Starting phenix.real_space_refine on Mon Jun 23 03:28:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xy4_33510/06_2025/7xy4_33510.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xy4_33510/06_2025/7xy4_33510.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xy4_33510/06_2025/7xy4_33510.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xy4_33510/06_2025/7xy4_33510.map" model { file = "/net/cci-nas-00/data/ceres_data/7xy4_33510/06_2025/7xy4_33510.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xy4_33510/06_2025/7xy4_33510.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 124 5.16 5 C 17349 2.51 5 N 4524 2.21 5 O 5300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27297 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8299 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 50, 'TRANS': 1009} Chain breaks: 5 Chain: "B" Number of atoms: 8299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8299 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 50, 'TRANS': 1009} Chain breaks: 5 Chain: "C" Number of atoms: 8299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8299 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 50, 'TRANS': 1009} Chain breaks: 5 Chain: "D" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 920 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "E" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 920 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 15.87, per 1000 atoms: 0.58 Number of scatterers: 27297 At special positions: 0 Unit cell: (153.92, 158.08, 197.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 124 16.00 O 5300 8.00 N 4524 7.00 C 17349 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.89 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=1.33 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=1.97 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 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " 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 A1201 " - " ASN A 61 " " NAG A1202 " - " ASN A 234 " " NAG A1203 " - " ASN A 282 " " NAG A1204 " - " ASN A 331 " " NAG A1205 " - " ASN A 343 " " NAG A1206 " - " ASN A 616 " " NAG A1207 " - " ASN A 657 " " NAG A1208 " - " ASN A 709 " " NAG A1209 " - " ASN A1074 " " NAG A1210 " - " ASN A 717 " " NAG A1211 " - " ASN A 801 " " NAG A1212 " - " ASN A1098 " " NAG A1213 " - " ASN A1134 " " NAG B1201 " - " ASN B 61 " " NAG B1202 " - " ASN B 282 " " NAG B1203 " - " ASN B 331 " " NAG B1204 " - " ASN B 343 " " NAG B1205 " - " ASN B 603 " " NAG B1206 " - " ASN B 616 " " NAG B1207 " - " ASN B 657 " " NAG B1208 " - " ASN B 709 " " NAG B1209 " - " ASN B1074 " " NAG B1210 " - " ASN B 717 " " NAG B1211 " - " ASN B 801 " " NAG B1212 " - " ASN B1098 " " NAG B1213 " - " ASN B1134 " " NAG C1201 " - " ASN C 122 " " NAG C1202 " - " ASN C 234 " " NAG C1203 " - " ASN C 282 " " NAG C1204 " - " ASN C 343 " " NAG C1205 " - " ASN C 603 " " NAG C1206 " - " ASN C 616 " " NAG C1207 " - " ASN C 657 " " NAG C1208 " - " ASN C 709 " " NAG C1209 " - " ASN C 717 " " NAG C1210 " - " ASN C1074 " " NAG C1211 " - " ASN C 165 " " NAG C1212 " - " ASN C 801 " " NAG C1213 " - " ASN C1098 " " NAG C1214 " - " ASN C1134 " Time building additional restraints: 6.82 Conformation dependent library (CDL) restraints added in 3.4 seconds 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6394 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 53 sheets defined 20.1% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.10 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 385 through 389 removed outlier: 4.020A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.804A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.557A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.609A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 964 removed outlier: 4.116A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN A 954 " --> pdb=" O ASP A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.942A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.624A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.769A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.664A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.711A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.535A pdb=" N GLY B 908 " --> pdb=" O TYR B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.838A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.944A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.838A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.607A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.228A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 366 through 371 removed outlier: 3.754A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.743A pdb=" N LYS C 386 " --> pdb=" O SER C 383 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 383 through 387' Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.824A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN C 409 " --> pdb=" O GLU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.914A pdb=" N ASP C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 438 through 443' Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 755 Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.842A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.596A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.819A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.924A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.632A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 1032 removed outlier: 4.433A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.588A pdb=" N HIS D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.336A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR A 266 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 8.882A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.888A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.057A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.527A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.676A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.888A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.925A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN A 164 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 316 removed outlier: 7.057A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.523A pdb=" N LEU A 546 " --> pdb=" O PHE A 543 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AB1, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.649A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 573 through 575 removed outlier: 6.591A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 Processing sheet with id=AB6, first strand: chain 'A' and resid 703 through 704 removed outlier: 7.387A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.912A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.912A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.430A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC2, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AC3, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.743A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.577A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.773A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC6, first strand: chain 'B' and resid 116 through 120 removed outlier: 4.003A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE B 128 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 317 removed outlier: 6.995A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 327 through 328 Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.637A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLY B 431 " --> pdb=" O CYS B 379 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N CYS B 379 " --> pdb=" O GLY B 431 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL B 433 " --> pdb=" O PHE B 377 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE B 377 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALA B 435 " --> pdb=" O SER B 375 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 538 through 539 removed outlier: 5.748A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 656 removed outlier: 5.970A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.624A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 722 removed outlier: 6.650A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 725 through 728 removed outlier: 3.747A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.348A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.470A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY C 268 " --> pdb=" O TYR C 91 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE C 197 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 51 removed outlier: 6.479A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.941A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 318 removed outlier: 6.725A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 325 through 327 removed outlier: 3.607A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 355 removed outlier: 3.653A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.532A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.592A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 718 through 719 Processing sheet with id=AF1, first strand: chain 'C' and resid 718 through 719 removed outlier: 6.021A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF4, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.990A pdb=" N TYR D 80 " --> pdb=" O SER D 71 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 11 through 12 removed outlier: 7.552A pdb=" N MET D 34 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N THR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AF7, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.657A pdb=" N LEU E 20 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU E 81 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 58 through 60 removed outlier: 3.932A pdb=" N TYR E 59 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR E 50 " --> pdb=" O TYR E 59 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU E 46 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG E 38 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N THR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N MET E 34 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL E 37 " --> pdb=" O TYR E 95 " (cutoff:3.500A) 914 hydrogen bonds defined for protein. 2490 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.06 Time building geometry restraints manager: 8.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8733 1.34 - 1.47: 7281 1.47 - 1.60: 11731 1.60 - 1.73: 0 1.73 - 1.86: 160 Bond restraints: 27905 Sorted by residual: bond pdb=" C1 NAG B1203 " pdb=" O5 NAG B1203 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" C1 NAG B1204 " pdb=" O5 NAG B1204 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.53e+00 bond pdb=" C1 NAG C1204 " pdb=" O5 NAG C1204 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.47e+00 bond pdb=" CG LEU B 916 " pdb=" CD2 LEU B 916 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.41e+00 bond pdb=" C1 NAG B1209 " pdb=" O5 NAG B1209 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.07e+00 ... (remaining 27900 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 36818 2.28 - 4.56: 1018 4.56 - 6.84: 90 6.84 - 9.12: 15 9.12 - 11.40: 6 Bond angle restraints: 37947 Sorted by residual: angle pdb=" C GLU A 619 " pdb=" N VAL A 620 " pdb=" CA VAL A 620 " ideal model delta sigma weight residual 121.70 128.73 -7.03 1.80e+00 3.09e-01 1.53e+01 angle pdb=" C GLU B 619 " pdb=" N VAL B 620 " pdb=" CA VAL B 620 " ideal model delta sigma weight residual 121.70 128.38 -6.68 1.80e+00 3.09e-01 1.38e+01 angle pdb=" N ASP B 215 " pdb=" CA ASP B 215 " pdb=" C ASP B 215 " ideal model delta sigma weight residual 110.80 118.69 -7.89 2.13e+00 2.20e-01 1.37e+01 angle pdb=" C GLU C 619 " pdb=" N VAL C 620 " pdb=" CA VAL C 620 " ideal model delta sigma weight residual 121.70 128.26 -6.56 1.80e+00 3.09e-01 1.33e+01 angle pdb=" N ASN C 334 " pdb=" CA ASN C 334 " pdb=" C ASN C 334 " ideal model delta sigma weight residual 109.07 114.59 -5.52 1.61e+00 3.86e-01 1.18e+01 ... (remaining 37942 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.94: 16673 20.94 - 41.87: 376 41.87 - 62.80: 66 62.80 - 83.74: 5 83.74 - 104.67: 8 Dihedral angle restraints: 17128 sinusoidal: 7182 harmonic: 9946 Sorted by residual: dihedral pdb=" CA ARG B 214 " pdb=" C ARG B 214 " pdb=" N ASP B 215 " pdb=" CA ASP B 215 " ideal model delta harmonic sigma weight residual 180.00 151.88 28.12 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA PHE C 275 " pdb=" C PHE C 275 " pdb=" N LEU C 276 " pdb=" CA LEU C 276 " ideal model delta harmonic sigma weight residual 180.00 153.37 26.63 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA CYS C 525 " pdb=" C CYS C 525 " pdb=" N GLY C 526 " pdb=" CA GLY C 526 " ideal model delta harmonic sigma weight residual -180.00 -153.44 -26.56 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 17125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.163: 4360 0.163 - 0.326: 33 0.326 - 0.489: 5 0.489 - 0.652: 3 0.652 - 0.814: 1 Chirality restraints: 4402 Sorted by residual: chirality pdb=" C1 NAG C1202 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG C1202 " pdb=" O5 NAG C1202 " both_signs ideal model delta sigma weight residual False -2.40 -1.59 -0.81 2.00e-01 2.50e+01 1.66e+01 chirality pdb=" C1 NAG A1212 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG A1212 " pdb=" O5 NAG A1212 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.57e+00 chirality pdb=" C1 NAG C1208 " pdb=" ND2 ASN C 709 " pdb=" C2 NAG C1208 " pdb=" O5 NAG C1208 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.48e+00 ... (remaining 4399 not shown) Planarity restraints: 4902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 801 " -0.091 2.00e-02 2.50e+03 9.33e-02 1.09e+02 pdb=" CG ASN C 801 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN C 801 " 0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN C 801 " 0.152 2.00e-02 2.50e+03 pdb=" C1 NAG C1212 " -0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1212 " 0.081 2.00e-02 2.50e+03 6.66e-02 5.54e+01 pdb=" C7 NAG C1212 " -0.022 2.00e-02 2.50e+03 pdb=" C8 NAG C1212 " 0.061 2.00e-02 2.50e+03 pdb=" N2 NAG C1212 " -0.105 2.00e-02 2.50e+03 pdb=" O7 NAG C1212 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 958 " 0.015 2.00e-02 2.50e+03 2.91e-02 8.49e+00 pdb=" C ALA A 958 " -0.050 2.00e-02 2.50e+03 pdb=" O ALA A 958 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU A 959 " 0.017 2.00e-02 2.50e+03 ... (remaining 4899 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4080 2.76 - 3.30: 23940 3.30 - 3.83: 44108 3.83 - 4.37: 50218 4.37 - 4.90: 88591 Nonbonded interactions: 210937 Sorted by model distance: nonbonded pdb=" OG1 THR A 108 " pdb=" O ASN A 234 " model vdw 2.227 3.040 nonbonded pdb=" OG1 THR A 645 " pdb=" O GLY A 648 " model vdw 2.279 3.040 nonbonded pdb=" OG1 THR C 393 " pdb=" O GLU C 516 " model vdw 2.289 3.040 nonbonded pdb=" OG1 THR B 393 " pdb=" O GLU B 516 " model vdw 2.300 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.302 3.040 ... (remaining 210932 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' selection = chain 'B' selection = (chain 'C' and (resid 14 through 1145 or resid 1201 through 1213)) } ncs_group { reference = chain 'D' selection = chain 'E' } 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.010 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 62.450 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.110 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 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 : 0.010 0.859 27986 Z= 0.466 Angle : 0.984 33.399 38149 Z= 0.497 Chirality : 0.061 0.814 4402 Planarity : 0.006 0.067 4862 Dihedral : 9.934 104.675 10611 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.07 % Allowed : 1.28 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.12), residues: 3382 helix: -1.90 (0.16), residues: 620 sheet: -2.36 (0.18), residues: 684 loop : -2.95 (0.11), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 64 HIS 0.009 0.002 HIS C1064 PHE 0.047 0.004 PHE A 906 TYR 0.042 0.003 TYR B 204 ARG 0.012 0.001 ARG C 815 Details of bonding type rmsd link_NAG-ASN : bond 0.04759 ( 40) link_NAG-ASN : angle 6.53920 ( 120) hydrogen bonds : bond 0.21012 ( 893) hydrogen bonds : angle 8.68445 ( 2490) SS BOND : bond 0.17315 ( 41) SS BOND : angle 6.46226 ( 82) covalent geometry : bond 0.00742 (27905) covalent geometry : angle 0.86534 (37947) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 528 time to evaluate : 3.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 PRO cc_start: 0.7086 (Cg_endo) cc_final: 0.6687 (Cg_exo) REVERT: A 153 MET cc_start: 0.4109 (ptp) cc_final: 0.3547 (tpt) REVERT: A 238 PHE cc_start: 0.7346 (p90) cc_final: 0.6953 (p90) REVERT: A 409 GLN cc_start: 0.8267 (mt0) cc_final: 0.8061 (mt0) REVERT: A 503 VAL cc_start: 0.8336 (m) cc_final: 0.8088 (t) REVERT: A 734 THR cc_start: 0.8617 (m) cc_final: 0.8299 (p) REVERT: B 177 MET cc_start: -0.0442 (tpp) cc_final: -0.0977 (mtt) REVERT: B 453 TYR cc_start: 0.4873 (p90) cc_final: 0.4197 (p90) REVERT: B 547 THR cc_start: 0.7946 (m) cc_final: 0.7372 (p) REVERT: B 574 ASP cc_start: 0.6844 (t70) cc_final: 0.6587 (t0) REVERT: B 1138 TYR cc_start: 0.6986 (t80) cc_final: 0.6634 (t80) REVERT: C 133 PHE cc_start: 0.7038 (m-10) cc_final: 0.6630 (m-10) REVERT: C 269 TYR cc_start: 0.6932 (m-10) cc_final: 0.6658 (m-10) REVERT: C 340 GLU cc_start: 0.6355 (mt-10) cc_final: 0.6101 (mp0) REVERT: C 614 ASP cc_start: 0.6362 (t70) cc_final: 0.6072 (t0) REVERT: C 809 PRO cc_start: 0.6620 (Cg_endo) cc_final: 0.6246 (Cg_exo) REVERT: C 859 THR cc_start: 0.8827 (m) cc_final: 0.8513 (p) REVERT: D 4 LEU cc_start: 0.7182 (mt) cc_final: 0.6567 (mt) REVERT: D 18 LEU cc_start: 0.6265 (mt) cc_final: 0.5870 (tp) REVERT: D 20 LEU cc_start: 0.7446 (mt) cc_final: 0.7222 (mp) REVERT: D 38 ARG cc_start: 0.7634 (ptt180) cc_final: 0.7342 (ptt90) REVERT: D 39 GLN cc_start: 0.7383 (tt0) cc_final: 0.6831 (tm-30) REVERT: D 73 ASP cc_start: 0.6916 (t0) cc_final: 0.6422 (t0) REVERT: D 99 ASP cc_start: 0.7690 (t0) cc_final: 0.7482 (t0) REVERT: D 116 GLN cc_start: 0.7763 (tp40) cc_final: 0.7205 (tp40) outliers start: 2 outliers final: 0 residues processed: 530 average time/residue: 0.4313 time to fit residues: 349.1096 Evaluate side-chains 253 residues out of total 2977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 3.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 288 optimal weight: 4.9990 chunk 259 optimal weight: 40.0000 chunk 143 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 268 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 199 optimal weight: 0.9990 chunk 310 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 239 GLN A 448 ASN A 450 ASN A 474 GLN A 501 ASN A 544 ASN A 580 GLN A 613 GLN A 658 ASN A 856 ASN A 965 GLN A1005 GLN A1101 HIS B 234 ASN B 354 ASN B 655 HIS B 965 GLN B1048 HIS C 69 HIS C 81 ASN C 207 HIS C 239 GLN C 540 ASN C 655 HIS C 804 GLN C 949 GLN C1010 GLN C1101 HIS D 32 HIS E 32 HIS E 116 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.161935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.108659 restraints weight = 47058.410| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.71 r_work: 0.3198 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 27986 Z= 0.263 Angle : 0.741 12.025 38149 Z= 0.370 Chirality : 0.050 0.495 4402 Planarity : 0.005 0.045 4862 Dihedral : 8.820 122.994 4510 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.15 % Allowed : 6.48 % Favored : 91.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.13), residues: 3382 helix: -0.15 (0.20), residues: 621 sheet: -2.08 (0.18), residues: 713 loop : -2.58 (0.12), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 109 HIS 0.008 0.002 HIS B1058 PHE 0.023 0.003 PHE B 906 TYR 0.026 0.002 TYR B 204 ARG 0.005 0.001 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00727 ( 40) link_NAG-ASN : angle 4.01063 ( 120) hydrogen bonds : bond 0.05663 ( 893) hydrogen bonds : angle 6.15878 ( 2490) SS BOND : bond 0.00577 ( 41) SS BOND : angle 1.65327 ( 82) covalent geometry : bond 0.00622 (27905) covalent geometry : angle 0.70375 (37947) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 264 time to evaluate : 2.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8985 (mt) cc_final: 0.8755 (mp) REVERT: A 153 MET cc_start: 0.3971 (ptp) cc_final: 0.3534 (tpt) REVERT: A 378 LYS cc_start: 0.8635 (tptt) cc_final: 0.8334 (tppt) REVERT: A 415 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.7836 (t) REVERT: A 441 LEU cc_start: 0.9156 (tp) cc_final: 0.8853 (mt) REVERT: A 734 THR cc_start: 0.9037 (m) cc_final: 0.8603 (p) REVERT: B 150 LYS cc_start: 0.6425 (pttt) cc_final: 0.6099 (pttt) REVERT: B 177 MET cc_start: -0.0470 (tpp) cc_final: -0.1013 (mtt) REVERT: B 200 TYR cc_start: 0.6809 (m-80) cc_final: 0.6268 (t80) REVERT: B 226 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7845 (tt) REVERT: B 355 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7838 (mmm160) REVERT: B 392 PHE cc_start: 0.7763 (m-80) cc_final: 0.7542 (m-80) REVERT: B 453 TYR cc_start: 0.4801 (p90) cc_final: 0.4356 (p90) REVERT: B 532 ASN cc_start: 0.7004 (t0) cc_final: 0.6757 (t0) REVERT: B 547 THR cc_start: 0.7967 (m) cc_final: 0.7460 (p) REVERT: B 660 TYR cc_start: 0.8979 (m-80) cc_final: 0.8631 (m-10) REVERT: B 800 PHE cc_start: 0.9188 (OUTLIER) cc_final: 0.8917 (m-80) REVERT: B 1138 TYR cc_start: 0.7737 (t80) cc_final: 0.7252 (t80) REVERT: C 133 PHE cc_start: 0.7070 (m-10) cc_final: 0.6662 (m-10) REVERT: C 269 TYR cc_start: 0.7448 (m-10) cc_final: 0.7035 (m-10) REVERT: C 340 GLU cc_start: 0.6659 (mt-10) cc_final: 0.6237 (mp0) REVERT: C 571 ASP cc_start: 0.8060 (t0) cc_final: 0.7705 (t0) REVERT: C 614 ASP cc_start: 0.7416 (t70) cc_final: 0.6971 (t0) REVERT: C 809 PRO cc_start: 0.6595 (Cg_endo) cc_final: 0.6230 (Cg_exo) REVERT: C 859 THR cc_start: 0.9023 (m) cc_final: 0.8747 (p) REVERT: C 988 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7777 (mp0) REVERT: D 36 TRP cc_start: 0.6612 (m100) cc_final: 0.6132 (m100) REVERT: D 38 ARG cc_start: 0.7999 (ptt180) cc_final: 0.7695 (ptm160) REVERT: D 39 GLN cc_start: 0.7346 (tt0) cc_final: 0.6920 (mp10) REVERT: D 58 THR cc_start: 0.7983 (t) cc_final: 0.7361 (t) REVERT: D 73 ASP cc_start: 0.7445 (t0) cc_final: 0.7154 (t0) REVERT: D 93 MET cc_start: 0.6815 (tpt) cc_final: 0.4925 (tmm) REVERT: D 95 TYR cc_start: 0.7792 (m-80) cc_final: 0.7179 (m-10) REVERT: D 104 ASP cc_start: 0.7150 (t0) cc_final: 0.6843 (t0) outliers start: 64 outliers final: 32 residues processed: 311 average time/residue: 0.4040 time to fit residues: 205.3294 Evaluate side-chains 249 residues out of total 2977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 212 time to evaluate : 3.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 800 PHE Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 64 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 129 optimal weight: 10.0000 chunk 268 optimal weight: 9.9990 chunk 228 optimal weight: 30.0000 chunk 84 optimal weight: 0.9980 chunk 326 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 266 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 136 optimal weight: 20.0000 chunk 109 optimal weight: 7.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 450 ASN A1005 GLN C 99 ASN C 146 HIS C 207 HIS C 955 ASN D 32 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.161418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.108326 restraints weight = 47022.523| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.88 r_work: 0.3176 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 27986 Z= 0.219 Angle : 0.676 11.202 38149 Z= 0.334 Chirality : 0.047 0.465 4402 Planarity : 0.004 0.043 4862 Dihedral : 7.930 114.196 4510 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.32 % Allowed : 7.83 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.13), residues: 3382 helix: 0.54 (0.21), residues: 625 sheet: -1.82 (0.19), residues: 702 loop : -2.38 (0.12), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 109 HIS 0.006 0.001 HIS C 207 PHE 0.027 0.002 PHE C 135 TYR 0.019 0.002 TYR A 789 ARG 0.005 0.001 ARG C 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00584 ( 40) link_NAG-ASN : angle 3.90121 ( 120) hydrogen bonds : bond 0.05075 ( 893) hydrogen bonds : angle 5.72350 ( 2490) SS BOND : bond 0.00558 ( 41) SS BOND : angle 1.60319 ( 82) covalent geometry : bond 0.00517 (27905) covalent geometry : angle 0.63699 (37947) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 233 time to evaluate : 3.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9000 (mt) cc_final: 0.8783 (mp) REVERT: A 153 MET cc_start: 0.3862 (ptp) cc_final: 0.3422 (tpt) REVERT: A 177 MET cc_start: 0.1581 (tpp) cc_final: 0.1243 (ttm) REVERT: A 309 GLU cc_start: 0.7455 (pm20) cc_final: 0.7197 (pm20) REVERT: A 378 LYS cc_start: 0.8620 (tptt) cc_final: 0.8305 (tppt) REVERT: A 734 THR cc_start: 0.9027 (m) cc_final: 0.8581 (p) REVERT: A 983 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.7166 (mtt180) REVERT: B 150 LYS cc_start: 0.6467 (pttt) cc_final: 0.6174 (pttt) REVERT: B 177 MET cc_start: -0.0430 (tpp) cc_final: -0.1037 (mtt) REVERT: B 200 TYR cc_start: 0.6913 (m-80) cc_final: 0.6377 (t80) REVERT: B 226 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7812 (tt) REVERT: B 271 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7775 (mt0) REVERT: B 392 PHE cc_start: 0.7725 (m-80) cc_final: 0.7506 (m-80) REVERT: B 453 TYR cc_start: 0.4790 (p90) cc_final: 0.4407 (p90) REVERT: B 532 ASN cc_start: 0.7122 (t0) cc_final: 0.6864 (t0) REVERT: B 547 THR cc_start: 0.8014 (m) cc_final: 0.7519 (p) REVERT: B 660 TYR cc_start: 0.8974 (m-80) cc_final: 0.8665 (m-10) REVERT: B 979 ASP cc_start: 0.8084 (t0) cc_final: 0.7837 (t0) REVERT: B 983 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.8129 (mmm-85) REVERT: B 1138 TYR cc_start: 0.7786 (t80) cc_final: 0.7301 (t80) REVERT: C 133 PHE cc_start: 0.6971 (m-10) cc_final: 0.6610 (m-10) REVERT: C 269 TYR cc_start: 0.7458 (m-10) cc_final: 0.7023 (m-10) REVERT: C 340 GLU cc_start: 0.6531 (mt-10) cc_final: 0.6213 (mp0) REVERT: C 571 ASP cc_start: 0.8153 (t0) cc_final: 0.7833 (t0) REVERT: C 614 ASP cc_start: 0.7454 (t70) cc_final: 0.7006 (t0) REVERT: C 809 PRO cc_start: 0.6560 (Cg_endo) cc_final: 0.6193 (Cg_exo) REVERT: C 859 THR cc_start: 0.9049 (m) cc_final: 0.8818 (p) REVERT: D 36 TRP cc_start: 0.6612 (m100) cc_final: 0.5991 (m100) REVERT: D 38 ARG cc_start: 0.7774 (ptt180) cc_final: 0.7480 (ptm160) REVERT: D 39 GLN cc_start: 0.7356 (tt0) cc_final: 0.6916 (mp10) REVERT: D 67 ARG cc_start: 0.6083 (mtp180) cc_final: 0.5583 (mtp180) REVERT: D 73 ASP cc_start: 0.7475 (t0) cc_final: 0.7198 (t0) REVERT: D 93 MET cc_start: 0.6624 (tpt) cc_final: 0.4797 (tmm) REVERT: D 95 TYR cc_start: 0.7533 (m-80) cc_final: 0.6282 (m-10) REVERT: D 104 ASP cc_start: 0.7089 (t0) cc_final: 0.6686 (t0) outliers start: 69 outliers final: 47 residues processed: 287 average time/residue: 0.4504 time to fit residues: 214.3241 Evaluate side-chains 251 residues out of total 2977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 200 time to evaluate : 2.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 64 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 322 optimal weight: 0.5980 chunk 217 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 314 optimal weight: 0.0670 chunk 317 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 223 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 182 optimal weight: 4.9990 chunk 262 optimal weight: 0.3980 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 394 ASN A 450 ASN A1005 GLN B 245 HIS C 49 HIS C 207 HIS C 450 ASN D 32 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.164653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.113522 restraints weight = 47330.592| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.75 r_work: 0.3253 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 27986 Z= 0.099 Angle : 0.569 11.762 38149 Z= 0.278 Chirality : 0.045 0.427 4402 Planarity : 0.004 0.042 4862 Dihedral : 6.910 113.088 4510 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.71 % Allowed : 8.97 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.14), residues: 3382 helix: 1.24 (0.21), residues: 625 sheet: -1.51 (0.19), residues: 684 loop : -2.18 (0.12), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 109 HIS 0.007 0.001 HIS C 207 PHE 0.032 0.001 PHE C 135 TYR 0.022 0.001 TYR A1138 ARG 0.005 0.000 ARG D 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00560 ( 40) link_NAG-ASN : angle 3.61468 ( 120) hydrogen bonds : bond 0.03851 ( 893) hydrogen bonds : angle 5.16945 ( 2490) SS BOND : bond 0.00374 ( 41) SS BOND : angle 1.25350 ( 82) covalent geometry : bond 0.00213 (27905) covalent geometry : angle 0.53000 (37947) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 248 time to evaluate : 5.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.3768 (ptp) cc_final: 0.3311 (tpt) REVERT: A 177 MET cc_start: 0.1328 (tpp) cc_final: 0.0958 (ttm) REVERT: A 309 GLU cc_start: 0.7417 (pm20) cc_final: 0.7068 (pm20) REVERT: A 378 LYS cc_start: 0.8552 (tptt) cc_final: 0.8151 (tppt) REVERT: A 529 LYS cc_start: 0.8902 (tttt) cc_final: 0.8686 (mmmt) REVERT: A 734 THR cc_start: 0.9089 (m) cc_final: 0.8712 (p) REVERT: B 150 LYS cc_start: 0.6446 (pttt) cc_final: 0.6141 (pttt) REVERT: B 177 MET cc_start: -0.0438 (tpp) cc_final: -0.1016 (mtt) REVERT: B 226 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7790 (tt) REVERT: B 271 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7811 (mt0) REVERT: B 392 PHE cc_start: 0.7685 (m-80) cc_final: 0.7445 (m-80) REVERT: B 453 TYR cc_start: 0.4589 (p90) cc_final: 0.4267 (p90) REVERT: B 532 ASN cc_start: 0.6924 (t0) cc_final: 0.6639 (t0) REVERT: B 547 THR cc_start: 0.7813 (m) cc_final: 0.7328 (p) REVERT: B 660 TYR cc_start: 0.8981 (m-80) cc_final: 0.8705 (m-10) REVERT: B 904 TYR cc_start: 0.7771 (m-10) cc_final: 0.7219 (m-10) REVERT: B 1119 ASN cc_start: 0.8722 (m-40) cc_final: 0.8502 (m110) REVERT: B 1138 TYR cc_start: 0.7757 (t80) cc_final: 0.7355 (t80) REVERT: C 133 PHE cc_start: 0.6998 (m-10) cc_final: 0.6684 (m-10) REVERT: C 269 TYR cc_start: 0.7288 (m-10) cc_final: 0.7080 (m-10) REVERT: C 340 GLU cc_start: 0.6708 (mt-10) cc_final: 0.6339 (mp0) REVERT: C 571 ASP cc_start: 0.8162 (t0) cc_final: 0.7834 (t0) REVERT: C 614 ASP cc_start: 0.7147 (t70) cc_final: 0.6664 (t0) REVERT: C 809 PRO cc_start: 0.6745 (Cg_endo) cc_final: 0.6397 (Cg_exo) REVERT: C 859 THR cc_start: 0.9069 (m) cc_final: 0.8839 (p) REVERT: D 13 GLN cc_start: 0.7423 (mp10) cc_final: 0.7212 (mp10) REVERT: D 36 TRP cc_start: 0.6519 (m100) cc_final: 0.5795 (m100) REVERT: D 38 ARG cc_start: 0.8059 (ptt180) cc_final: 0.7637 (ptm160) REVERT: D 39 GLN cc_start: 0.7350 (tt0) cc_final: 0.6848 (mp10) REVERT: D 67 ARG cc_start: 0.5762 (mtp180) cc_final: 0.5383 (mtp180) REVERT: D 73 ASP cc_start: 0.7654 (t0) cc_final: 0.7376 (t0) REVERT: D 93 MET cc_start: 0.6592 (tpt) cc_final: 0.4657 (tmm) REVERT: D 104 ASP cc_start: 0.7264 (t0) cc_final: 0.7005 (t0) REVERT: D 105 TRP cc_start: 0.8388 (p-90) cc_final: 0.8085 (p-90) outliers start: 51 outliers final: 28 residues processed: 286 average time/residue: 0.4991 time to fit residues: 237.0435 Evaluate side-chains 236 residues out of total 2977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 206 time to evaluate : 5.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain E residue 64 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 144 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 308 optimal weight: 0.2980 chunk 317 optimal weight: 9.9990 chunk 214 optimal weight: 10.0000 chunk 210 optimal weight: 1.9990 chunk 298 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 200 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A1005 GLN C 207 HIS C 354 ASN D 32 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.161509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.108862 restraints weight = 47133.358| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.78 r_work: 0.3182 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 27986 Z= 0.200 Angle : 0.627 11.349 38149 Z= 0.307 Chirality : 0.046 0.449 4402 Planarity : 0.004 0.041 4862 Dihedral : 6.846 112.193 4510 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.45 % Allowed : 9.47 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.14), residues: 3382 helix: 1.16 (0.21), residues: 630 sheet: -1.41 (0.19), residues: 675 loop : -2.18 (0.12), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 109 HIS 0.006 0.001 HIS B1058 PHE 0.027 0.002 PHE C 135 TYR 0.017 0.002 TYR A 265 ARG 0.005 0.000 ARG D 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00508 ( 40) link_NAG-ASN : angle 3.73246 ( 120) hydrogen bonds : bond 0.04555 ( 893) hydrogen bonds : angle 5.24559 ( 2490) SS BOND : bond 0.00481 ( 41) SS BOND : angle 1.53696 ( 82) covalent geometry : bond 0.00477 (27905) covalent geometry : angle 0.58793 (37947) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 207 time to evaluate : 2.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.3777 (ptp) cc_final: 0.3346 (tpt) REVERT: A 177 MET cc_start: 0.1431 (tpp) cc_final: 0.0961 (ttm) REVERT: A 378 LYS cc_start: 0.8608 (tptt) cc_final: 0.8292 (tppt) REVERT: A 734 THR cc_start: 0.9069 (m) cc_final: 0.8661 (p) REVERT: B 150 LYS cc_start: 0.6708 (pttt) cc_final: 0.6356 (pttt) REVERT: B 177 MET cc_start: -0.0285 (tpp) cc_final: -0.0942 (mtt) REVERT: B 200 TYR cc_start: 0.6898 (m-80) cc_final: 0.6670 (t80) REVERT: B 226 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7789 (tt) REVERT: B 271 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7774 (mt0) REVERT: B 392 PHE cc_start: 0.7839 (m-80) cc_final: 0.7636 (m-80) REVERT: B 453 TYR cc_start: 0.4705 (p90) cc_final: 0.4340 (p90) REVERT: B 532 ASN cc_start: 0.7062 (t0) cc_final: 0.6735 (t0) REVERT: B 547 THR cc_start: 0.8038 (m) cc_final: 0.7537 (p) REVERT: B 660 TYR cc_start: 0.9004 (m-80) cc_final: 0.8753 (m-10) REVERT: B 904 TYR cc_start: 0.7735 (m-10) cc_final: 0.6985 (m-10) REVERT: B 1138 TYR cc_start: 0.7730 (t80) cc_final: 0.7417 (t80) REVERT: C 133 PHE cc_start: 0.6983 (m-10) cc_final: 0.6692 (m-10) REVERT: C 269 TYR cc_start: 0.7545 (m-10) cc_final: 0.7023 (m-10) REVERT: C 340 GLU cc_start: 0.6724 (mt-10) cc_final: 0.6351 (mp0) REVERT: C 571 ASP cc_start: 0.8106 (t0) cc_final: 0.7760 (t0) REVERT: C 614 ASP cc_start: 0.7277 (t70) cc_final: 0.6886 (t0) REVERT: C 809 PRO cc_start: 0.6647 (Cg_endo) cc_final: 0.6282 (Cg_exo) REVERT: D 3 GLN cc_start: 0.6358 (mm-40) cc_final: 0.6120 (mm110) REVERT: D 36 TRP cc_start: 0.6507 (m100) cc_final: 0.5849 (m100) REVERT: D 38 ARG cc_start: 0.7891 (ptt180) cc_final: 0.7314 (ptm160) REVERT: D 39 GLN cc_start: 0.7376 (tt0) cc_final: 0.6911 (mp10) REVERT: D 73 ASP cc_start: 0.7650 (t0) cc_final: 0.7409 (t0) REVERT: D 90 ASP cc_start: 0.5836 (OUTLIER) cc_final: 0.5512 (t0) REVERT: D 95 TYR cc_start: 0.7348 (m-80) cc_final: 0.6965 (m-10) REVERT: D 104 ASP cc_start: 0.7288 (t0) cc_final: 0.6991 (t0) outliers start: 73 outliers final: 53 residues processed: 262 average time/residue: 0.3622 time to fit residues: 155.4696 Evaluate side-chains 251 residues out of total 2977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 195 time to evaluate : 2.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain E residue 64 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 300 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 334 optimal weight: 9.9990 chunk 73 optimal weight: 0.9990 chunk 127 optimal weight: 10.0000 chunk 313 optimal weight: 0.6980 chunk 305 optimal weight: 1.9990 chunk 282 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 45 optimal weight: 20.0000 chunk 34 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN A1005 GLN C 207 HIS D 32 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.163369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.113405 restraints weight = 47152.763| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.75 r_work: 0.3222 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 27986 Z= 0.118 Angle : 0.562 11.691 38149 Z= 0.275 Chirality : 0.044 0.426 4402 Planarity : 0.003 0.041 4862 Dihedral : 6.489 111.768 4510 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.12 % Allowed : 10.04 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.14), residues: 3382 helix: 1.48 (0.22), residues: 623 sheet: -1.31 (0.19), residues: 676 loop : -2.06 (0.12), residues: 2083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 109 HIS 0.004 0.001 HIS C 207 PHE 0.024 0.001 PHE C 135 TYR 0.017 0.001 TYR A1138 ARG 0.008 0.000 ARG B 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00526 ( 40) link_NAG-ASN : angle 3.52508 ( 120) hydrogen bonds : bond 0.03911 ( 893) hydrogen bonds : angle 4.98477 ( 2490) SS BOND : bond 0.00353 ( 41) SS BOND : angle 1.45692 ( 82) covalent geometry : bond 0.00271 (27905) covalent geometry : angle 0.52284 (37947) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 210 time to evaluate : 2.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7966 (t70) REVERT: A 153 MET cc_start: 0.3772 (ptp) cc_final: 0.3316 (tpt) REVERT: A 177 MET cc_start: 0.1328 (tpp) cc_final: 0.0885 (ttm) REVERT: A 378 LYS cc_start: 0.8565 (tptt) cc_final: 0.8154 (tppt) REVERT: A 734 THR cc_start: 0.9145 (m) cc_final: 0.8736 (p) REVERT: B 150 LYS cc_start: 0.6453 (pttt) cc_final: 0.6198 (pttt) REVERT: B 177 MET cc_start: -0.0364 (tpp) cc_final: -0.1074 (mtt) REVERT: B 200 TYR cc_start: 0.6823 (m-80) cc_final: 0.6580 (t80) REVERT: B 226 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7810 (tt) REVERT: B 271 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7818 (mt0) REVERT: B 453 TYR cc_start: 0.4606 (p90) cc_final: 0.4285 (p90) REVERT: B 532 ASN cc_start: 0.6999 (t0) cc_final: 0.6627 (t0) REVERT: B 547 THR cc_start: 0.7985 (m) cc_final: 0.7483 (p) REVERT: B 660 TYR cc_start: 0.8993 (m-80) cc_final: 0.8741 (m-10) REVERT: B 904 TYR cc_start: 0.7761 (m-10) cc_final: 0.6991 (m-10) REVERT: B 1138 TYR cc_start: 0.7712 (t80) cc_final: 0.7226 (t80) REVERT: C 133 PHE cc_start: 0.6967 (m-10) cc_final: 0.6638 (m-10) REVERT: C 170 TYR cc_start: 0.6556 (t80) cc_final: 0.6167 (t80) REVERT: C 269 TYR cc_start: 0.7513 (m-10) cc_final: 0.7083 (m-10) REVERT: C 340 GLU cc_start: 0.6742 (mt-10) cc_final: 0.6364 (mp0) REVERT: C 571 ASP cc_start: 0.8137 (t0) cc_final: 0.7795 (t0) REVERT: C 574 ASP cc_start: 0.7580 (p0) cc_final: 0.7314 (p0) REVERT: C 809 PRO cc_start: 0.6615 (Cg_endo) cc_final: 0.6256 (Cg_exo) REVERT: D 3 GLN cc_start: 0.6012 (mm-40) cc_final: 0.5635 (mm110) REVERT: D 13 GLN cc_start: 0.7397 (mp10) cc_final: 0.7054 (mp10) REVERT: D 36 TRP cc_start: 0.6467 (m100) cc_final: 0.5762 (m100) REVERT: D 38 ARG cc_start: 0.7817 (ptt180) cc_final: 0.7400 (ptm160) REVERT: D 39 GLN cc_start: 0.7391 (tt0) cc_final: 0.6941 (mp10) REVERT: D 73 ASP cc_start: 0.7604 (t0) cc_final: 0.7316 (t0) REVERT: D 95 TYR cc_start: 0.7257 (m-80) cc_final: 0.6780 (m-10) REVERT: D 104 ASP cc_start: 0.7410 (t0) cc_final: 0.7156 (t0) outliers start: 63 outliers final: 47 residues processed: 261 average time/residue: 0.5190 time to fit residues: 221.8139 Evaluate side-chains 249 residues out of total 2977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 199 time to evaluate : 3.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 58 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 48 optimal weight: 1.9990 chunk 247 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 218 optimal weight: 0.5980 chunk 272 optimal weight: 3.9990 chunk 337 optimal weight: 30.0000 chunk 315 optimal weight: 9.9990 chunk 237 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 327 optimal weight: 9.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN D 32 HIS D 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.162470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.112226 restraints weight = 46841.721| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.88 r_work: 0.3188 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 27986 Z= 0.148 Angle : 0.578 11.438 38149 Z= 0.282 Chirality : 0.045 0.430 4402 Planarity : 0.004 0.039 4862 Dihedral : 6.376 110.713 4510 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.18 % Allowed : 9.98 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.14), residues: 3382 helix: 1.48 (0.22), residues: 623 sheet: -1.18 (0.19), residues: 679 loop : -2.01 (0.12), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 886 HIS 0.004 0.001 HIS B1058 PHE 0.021 0.001 PHE C 135 TYR 0.016 0.001 TYR A 265 ARG 0.006 0.000 ARG B 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00490 ( 40) link_NAG-ASN : angle 3.52215 ( 120) hydrogen bonds : bond 0.04110 ( 893) hydrogen bonds : angle 4.95005 ( 2490) SS BOND : bond 0.00456 ( 41) SS BOND : angle 1.49929 ( 82) covalent geometry : bond 0.00349 (27905) covalent geometry : angle 0.53980 (37947) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 197 time to evaluate : 2.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.8003 (t70) REVERT: A 153 MET cc_start: 0.3753 (ptp) cc_final: 0.3289 (tpt) REVERT: A 177 MET cc_start: 0.1284 (tpp) cc_final: 0.0813 (ttm) REVERT: A 269 TYR cc_start: 0.7506 (m-80) cc_final: 0.7109 (m-80) REVERT: A 378 LYS cc_start: 0.8605 (tptt) cc_final: 0.8205 (tppt) REVERT: A 734 THR cc_start: 0.9184 (m) cc_final: 0.8723 (p) REVERT: B 150 LYS cc_start: 0.6641 (pttt) cc_final: 0.6355 (ptmt) REVERT: B 177 MET cc_start: -0.0304 (tpp) cc_final: -0.1045 (mtt) REVERT: B 200 TYR cc_start: 0.6950 (m-80) cc_final: 0.6648 (t80) REVERT: B 226 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7779 (tt) REVERT: B 271 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7807 (mt0) REVERT: B 338 PHE cc_start: 0.7339 (OUTLIER) cc_final: 0.6556 (m-80) REVERT: B 453 TYR cc_start: 0.4607 (p90) cc_final: 0.4285 (p90) REVERT: B 532 ASN cc_start: 0.7024 (t0) cc_final: 0.6606 (t0) REVERT: B 547 THR cc_start: 0.8167 (m) cc_final: 0.7628 (p) REVERT: B 660 TYR cc_start: 0.9014 (m-80) cc_final: 0.8773 (m-10) REVERT: B 904 TYR cc_start: 0.7831 (m-10) cc_final: 0.7063 (m-10) REVERT: B 1138 TYR cc_start: 0.7735 (t80) cc_final: 0.7408 (t80) REVERT: C 133 PHE cc_start: 0.6979 (m-10) cc_final: 0.6685 (m-10) REVERT: C 170 TYR cc_start: 0.6646 (t80) cc_final: 0.6268 (t80) REVERT: C 269 TYR cc_start: 0.7683 (m-10) cc_final: 0.7103 (m-10) REVERT: C 740 MET cc_start: 0.9123 (tpt) cc_final: 0.8844 (tpp) REVERT: C 809 PRO cc_start: 0.6538 (Cg_endo) cc_final: 0.6186 (Cg_exo) REVERT: C 916 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8445 (tp) REVERT: D 3 GLN cc_start: 0.6161 (mm-40) cc_final: 0.5893 (mm-40) REVERT: D 36 TRP cc_start: 0.6465 (m100) cc_final: 0.5794 (m100) REVERT: D 38 ARG cc_start: 0.7796 (ptt180) cc_final: 0.7348 (ptm160) REVERT: D 39 GLN cc_start: 0.7604 (tt0) cc_final: 0.7255 (mp10) REVERT: D 73 ASP cc_start: 0.7606 (t0) cc_final: 0.7311 (t0) REVERT: D 85 SER cc_start: 0.8102 (m) cc_final: 0.7820 (t) REVERT: D 95 TYR cc_start: 0.7273 (m-80) cc_final: 0.6856 (m-10) REVERT: D 104 ASP cc_start: 0.7446 (t0) cc_final: 0.7192 (t0) outliers start: 65 outliers final: 52 residues processed: 248 average time/residue: 0.3632 time to fit residues: 149.0569 Evaluate side-chains 247 residues out of total 2977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 190 time to evaluate : 2.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 108 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 230 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 173 optimal weight: 0.9980 chunk 170 optimal weight: 10.0000 chunk 169 optimal weight: 7.9990 chunk 102 optimal weight: 0.9990 chunk 99 optimal weight: 0.0770 chunk 267 optimal weight: 10.0000 chunk 328 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 chunk 201 optimal weight: 7.9990 overall best weight: 2.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.162085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.109912 restraints weight = 46984.209| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.72 r_work: 0.3194 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 27986 Z= 0.162 Angle : 0.580 11.413 38149 Z= 0.284 Chirality : 0.045 0.429 4402 Planarity : 0.003 0.040 4862 Dihedral : 6.355 110.532 4510 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.35 % Allowed : 9.88 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.14), residues: 3382 helix: 1.50 (0.22), residues: 623 sheet: -1.15 (0.19), residues: 679 loop : -1.98 (0.12), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 886 HIS 0.004 0.001 HIS B1058 PHE 0.019 0.001 PHE B 135 TYR 0.016 0.001 TYR A 265 ARG 0.006 0.000 ARG B 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 40) link_NAG-ASN : angle 3.48496 ( 120) hydrogen bonds : bond 0.04183 ( 893) hydrogen bonds : angle 4.95852 ( 2490) SS BOND : bond 0.00430 ( 41) SS BOND : angle 1.47032 ( 82) covalent geometry : bond 0.00383 (27905) covalent geometry : angle 0.54327 (37947) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 199 time to evaluate : 2.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ASN cc_start: 0.6959 (m-40) cc_final: 0.6686 (t0) REVERT: A 153 MET cc_start: 0.3749 (ptp) cc_final: 0.3222 (tpt) REVERT: A 177 MET cc_start: 0.1342 (tpp) cc_final: 0.0861 (ttm) REVERT: A 241 LEU cc_start: 0.8159 (mt) cc_final: 0.7957 (pp) REVERT: A 378 LYS cc_start: 0.8594 (tptt) cc_final: 0.8267 (tppt) REVERT: A 460 ASN cc_start: 0.8119 (OUTLIER) cc_final: 0.7571 (m-40) REVERT: A 734 THR cc_start: 0.9090 (m) cc_final: 0.8648 (p) REVERT: B 150 LYS cc_start: 0.6652 (pttt) cc_final: 0.6364 (ptmt) REVERT: B 177 MET cc_start: -0.0384 (tpp) cc_final: -0.1185 (mtt) REVERT: B 226 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7765 (tt) REVERT: B 271 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7748 (mt0) REVERT: B 338 PHE cc_start: 0.7155 (OUTLIER) cc_final: 0.6457 (m-80) REVERT: B 453 TYR cc_start: 0.4652 (p90) cc_final: 0.4315 (p90) REVERT: B 532 ASN cc_start: 0.7066 (t0) cc_final: 0.6652 (t0) REVERT: B 547 THR cc_start: 0.8152 (m) cc_final: 0.7663 (p) REVERT: B 660 TYR cc_start: 0.8990 (m-80) cc_final: 0.8750 (m-10) REVERT: B 904 TYR cc_start: 0.7737 (m-10) cc_final: 0.6975 (m-10) REVERT: B 1138 TYR cc_start: 0.7703 (t80) cc_final: 0.7410 (t80) REVERT: C 133 PHE cc_start: 0.7007 (m-10) cc_final: 0.6712 (m-10) REVERT: C 170 TYR cc_start: 0.6703 (t80) cc_final: 0.6318 (t80) REVERT: C 269 TYR cc_start: 0.7652 (m-10) cc_final: 0.7056 (m-10) REVERT: C 740 MET cc_start: 0.9139 (tpt) cc_final: 0.8836 (tpp) REVERT: C 809 PRO cc_start: 0.6538 (Cg_endo) cc_final: 0.6188 (Cg_exo) REVERT: C 916 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8437 (tp) REVERT: D 3 GLN cc_start: 0.5988 (mm-40) cc_final: 0.5729 (mm-40) REVERT: D 36 TRP cc_start: 0.6507 (m100) cc_final: 0.5814 (m100) REVERT: D 38 ARG cc_start: 0.7786 (ptt180) cc_final: 0.7218 (ptm160) REVERT: D 39 GLN cc_start: 0.7580 (tt0) cc_final: 0.7227 (mp10) REVERT: D 73 ASP cc_start: 0.7611 (t0) cc_final: 0.7161 (t0) REVERT: D 85 SER cc_start: 0.8108 (m) cc_final: 0.7839 (t) REVERT: D 95 TYR cc_start: 0.7282 (m-80) cc_final: 0.6957 (m-10) outliers start: 70 outliers final: 56 residues processed: 254 average time/residue: 0.3613 time to fit residues: 153.5276 Evaluate side-chains 255 residues out of total 2977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 194 time to evaluate : 2.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain E residue 64 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 310 optimal weight: 1.9990 chunk 340 optimal weight: 10.0000 chunk 315 optimal weight: 0.1980 chunk 106 optimal weight: 30.0000 chunk 265 optimal weight: 7.9990 chunk 317 optimal weight: 6.9990 chunk 194 optimal weight: 1.9990 chunk 333 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 213 optimal weight: 8.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN D 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.161348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.111486 restraints weight = 46716.767| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.71 r_work: 0.3185 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 27986 Z= 0.174 Angle : 0.590 11.508 38149 Z= 0.290 Chirality : 0.045 0.432 4402 Planarity : 0.004 0.050 4862 Dihedral : 6.369 110.120 4510 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.45 % Allowed : 10.04 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.14), residues: 3382 helix: 1.55 (0.22), residues: 614 sheet: -1.21 (0.19), residues: 696 loop : -1.94 (0.12), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 886 HIS 0.004 0.001 HIS B1058 PHE 0.019 0.001 PHE D 27 TYR 0.016 0.001 TYR A 265 ARG 0.005 0.000 ARG B 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00486 ( 40) link_NAG-ASN : angle 3.49445 ( 120) hydrogen bonds : bond 0.04307 ( 893) hydrogen bonds : angle 4.97619 ( 2490) SS BOND : bond 0.00457 ( 41) SS BOND : angle 1.54900 ( 82) covalent geometry : bond 0.00414 (27905) covalent geometry : angle 0.55384 (37947) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 197 time to evaluate : 2.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.3747 (ptp) cc_final: 0.3226 (tpt) REVERT: A 177 MET cc_start: 0.1304 (tpp) cc_final: 0.0808 (ttm) REVERT: A 378 LYS cc_start: 0.8549 (tptt) cc_final: 0.8160 (tppt) REVERT: A 460 ASN cc_start: 0.8102 (OUTLIER) cc_final: 0.7585 (m-40) REVERT: B 150 LYS cc_start: 0.6679 (pttt) cc_final: 0.6389 (ptmt) REVERT: B 177 MET cc_start: -0.0345 (tpp) cc_final: -0.1168 (mtt) REVERT: B 200 TYR cc_start: 0.6927 (OUTLIER) cc_final: 0.6368 (t80) REVERT: B 226 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7786 (tt) REVERT: B 271 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7762 (mt0) REVERT: B 338 PHE cc_start: 0.7396 (OUTLIER) cc_final: 0.6898 (m-80) REVERT: B 453 TYR cc_start: 0.4615 (p90) cc_final: 0.4291 (p90) REVERT: B 532 ASN cc_start: 0.7083 (t0) cc_final: 0.6641 (t0) REVERT: B 547 THR cc_start: 0.8176 (m) cc_final: 0.7694 (p) REVERT: B 660 TYR cc_start: 0.9014 (m-80) cc_final: 0.8782 (m-10) REVERT: B 904 TYR cc_start: 0.7820 (m-10) cc_final: 0.7047 (m-10) REVERT: B 1138 TYR cc_start: 0.7672 (t80) cc_final: 0.7336 (t80) REVERT: C 133 PHE cc_start: 0.7015 (m-10) cc_final: 0.6677 (m-10) REVERT: C 170 TYR cc_start: 0.6708 (t80) cc_final: 0.6318 (t80) REVERT: C 269 TYR cc_start: 0.7613 (m-10) cc_final: 0.7060 (m-10) REVERT: C 740 MET cc_start: 0.9160 (tpt) cc_final: 0.8798 (tpp) REVERT: C 809 PRO cc_start: 0.6516 (Cg_endo) cc_final: 0.6166 (Cg_exo) REVERT: C 902 MET cc_start: 0.8808 (mmt) cc_final: 0.8547 (mmt) REVERT: C 916 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8502 (tp) REVERT: D 3 GLN cc_start: 0.6054 (mm-40) cc_final: 0.5775 (mm-40) REVERT: D 36 TRP cc_start: 0.6579 (m100) cc_final: 0.5911 (m100) REVERT: D 38 ARG cc_start: 0.7758 (ptt180) cc_final: 0.7120 (ptm160) REVERT: D 39 GLN cc_start: 0.7549 (tt0) cc_final: 0.7214 (mp10) REVERT: D 73 ASP cc_start: 0.7443 (t0) cc_final: 0.7042 (t0) REVERT: D 85 SER cc_start: 0.8065 (m) cc_final: 0.7801 (t) REVERT: D 90 ASP cc_start: 0.5836 (OUTLIER) cc_final: 0.5427 (t0) REVERT: D 95 TYR cc_start: 0.7303 (m-80) cc_final: 0.6979 (m-10) outliers start: 73 outliers final: 59 residues processed: 252 average time/residue: 0.3592 time to fit residues: 149.7149 Evaluate side-chains 252 residues out of total 2977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 186 time to evaluate : 2.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 108 ASN Chi-restraints excluded: chain E residue 64 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 291 optimal weight: 2.9990 chunk 138 optimal weight: 7.9990 chunk 190 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 chunk 44 optimal weight: 0.0040 chunk 51 optimal weight: 2.9990 chunk 256 optimal weight: 30.0000 chunk 80 optimal weight: 0.9990 chunk 313 optimal weight: 1.9990 chunk 296 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN D 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.162569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.110386 restraints weight = 46573.360| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 3.00 r_work: 0.3187 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 27986 Z= 0.122 Angle : 0.560 11.591 38149 Z= 0.274 Chirality : 0.044 0.422 4402 Planarity : 0.003 0.049 4862 Dihedral : 6.210 109.871 4510 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.02 % Allowed : 10.75 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.14), residues: 3382 helix: 1.72 (0.22), residues: 614 sheet: -1.10 (0.19), residues: 691 loop : -1.89 (0.13), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 886 HIS 0.003 0.001 HIS B 519 PHE 0.017 0.001 PHE B 140 TYR 0.017 0.001 TYR B 265 ARG 0.005 0.000 ARG B 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00496 ( 40) link_NAG-ASN : angle 3.38445 ( 120) hydrogen bonds : bond 0.03943 ( 893) hydrogen bonds : angle 4.86426 ( 2490) SS BOND : bond 0.00375 ( 41) SS BOND : angle 1.42899 ( 82) covalent geometry : bond 0.00283 (27905) covalent geometry : angle 0.52366 (37947) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 206 time to evaluate : 2.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.3703 (ptp) cc_final: 0.3231 (tpt) REVERT: A 177 MET cc_start: 0.1340 (tpp) cc_final: 0.0814 (ttm) REVERT: A 319 ARG cc_start: 0.7648 (tpp80) cc_final: 0.7397 (tpp80) REVERT: A 378 LYS cc_start: 0.8535 (tptt) cc_final: 0.8130 (tppt) REVERT: A 460 ASN cc_start: 0.8083 (OUTLIER) cc_final: 0.7618 (m-40) REVERT: A 734 THR cc_start: 0.9177 (m) cc_final: 0.8698 (p) REVERT: B 150 LYS cc_start: 0.6671 (pttt) cc_final: 0.6375 (ptmt) REVERT: B 177 MET cc_start: -0.0365 (tpp) cc_final: -0.1207 (mtt) REVERT: B 226 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7775 (tt) REVERT: B 271 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7775 (mt0) REVERT: B 338 PHE cc_start: 0.7400 (OUTLIER) cc_final: 0.6968 (m-80) REVERT: B 453 TYR cc_start: 0.4712 (p90) cc_final: 0.4392 (p90) REVERT: B 532 ASN cc_start: 0.7064 (t0) cc_final: 0.6595 (t0) REVERT: B 547 THR cc_start: 0.8123 (m) cc_final: 0.7645 (p) REVERT: B 660 TYR cc_start: 0.9016 (m-80) cc_final: 0.8790 (m-10) REVERT: B 904 TYR cc_start: 0.7804 (m-10) cc_final: 0.7066 (m-10) REVERT: B 1138 TYR cc_start: 0.7678 (t80) cc_final: 0.7144 (t80) REVERT: C 133 PHE cc_start: 0.7010 (m-10) cc_final: 0.6684 (m-10) REVERT: C 170 TYR cc_start: 0.6627 (t80) cc_final: 0.6264 (t80) REVERT: C 269 TYR cc_start: 0.7613 (m-10) cc_final: 0.7054 (m-10) REVERT: C 740 MET cc_start: 0.9156 (tpt) cc_final: 0.8753 (tpp) REVERT: C 809 PRO cc_start: 0.6509 (Cg_endo) cc_final: 0.6166 (Cg_exo) REVERT: C 916 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8417 (tp) REVERT: D 3 GLN cc_start: 0.6096 (mm-40) cc_final: 0.5895 (mm-40) REVERT: D 36 TRP cc_start: 0.6572 (m100) cc_final: 0.5902 (m100) REVERT: D 38 ARG cc_start: 0.7722 (ptt180) cc_final: 0.7102 (ptm160) REVERT: D 39 GLN cc_start: 0.7600 (tt0) cc_final: 0.7322 (mp10) REVERT: D 73 ASP cc_start: 0.7379 (t0) cc_final: 0.6993 (t0) REVERT: D 85 SER cc_start: 0.8068 (m) cc_final: 0.7812 (t) REVERT: D 90 ASP cc_start: 0.5681 (OUTLIER) cc_final: 0.5278 (t0) REVERT: D 95 TYR cc_start: 0.7286 (m-80) cc_final: 0.6946 (m-10) outliers start: 60 outliers final: 52 residues processed: 251 average time/residue: 0.3781 time to fit residues: 157.7189 Evaluate side-chains 253 residues out of total 2977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 195 time to evaluate : 3.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 108 ASN Chi-restraints excluded: chain E residue 64 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 326 optimal weight: 1.9990 chunk 65 optimal weight: 0.2980 chunk 252 optimal weight: 5.9990 chunk 188 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 248 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 chunk 335 optimal weight: 30.0000 chunk 189 optimal weight: 0.9980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.162486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.111043 restraints weight = 46644.370| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.83 r_work: 0.3202 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27986 Z= 0.132 Angle : 0.562 11.469 38149 Z= 0.275 Chirality : 0.045 0.421 4402 Planarity : 0.003 0.048 4862 Dihedral : 6.149 109.210 4510 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.12 % Allowed : 10.98 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.14), residues: 3382 helix: 1.69 (0.22), residues: 613 sheet: -1.05 (0.19), residues: 686 loop : -1.87 (0.12), residues: 2083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 886 HIS 0.003 0.001 HIS C1048 PHE 0.019 0.001 PHE D 27 TYR 0.016 0.001 TYR A 265 ARG 0.005 0.000 ARG B 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00487 ( 40) link_NAG-ASN : angle 3.36153 ( 120) hydrogen bonds : bond 0.03968 ( 893) hydrogen bonds : angle 4.83570 ( 2490) SS BOND : bond 0.00386 ( 41) SS BOND : angle 1.40924 ( 82) covalent geometry : bond 0.00310 (27905) covalent geometry : angle 0.52680 (37947) =============================================================================== Job complete usr+sys time: 15650.68 seconds wall clock time: 275 minutes 43.26 seconds (16543.26 seconds total)