645 helix: 1.63 (0.19), residues: 669 sheet: -0.58 (0.16), residues: 1050 loop : -0.90 (0.13), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 237 TYR 0.021 0.001 TYR B1067 PHE 0.023 0.001 PHE C 192 TRP 0.015 0.001 TRP A 64 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00283 (30063) covalent geometry : angle 0.55316 (40890) SS BOND : bond 0.00187 ( 39) SS BOND : angle 1.42103 ( 78) hydrogen bonds : bond 0.03576 ( 1049) hydrogen bonds : angle 5.23585 ( 3012) link_NAG-ASN : bond 0.00610 ( 45) link_NAG-ASN : angle 3.64164 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 190 ARG cc_start: 0.5582 (mtm180) cc_final: 0.5175 (mtt180) REVERT: B 563 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8140 (tt0) REVERT: B 590 CYS cc_start: 0.8417 (OUTLIER) cc_final: 0.7352 (m) REVERT: B 902 MET cc_start: 0.8409 (tpt) cc_final: 0.8164 (tpt) REVERT: B 987 PRO cc_start: 0.8416 (Cg_exo) cc_final: 0.8210 (Cg_endo) REVERT: M 100 MET cc_start: 0.0836 (OUTLIER) cc_final: 0.0630 (ptm) REVERT: C 556 ASN cc_start: 0.8620 (t0) cc_final: 0.8386 (t0) REVERT: C 661 GLU cc_start: 0.8340 (mt-10) cc_final: 0.7973 (mp0) REVERT: C 878 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8068 (tp) REVERT: P 100 MET cc_start: 0.0676 (ptm) cc_final: -0.0673 (tpt) outliers start: 37 outliers final: 27 residues processed: 178 average time/residue: 0.1681 time to fit residues: 52.1161 Evaluate side-chains 166 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain M residue 100 MET Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 73 optimal weight: 1.9990 chunk 179 optimal weight: 0.9980 chunk 42 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 200 optimal weight: 0.6980 chunk 297 optimal weight: 0.5980 chunk 215 optimal weight: 3.9990 chunk 93 optimal weight: 0.0000 chunk 1 optimal weight: 1.9990 chunk 305 optimal weight: 0.6980 chunk 346 optimal weight: 8.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.223768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.128392 restraints weight = 39860.729| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 3.69 r_work: 0.3346 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 30147 Z= 0.109 Angle : 0.566 11.022 41103 Z= 0.270 Chirality : 0.045 0.376 4773 Planarity : 0.004 0.049 5226 Dihedral : 8.492 101.213 4917 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.09 % Allowed : 12.26 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.13), residues: 3645 helix: 1.85 (0.19), residues: 672 sheet: -0.46 (0.16), residues: 1044 loop : -0.83 (0.13), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 102 TYR 0.019 0.001 TYR B1067 PHE 0.018 0.001 PHE C 192 TRP 0.015 0.001 TRP B 104 HIS 0.002 0.000 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00252 (30063) covalent geometry : angle 0.52792 (40890) SS BOND : bond 0.00165 ( 39) SS BOND : angle 1.03241 ( 78) hydrogen bonds : bond 0.03307 ( 1049) hydrogen bonds : angle 4.90944 ( 3012) link_NAG-ASN : bond 0.00607 ( 45) link_NAG-ASN : angle 3.52102 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 164 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 583 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7866 (pm20) REVERT: A 811 LYS cc_start: 0.8236 (mttt) cc_final: 0.7594 (ttpp) REVERT: B 190 ARG cc_start: 0.5495 (mtm180) cc_final: 0.5062 (mtt180) REVERT: B 556 ASN cc_start: 0.8636 (t0) cc_final: 0.8408 (t0) REVERT: B 563 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8047 (mt0) REVERT: B 583 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.8056 (pm20) REVERT: B 590 CYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7360 (m) REVERT: B 643 PHE cc_start: 0.7959 (t80) cc_final: 0.7753 (t80) REVERT: B 661 GLU cc_start: 0.8179 (mp0) cc_final: 0.7972 (mt-10) REVERT: B 987 PRO cc_start: 0.8378 (Cg_exo) cc_final: 0.8127 (Cg_endo) REVERT: B 1111 GLU cc_start: 0.8772 (tp30) cc_final: 0.8534 (tt0) REVERT: C 556 ASN cc_start: 0.8633 (t0) cc_final: 0.8401 (t0) REVERT: C 661 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8001 (mp0) REVERT: C 878 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8060 (mt) REVERT: C 934 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7774 (mm) REVERT: C 988 GLU cc_start: 0.8538 (pm20) cc_final: 0.8324 (pm20) REVERT: P 100 MET cc_start: 0.0520 (ptm) cc_final: -0.0787 (tpt) outliers start: 35 outliers final: 25 residues processed: 193 average time/residue: 0.1495 time to fit residues: 50.0030 Evaluate side-chains 178 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 233 optimal weight: 20.0000 chunk 83 optimal weight: 6.9990 chunk 341 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 362 optimal weight: 50.0000 chunk 37 optimal weight: 30.0000 chunk 363 optimal weight: 8.9990 chunk 249 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.218947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.124759 restraints weight = 39427.221| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 3.77 r_work: 0.3264 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 30147 Z= 0.282 Angle : 0.668 11.194 41103 Z= 0.326 Chirality : 0.049 0.365 4773 Planarity : 0.004 0.053 5226 Dihedral : 8.646 101.355 4917 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.06 % Allowed : 12.61 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.13), residues: 3645 helix: 1.30 (0.19), residues: 693 sheet: -0.54 (0.16), residues: 1041 loop : -0.91 (0.13), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1039 TYR 0.024 0.001 TYR A1067 PHE 0.027 0.002 PHE A1121 TRP 0.037 0.002 TRP H 36 HIS 0.003 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00685 (30063) covalent geometry : angle 0.63036 (40890) SS BOND : bond 0.00302 ( 39) SS BOND : angle 1.34747 ( 78) hydrogen bonds : bond 0.04048 ( 1049) hydrogen bonds : angle 5.30701 ( 3012) link_NAG-ASN : bond 0.00615 ( 45) link_NAG-ASN : angle 3.80299 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 583 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7804 (pm20) REVERT: A 984 LEU cc_start: 0.8743 (mm) cc_final: 0.8295 (tp) REVERT: B 190 ARG cc_start: 0.5590 (mtm180) cc_final: 0.5099 (mtt180) REVERT: B 556 ASN cc_start: 0.8644 (t0) cc_final: 0.8432 (t0) REVERT: B 563 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8122 (tt0) REVERT: B 583 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7655 (pm20) REVERT: B 987 PRO cc_start: 0.8409 (Cg_exo) cc_final: 0.8191 (Cg_endo) REVERT: B 1138 TYR cc_start: 0.7553 (t80) cc_final: 0.7268 (t80) REVERT: C 556 ASN cc_start: 0.8618 (t0) cc_final: 0.8392 (t0) REVERT: C 661 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8035 (mp0) REVERT: C 878 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8205 (tp) REVERT: P 100 MET cc_start: 0.0189 (ptm) cc_final: -0.1030 (tpt) outliers start: 34 outliers final: 30 residues processed: 174 average time/residue: 0.1598 time to fit residues: 48.5994 Evaluate side-chains 179 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 84 optimal weight: 0.7980 chunk 292 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 211 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 235 optimal weight: 10.0000 chunk 184 optimal weight: 2.9990 chunk 347 optimal weight: 30.0000 chunk 115 optimal weight: 30.0000 chunk 149 optimal weight: 8.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.222412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.125173 restraints weight = 39606.660| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 3.37 r_work: 0.3341 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 30147 Z= 0.141 Angle : 0.587 11.131 41103 Z= 0.281 Chirality : 0.045 0.365 4773 Planarity : 0.004 0.050 5226 Dihedral : 8.392 99.635 4917 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.12 % Allowed : 12.70 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.13), residues: 3645 helix: 1.67 (0.19), residues: 675 sheet: -0.49 (0.16), residues: 1038 loop : -0.85 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1039 TYR 0.021 0.001 TYR B1067 PHE 0.019 0.001 PHE C 192 TRP 0.016 0.001 TRP A 64 HIS 0.002 0.000 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00334 (30063) covalent geometry : angle 0.54971 (40890) SS BOND : bond 0.00203 ( 39) SS BOND : angle 1.00778 ( 78) hydrogen bonds : bond 0.03452 ( 1049) hydrogen bonds : angle 5.03455 ( 3012) link_NAG-ASN : bond 0.00580 ( 45) link_NAG-ASN : angle 3.58319 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10391.64 seconds wall clock time: 177 minutes 51.44 seconds (10671.44 seconds total)