Starting phenix.real_space_refine on Sun Jul 5 08:35:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xy4_33510/07_2026/7xy4_33510.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xy4_33510/07_2026/7xy4_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_33510/07_2026/7xy4_33510.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xy4_33510/07_2026/7xy4_33510.map" model { file = "/net/cci-nas-00/data/ceres_data/7xy4_33510/07_2026/7xy4_33510.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xy4_33510/07_2026/7xy4_33510.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7xy4_33510/07_2026/7xy4_33510.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xy4_33510/07_2026/7xy4_33510.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 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 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 chiralities: 14 Time building chain proxies: 5.73, per 1000 atoms: 0.21 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: 2.27 Conformation dependent library (CDL) restraints added in 1.1 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: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 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: 6.82 Time building geometry restraints manager: 3.08 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 - 15.26: 15552 15.26 - 30.52: 576 30.52 - 45.79: 144 45.79 - 61.05: 11 61.05 - 76.31: 5 Dihedral angle restraints: 16288 sinusoidal: 6342 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 16285 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 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: 1.700 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: 0.030 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 26.630 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 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 : 9.044 76.312 9771 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.012 0.001 ARG C 815 TYR 0.042 0.003 TYR B 204 PHE 0.047 0.004 PHE A 906 TRP 0.027 0.002 TRP A 64 HIS 0.009 0.002 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00742 / 0.32 (27905) covalent geometry : angle 0.86534 / 0.46 (37947) SS BOND : bond 0.17315 / 13.47 ( 41) SS BOND : angle 6.46226 / 3.62 ( 82) hydrogen bonds : bond 0.21012 / 14.35 ( 893) hydrogen bonds : angle 8.68445 / 5.97 ( 2490) link_NAG-ASN : bond 0.04759 / 1.52 ( 40) link_NAG-ASN : angle 6.53920 / 5.04 ( 120) *********************** 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 : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 PRO cc_start: 0.7086 (Cg_endo) cc_final: 0.6686 (Cg_exo) REVERT: A 153 MET cc_start: 0.4109 (ptp) cc_final: 0.3546 (tpt) REVERT: A 238 PHE cc_start: 0.7346 (p90) cc_final: 0.6954 (p90) REVERT: A 409 GLN cc_start: 0.8267 (mt0) cc_final: 0.8062 (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: 0.8298 (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: 0.4198 (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: 0.6588 (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: 0.6629 (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: 0.6100 (mp0) REVERT: C 614 ASP cc_start: 0.6362 (t70) cc_final: 0.6068 (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: 0.8512 (p) REVERT: D 4 LEU cc_start: 0.7182 (mt) cc_final: 0.6566 (mt) REVERT: D 18 LEU cc_start: 0.6265 (mt) cc_final: 0.5871 (tp) REVERT: D 20 LEU cc_start: 0.7446 (mt) cc_final: 0.7216 (mp) REVERT: D 38 ARG cc_start: 0.7634 (ptt180) cc_final: 0.7341 (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: 0.6424 (t0) REVERT: D 99 ASP cc_start: 0.7690 (t0) cc_final: 0.7484 (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: 0.2019 time to fit residues: 165.0951 Evaluate side-chains 252 residues out of total 2977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN A 448 ASN A 450 ASN A 501 ASN A 544 ASN A 580 GLN A 613 GLN A 658 ASN A 965 GLN A1005 GLN A1101 HIS B 66 HIS B 234 ASN B 245 HIS B 354 ASN B 655 HIS B 965 GLN B1048 HIS C 69 HIS C 81 ASN C 207 HIS C 239 GLN C 450 ASN C 540 ASN C 655 HIS C 804 GLN C 949 GLN C1010 GLN C1101 HIS D 32 HIS E 32 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.163988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.111501 restraints weight = 47159.542| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.88 r_work: 0.3224 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 27986 Z= 0.187 Angle : 0.672 10.705 38149 Z= 0.338 Chirality : 0.048 0.450 4402 Planarity : 0.005 0.043 4862 Dihedral : 5.439 26.420 3670 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.88 % Allowed : 6.52 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.79 (0.13), residues: 3382 helix: 0.04 (0.20), residues: 618 sheet: -1.90 (0.18), residues: 700 loop : -2.56 (0.11), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 765 TYR 0.023 0.002 TYR A1138 PHE 0.017 0.002 PHE C 135 TRP 0.017 0.001 TRP D 109 HIS 0.008 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 (27905) covalent geometry : angle 0.63863 / 0.33 (37947) SS BOND : bond 0.00467 / 0.34 ( 41) SS BOND : angle 1.56794 / 0.98 ( 82) hydrogen bonds : bond 0.05192 / 3.47 ( 893) hydrogen bonds : angle 6.08970 / 4.23 ( 2490) link_NAG-ASN : bond 0.00521 / 0.31 ( 40) link_NAG-ASN : angle 3.61668 / 2.35 ( 120) *********************** 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 331 residues out of total 2977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 275 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8961 (mt) cc_final: 0.8726 (mp) REVERT: A 153 MET cc_start: 0.4023 (ptp) cc_final: 0.3496 (tpt) REVERT: A 238 PHE cc_start: 0.7061 (p90) cc_final: 0.6556 (p90) REVERT: A 269 TYR cc_start: 0.8144 (m-10) cc_final: 0.7932 (m-10) REVERT: A 378 LYS cc_start: 0.8643 (tptt) cc_final: 0.8335 (tppt) REVERT: A 493 GLN cc_start: 0.7905 (tt0) cc_final: 0.7504 (tt0) REVERT: A 642 VAL cc_start: 0.9175 (t) cc_final: 0.8963 (p) REVERT: A 734 THR cc_start: 0.8996 (m) cc_final: 0.8608 (p) REVERT: B 150 LYS cc_start: 0.6156 (pttt) cc_final: 0.5880 (pttt) REVERT: B 177 MET cc_start: -0.0541 (tpp) cc_final: -0.1059 (mtt) REVERT: B 200 TYR cc_start: 0.6694 (OUTLIER) cc_final: 0.6116 (t80) REVERT: B 226 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7783 (tt) REVERT: B 355 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7937 (mmm160) REVERT: B 390 LEU cc_start: 0.8313 (tp) cc_final: 0.7869 (tp) REVERT: B 453 TYR cc_start: 0.4634 (p90) cc_final: 0.4244 (p90) REVERT: B 532 ASN cc_start: 0.6942 (t0) cc_final: 0.6693 (t0) REVERT: B 547 THR cc_start: 0.8013 (m) cc_final: 0.7443 (p) REVERT: B 1138 TYR cc_start: 0.7761 (t80) cc_final: 0.7268 (t80) REVERT: C 133 PHE cc_start: 0.7074 (m-10) cc_final: 0.6688 (m-10) REVERT: C 269 TYR cc_start: 0.7330 (m-10) cc_final: 0.6997 (m-10) REVERT: C 340 GLU cc_start: 0.6782 (mt-10) cc_final: 0.6317 (mp0) REVERT: C 436 TRP cc_start: 0.1610 (p90) cc_final: 0.1370 (p90) REVERT: C 571 ASP cc_start: 0.8089 (t0) cc_final: 0.7688 (t0) REVERT: C 614 ASP cc_start: 0.7343 (t70) cc_final: 0.6905 (t0) REVERT: C 809 PRO cc_start: 0.6577 (Cg_endo) cc_final: 0.6227 (Cg_exo) REVERT: C 859 THR cc_start: 0.9016 (m) cc_final: 0.8732 (p) REVERT: C 988 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7730 (mp0) REVERT: D 20 LEU cc_start: 0.7365 (mt) cc_final: 0.5900 (mp) REVERT: D 36 TRP cc_start: 0.6573 (m100) cc_final: 0.6035 (m100) REVERT: D 38 ARG cc_start: 0.7998 (ptt180) cc_final: 0.7727 (ptm160) REVERT: D 39 GLN cc_start: 0.7323 (tt0) cc_final: 0.6867 (mp10) REVERT: D 58 THR cc_start: 0.8002 (t) cc_final: 0.7405 (t) REVERT: D 73 ASP cc_start: 0.7430 (t0) cc_final: 0.7146 (t0) REVERT: D 93 MET cc_start: 0.6765 (tpt) cc_final: 0.4933 (tmm) REVERT: D 95 TYR cc_start: 0.7815 (m-80) cc_final: 0.6568 (m-10) REVERT: D 104 ASP cc_start: 0.6982 (t0) cc_final: 0.6654 (t0) REVERT: E 63 SER cc_start: 0.2300 (p) cc_final: 0.2041 (m) REVERT: E 83 MET cc_start: 0.1619 (mtm) cc_final: 0.0992 (mmt) outliers start: 56 outliers final: 27 residues processed: 317 average time/residue: 0.1760 time to fit residues: 91.0226 Evaluate side-chains 242 residues out of total 2977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 211 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN 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 353 TRP 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 B residue 116 SER Chi-restraints excluded: chain B residue 200 TYR 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 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 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 7 optimal weight: 20.0000 chunk 160 optimal weight: 0.0270 chunk 128 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 233 optimal weight: 6.9990 chunk 189 optimal weight: 2.9990 chunk 335 optimal weight: 0.8980 chunk 296 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 overall best weight: 1.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 450 ASN A 913 GLN A1005 GLN C 99 ASN C 207 HIS C 935 GLN D 32 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.163999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.114968 restraints weight = 47312.181| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.86 r_work: 0.3232 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 27986 Z= 0.140 Angle : 0.595 10.730 38149 Z= 0.297 Chirality : 0.046 0.417 4402 Planarity : 0.004 0.048 4862 Dihedral : 4.932 25.007 3670 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.58 % Allowed : 7.96 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.13), residues: 3382 helix: 0.82 (0.21), residues: 629 sheet: -1.60 (0.19), residues: 685 loop : -2.36 (0.12), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 106 TYR 0.017 0.001 TYR A 170 PHE 0.026 0.002 PHE C 135 TRP 0.033 0.001 TRP D 109 HIS 0.007 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (27905) covalent geometry : angle 0.56168 / 0.29 (37947) SS BOND : bond 0.00515 / 0.36 ( 41) SS BOND : angle 1.41525 / 0.89 ( 82) hydrogen bonds : bond 0.04412 / 2.95 ( 893) hydrogen bonds : angle 5.50157 / 3.83 ( 2490) link_NAG-ASN : bond 0.00611 / 0.35 ( 40) link_NAG-ASN : angle 3.35963 / 2.21 ( 120) *********************** 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 294 residues out of total 2977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 247 time to evaluate : 1.032 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: 0.3890 (ptp) cc_final: 0.3532 (tpt) REVERT: A 177 MET cc_start: 0.1633 (tpp) cc_final: 0.1161 (ttm) REVERT: A 238 PHE cc_start: 0.7056 (p90) cc_final: 0.6453 (p90) REVERT: A 269 TYR cc_start: 0.8150 (m-10) cc_final: 0.7836 (m-10) REVERT: A 378 LYS cc_start: 0.8587 (tptt) cc_final: 0.8220 (tppt) REVERT: A 642 VAL cc_start: 0.9104 (t) cc_final: 0.8903 (p) REVERT: A 734 THR cc_start: 0.9077 (m) cc_final: 0.8685 (p) REVERT: B 150 LYS cc_start: 0.6367 (pttt) cc_final: 0.6100 (pttt) REVERT: B 177 MET cc_start: -0.0503 (tpp) cc_final: -0.1067 (mtt) REVERT: B 200 TYR cc_start: 0.6725 (m-80) cc_final: 0.6327 (t80) REVERT: B 201 PHE cc_start: 0.6736 (OUTLIER) cc_final: 0.6169 (m-80) REVERT: B 226 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7770 (tt) REVERT: B 453 TYR cc_start: 0.4578 (p90) cc_final: 0.4239 (p90) REVERT: B 532 ASN cc_start: 0.7034 (t0) cc_final: 0.6711 (t0) REVERT: B 547 THR cc_start: 0.7774 (m) cc_final: 0.7251 (p) REVERT: B 1138 TYR cc_start: 0.7810 (t80) cc_final: 0.7378 (t80) REVERT: C 133 PHE cc_start: 0.7102 (m-10) cc_final: 0.6711 (m-10) REVERT: C 269 TYR cc_start: 0.7268 (m-10) cc_final: 0.6680 (m-10) REVERT: C 340 GLU cc_start: 0.6724 (mt-10) cc_final: 0.6271 (mp0) REVERT: C 571 ASP cc_start: 0.8137 (t0) cc_final: 0.7830 (t0) REVERT: C 614 ASP cc_start: 0.7256 (t70) cc_final: 0.6764 (t0) REVERT: C 809 PRO cc_start: 0.6546 (Cg_endo) cc_final: 0.6180 (Cg_exo) REVERT: C 859 THR cc_start: 0.9089 (m) cc_final: 0.8808 (p) REVERT: D 3 GLN cc_start: 0.6286 (mm-40) cc_final: 0.6032 (mm-40) REVERT: D 20 LEU cc_start: 0.7407 (mt) cc_final: 0.7147 (mp) REVERT: D 36 TRP cc_start: 0.6454 (m100) cc_final: 0.5772 (m100) REVERT: D 38 ARG cc_start: 0.7996 (ptt180) cc_final: 0.7673 (ptm160) REVERT: D 39 GLN cc_start: 0.7303 (tt0) cc_final: 0.6853 (mp10) REVERT: D 67 ARG cc_start: 0.5773 (mtp180) cc_final: 0.5335 (mtp180) REVERT: D 73 ASP cc_start: 0.7502 (t0) cc_final: 0.7204 (t0) REVERT: D 93 MET cc_start: 0.6531 (tpt) cc_final: 0.4908 (tmm) REVERT: D 104 ASP cc_start: 0.7108 (t0) cc_final: 0.6677 (t0) REVERT: E 83 MET cc_start: 0.1729 (mtm) cc_final: 0.1041 (mmt) outliers start: 47 outliers final: 27 residues processed: 285 average time/residue: 0.1751 time to fit residues: 81.8147 Evaluate side-chains 237 residues out of total 2977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 208 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN 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 430 THR Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 753 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 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 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 709 ASN Chi-restraints excluded: chain C residue 878 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 37 VAL Chi-restraints excluded: chain D residue 70 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 178 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 95 optimal weight: 0.9980 chunk 331 optimal weight: 6.9990 chunk 341 optimal weight: 5.9990 chunk 209 optimal weight: 0.4980 chunk 117 optimal weight: 1.9990 chunk 252 optimal weight: 5.9990 chunk 249 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 259 optimal weight: 9.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 450 ASN A 856 ASN A1005 GLN A1048 HIS 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 = 0.4155 r_free = 0.4155 target = 0.162358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.107971 restraints weight = 46934.949| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.58 r_work: 0.3222 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 27986 Z= 0.184 Angle : 0.615 10.825 38149 Z= 0.306 Chirality : 0.046 0.430 4402 Planarity : 0.004 0.054 4862 Dihedral : 4.866 24.854 3670 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.15 % Allowed : 8.63 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.14), residues: 3382 helix: 0.96 (0.21), residues: 636 sheet: -1.44 (0.19), residues: 680 loop : -2.27 (0.12), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 983 TYR 0.019 0.002 TYR A1138 PHE 0.029 0.002 PHE C 135 TRP 0.034 0.002 TRP D 109 HIS 0.007 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 (27905) covalent geometry : angle 0.58438 / 0.30 (37947) SS BOND : bond 0.00475 / 0.36 ( 41) SS BOND : angle 1.42288 / 0.89 ( 82) hydrogen bonds : bond 0.04573 / 3.05 ( 893) hydrogen bonds : angle 5.32188 / 3.71 ( 2490) link_NAG-ASN : bond 0.00545 / 0.33 ( 40) link_NAG-ASN : angle 3.32092 / 2.20 ( 120) *********************** 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 280 residues out of total 2977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 216 time to evaluate : 0.952 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: 0.3921 (ptp) cc_final: 0.3408 (tpt) REVERT: A 177 MET cc_start: 0.1340 (tpp) cc_final: 0.0974 (ttm) REVERT: A 238 PHE cc_start: 0.7218 (p90) cc_final: 0.6622 (p90) REVERT: A 378 LYS cc_start: 0.8655 (tptt) cc_final: 0.8321 (tppt) REVERT: A 529 LYS cc_start: 0.8998 (tttt) cc_final: 0.8784 (mmmt) REVERT: A 734 THR cc_start: 0.9141 (m) cc_final: 0.8744 (p) REVERT: A 983 ARG cc_start: 0.7841 (ttm110) cc_final: 0.7581 (mtm180) REVERT: B 150 LYS cc_start: 0.6491 (pttt) cc_final: 0.6156 (pttt) REVERT: B 157 PHE cc_start: 0.6633 (m-80) cc_final: 0.6399 (t80) REVERT: B 177 MET cc_start: -0.0412 (tpp) cc_final: -0.0997 (mtt) REVERT: B 200 TYR cc_start: 0.7085 (m-80) cc_final: 0.6727 (t80) REVERT: B 226 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7859 (tt) REVERT: B 453 TYR cc_start: 0.4824 (p90) cc_final: 0.4383 (p90) REVERT: B 532 ASN cc_start: 0.7163 (t0) cc_final: 0.6838 (t0) REVERT: B 547 THR cc_start: 0.8042 (m) cc_final: 0.7580 (p) REVERT: B 660 TYR cc_start: 0.9003 (m-80) cc_final: 0.8780 (m-10) REVERT: B 1138 TYR cc_start: 0.8018 (t80) cc_final: 0.7520 (t80) REVERT: C 133 PHE cc_start: 0.6994 (m-10) cc_final: 0.6615 (m-10) REVERT: C 269 TYR cc_start: 0.7601 (m-10) cc_final: 0.6913 (m-10) REVERT: C 340 GLU cc_start: 0.6690 (mt-10) cc_final: 0.6296 (mp0) REVERT: C 571 ASP cc_start: 0.8200 (t0) cc_final: 0.7868 (t0) REVERT: C 614 ASP cc_start: 0.7691 (t70) cc_final: 0.7245 (t0) REVERT: C 809 PRO cc_start: 0.6546 (Cg_endo) cc_final: 0.6179 (Cg_exo) REVERT: C 859 THR cc_start: 0.9154 (m) cc_final: 0.8954 (p) REVERT: D 3 GLN cc_start: 0.6150 (mm-40) cc_final: 0.5889 (mm-40) REVERT: D 20 LEU cc_start: 0.7292 (mt) cc_final: 0.7045 (mp) REVERT: D 36 TRP cc_start: 0.6532 (m100) cc_final: 0.5982 (m100) REVERT: D 38 ARG cc_start: 0.7946 (ptt180) cc_final: 0.7569 (ptm160) REVERT: D 39 GLN cc_start: 0.7402 (tt0) cc_final: 0.6975 (mp10) REVERT: D 67 ARG cc_start: 0.6017 (mtp180) cc_final: 0.5543 (mtp180) REVERT: D 73 ASP cc_start: 0.7546 (t0) cc_final: 0.7274 (t0) REVERT: D 93 MET cc_start: 0.6644 (tpt) cc_final: 0.4612 (tmm) REVERT: D 104 ASP cc_start: 0.7297 (t0) cc_final: 0.7025 (t0) REVERT: E 63 SER cc_start: 0.2301 (p) cc_final: 0.2083 (m) REVERT: E 83 MET cc_start: 0.1723 (mtm) cc_final: 0.1108 (mmt) outliers start: 64 outliers final: 45 residues processed: 261 average time/residue: 0.1464 time to fit residues: 61.7925 Evaluate side-chains 249 residues out of total 2977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 203 time to evaluate : 0.599 ------------------------------------------------------------------------------- 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 430 THR Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 753 LEU 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 385 THR Chi-restraints excluded: chain B residue 515 PHE 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 738 CYS Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain C residue 24 LEU 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 709 ASN Chi-restraints excluded: chain C residue 723 THR 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 5 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 83 MET 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 190 optimal weight: 4.9990 chunk 294 optimal weight: 0.9990 chunk 335 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 112 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 293 optimal weight: 0.6980 chunk 238 optimal weight: 6.9990 chunk 186 optimal weight: 6.9990 chunk 164 optimal weight: 0.6980 chunk 179 optimal weight: 0.4980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 450 ASN A1005 GLN B 580 GLN C 49 HIS C 207 HIS D 32 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.164737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.115869 restraints weight = 46767.401| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.73 r_work: 0.3244 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 27986 Z= 0.097 Angle : 0.533 11.134 38149 Z= 0.264 Chirality : 0.045 0.396 4402 Planarity : 0.003 0.041 4862 Dihedral : 4.427 24.520 3670 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.68 % Allowed : 9.81 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.14), residues: 3382 helix: 1.45 (0.21), residues: 632 sheet: -1.34 (0.19), residues: 679 loop : -2.08 (0.12), residues: 2071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 983 TYR 0.017 0.001 TYR A 265 PHE 0.032 0.001 PHE C 135 TRP 0.030 0.001 TRP D 109 HIS 0.007 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 (27905) covalent geometry : angle 0.50317 / 0.26 (37947) SS BOND : bond 0.00337 / 0.26 ( 41) SS BOND : angle 1.09186 / 0.68 ( 82) hydrogen bonds : bond 0.03729 / 2.49 ( 893) hydrogen bonds : angle 4.92763 / 3.44 ( 2490) link_NAG-ASN : bond 0.00560 / 0.33 ( 40) link_NAG-ASN : angle 3.05905 / 2.04 ( 120) *********************** 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 288 residues out of total 2977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 238 time to evaluate : 1.129 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: 0.8498 (OUTLIER) cc_final: 0.8136 (t70) REVERT: A 87 ASN cc_start: 0.6509 (OUTLIER) cc_final: 0.5997 (t0) REVERT: A 153 MET cc_start: 0.3696 (ptp) cc_final: 0.3289 (tpt) REVERT: A 177 MET cc_start: 0.1339 (tpp) cc_final: 0.0848 (ttm) REVERT: A 238 PHE cc_start: 0.6513 (p90) cc_final: 0.5824 (p90) REVERT: A 378 LYS cc_start: 0.8540 (tptt) cc_final: 0.8117 (tppt) REVERT: A 734 THR cc_start: 0.9095 (m) cc_final: 0.8739 (p) REVERT: B 150 LYS cc_start: 0.6432 (pttt) cc_final: 0.6120 (pttt) REVERT: B 177 MET cc_start: -0.0438 (tpp) cc_final: -0.1007 (mtt) REVERT: B 200 TYR cc_start: 0.6722 (m-80) cc_final: 0.6470 (t80) REVERT: B 226 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7770 (tt) REVERT: B 453 TYR cc_start: 0.4481 (p90) cc_final: 0.4157 (p90) REVERT: B 532 ASN cc_start: 0.7069 (t0) cc_final: 0.6695 (t0) REVERT: B 547 THR cc_start: 0.7928 (m) cc_final: 0.7456 (p) REVERT: B 904 TYR cc_start: 0.7754 (m-10) cc_final: 0.7104 (m-10) REVERT: B 1119 ASN cc_start: 0.8703 (m-40) cc_final: 0.8492 (m110) REVERT: B 1138 TYR cc_start: 0.7711 (t80) cc_final: 0.7206 (t80) REVERT: C 105 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.8005 (mp) REVERT: C 133 PHE cc_start: 0.6933 (m-10) cc_final: 0.6703 (m-10) REVERT: C 269 TYR cc_start: 0.7410 (m-10) cc_final: 0.6875 (m-10) REVERT: C 273 ARG cc_start: 0.7792 (mmt180) cc_final: 0.7448 (mmp80) REVERT: C 340 GLU cc_start: 0.6737 (mt-10) cc_final: 0.6343 (mp0) REVERT: C 571 ASP cc_start: 0.8127 (t0) cc_final: 0.7808 (t0) REVERT: C 614 ASP cc_start: 0.7127 (t70) cc_final: 0.6679 (t0) REVERT: C 809 PRO cc_start: 0.6768 (Cg_endo) cc_final: 0.6410 (Cg_exo) REVERT: C 859 THR cc_start: 0.9102 (m) cc_final: 0.8887 (p) REVERT: D 4 LEU cc_start: 0.6839 (mt) cc_final: 0.6617 (mm) REVERT: D 36 TRP cc_start: 0.6453 (m100) cc_final: 0.5816 (m100) REVERT: D 38 ARG cc_start: 0.8030 (ptt180) cc_final: 0.7638 (ptm160) REVERT: D 39 GLN cc_start: 0.7362 (tt0) cc_final: 0.6861 (mp10) REVERT: D 73 ASP cc_start: 0.7623 (t0) cc_final: 0.7350 (t0) REVERT: D 95 TYR cc_start: 0.7214 (m-80) cc_final: 0.6880 (m-10) REVERT: D 104 ASP cc_start: 0.7298 (t0) cc_final: 0.6960 (t0) outliers start: 50 outliers final: 32 residues processed: 279 average time/residue: 0.1686 time to fit residues: 76.9420 Evaluate side-chains 246 residues out of total 2977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 210 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP 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 430 THR 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 740 MET Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 1128 VAL 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 312 ILE Chi-restraints excluded: chain B residue 515 PHE 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 C residue 24 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 723 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 37 VAL 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 272 optimal weight: 10.0000 chunk 177 optimal weight: 3.9990 chunk 174 optimal weight: 0.9980 chunk 236 optimal weight: 0.8980 chunk 215 optimal weight: 0.4980 chunk 326 optimal weight: 6.9990 chunk 206 optimal weight: 10.0000 chunk 316 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 185 optimal weight: 0.1980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1005 GLN C 17 ASN D 32 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.164407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.115135 restraints weight = 47167.420| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.89 r_work: 0.3228 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3278 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= 0.110 Angle : 0.537 10.708 38149 Z= 0.265 Chirality : 0.045 0.398 4402 Planarity : 0.003 0.038 4862 Dihedral : 4.329 23.842 3670 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.95 % Allowed : 9.81 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.14), residues: 3382 helix: 1.60 (0.21), residues: 633 sheet: -1.17 (0.19), residues: 677 loop : -2.03 (0.12), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 106 TYR 0.015 0.001 TYR A 265 PHE 0.028 0.001 PHE C 135 TRP 0.029 0.001 TRP D 109 HIS 0.003 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (27905) covalent geometry : angle 0.50723 / 0.26 (37947) SS BOND : bond 0.00378 / 0.29 ( 41) SS BOND : angle 1.31412 / 0.89 ( 82) hydrogen bonds : bond 0.03753 / 2.50 ( 893) hydrogen bonds : angle 4.83519 / 3.39 ( 2490) link_NAG-ASN : bond 0.00527 / 0.31 ( 40) link_NAG-ASN : angle 3.00743 / 2.01 ( 120) *********************** 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 277 residues out of total 2977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 219 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8493 (OUTLIER) cc_final: 0.8131 (t70) REVERT: A 153 MET cc_start: 0.3686 (ptp) cc_final: 0.3277 (tpt) REVERT: A 177 MET cc_start: 0.1242 (tpp) cc_final: 0.0747 (ttm) REVERT: A 378 LYS cc_start: 0.8560 (tptt) cc_final: 0.8156 (tppt) REVERT: A 460 ASN cc_start: 0.8147 (OUTLIER) cc_final: 0.7663 (m-40) REVERT: A 734 THR cc_start: 0.9121 (m) cc_final: 0.8765 (p) REVERT: A 1050 MET cc_start: 0.8710 (ptt) cc_final: 0.8298 (ptt) REVERT: B 150 LYS cc_start: 0.6434 (pttt) cc_final: 0.6124 (pttt) REVERT: B 157 PHE cc_start: 0.6744 (m-80) cc_final: 0.6479 (t80) REVERT: B 177 MET cc_start: -0.0418 (tpp) cc_final: -0.1058 (tmm) REVERT: B 200 TYR cc_start: 0.6787 (m-80) cc_final: 0.6491 (t80) REVERT: B 226 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7813 (tt) REVERT: B 453 TYR cc_start: 0.4456 (p90) cc_final: 0.4137 (p90) REVERT: B 532 ASN cc_start: 0.7057 (t0) cc_final: 0.6645 (t0) REVERT: B 547 THR cc_start: 0.7965 (m) cc_final: 0.7449 (p) REVERT: B 904 TYR cc_start: 0.7739 (m-10) cc_final: 0.7085 (m-10) REVERT: B 1138 TYR cc_start: 0.7734 (t80) cc_final: 0.7392 (t80) REVERT: C 133 PHE cc_start: 0.6973 (m-10) cc_final: 0.6740 (m-10) REVERT: C 269 TYR cc_start: 0.7525 (m-10) cc_final: 0.6965 (m-10) REVERT: C 273 ARG cc_start: 0.7822 (mmt180) cc_final: 0.7473 (mmp80) REVERT: C 340 GLU cc_start: 0.6745 (mt-10) cc_final: 0.6335 (mp0) REVERT: C 571 ASP cc_start: 0.8134 (t0) cc_final: 0.7815 (t0) REVERT: C 586 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7600 (m-30) REVERT: C 614 ASP cc_start: 0.7118 (t70) cc_final: 0.6677 (t0) REVERT: C 740 MET cc_start: 0.9046 (ttp) cc_final: 0.8745 (tpp) REVERT: C 809 PRO cc_start: 0.6633 (Cg_endo) cc_final: 0.6284 (Cg_exo) REVERT: C 1050 MET cc_start: 0.9044 (ptp) cc_final: 0.8743 (ptm) REVERT: D 4 LEU cc_start: 0.6826 (mt) cc_final: 0.6580 (mm) REVERT: D 36 TRP cc_start: 0.6465 (m100) cc_final: 0.5704 (m100) REVERT: D 38 ARG cc_start: 0.8015 (ptt180) cc_final: 0.7621 (ptm160) REVERT: D 39 GLN cc_start: 0.7509 (tt0) cc_final: 0.7089 (mp10) REVERT: D 73 ASP cc_start: 0.7593 (t0) cc_final: 0.7286 (t0) REVERT: D 93 MET cc_start: 0.6597 (tpt) cc_final: 0.4861 (tpt) REVERT: D 95 TYR cc_start: 0.7211 (m-80) cc_final: 0.6709 (m-10) REVERT: D 104 ASP cc_start: 0.7429 (t0) cc_final: 0.7067 (t0) outliers start: 58 outliers final: 43 residues processed: 261 average time/residue: 0.1662 time to fit residues: 71.2744 Evaluate side-chains 244 residues out of total 2977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 197 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 430 THR Chi-restraints excluded: chain A residue 460 ASN 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 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 A residue 1128 VAL 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 312 ILE Chi-restraints excluded: chain B residue 515 PHE 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 231 ILE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 586 ASP 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 709 ASN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 878 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 E residue 64 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 16 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 284 optimal weight: 0.5980 chunk 144 optimal weight: 0.0970 chunk 100 optimal weight: 3.9990 chunk 238 optimal weight: 6.9990 chunk 338 optimal weight: 0.0980 chunk 277 optimal weight: 6.9990 chunk 150 optimal weight: 30.0000 chunk 211 optimal weight: 6.9990 overall best weight: 2.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1005 GLN C 354 ASN D 32 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.162289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.112590 restraints weight = 46569.431| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.60 r_work: 0.3209 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 27986 Z= 0.170 Angle : 0.576 10.656 38149 Z= 0.285 Chirality : 0.046 0.407 4402 Planarity : 0.003 0.043 4862 Dihedral : 4.469 23.976 3670 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.18 % Allowed : 9.91 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.14), residues: 3382 helix: 1.51 (0.21), residues: 629 sheet: -1.13 (0.19), residues: 682 loop : -2.00 (0.12), residues: 2071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 67 TYR 0.013 0.001 TYR A 265 PHE 0.026 0.001 PHE C 135 TRP 0.019 0.001 TRP D 109 HIS 0.004 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (27905) covalent geometry : angle 0.54779 / 0.28 (37947) SS BOND : bond 0.00478 / 0.35 ( 41) SS BOND : angle 1.40601 / 0.92 ( 82) hydrogen bonds : bond 0.04195 / 2.79 ( 893) hydrogen bonds : angle 4.91212 / 3.44 ( 2490) link_NAG-ASN : bond 0.00528 / 0.31 ( 40) link_NAG-ASN : angle 3.05938 / 2.05 ( 120) *********************** 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 259 residues out of total 2977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 194 time to evaluate : 1.028 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: 0.3807 (ptp) cc_final: 0.3280 (tpt) REVERT: A 378 LYS cc_start: 0.8668 (tptt) cc_final: 0.8282 (tppt) REVERT: A 460 ASN cc_start: 0.8198 (OUTLIER) cc_final: 0.7738 (m-40) REVERT: A 734 THR cc_start: 0.9248 (m) cc_final: 0.8857 (p) REVERT: B 150 LYS cc_start: 0.6655 (pttt) cc_final: 0.6261 (ptmt) REVERT: B 157 PHE cc_start: 0.6796 (m-80) cc_final: 0.6523 (t80) REVERT: B 177 MET cc_start: -0.0352 (tpp) cc_final: -0.1055 (tmm) REVERT: B 200 TYR cc_start: 0.7085 (m-80) cc_final: 0.6666 (t80) REVERT: B 226 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7853 (tt) REVERT: B 453 TYR cc_start: 0.4660 (p90) cc_final: 0.4290 (p90) REVERT: B 532 ASN cc_start: 0.7145 (t0) cc_final: 0.6708 (t0) REVERT: B 547 THR cc_start: 0.8211 (m) cc_final: 0.7683 (p) REVERT: B 904 TYR cc_start: 0.8107 (m-10) cc_final: 0.7419 (m-10) REVERT: B 1138 TYR cc_start: 0.7897 (t80) cc_final: 0.7538 (t80) REVERT: C 133 PHE cc_start: 0.7000 (m-10) cc_final: 0.6739 (m-10) REVERT: C 269 TYR cc_start: 0.7711 (m-10) cc_final: 0.7001 (m-10) REVERT: C 340 GLU cc_start: 0.6766 (mt-10) cc_final: 0.6354 (mp0) REVERT: C 571 ASP cc_start: 0.8246 (t0) cc_final: 0.7887 (t0) REVERT: C 614 ASP cc_start: 0.7558 (t70) cc_final: 0.7111 (t0) REVERT: C 740 MET cc_start: 0.9285 (ttp) cc_final: 0.8984 (tpp) REVERT: C 809 PRO cc_start: 0.6530 (Cg_endo) cc_final: 0.6196 (Cg_exo) REVERT: C 954 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8191 (tt0) REVERT: D 36 TRP cc_start: 0.6541 (m100) cc_final: 0.5809 (m100) REVERT: D 38 ARG cc_start: 0.7930 (ptt180) cc_final: 0.7508 (ptm160) REVERT: D 39 GLN cc_start: 0.7618 (tt0) cc_final: 0.7242 (mp10) REVERT: D 73 ASP cc_start: 0.7597 (t0) cc_final: 0.7259 (t0) REVERT: D 93 MET cc_start: 0.6698 (tpt) cc_final: 0.4957 (tpt) REVERT: D 95 TYR cc_start: 0.7226 (m-80) cc_final: 0.6793 (m-10) REVERT: D 104 ASP cc_start: 0.7487 (t0) cc_final: 0.7140 (t0) outliers start: 65 outliers final: 50 residues processed: 243 average time/residue: 0.1604 time to fit residues: 64.8357 Evaluate side-chains 242 residues out of total 2977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 189 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 430 THR Chi-restraints excluded: chain A residue 460 ASN 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 740 MET Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1128 VAL 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 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 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 231 ILE 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 620 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 709 ASN 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 954 GLN 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 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 Chi-restraints excluded: chain E residue 68 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 175 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 123 optimal weight: 0.7980 chunk 200 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 255 optimal weight: 2.9990 chunk 122 optimal weight: 0.0770 chunk 59 optimal weight: 10.0000 chunk 322 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN D 32 HIS 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 = 0.162674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.113409 restraints weight = 46856.012| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.62 r_work: 0.3219 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 27986 Z= 0.139 Angle : 0.554 10.621 38149 Z= 0.274 Chirality : 0.045 0.402 4402 Planarity : 0.003 0.048 4862 Dihedral : 4.407 23.873 3670 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.18 % Allowed : 10.11 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.14), residues: 3382 helix: 1.58 (0.21), residues: 630 sheet: -1.06 (0.19), residues: 669 loop : -1.97 (0.12), residues: 2083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 577 TYR 0.021 0.001 TYR A1138 PHE 0.022 0.001 PHE C 135 TRP 0.023 0.001 TRP C 886 HIS 0.003 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (27905) covalent geometry : angle 0.52659 / 0.27 (37947) SS BOND : bond 0.00394 / 0.30 ( 41) SS BOND : angle 1.22916 / 0.81 ( 82) hydrogen bonds : bond 0.04021 / 2.67 ( 893) hydrogen bonds : angle 4.82425 / 3.38 ( 2490) link_NAG-ASN : bond 0.00509 / 0.30 ( 40) link_NAG-ASN : angle 2.98669 / 2.01 ( 120) *********************** 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 268 residues out of total 2977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 203 time to evaluate : 1.036 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: 0.3827 (ptp) cc_final: 0.3250 (tpt) REVERT: A 177 MET cc_start: 0.1976 (tpp) cc_final: 0.0185 (ttp) REVERT: A 269 TYR cc_start: 0.7598 (m-80) cc_final: 0.7100 (m-80) REVERT: A 378 LYS cc_start: 0.8659 (tptt) cc_final: 0.8272 (tppt) REVERT: A 427 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7941 (t0) REVERT: A 460 ASN cc_start: 0.8171 (OUTLIER) cc_final: 0.7699 (m-40) REVERT: A 734 THR cc_start: 0.9257 (m) cc_final: 0.8852 (p) REVERT: B 150 LYS cc_start: 0.6630 (pttt) cc_final: 0.6314 (ptmt) REVERT: B 177 MET cc_start: -0.0290 (tpp) cc_final: -0.1016 (tmm) REVERT: B 200 TYR cc_start: 0.7108 (m-80) cc_final: 0.6717 (t80) REVERT: B 226 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7860 (tt) REVERT: B 453 TYR cc_start: 0.4722 (p90) cc_final: 0.4351 (p90) REVERT: B 532 ASN cc_start: 0.7151 (t0) cc_final: 0.6688 (t0) REVERT: B 547 THR cc_start: 0.8189 (m) cc_final: 0.7692 (p) REVERT: B 904 TYR cc_start: 0.8081 (m-10) cc_final: 0.7416 (m-10) REVERT: B 988 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7953 (mp0) REVERT: B 1138 TYR cc_start: 0.7848 (t80) cc_final: 0.7319 (t80) REVERT: C 133 PHE cc_start: 0.7042 (m-10) cc_final: 0.6742 (m-10) REVERT: C 269 TYR cc_start: 0.7712 (m-10) cc_final: 0.7060 (m-10) REVERT: C 340 GLU cc_start: 0.6745 (mt-10) cc_final: 0.6340 (mp0) REVERT: C 571 ASP cc_start: 0.8254 (t0) cc_final: 0.7891 (t0) REVERT: C 614 ASP cc_start: 0.7494 (t70) cc_final: 0.7024 (t0) REVERT: C 740 MET cc_start: 0.9303 (ttp) cc_final: 0.9026 (tpp) REVERT: C 809 PRO cc_start: 0.6547 (Cg_endo) cc_final: 0.6209 (Cg_exo) REVERT: C 916 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8501 (tp) REVERT: D 4 LEU cc_start: 0.6922 (mt) cc_final: 0.6694 (mm) REVERT: D 36 TRP cc_start: 0.6558 (m100) cc_final: 0.5822 (m100) REVERT: D 38 ARG cc_start: 0.7907 (ptt180) cc_final: 0.7487 (ptm160) REVERT: D 39 GLN cc_start: 0.7604 (tt0) cc_final: 0.7237 (mp10) REVERT: D 73 ASP cc_start: 0.7399 (t0) cc_final: 0.7081 (t0) REVERT: D 93 MET cc_start: 0.6633 (tpt) cc_final: 0.4956 (tpt) REVERT: D 95 TYR cc_start: 0.7223 (m-80) cc_final: 0.6738 (m-10) REVERT: D 104 ASP cc_start: 0.7529 (t0) cc_final: 0.7191 (t0) outliers start: 65 outliers final: 48 residues processed: 253 average time/residue: 0.1695 time to fit residues: 71.5204 Evaluate side-chains 248 residues out of total 2977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 195 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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 427 ASP 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 645 THR 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 969 ASN Chi-restraints excluded: chain A residue 1128 VAL 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 312 ILE 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 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 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 705 VAL Chi-restraints excluded: chain C residue 709 ASN 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 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 Chi-restraints excluded: chain E residue 68 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 149 optimal weight: 0.1980 chunk 2 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 chunk 128 optimal weight: 8.9990 chunk 283 optimal weight: 0.9990 chunk 299 optimal weight: 3.9990 chunk 293 optimal weight: 0.8980 chunk 211 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 223 optimal weight: 20.0000 chunk 141 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN D 32 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.165226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.115613 restraints weight = 47102.472| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.82 r_work: 0.3247 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 27986 Z= 0.095 Angle : 0.520 10.626 38149 Z= 0.256 Chirality : 0.044 0.385 4402 Planarity : 0.003 0.046 4862 Dihedral : 4.153 23.287 3670 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.75 % Allowed : 10.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.14), residues: 3382 helix: 1.89 (0.22), residues: 618 sheet: -0.93 (0.19), residues: 673 loop : -1.86 (0.12), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 577 TYR 0.013 0.001 TYR A 265 PHE 0.022 0.001 PHE C 135 TRP 0.027 0.001 TRP D 109 HIS 0.002 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.09 (27905) covalent geometry : angle 0.49431 / 0.25 (37947) SS BOND : bond 0.00301 / 0.23 ( 41) SS BOND : angle 1.01375 / 0.66 ( 82) hydrogen bonds : bond 0.03519 / 2.34 ( 893) hydrogen bonds : angle 4.60832 / 3.23 ( 2490) link_NAG-ASN : bond 0.00528 / 0.32 ( 40) link_NAG-ASN : angle 2.81059 / 1.90 ( 120) *********************** 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 273 residues out of total 2977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 221 time to evaluate : 0.915 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: 0.3736 (ptp) cc_final: 0.3254 (tpt) REVERT: A 177 MET cc_start: 0.2257 (tpp) cc_final: 0.0382 (ttp) REVERT: A 238 PHE cc_start: 0.6997 (p90) cc_final: 0.6302 (p90) REVERT: A 378 LYS cc_start: 0.8565 (tptt) cc_final: 0.8188 (tppt) REVERT: A 460 ASN cc_start: 0.7955 (OUTLIER) cc_final: 0.7572 (m-40) REVERT: A 734 THR cc_start: 0.9145 (m) cc_final: 0.8769 (p) REVERT: B 150 LYS cc_start: 0.6367 (pttt) cc_final: 0.6155 (ptmt) REVERT: B 157 PHE cc_start: 0.6715 (m-80) cc_final: 0.6472 (t80) REVERT: B 177 MET cc_start: -0.0311 (tpp) cc_final: -0.0968 (tmm) REVERT: B 200 TYR cc_start: 0.6748 (m-80) cc_final: 0.6521 (t80) REVERT: B 226 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7768 (tt) REVERT: B 453 TYR cc_start: 0.4478 (p90) cc_final: 0.4176 (p90) REVERT: B 532 ASN cc_start: 0.7077 (t0) cc_final: 0.6633 (t0) REVERT: B 547 THR cc_start: 0.8141 (m) cc_final: 0.7664 (p) REVERT: B 734 THR cc_start: 0.9092 (m) cc_final: 0.8773 (p) REVERT: B 904 TYR cc_start: 0.7660 (m-10) cc_final: 0.7027 (m-10) REVERT: B 1029 MET cc_start: 0.9423 (tpp) cc_final: 0.9062 (tpp) REVERT: B 1138 TYR cc_start: 0.7671 (t80) cc_final: 0.7334 (t80) REVERT: C 133 PHE cc_start: 0.6939 (m-10) cc_final: 0.6665 (m-10) REVERT: C 273 ARG cc_start: 0.7823 (mmt180) cc_final: 0.7507 (mmp80) REVERT: C 571 ASP cc_start: 0.8153 (t0) cc_final: 0.7816 (t0) REVERT: C 614 ASP cc_start: 0.7118 (t70) cc_final: 0.6651 (t0) REVERT: C 740 MET cc_start: 0.8980 (ttp) cc_final: 0.8689 (tpp) REVERT: C 809 PRO cc_start: 0.6501 (Cg_endo) cc_final: 0.6178 (Cg_exo) REVERT: C 916 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8307 (tp) REVERT: C 954 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.8059 (tt0) REVERT: D 4 LEU cc_start: 0.6807 (mt) cc_final: 0.6555 (mm) REVERT: D 36 TRP cc_start: 0.6403 (m100) cc_final: 0.5852 (m100) REVERT: D 38 ARG cc_start: 0.7892 (ptt180) cc_final: 0.7507 (ptm160) REVERT: D 39 GLN cc_start: 0.7619 (tt0) cc_final: 0.7328 (mp10) REVERT: D 73 ASP cc_start: 0.7401 (t0) cc_final: 0.7021 (t0) REVERT: D 91 THR cc_start: 0.6843 (p) cc_final: 0.6582 (p) REVERT: D 93 MET cc_start: 0.6590 (tpt) cc_final: 0.5006 (tpt) REVERT: D 95 TYR cc_start: 0.7120 (m-80) cc_final: 0.6614 (m-10) REVERT: D 104 ASP cc_start: 0.7632 (t0) cc_final: 0.7417 (t0) outliers start: 52 outliers final: 38 residues processed: 260 average time/residue: 0.1627 time to fit residues: 69.9632 Evaluate side-chains 246 residues out of total 2977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 204 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 430 THR Chi-restraints excluded: chain A residue 460 ASN 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 753 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1128 VAL 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 312 ILE 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 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 208 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 954 GLN 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 68 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 174 optimal weight: 0.2980 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 299 optimal weight: 3.9990 chunk 333 optimal weight: 50.0000 chunk 338 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 170 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 317 optimal weight: 10.0000 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.162703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.112230 restraints weight = 46912.734| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.74 r_work: 0.3199 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 27986 Z= 0.176 Angle : 0.579 10.370 38149 Z= 0.286 Chirality : 0.046 0.401 4402 Planarity : 0.004 0.045 4862 Dihedral : 4.378 23.223 3670 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.71 % Allowed : 10.98 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.14), residues: 3382 helix: 1.67 (0.22), residues: 622 sheet: -0.91 (0.19), residues: 670 loop : -1.89 (0.12), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 577 TYR 0.024 0.001 TYR A1138 PHE 0.019 0.002 PHE B 135 TRP 0.030 0.002 TRP C 886 HIS 0.004 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (27905) covalent geometry : angle 0.55232 / 0.28 (37947) SS BOND : bond 0.00427 / 0.31 ( 41) SS BOND : angle 1.41800 / 0.93 ( 82) hydrogen bonds : bond 0.04204 / 2.79 ( 893) hydrogen bonds : angle 4.81746 / 3.37 ( 2490) link_NAG-ASN : bond 0.00494 / 0.31 ( 40) link_NAG-ASN : angle 2.93468 / 1.98 ( 120) ********************** 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 245 residues out of total 2977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 194 time to evaluate : 0.814 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: 0.3745 (ptp) cc_final: 0.3225 (tpt) REVERT: A 177 MET cc_start: 0.2205 (tpp) cc_final: 0.0358 (ttp) REVERT: A 269 TYR cc_start: 0.7475 (m-80) cc_final: 0.7017 (m-80) REVERT: A 378 LYS cc_start: 0.8540 (tptt) cc_final: 0.8166 (tppt) REVERT: A 734 THR cc_start: 0.9162 (m) cc_final: 0.8721 (p) REVERT: B 150 LYS cc_start: 0.6647 (pttt) cc_final: 0.6380 (ptmt) REVERT: B 157 PHE cc_start: 0.6783 (m-80) cc_final: 0.6511 (t80) REVERT: B 177 MET cc_start: -0.0266 (tpp) cc_final: -0.0926 (mtt) REVERT: B 200 TYR cc_start: 0.6934 (m-80) cc_final: 0.6687 (t80) REVERT: B 226 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7779 (tt) REVERT: B 453 TYR cc_start: 0.4529 (p90) cc_final: 0.4223 (p90) REVERT: B 532 ASN cc_start: 0.7129 (t0) cc_final: 0.6669 (t0) REVERT: B 547 THR cc_start: 0.8183 (m) cc_final: 0.7710 (p) REVERT: B 904 TYR cc_start: 0.7764 (m-10) cc_final: 0.7091 (m-10) REVERT: B 1138 TYR cc_start: 0.7682 (t80) cc_final: 0.7337 (t80) REVERT: C 133 PHE cc_start: 0.6958 (m-10) cc_final: 0.6688 (m-10) REVERT: C 571 ASP cc_start: 0.8148 (t0) cc_final: 0.7795 (t0) REVERT: C 614 ASP cc_start: 0.7182 (t70) cc_final: 0.6738 (t0) REVERT: C 740 MET cc_start: 0.9078 (ttp) cc_final: 0.8785 (tpp) REVERT: C 809 PRO cc_start: 0.6508 (Cg_endo) cc_final: 0.6177 (Cg_exo) REVERT: C 916 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8473 (tp) REVERT: C 954 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.8071 (tt0) REVERT: D 4 LEU cc_start: 0.6742 (mt) cc_final: 0.6502 (mm) REVERT: D 36 TRP cc_start: 0.6527 (m100) cc_final: 0.6003 (m100) REVERT: D 38 ARG cc_start: 0.7799 (ptt180) cc_final: 0.7360 (ptm160) REVERT: D 39 GLN cc_start: 0.7597 (tt0) cc_final: 0.7326 (mp10) REVERT: D 73 ASP cc_start: 0.7426 (t0) cc_final: 0.7023 (t0) REVERT: D 91 THR cc_start: 0.6981 (p) cc_final: 0.6699 (p) REVERT: D 93 MET cc_start: 0.6618 (tpt) cc_final: 0.5068 (tpt) REVERT: D 95 TYR cc_start: 0.7115 (m-80) cc_final: 0.6574 (m-10) REVERT: D 104 ASP cc_start: 0.7540 (t0) cc_final: 0.7161 (t0) outliers start: 51 outliers final: 44 residues processed: 234 average time/residue: 0.1685 time to fit residues: 65.6660 Evaluate side-chains 237 residues out of total 2977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 190 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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 430 THR 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 753 LEU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1128 VAL 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 312 ILE 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 987 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 24 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 553 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 709 ASN 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 954 GLN 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 Chi-restraints excluded: chain E residue 68 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 119 optimal weight: 10.0000 chunk 177 optimal weight: 3.9990 chunk 266 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 186 optimal weight: 0.0980 chunk 188 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 179 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.165168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.116180 restraints weight = 46809.502| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.85 r_work: 0.3252 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 27986 Z= 0.092 Angle : 0.517 10.519 38149 Z= 0.255 Chirality : 0.044 0.386 4402 Planarity : 0.003 0.045 4862 Dihedral : 4.116 22.871 3670 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.55 % Allowed : 11.12 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.14), residues: 3382 helix: 1.91 (0.22), residues: 621 sheet: -0.77 (0.20), residues: 655 loop : -1.81 (0.12), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 577 TYR 0.013 0.001 TYR A 351 PHE 0.016 0.001 PHE D 27 TRP 0.028 0.001 TRP D 109 HIS 0.002 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 (27905) covalent geometry : angle 0.49211 / 0.25 (37947) SS BOND : bond 0.00291 / 0.23 ( 41) SS BOND : angle 1.13790 / 0.75 ( 82) hydrogen bonds : bond 0.03486 / 2.33 ( 893) hydrogen bonds : angle 4.58964 / 3.22 ( 2490) link_NAG-ASN : bond 0.00529 / 0.32 ( 40) link_NAG-ASN : angle 2.76217 / 1.88 ( 120) =============================================================================== Job complete usr+sys time: 7544.98 seconds wall clock time: 144 minutes 52.13 seconds (8692.13 seconds total)