Starting phenix.real_space_refine on Thu Mar 5 13:39:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kdh_22822/03_2026/7kdh_22822.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kdh_22822/03_2026/7kdh_22822.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7kdh_22822/03_2026/7kdh_22822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kdh_22822/03_2026/7kdh_22822.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kdh_22822/03_2026/7kdh_22822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kdh_22822/03_2026/7kdh_22822.map" } resolution = 3.33 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= 0.050 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 98 5.16 5 C 14449 2.51 5 N 3731 2.21 5 O 4420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 194 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22698 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 970, 7486 Classifications: {'peptide': 970} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 45, 'TRANS': 924} Chain breaks: 11 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 4, 'PHE:plan': 1, 'GLU:plan': 9, 'ASP:plan': 8, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 90 Chain: "B" Number of atoms: 7033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 958, 7033 Classifications: {'peptide': 958} Incomplete info: {'truncation_to_alanine': 122} Link IDs: {'PTRANS': 44, 'TRANS': 913} Chain breaks: 11 Unresolved non-hydrogen bonds: 471 Unresolved non-hydrogen angles: 608 Unresolved non-hydrogen dihedrals: 393 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'ASP:plan': 12, 'GLU:plan': 4, 'GLN:plan1': 9, 'ASN:plan1': 14, 'ARG:plan': 9, 'PHE:plan': 8, 'TYR:plan': 12, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 316 Chain: "C" Number of atoms: 7367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 963, 7367 Classifications: {'peptide': 963} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 45, 'TRANS': 917} Chain breaks: 11 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 11, 'GLN:plan1': 3, 'GLU:plan': 8, 'ASN:plan1': 4, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 103 Chain: "A" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 252 Unusual residues: {'NAG': 18} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 18 Chain: "B" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 266 Unusual residues: {'NAG': 19} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 19 Chain: "C" Number of atoms: 294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 294 Unusual residues: {'NAG': 21} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 21 Time building chain proxies: 5.15, per 1000 atoms: 0.23 Number of scatterers: 22698 At special positions: 0 Unit cell: (137.385, 126.735, 177.855, 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 98 16.00 O 4420 8.00 N 3731 7.00 C 14449 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.01 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=2.04 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 B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.01 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.01 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=1.99 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A 717 " " NAG A1312 " - " ASN A 801 " " NAG A1314 " - " ASN A1074 " " NAG A1315 " - " ASN A1098 " " NAG A1317 " - " ASN A1134 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 717 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B 343 " " NAG B1310 " - " ASN B1134 " " NAG B1311 " - " ASN B 61 " " NAG B1313 " - " ASN B 165 " " NAG B1314 " - " ASN B 801 " " NAG B1315 " - " ASN B 657 " " NAG B1317 " - " ASN B 709 " " NAG B1318 " - " ASN B1098 " " NAG B1319 " - " ASN B 282 " " NAG C1302 " - " ASN C1074 " " NAG C1303 " - " ASN C 331 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 234 " " NAG C1307 " - " ASN C 61 " " NAG C1308 " - " ASN C 122 " " NAG C1309 " - " ASN C 717 " " NAG C1310 " - " ASN C 282 " " NAG C1311 " - " ASN C 343 " " NAG C1312 " - " ASN C 603 " " NAG C1315 " - " ASN C 657 " " NAG C1317 " - " ASN C1134 " " NAG C1319 " - " ASN C 801 " " NAG C1320 " - " ASN C 616 " " NAG C1321 " - " ASN C1098 " Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 773.3 milliseconds 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5432 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 42 sheets defined 28.0% alpha, 27.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.635A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.679A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.804A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.253A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.946A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.998A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.856A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.722A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.756A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.479A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1129 Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.432A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 142 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.688A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.073A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.959A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 411 removed outlier: 3.674A pdb=" N ALA B 411 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 437 through 441 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.704A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.727A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.820A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.290A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 4.303A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.011A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.345A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.618A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.660A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.620A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.679A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.726A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 907 removed outlier: 3.679A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 908 through 910 No H-bonds generated for 'chain 'C' and resid 908 through 910' Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.613A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.865A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.807A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.587A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.624A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 65 through 66 removed outlier: 3.516A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.321A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.539A 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: 5.579A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.814A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.769A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) 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 654 through 655 removed outlier: 6.161A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.823A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.786A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.336A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1123 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.275A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.471A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.296A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 10.066A pdb=" N SER B 221 " --> pdb=" O PRO B 209 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ARG B 34 " --> pdb=" O SER B 221 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N LEU B 223 " --> pdb=" O ARG B 34 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.719A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.261A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.329A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 357 removed outlier: 5.415A pdb=" N PHE B 515 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N TYR B 396 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU B 513 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASP B 398 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL B 511 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE B 400 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ARG B 509 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE B 402 " --> pdb=" O PRO B 507 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 357 Processing sheet with id=AC6, first strand: chain 'B' and resid 448 through 453 removed outlier: 3.657A pdb=" N ASN B 450 " --> pdb=" O TYR B 495 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N TYR B 495 " --> pdb=" O ASN B 450 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU B 452 " --> pdb=" O GLN B 493 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLN B 493 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.148A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 704 removed outlier: 6.751A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.543A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.543A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 3.906A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.006A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 52 removed outlier: 3.827A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.615A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 310 through 319 removed outlier: 5.720A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.738A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.148A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.832A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.656A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 5.510A pdb=" N VAL C1122 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N PHE C1089 " --> pdb=" O VAL C1122 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N GLY C1124 " --> pdb=" O ALA C1087 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1094 through 1097 1009 hydrogen bonds defined for protein. 2757 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: 5.04 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5458 1.33 - 1.45: 4645 1.45 - 1.58: 12930 1.58 - 1.70: 0 1.70 - 1.82: 122 Bond restraints: 23155 Sorted by residual: bond pdb=" C1 NAG B1309 " pdb=" O5 NAG B1309 " ideal model delta sigma weight residual 1.406 1.488 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" C1 NAG A1313 " pdb=" O5 NAG A1313 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C1 NAG A1316 " pdb=" O5 NAG A1316 " ideal model delta sigma weight residual 1.406 1.483 -0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C1 NAG B1312 " pdb=" O5 NAG B1312 " ideal model delta sigma weight residual 1.406 1.483 -0.077 2.00e-02 2.50e+03 1.49e+01 ... (remaining 23150 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.44: 31410 5.44 - 10.89: 122 10.89 - 16.33: 0 16.33 - 21.77: 3 21.77 - 27.21: 1 Bond angle restraints: 31536 Sorted by residual: angle pdb=" CA VAL B 510 " pdb=" CB VAL B 510 " pdb=" CG1 VAL B 510 " ideal model delta sigma weight residual 110.40 130.86 -20.46 1.70e+00 3.46e-01 1.45e+02 angle pdb=" CA VAL B 433 " pdb=" CB VAL B 433 " pdb=" CG1 VAL B 433 " ideal model delta sigma weight residual 110.40 130.35 -19.95 1.70e+00 3.46e-01 1.38e+02 angle pdb=" CA VAL B 512 " pdb=" CB VAL B 512 " pdb=" CG1 VAL B 512 " ideal model delta sigma weight residual 110.40 127.16 -16.76 1.70e+00 3.46e-01 9.72e+01 angle pdb=" CB LEU B 141 " pdb=" CG LEU B 141 " pdb=" CD1 LEU B 141 " ideal model delta sigma weight residual 110.70 137.91 -27.21 3.00e+00 1.11e-01 8.23e+01 angle pdb=" CA ASN A 331 " pdb=" CB ASN A 331 " pdb=" CG ASN A 331 " ideal model delta sigma weight residual 112.60 119.49 -6.89 1.00e+00 1.00e+00 4.74e+01 ... (remaining 31531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.58: 13562 18.58 - 37.16: 759 37.16 - 55.73: 131 55.73 - 74.31: 41 74.31 - 92.89: 22 Dihedral angle restraints: 14515 sinusoidal: 6120 harmonic: 8395 Sorted by residual: 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 -174.62 88.62 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual 93.00 179.87 -86.87 1 1.00e+01 1.00e-02 9.08e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 177.15 -84.15 1 1.00e+01 1.00e-02 8.62e+01 ... (remaining 14512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.697: 3814 0.697 - 1.394: 1 1.394 - 2.090: 20 2.090 - 2.787: 2 2.787 - 3.484: 3 Chirality restraints: 3840 Sorted by residual: chirality pdb=" C1 NAG C1312 " pdb=" ND2 ASN C 603 " pdb=" C2 NAG C1312 " pdb=" O5 NAG C1312 " both_signs ideal model delta sigma weight residual False -2.40 -5.88 3.48 2.00e-01 2.50e+01 3.03e+02 chirality pdb=" C1 NAG C1307 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1307 " pdb=" O5 NAG C1307 " both_signs ideal model delta sigma weight residual False -2.40 -5.74 3.34 2.00e-01 2.50e+01 2.79e+02 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -5.25 2.85 2.00e-01 2.50e+01 2.03e+02 ... (remaining 3837 not shown) Planarity restraints: 4032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 657 " 0.162 2.00e-02 2.50e+03 1.70e-01 3.60e+02 pdb=" CG ASN C 657 " -0.101 2.00e-02 2.50e+03 pdb=" OD1 ASN C 657 " -0.258 2.00e-02 2.50e+03 pdb=" ND2 ASN C 657 " -0.005 2.00e-02 2.50e+03 pdb=" C1 NAG C1315 " 0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 282 " -0.160 2.00e-02 2.50e+03 1.67e-01 3.50e+02 pdb=" CG ASN B 282 " 0.093 2.00e-02 2.50e+03 pdb=" OD1 ASN B 282 " 0.257 2.00e-02 2.50e+03 pdb=" ND2 ASN B 282 " 0.009 2.00e-02 2.50e+03 pdb=" C1 NAG B1319 " -0.199 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1074 " 0.143 2.00e-02 2.50e+03 1.52e-01 2.88e+02 pdb=" CG ASN C1074 " -0.084 2.00e-02 2.50e+03 pdb=" OD1 ASN C1074 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN C1074 " -0.233 2.00e-02 2.50e+03 pdb=" C1 NAG C1302 " 0.182 2.00e-02 2.50e+03 ... (remaining 4029 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 22 2.14 - 2.83: 5788 2.83 - 3.52: 30638 3.52 - 4.21: 52473 4.21 - 4.90: 91177 Nonbonded interactions: 180098 Sorted by model distance: nonbonded pdb=" OD1 ASN A1134 " pdb=" C1 NAG A1317 " model vdw 1.454 2.776 nonbonded pdb=" OD1 ASN B 657 " pdb=" C1 NAG B1315 " model vdw 1.462 2.776 nonbonded pdb=" OD1 ASN B 61 " pdb=" C1 NAG B1311 " model vdw 1.465 2.776 nonbonded pdb=" OD1 ASN C 282 " pdb=" C1 NAG C1310 " model vdw 1.469 2.776 nonbonded pdb=" OD1 ASN A 343 " pdb=" C1 NAG A1305 " model vdw 1.470 2.776 ... (remaining 180093 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 95 or (resid 96 through 97 and (name N or name CA or name C or name O or name \ CB )) or resid 98 through 109 or (resid 110 and (name N or name CA or name C or \ name O or name CB )) or resid 111 through 114 or (resid 115 and (name N or name \ CA or name C or name O or name CB )) or resid 116 through 131 or (resid 132 and \ (name N or name CA or name C or name O or name CB )) or resid 133 or (resid 134 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 143 or (resid 165 and (name N or name CA or name C or name O or name C \ B )) or resid 166 through 168 or (resid 169 and (name N or name CA or name C or \ name O or name CB )) or resid 170 through 171 or (resid 172 and (name N or name \ CA or name C or name O or name CB )) or resid 186 through 190 or (resid 191 and \ (name N or name CA or name C or name O or name CB )) or resid 192 through 196 or \ (resid 197 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 8 through 213 or (resid 214 through 215 and (name N or name CA or name C or name \ O or name CB )) or resid 216 through 217 or (resid 218 and (name N or name CA o \ r name C or name O or name CB )) or resid 219 through 238 or (resid 239 and (nam \ e N or name CA or name C or name O or name CB )) or resid 240 through 308 or (re \ sid 309 and (name N or name CA or name C or name O or name CB )) or resid 310 th \ rough 333 or (resid 334 and (name N or name CA or name C or name O or name CB )) \ or resid 335 through 345 or (resid 346 through 355 and (name N or name CA or na \ me C or name O or name CB )) or resid 356 or (resid 357 through 360 and (name N \ or name CA or name C or name O or name CB )) or resid 361 or (resid 362 through \ 376 and (name N or name CA or name C or name O or name CB )) or resid 377 or (re \ sid 378 and (name N or name CA or name C or name O or name CB )) or resid 379 or \ (resid 380 and (name N or name CA or name C or name O or name CB )) or resid 38 \ 1 or (resid 382 through 383 and (name N or name CA or name C or name O or name C \ B )) or resid 384 or (resid 385 through 387 and (name N or name CA or name C or \ name O or name CB )) or resid 388 or (resid 389 through 390 and (name N or name \ CA or name C or name O or name CB )) or resid 391 or (resid 392 and (name N or n \ ame CA or name C or name O or name CB )) or resid 393 or (resid 394 through 403 \ and (name N or name CA or name C or name O or name CB )) or (resid 404 through 4 \ 11 and (name N or name CA or name C or name O or name CB )) or resid 412 through \ 413 or (resid 414 through 415 and (name N or name CA or name C or name O or nam \ e CB )) or resid 416 or (resid 417 through 425 and (name N or name CA or name C \ or name O or name CB )) or resid 426 or (resid 427 through 430 and (name N or na \ me CA or name C or name O or name CB )) or resid 431 through 433 or (resid 434 t \ hrough 435 and (name N or name CA or name C or name O or name CB )) or resid 436 \ or (resid 437 through 454 and (name N or name CA or name C or name O or name CB \ )) or (resid 462 and (name N or name CA or name C or name O or name CB )) or re \ sid 463 or (resid 464 through 466 and (name N or name CA or name C or name O or \ name CB )) or resid 491 or (resid 492 through 495 and (name N or name CA or name \ C or name O or name CB )) or resid 496 or (resid 497 through 498 and (name N or \ name CA or name C or name O or name CB )) or resid 499 or (resid 500 through 50 \ 3 and (name N or name CA or name C or name O or name CB )) or (resid 504 through \ 506 and (name N or name CA or name C or name O or name CB )) or resid 507 throu \ gh 508 or (resid 509 and (name N or name CA or name C or name O or name CB )) or \ resid 510 or (resid 511 and (name N or name CA or name C or name O or name CB ) \ ) or resid 512 or (resid 513 through 515 and (name N or name CA or name C or nam \ e O or name CB )) or (resid 522 through 524 and (name N or name CA or name C or \ name O or name CB )) or resid 525 through 527 or (resid 528 and (name N or name \ CA or name C or name O or name CB )) or resid 529 through 810 or (resid 811 and \ (name N or name CA or name C or name O or name CB )) or resid 813 through 827 or \ resid 855 through 866 or (resid 867 through 868 and (name N or name CA or name \ C or name O or name CB )) or resid 869 through 1141 or (resid 1142 and (name N o \ r name CA or name C or name O or name CB )) or resid 1143 through 1144 or (resid \ 1145 through 1146 and (name N or name CA or name C or name O or name CB )) or r \ esid 1147 through 1318)) selection = (chain 'B' and (resid 27 through 66 or resid 82 through 87 or (resid 88 and (nam \ e N or name CA or name C or name O or name CB )) or resid 89 through 96 or (resi \ d 97 and (name N or name CA or name C or name O or name CB )) or resid 98 or (re \ sid 99 and (name N or name CA or name C or name O or name CB )) or resid 100 thr \ ough 109 or (resid 110 and (name N or name CA or name C or name O or name CB )) \ or resid 111 through 114 or (resid 115 and (name N or name CA or name C or name \ O or name CB )) or resid 116 through 134 or (resid 135 through 138 and (name N o \ r name CA or name C or name O or name CB )) or resid 139 through 164 or resid 16 \ 6 through 168 or (resid 169 and (name N or name CA or name C or name O or name C \ B )) or resid 170 through 190 or (resid 191 and (name N or name CA or name C or \ name O or name CB )) or resid 192 through 195 or (resid 196 through 197 and (nam \ e N or name CA or name C or name O or name CB )) or resid 198 through 241 or (re \ sid 242 through 264 and (name N or name CA or name C or name O or name CB )) or \ resid 265 through 280 or (resid 281 and (name N or name CA or name C or name O o \ r name CB )) or resid 282 through 339 or (resid 340 and (name N or name CA or na \ me C or name O or name CB )) or resid 341 through 442 or resid 448 through 464 o \ r (resid 465 through 466 and (name N or name CA or name C or name O or name CB ) \ ) or resid 491 through 501 or resid 503 through 567 or (resid 568 and (name N or \ name CA or name C or name O or name CB )) or resid 569 through 582 or (resid 58 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 584 through \ 585 or (resid 586 and (name N or name CA or name C or name O or name CB )) or re \ sid 587 through 613 or (resid 614 and (name N or name CA or name C or name O or \ name CB )) or resid 615 through 618 or (resid 619 and (name N or name CA or name \ C or name O or name CB )) or resid 620 through 676 or resid 690 through 744 or \ (resid 745 and (name N or name CA or name C or name O or name CB )) or resid 746 \ through 747 or (resid 748 and (name N or name CA or name C or name O or name CB \ )) or resid 749 through 810 or (resid 811 and (name N or name CA or name C or n \ ame O or name CB )) or resid 813 or (resid 814 and (name N or name CA or name C \ or name O or name CB )) or resid 815 through 827 or resid 855 through 866 or (re \ sid 867 through 868 and (name N or name CA or name C or name O or name CB )) or \ resid 869 through 1091 or (resid 1092 and (name N or name CA or name C or name O \ or name CB )) or resid 1093 through 1143 or (resid 1144 through 1146 and (name \ N or name CA or name C or name O or name CB )) or resid 1147 through 1318)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 134 or (resid 135 through 138 and (name N or name CA or name C o \ r name O or name CB )) or resid 139 through 143 or (resid 165 and (name N or nam \ e CA or name C or name O or name CB )) or resid 166 through 195 or (resid 196 th \ rough 197 and (name N or name CA or name C or name O or name CB )) or resid 198 \ through 213 or (resid 214 through 215 and (name N or name CA or name C or name O \ or name CB )) or resid 216 through 217 or (resid 218 and (name N or name CA or \ name C or name O or name CB )) or resid 219 through 238 or (resid 239 and (name \ N or name CA or name C or name O or name CB )) or resid 240 through 308 or (resi \ d 309 and (name N or name CA or name C or name O or name CB )) or resid 310 thro \ ugh 333 or (resid 334 and (name N or name CA or name C or name O or name CB )) o \ r resid 335 through 339 or (resid 340 and (name N or name CA or name C or name O \ or name CB )) or resid 341 through 345 or (resid 346 through 355 and (name N or \ name CA or name C or name O or name CB )) or resid 356 or (resid 357 through 36 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 361 or (resi \ d 362 through 376 and (name N or name CA or name C or name O or name CB )) or re \ sid 377 through 379 or (resid 380 and (name N or name CA or name C or name O or \ name CB )) or resid 381 or (resid 382 through 383 and (name N or name CA or name \ C or name O or name CB )) or resid 384 or (resid 385 through 387 and (name N or \ name CA or name C or name O or name CB )) or resid 388 or (resid 389 through 39 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 391 or (resi \ d 392 and (name N or name CA or name C or name O or name CB )) or resid 393 or ( \ resid 394 through 403 and (name N or name CA or name C or name O or name CB )) o \ r (resid 404 through 411 and (name N or name CA or name C or name O or name CB ) \ ) or resid 412 through 413 or (resid 414 through 415 and (name N or name CA or n \ ame C or name O or name CB )) or (resid 416 through 425 and (name N or name CA o \ r name C or name O or name CB )) or resid 426 or (resid 427 through 430 and (nam \ e N or name CA or name C or name O or name CB )) or resid 431 through 433 or (re \ sid 434 through 435 and (name N or name CA or name C or name O or name CB )) or \ resid 436 through 437 or (resid 438 through 442 and (name N or name CA or name C \ or name O or name CB )) or (resid 448 through 462 and (name N or name CA or nam \ e C or name O or name CB )) or resid 463 or (resid 464 through 466 and (name N o \ r name CA or name C or name O or name CB )) or resid 491 or (resid 492 through 4 \ 95 and (name N or name CA or name C or name O or name CB )) or resid 496 or (res \ id 497 through 498 and (name N or name CA or name C or name O or name CB )) or r \ esid 499 through 500 or (resid 501 and (name N or name CA or name C or name O or \ name CB )) or (resid 503 and (name N or name CA or name C or name O or name CB \ )) or (resid 504 through 506 and (name N or name CA or name C or name O or name \ CB )) or resid 507 through 508 or (resid 509 and (name N or name CA or name C or \ name O or name CB )) or resid 510 or (resid 511 and (name N or name CA or name \ C or name O or name CB )) or resid 512 or (resid 513 through 515 and (name N or \ name CA or name C or name O or name CB )) or (resid 522 through 524 and (name N \ or name CA or name C or name O or name CB )) or resid 525 through 527 or (resid \ 528 and (name N or name CA or name C or name O or name CB )) or resid 529 throug \ h 567 or (resid 568 and (name N or name CA or name C or name O or name CB )) or \ resid 569 through 582 or (resid 583 and (name N or name CA or name C or name O o \ r name CB )) or resid 584 through 585 or (resid 586 and (name N or name CA or na \ me C or name O or name CB )) or resid 587 through 618 or (resid 619 and (name N \ or name CA or name C or name O or name CB )) or resid 620 through 813 or (resid \ 814 and (name N or name CA or name C or name O or name CB )) or resid 815 throug \ h 1091 or (resid 1092 and (name N or name CA or name C or name O or name CB )) o \ r resid 1093 through 1141 or (resid 1142 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1143 or (resid 1144 through 1146 and (name N or name \ CA or name C or name O or name CB )) or resid 1147 through 1318)) } 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: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.330 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 21.140 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 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 : 0.045 1.463 23235 Z= 2.287 Angle : 2.581 65.181 31741 Z= 1.324 Chirality : 0.191 3.484 3840 Planarity : 0.014 0.155 3987 Dihedral : 12.764 92.889 8978 Min Nonbonded Distance : 1.454 Molprobity Statistics. All-atom Clashscore : 0.56 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.31 % Favored : 92.30 % Rotamer: Outliers : 0.56 % Allowed : 2.83 % Favored : 96.62 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.14), residues: 2819 helix: -0.57 (0.17), residues: 665 sheet: -0.02 (0.23), residues: 477 loop : -1.23 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 273 TYR 0.203 0.022 TYR C 904 PHE 0.095 0.013 PHE B 927 TRP 0.203 0.030 TRP C 886 HIS 0.017 0.003 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.01342 (23155) covalent geometry : angle 1.76990 (31536) SS BOND : bond 0.01015 ( 35) SS BOND : angle 1.77517 ( 70) hydrogen bonds : bond 0.15779 ( 994) hydrogen bonds : angle 8.66721 ( 2757) link_NAG-ASN : bond 0.98010 ( 45) link_NAG-ASN : angle 28.86468 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 196 time to evaluate : 0.772 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: B 1081 ILE cc_start: 0.7689 (OUTLIER) cc_final: 0.7317 (pt) REVERT: B 1135 ASN cc_start: 0.7482 (OUTLIER) cc_final: 0.7202 (t0) outliers start: 13 outliers final: 3 residues processed: 206 average time/residue: 0.1425 time to fit residues: 47.3463 Evaluate side-chains 97 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1135 ASN Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A1088 HIS B1005 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.092401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.063146 restraints weight = 59972.295| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.53 r_work: 0.2975 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 23235 Z= 0.147 Angle : 0.752 15.269 31741 Z= 0.379 Chirality : 0.048 0.361 3840 Planarity : 0.004 0.034 3987 Dihedral : 6.993 52.975 4276 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.87 % Favored : 96.10 % Rotamer: Outliers : 1.11 % Allowed : 5.82 % Favored : 93.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.41 (0.15), residues: 2819 helix: 1.38 (0.20), residues: 653 sheet: -0.25 (0.19), residues: 653 loop : -1.02 (0.15), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 237 TYR 0.019 0.002 TYR B 170 PHE 0.018 0.002 PHE B 565 TRP 0.012 0.002 TRP C 436 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00298 (23155) covalent geometry : angle 0.69420 (31536) SS BOND : bond 0.00394 ( 35) SS BOND : angle 2.02906 ( 70) hydrogen bonds : bond 0.04945 ( 994) hydrogen bonds : angle 6.56229 ( 2757) link_NAG-ASN : bond 0.01181 ( 45) link_NAG-ASN : angle 4.25406 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7762 (OUTLIER) cc_final: 0.7048 (t80) REVERT: A 270 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7897 (mp) REVERT: B 241 LEU cc_start: 0.8192 (mt) cc_final: 0.7946 (mp) REVERT: B 1045 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8356 (tptp) REVERT: C 270 LEU cc_start: 0.8489 (mt) cc_final: 0.8228 (mp) outliers start: 26 outliers final: 10 residues processed: 124 average time/residue: 0.1445 time to fit residues: 29.2581 Evaluate side-chains 93 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 724 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 110 optimal weight: 5.9990 chunk 285 optimal weight: 1.9990 chunk 236 optimal weight: 9.9990 chunk 274 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 273 optimal weight: 4.9990 chunk 233 optimal weight: 0.4980 chunk 165 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN C 207 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.089878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.060821 restraints weight = 60485.369| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 3.44 r_work: 0.2917 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 23235 Z= 0.219 Angle : 0.667 14.232 31741 Z= 0.338 Chirality : 0.047 0.324 3840 Planarity : 0.004 0.056 3987 Dihedral : 6.314 52.887 4270 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.63 % Allowed : 6.77 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.26 (0.15), residues: 2819 helix: 1.55 (0.20), residues: 667 sheet: -0.29 (0.19), residues: 694 loop : -0.92 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 328 TYR 0.023 0.002 TYR A1067 PHE 0.025 0.002 PHE B1121 TRP 0.018 0.002 TRP C 104 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00509 (23155) covalent geometry : angle 0.63416 (31536) SS BOND : bond 0.00369 ( 35) SS BOND : angle 1.09604 ( 70) hydrogen bonds : bond 0.04372 ( 994) hydrogen bonds : angle 6.15172 ( 2757) link_NAG-ASN : bond 0.00846 ( 45) link_NAG-ASN : angle 3.15734 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 87 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8119 (mp) REVERT: B 241 LEU cc_start: 0.8184 (mt) cc_final: 0.7934 (mp) REVERT: B 331 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.8323 (m110) REVERT: B 1045 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8599 (tptp) outliers start: 38 outliers final: 19 residues processed: 118 average time/residue: 0.1318 time to fit residues: 26.5668 Evaluate side-chains 98 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 724 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 226 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 254 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 260 optimal weight: 0.3980 chunk 252 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 212 optimal weight: 5.9990 chunk 108 optimal weight: 20.0000 chunk 139 optimal weight: 8.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 907 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.091639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.062857 restraints weight = 60379.356| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.32 r_work: 0.3007 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 23235 Z= 0.134 Angle : 0.589 13.907 31741 Z= 0.297 Chirality : 0.044 0.210 3840 Planarity : 0.003 0.047 3987 Dihedral : 5.796 62.962 4270 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.20 % Allowed : 8.05 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.15), residues: 2819 helix: 1.89 (0.20), residues: 660 sheet: -0.24 (0.19), residues: 689 loop : -0.84 (0.15), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 237 TYR 0.019 0.001 TYR B1067 PHE 0.028 0.001 PHE B 201 TRP 0.026 0.001 TRP A 104 HIS 0.002 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00300 (23155) covalent geometry : angle 0.55272 (31536) SS BOND : bond 0.00364 ( 35) SS BOND : angle 1.96209 ( 70) hydrogen bonds : bond 0.03831 ( 994) hydrogen bonds : angle 5.82431 ( 2757) link_NAG-ASN : bond 0.00643 ( 45) link_NAG-ASN : angle 2.86511 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 87 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8222 (mp) REVERT: B 973 ILE cc_start: 0.9442 (OUTLIER) cc_final: 0.9229 (pt) REVERT: B 1045 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8505 (tptp) REVERT: C 773 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8623 (tt0) outliers start: 28 outliers final: 13 residues processed: 108 average time/residue: 0.1289 time to fit residues: 23.6193 Evaluate side-chains 90 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 773 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 210 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 108 optimal weight: 20.0000 chunk 96 optimal weight: 1.9990 chunk 243 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 230 optimal weight: 10.0000 chunk 236 optimal weight: 4.9990 chunk 222 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 901 GLN B 907 ASN B1106 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.090358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.061385 restraints weight = 60396.112| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.30 r_work: 0.2974 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 23235 Z= 0.197 Angle : 0.605 13.781 31741 Z= 0.305 Chirality : 0.045 0.223 3840 Planarity : 0.004 0.041 3987 Dihedral : 5.681 66.622 4270 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.54 % Allowed : 8.48 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.10 (0.16), residues: 2819 helix: 1.76 (0.20), residues: 669 sheet: -0.27 (0.19), residues: 701 loop : -0.81 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 319 TYR 0.021 0.002 TYR A1067 PHE 0.022 0.002 PHE B1121 TRP 0.021 0.002 TRP B 104 HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00456 (23155) covalent geometry : angle 0.57566 (31536) SS BOND : bond 0.00332 ( 35) SS BOND : angle 1.60700 ( 70) hydrogen bonds : bond 0.03935 ( 994) hydrogen bonds : angle 5.76203 ( 2757) link_NAG-ASN : bond 0.00628 ( 45) link_NAG-ASN : angle 2.70238 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 85 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ILE cc_start: 0.7853 (OUTLIER) cc_final: 0.7589 (tt) REVERT: A 270 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8246 (mp) REVERT: A 1002 GLN cc_start: 0.8544 (tt0) cc_final: 0.8209 (tm-30) REVERT: B 133 PHE cc_start: 0.7537 (m-80) cc_final: 0.7213 (m-10) REVERT: B 210 ILE cc_start: 0.7286 (pt) cc_final: 0.7030 (pt) REVERT: B 331 ASN cc_start: 0.8499 (OUTLIER) cc_final: 0.8290 (m110) REVERT: B 912 THR cc_start: 0.8764 (OUTLIER) cc_final: 0.8536 (p) REVERT: B 973 ILE cc_start: 0.9444 (OUTLIER) cc_final: 0.9196 (tp) REVERT: B 1045 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8626 (tptp) REVERT: C 773 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8556 (tt0) outliers start: 36 outliers final: 18 residues processed: 114 average time/residue: 0.1388 time to fit residues: 27.0700 Evaluate side-chains 99 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 255 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 174 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 195 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 22 optimal weight: 0.0970 chunk 77 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 140 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 901 GLN B 907 ASN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.091812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.062959 restraints weight = 60336.691| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.32 r_work: 0.3012 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 23235 Z= 0.116 Angle : 0.556 13.427 31741 Z= 0.280 Chirality : 0.043 0.233 3840 Planarity : 0.003 0.040 3987 Dihedral : 5.334 72.810 4270 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.46 % Allowed : 8.82 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.16), residues: 2819 helix: 1.99 (0.20), residues: 669 sheet: -0.30 (0.19), residues: 726 loop : -0.68 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 567 TYR 0.019 0.001 TYR A 351 PHE 0.032 0.001 PHE B 201 TRP 0.034 0.001 TRP A 104 HIS 0.002 0.000 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00257 (23155) covalent geometry : angle 0.52728 (31536) SS BOND : bond 0.00289 ( 35) SS BOND : angle 1.71924 ( 70) hydrogen bonds : bond 0.03626 ( 994) hydrogen bonds : angle 5.48993 ( 2757) link_NAG-ASN : bond 0.00613 ( 45) link_NAG-ASN : angle 2.50509 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 85 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.8249 (m) cc_final: 0.7973 (p) REVERT: A 233 ILE cc_start: 0.7798 (OUTLIER) cc_final: 0.7548 (tt) REVERT: A 452 LEU cc_start: 0.8973 (mm) cc_final: 0.8500 (tp) REVERT: A 979 ASP cc_start: 0.8270 (m-30) cc_final: 0.7871 (t70) REVERT: A 1002 GLN cc_start: 0.8528 (tt0) cc_final: 0.8125 (tm-30) REVERT: B 133 PHE cc_start: 0.7471 (m-80) cc_final: 0.7055 (m-10) REVERT: B 210 ILE cc_start: 0.7231 (pt) cc_final: 0.6871 (pt) REVERT: B 238 PHE cc_start: 0.5667 (OUTLIER) cc_final: 0.3963 (p90) REVERT: B 900 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8368 (mtp) REVERT: B 912 THR cc_start: 0.8777 (OUTLIER) cc_final: 0.8527 (p) REVERT: B 973 ILE cc_start: 0.9449 (OUTLIER) cc_final: 0.9214 (pt) REVERT: B 1045 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8670 (tptp) REVERT: C 773 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8619 (tt0) outliers start: 34 outliers final: 16 residues processed: 111 average time/residue: 0.1308 time to fit residues: 24.8377 Evaluate side-chains 98 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 773 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 137 optimal weight: 0.0020 chunk 114 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 190 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 142 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 182 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 overall best weight: 3.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS A 901 GLN A1088 HIS A1119 ASN B 901 GLN B 907 ASN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.088675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.059574 restraints weight = 61022.126| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.31 r_work: 0.2931 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.107 23235 Z= 0.302 Angle : 0.694 13.748 31741 Z= 0.347 Chirality : 0.047 0.247 3840 Planarity : 0.004 0.049 3987 Dihedral : 5.799 71.949 4270 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.63 % Allowed : 9.85 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.15), residues: 2819 helix: 1.53 (0.20), residues: 670 sheet: -0.44 (0.19), residues: 721 loop : -0.90 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1107 TYR 0.022 0.002 TYR A1067 PHE 0.032 0.002 PHE B1121 TRP 0.024 0.002 TRP A 104 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00705 (23155) covalent geometry : angle 0.66467 (31536) SS BOND : bond 0.00495 ( 35) SS BOND : angle 2.39652 ( 70) hydrogen bonds : bond 0.04237 ( 994) hydrogen bonds : angle 5.87470 ( 2757) link_NAG-ASN : bond 0.00685 ( 45) link_NAG-ASN : angle 2.66740 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 75 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.7580 (tt) REVERT: A 452 LEU cc_start: 0.8982 (mm) cc_final: 0.8631 (pp) REVERT: A 979 ASP cc_start: 0.8313 (m-30) cc_final: 0.7923 (t70) REVERT: A 1002 GLN cc_start: 0.8648 (tt0) cc_final: 0.8376 (tm-30) REVERT: B 210 ILE cc_start: 0.7134 (pt) cc_final: 0.6804 (pt) REVERT: B 973 ILE cc_start: 0.9480 (OUTLIER) cc_final: 0.9234 (tp) REVERT: B 1045 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8571 (tptp) REVERT: B 1050 MET cc_start: 0.8417 (ptt) cc_final: 0.8210 (ptt) REVERT: C 759 PHE cc_start: 0.8314 (m-80) cc_final: 0.8108 (m-80) REVERT: C 773 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8615 (tt0) outliers start: 38 outliers final: 27 residues processed: 106 average time/residue: 0.1287 time to fit residues: 23.6890 Evaluate side-chains 103 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 72 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 31 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 173 optimal weight: 3.9990 chunk 165 optimal weight: 0.7980 chunk 212 optimal weight: 0.0670 chunk 144 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 236 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN B 901 GLN B 907 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.091210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.062565 restraints weight = 59910.886| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.30 r_work: 0.3006 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 23235 Z= 0.112 Angle : 0.556 13.240 31741 Z= 0.279 Chirality : 0.043 0.246 3840 Planarity : 0.003 0.038 3987 Dihedral : 5.237 63.243 4270 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.07 % Allowed : 10.41 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.16), residues: 2819 helix: 1.96 (0.21), residues: 666 sheet: -0.29 (0.19), residues: 709 loop : -0.71 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1107 TYR 0.020 0.001 TYR B1067 PHE 0.025 0.001 PHE B 201 TRP 0.029 0.002 TRP A 104 HIS 0.002 0.000 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00249 (23155) covalent geometry : angle 0.52627 (31536) SS BOND : bond 0.00238 ( 35) SS BOND : angle 1.92159 ( 70) hydrogen bonds : bond 0.03572 ( 994) hydrogen bonds : angle 5.45428 ( 2757) link_NAG-ASN : bond 0.00646 ( 45) link_NAG-ASN : angle 2.46299 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.8141 (m) cc_final: 0.7844 (p) REVERT: A 233 ILE cc_start: 0.7805 (OUTLIER) cc_final: 0.7529 (tt) REVERT: A 452 LEU cc_start: 0.8962 (mm) cc_final: 0.8495 (tp) REVERT: A 979 ASP cc_start: 0.8236 (m-30) cc_final: 0.7919 (t70) REVERT: A 1002 GLN cc_start: 0.8541 (tt0) cc_final: 0.8238 (tm-30) REVERT: B 133 PHE cc_start: 0.7314 (m-80) cc_final: 0.7018 (m-10) REVERT: B 238 PHE cc_start: 0.5937 (OUTLIER) cc_final: 0.4406 (p90) REVERT: B 973 ILE cc_start: 0.9439 (OUTLIER) cc_final: 0.9181 (tp) REVERT: B 1045 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8709 (tptp) REVERT: B 1050 MET cc_start: 0.8247 (ptt) cc_final: 0.7900 (ptt) REVERT: C 773 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8580 (tt0) outliers start: 25 outliers final: 17 residues processed: 100 average time/residue: 0.1364 time to fit residues: 23.3079 Evaluate side-chains 100 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 987 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 236 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 241 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 217 optimal weight: 0.6980 chunk 104 optimal weight: 9.9990 chunk 249 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 chunk 197 optimal weight: 6.9990 chunk 243 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN A1088 HIS B 901 GLN B 907 ASN C1048 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.089320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.060162 restraints weight = 61104.055| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.32 r_work: 0.2945 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 23235 Z= 0.264 Angle : 0.633 13.428 31741 Z= 0.316 Chirality : 0.046 0.255 3840 Planarity : 0.004 0.038 3987 Dihedral : 5.465 61.898 4270 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.11 % Allowed : 10.54 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.16), residues: 2819 helix: 1.70 (0.20), residues: 672 sheet: -0.39 (0.19), residues: 716 loop : -0.83 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1107 TYR 0.021 0.002 TYR B1067 PHE 0.028 0.002 PHE B1121 TRP 0.017 0.002 TRP A 104 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00612 (23155) covalent geometry : angle 0.60535 (31536) SS BOND : bond 0.00360 ( 35) SS BOND : angle 2.02126 ( 70) hydrogen bonds : bond 0.03926 ( 994) hydrogen bonds : angle 5.66730 ( 2757) link_NAG-ASN : bond 0.00607 ( 45) link_NAG-ASN : angle 2.53575 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ILE cc_start: 0.7885 (OUTLIER) cc_final: 0.7568 (tt) REVERT: A 452 LEU cc_start: 0.8960 (mm) cc_final: 0.8637 (pp) REVERT: A 979 ASP cc_start: 0.8304 (m-30) cc_final: 0.7958 (t70) REVERT: A 1002 GLN cc_start: 0.8654 (tt0) cc_final: 0.8368 (tm-30) REVERT: B 133 PHE cc_start: 0.7318 (m-80) cc_final: 0.7022 (m-10) REVERT: B 238 PHE cc_start: 0.5934 (OUTLIER) cc_final: 0.4327 (p90) REVERT: B 973 ILE cc_start: 0.9448 (OUTLIER) cc_final: 0.9211 (tp) REVERT: B 1045 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8588 (tptp) REVERT: C 759 PHE cc_start: 0.8224 (m-80) cc_final: 0.8010 (m-80) REVERT: C 773 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8612 (tt0) outliers start: 26 outliers final: 19 residues processed: 92 average time/residue: 0.1358 time to fit residues: 21.6797 Evaluate side-chains 93 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 261 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 135 optimal weight: 40.0000 chunk 23 optimal weight: 0.9990 chunk 222 optimal weight: 9.9990 chunk 131 optimal weight: 30.0000 chunk 161 optimal weight: 0.4980 chunk 75 optimal weight: 0.9980 chunk 43 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN A1088 HIS B 907 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.090549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.061842 restraints weight = 60523.269| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 3.31 r_work: 0.2991 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 23235 Z= 0.130 Angle : 0.555 13.151 31741 Z= 0.278 Chirality : 0.044 0.250 3840 Planarity : 0.003 0.037 3987 Dihedral : 5.183 54.563 4270 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.11 % Allowed : 10.45 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.16), residues: 2819 helix: 1.91 (0.21), residues: 666 sheet: -0.31 (0.19), residues: 710 loop : -0.74 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1107 TYR 0.020 0.001 TYR B1067 PHE 0.031 0.001 PHE B 201 TRP 0.025 0.001 TRP A 104 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00299 (23155) covalent geometry : angle 0.52700 (31536) SS BOND : bond 0.00272 ( 35) SS BOND : angle 1.80088 ( 70) hydrogen bonds : bond 0.03591 ( 994) hydrogen bonds : angle 5.46267 ( 2757) link_NAG-ASN : bond 0.00608 ( 45) link_NAG-ASN : angle 2.43045 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.8196 (m) cc_final: 0.7863 (p) REVERT: A 233 ILE cc_start: 0.7811 (OUTLIER) cc_final: 0.7577 (tt) REVERT: A 452 LEU cc_start: 0.8981 (mm) cc_final: 0.8636 (pp) REVERT: A 979 ASP cc_start: 0.8240 (m-30) cc_final: 0.7944 (t70) REVERT: A 1002 GLN cc_start: 0.8581 (tt0) cc_final: 0.8363 (tm-30) REVERT: B 133 PHE cc_start: 0.7193 (m-80) cc_final: 0.6902 (m-10) REVERT: B 238 PHE cc_start: 0.5999 (OUTLIER) cc_final: 0.4470 (p90) REVERT: B 242 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7819 (mm) REVERT: B 973 ILE cc_start: 0.9445 (OUTLIER) cc_final: 0.9193 (tp) REVERT: B 1045 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8669 (tptp) REVERT: C 773 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8596 (tt0) outliers start: 26 outliers final: 17 residues processed: 96 average time/residue: 0.1328 time to fit residues: 22.1996 Evaluate side-chains 94 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 987 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 22 optimal weight: 0.9980 chunk 191 optimal weight: 0.5980 chunk 169 optimal weight: 0.9990 chunk 188 optimal weight: 0.9990 chunk 227 optimal weight: 20.0000 chunk 220 optimal weight: 0.0870 chunk 251 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 115 optimal weight: 0.0020 chunk 13 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.5366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 901 GLN B 907 ASN C1135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.091918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.063511 restraints weight = 60210.796| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 3.30 r_work: 0.3018 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 23235 Z= 0.100 Angle : 0.533 12.819 31741 Z= 0.266 Chirality : 0.043 0.245 3840 Planarity : 0.003 0.038 3987 Dihedral : 4.814 44.910 4270 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.99 % Allowed : 10.75 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.16), residues: 2819 helix: 2.03 (0.21), residues: 664 sheet: -0.20 (0.19), residues: 712 loop : -0.60 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1107 TYR 0.018 0.001 TYR B1067 PHE 0.031 0.001 PHE B 201 TRP 0.026 0.002 TRP A 104 HIS 0.005 0.000 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00218 (23155) covalent geometry : angle 0.50645 (31536) SS BOND : bond 0.00235 ( 35) SS BOND : angle 1.67937 ( 70) hydrogen bonds : bond 0.03424 ( 994) hydrogen bonds : angle 5.28233 ( 2757) link_NAG-ASN : bond 0.00602 ( 45) link_NAG-ASN : angle 2.33855 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4893.12 seconds wall clock time: 84 minutes 36.39 seconds (5076.39 seconds total)