Starting phenix.real_space_refine on Thu Mar 5 23:05:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xy3_33509/03_2026/7xy3_33509.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xy3_33509/03_2026/7xy3_33509.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xy3_33509/03_2026/7xy3_33509.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xy3_33509/03_2026/7xy3_33509.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xy3_33509/03_2026/7xy3_33509.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xy3_33509/03_2026/7xy3_33509.map" } resolution = 4.6 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= 0.003 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 120 5.16 5 C 16773 2.51 5 N 4355 2.21 5 O 5115 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26363 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 8266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8266 Classifications: {'peptide': 1056} Link IDs: {'PTRANS': 51, 'TRANS': 1004} Chain breaks: 7 Chain: "B" Number of atoms: 8297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8297 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 52, 'TRANS': 1007} Chain breaks: 5 Chain: "C" Number of atoms: 8268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8268 Classifications: {'peptide': 1056} Link IDs: {'PTRANS': 51, 'TRANS': 1004} Chain breaks: 6 Chain: "D" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1000 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 5.60, per 1000 atoms: 0.21 Number of scatterers: 26363 At special positions: 0 Unit cell: (156, 157.04, 195.52, 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 120 16.00 O 5115 8.00 N 4355 7.00 C 16773 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 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=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 99 " 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 616 " " NAG A1205 " - " ASN A 657 " " NAG A1206 " - " ASN A 709 " " NAG A1207 " - " ASN A1074 " " NAG A1208 " - " ASN A 717 " " NAG A1209 " - " ASN A 801 " " NAG A1210 " - " ASN A1098 " " NAG A1211 " - " 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 331 " " 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: 2.16 Conformation dependent library (CDL) restraints added in 1.1 seconds 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6174 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 51 sheets defined 21.1% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 403 through 408 removed outlier: 3.529A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 403 through 408' Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 746 through 756 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 886 through 891 removed outlier: 3.600A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.580A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.561A 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 965 removed outlier: 3.865A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN A 954 " --> pdb=" O ASP A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.989A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'A' and resid 1141 through 1145 removed outlier: 3.708A pdb=" N LEU A1145 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.905A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN B 409 " --> pdb=" O GLU B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 442 Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 747 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.866A 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 removed outlier: 3.514A pdb=" N ILE B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 885 through 891 removed outlier: 4.154A pdb=" N PHE B 888 " --> pdb=" O GLY B 885 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.676A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.519A pdb=" N ILE B 923 " --> pdb=" O ASN B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.734A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.237A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.757A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 removed outlier: 4.250A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 removed outlier: 3.635A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 417 through 422' Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.597A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) 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 783 removed outlier: 3.674A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.962A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 887 through 891 removed outlier: 4.001A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.798A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.639A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1032 Processing helix chain 'C' and resid 1141 through 1145 removed outlier: 3.919A pdb=" N LEU C1145 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 117 removed outlier: 4.256A pdb=" N GLY D 116 " --> pdb=" O ARG D 113 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR D 117 " --> pdb=" O SER D 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 113 through 117' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.731A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.863A 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 55 removed outlier: 7.076A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.748A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 225 removed outlier: 3.779A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 95 through 96 removed outlier: 4.233A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 143 through 144 removed outlier: 3.588A pdb=" N TYR A 144 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N MET A 153 " --> pdb=" O TYR A 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 317 removed outlier: 7.077A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 327 removed outlier: 6.524A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 546 " --> pdb=" O PHE A 543 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 325 through 327 removed outlier: 6.524A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.003A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB4, first strand: chain 'A' and resid 573 through 575 removed outlier: 5.739A 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 removed outlier: 5.661A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 701 through 704 removed outlier: 3.557A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 728 removed outlier: 4.008A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 711 through 728 removed outlier: 4.008A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A1105 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AC1, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.913A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.258A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.588A 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 118 through 121 removed outlier: 3.636A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 317 removed outlier: 6.663A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.581A pdb=" N ILE B 326 " --> pdb=" O ASN B 540 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.687A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE B 434 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N VAL B 433 " --> pdb=" O PHE B 377 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE B 377 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA B 435 " --> pdb=" O SER B 375 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 584 through 586 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.892A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 703 removed outlier: 5.988A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 719 removed outlier: 3.646A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 722 through 728 removed outlier: 4.390A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 5.209A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.687A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU C 226 " --> pdb=" O ILE C 203 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 55 removed outlier: 6.554A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.740A pdb=" N ARG C 237 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE C 119 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 154 through 157 removed outlier: 3.892A pdb=" N SER C 155 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU C 244 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL C 143 " --> pdb=" O LEU C 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 313 through 319 removed outlier: 5.803A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.710A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA C 435 " --> pdb=" O SER C 375 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 538 through 542 removed outlier: 3.676A pdb=" N ASP C 586 " --> pdb=" O THR C 553 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 664 through 667 removed outlier: 6.335A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY C 667 " --> pdb=" O ILE C 670 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 719 removed outlier: 3.641A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 722 through 728 removed outlier: 4.019A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 735 removed outlier: 3.576A pdb=" N SER C 735 " --> pdb=" O THR C 859 " (cutoff:3.500A) 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 2 through 7 removed outlier: 3.625A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 61 through 63 removed outlier: 3.655A pdb=" N VAL D 52 " --> pdb=" O TRP D 40 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TRP D 40 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ALA D 54 " --> pdb=" O MET D 38 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N MET D 38 " --> pdb=" O ALA D 54 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY D 39 " --> pdb=" O ALA D 100 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR D 119 " --> pdb=" O ALA D 101 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 61 through 63 removed outlier: 3.655A pdb=" N VAL D 52 " --> pdb=" O TRP D 40 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TRP D 40 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ALA D 54 " --> pdb=" O MET D 38 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N MET D 38 " --> pdb=" O ALA D 54 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY D 39 " --> pdb=" O ALA D 100 " (cutoff:3.500A) 866 hydrogen bonds defined for protein. 2379 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.21 Time building geometry restraints manager: 2.91 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: 8428 1.34 - 1.47: 6788 1.47 - 1.59: 11587 1.59 - 1.72: 0 1.72 - 1.84: 154 Bond restraints: 26957 Sorted by residual: bond pdb=" C1 NAG A1202 " pdb=" O5 NAG A1202 " ideal model delta sigma weight residual 1.406 1.480 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C1 NAG C1211 " pdb=" O5 NAG C1211 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.83e+00 bond pdb=" C1 NAG C1210 " pdb=" O5 NAG C1210 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.92e+00 bond pdb=" C1 NAG B1209 " pdb=" O5 NAG B1209 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.81e+00 bond pdb=" C1 NAG C1201 " pdb=" O5 NAG C1201 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.73e+00 ... (remaining 26952 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 36054 2.45 - 4.89: 558 4.89 - 7.34: 40 7.34 - 9.79: 9 9.79 - 12.23: 2 Bond angle restraints: 36663 Sorted by residual: angle pdb=" N TYR D 32 " pdb=" CA TYR D 32 " pdb=" C TYR D 32 " ideal model delta sigma weight residual 113.02 103.80 9.22 1.20e+00 6.94e-01 5.90e+01 angle pdb=" N TYR D 29 " pdb=" CA TYR D 29 " pdb=" C TYR D 29 " ideal model delta sigma weight residual 108.49 98.11 10.38 1.65e+00 3.67e-01 3.96e+01 angle pdb=" N VAL C 382 " pdb=" CA VAL C 382 " pdb=" C VAL C 382 " ideal model delta sigma weight residual 108.81 116.99 -8.18 1.62e+00 3.81e-01 2.55e+01 angle pdb=" N GLY B 757 " pdb=" CA GLY B 757 " pdb=" C GLY B 757 " ideal model delta sigma weight residual 111.21 116.25 -5.04 1.04e+00 9.25e-01 2.35e+01 angle pdb=" C GLU C 619 " pdb=" N VAL C 620 " pdb=" CA VAL C 620 " ideal model delta sigma weight residual 121.70 128.64 -6.94 1.80e+00 3.09e-01 1.48e+01 ... (remaining 36658 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.67: 16168 20.67 - 41.34: 291 41.34 - 62.02: 68 62.02 - 82.69: 5 82.69 - 103.36: 8 Dihedral angle restraints: 16540 sinusoidal: 6937 harmonic: 9603 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual 93.00 146.34 -53.34 1 1.00e+01 1.00e-02 3.87e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual 93.00 141.02 -48.02 1 1.00e+01 1.00e-02 3.18e+01 dihedral pdb=" CA VAL A 951 " pdb=" C VAL A 951 " pdb=" N VAL A 952 " pdb=" CA VAL A 952 " ideal model delta harmonic sigma weight residual 180.00 -152.78 -27.22 0 5.00e+00 4.00e-02 2.96e+01 ... (remaining 16537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.183: 4230 0.183 - 0.366: 6 0.366 - 0.549: 5 0.549 - 0.732: 1 0.732 - 0.915: 1 Chirality restraints: 4243 Sorted by residual: chirality pdb=" C1 NAG C1204 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1204 " pdb=" O5 NAG C1204 " both_signs ideal model delta sigma weight residual False -2.40 -1.48 -0.92 2.00e-01 2.50e+01 2.09e+01 chirality pdb=" C1 NAG C1212 " pdb=" ND2 ASN C 801 " pdb=" C2 NAG C1212 " pdb=" O5 NAG C1212 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.09e+01 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 -1.86 -0.54 2.00e-01 2.50e+01 7.20e+00 ... (remaining 4240 not shown) Planarity restraints: 4742 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " -0.020 2.00e-02 2.50e+03 1.28e-01 2.04e+02 pdb=" CG ASN C 331 " -0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " 0.117 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " -0.212 2.00e-02 2.50e+03 pdb=" C1 NAG C1204 " 0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1204 " 0.127 2.00e-02 2.50e+03 1.05e-01 1.37e+02 pdb=" C7 NAG C1204 " -0.035 2.00e-02 2.50e+03 pdb=" C8 NAG C1204 " 0.095 2.00e-02 2.50e+03 pdb=" N2 NAG C1204 " -0.167 2.00e-02 2.50e+03 pdb=" O7 NAG C1204 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1212 " -0.106 2.00e-02 2.50e+03 8.70e-02 9.46e+01 pdb=" C7 NAG C1212 " 0.029 2.00e-02 2.50e+03 pdb=" C8 NAG C1212 " -0.080 2.00e-02 2.50e+03 pdb=" N2 NAG C1212 " 0.138 2.00e-02 2.50e+03 pdb=" O7 NAG C1212 " 0.018 2.00e-02 2.50e+03 ... (remaining 4739 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1954 2.74 - 3.28: 24971 3.28 - 3.82: 43735 3.82 - 4.36: 49701 4.36 - 4.90: 84689 Nonbonded interactions: 205050 Sorted by model distance: nonbonded pdb=" OE1 GLN C 804 " pdb=" CG2 ILE C 931 " model vdw 2.198 3.460 nonbonded pdb=" OG1 THR A 108 " pdb=" O ASN A 234 " model vdw 2.250 3.040 nonbonded pdb=" OG1 THR B 33 " pdb=" O GLY B 219 " model vdw 2.258 3.040 nonbonded pdb=" O TYR B 396 " pdb=" OG SER B 514 " model vdw 2.261 3.040 nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.271 3.040 ... (remaining 205045 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 525 or resid 530 through 1211)) selection = (chain 'B' and (resid 14 through 331 or resid 334 through 525 or resid 530 throu \ gh 1211)) selection = (chain 'C' and (resid 14 through 331 or resid 334 through 1211)) } 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 group one per residue 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: 1.920 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: 0.390 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 25.940 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.253 27035 Z= 0.239 Angle : 0.808 23.574 36857 Z= 0.423 Chirality : 0.056 0.915 4243 Planarity : 0.006 0.105 4704 Dihedral : 9.584 103.361 10246 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 0.07 % Allowed : 0.69 % Favored : 99.24 % 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: -3.84 (0.12), residues: 3258 helix: -1.23 (0.17), residues: 633 sheet: -2.34 (0.20), residues: 517 loop : -3.24 (0.11), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 815 TYR 0.022 0.002 TYR B 204 PHE 0.028 0.003 PHE B 823 TRP 0.017 0.002 TRP B 886 HIS 0.008 0.002 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00467 (26957) covalent geometry : angle 0.75293 (36663) SS BOND : bond 0.00354 ( 40) SS BOND : angle 1.18993 ( 80) hydrogen bonds : bond 0.22063 ( 854) hydrogen bonds : angle 9.45296 ( 2379) link_NAG-ASN : bond 0.04202 ( 38) link_NAG-ASN : angle 5.27686 ( 114) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 381 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.9456 (ttp) cc_final: 0.9212 (ttm) REVERT: A 772 VAL cc_start: 0.9607 (t) cc_final: 0.9390 (p) REVERT: A 773 GLU cc_start: 0.8511 (mm-30) cc_final: 0.7860 (tp30) REVERT: A 781 VAL cc_start: 0.9641 (t) cc_final: 0.9064 (m) REVERT: A 802 PHE cc_start: 0.8697 (m-10) cc_final: 0.8443 (m-10) REVERT: A 870 ILE cc_start: 0.9325 (pt) cc_final: 0.9116 (mp) REVERT: A 953 ASN cc_start: 0.8362 (m-40) cc_final: 0.7973 (m110) REVERT: A 1029 MET cc_start: 0.8800 (mtt) cc_final: 0.8569 (tpp) REVERT: A 1065 VAL cc_start: 0.9397 (t) cc_final: 0.8913 (t) REVERT: B 177 MET cc_start: 0.0219 (tpp) cc_final: -0.0145 (ttp) REVERT: B 192 PHE cc_start: 0.8985 (m-10) cc_final: 0.8742 (m-10) REVERT: B 389 ASP cc_start: 0.8463 (m-30) cc_final: 0.8247 (t0) REVERT: B 424 LYS cc_start: 0.8050 (tttt) cc_final: 0.7670 (tptp) REVERT: B 471 GLU cc_start: 0.9089 (tt0) cc_final: 0.8872 (mm-30) REVERT: B 731 MET cc_start: 0.9251 (ttp) cc_final: 0.8999 (ttm) REVERT: B 740 MET cc_start: 0.7691 (ttt) cc_final: 0.7064 (ttt) REVERT: B 774 GLN cc_start: 0.9105 (mm-40) cc_final: 0.8702 (mm110) REVERT: B 1006 THR cc_start: 0.9206 (m) cc_final: 0.8919 (p) REVERT: B 1033 VAL cc_start: 0.9334 (t) cc_final: 0.9111 (t) REVERT: B 1062 PHE cc_start: 0.8921 (m-80) cc_final: 0.8259 (m-10) REVERT: C 153 MET cc_start: 0.4711 (ptp) cc_final: 0.4159 (ppp) REVERT: C 214 ARG cc_start: 0.9036 (ptt180) cc_final: 0.8668 (tpm170) REVERT: C 353 TRP cc_start: 0.2348 (p90) cc_final: 0.1757 (p90) REVERT: C 731 MET cc_start: 0.8891 (ttp) cc_final: 0.7753 (ptm) REVERT: C 763 LEU cc_start: 0.9138 (mt) cc_final: 0.8814 (mt) REVERT: C 765 ARG cc_start: 0.8528 (ttp-170) cc_final: 0.7853 (ptm160) REVERT: C 966 LEU cc_start: 0.9565 (mt) cc_final: 0.9109 (mp) REVERT: C 1050 MET cc_start: 0.9024 (ptp) cc_final: 0.8715 (ptp) REVERT: D 94 MET cc_start: 0.7521 (ttm) cc_final: 0.7216 (ptt) outliers start: 2 outliers final: 0 residues processed: 383 average time/residue: 0.1819 time to fit residues: 106.3002 Evaluate side-chains 167 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 10.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 580 GLN A 762 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 953 ASN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS A1119 ASN B 14 GLN B 99 ASN B 115 GLN B 188 ASN B 474 GLN B 644 GLN B 655 HIS B 658 ASN ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B 901 GLN B 913 GLN B 965 GLN B1071 GLN B1083 HIS C 49 HIS C 487 ASN C 501 ASN C 710 ASN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 919 ASN C 965 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.061395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.043172 restraints weight = 181405.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.044394 restraints weight = 106322.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.045209 restraints weight = 73246.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.045747 restraints weight = 56469.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.046080 restraints weight = 47303.874| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 27035 Z= 0.300 Angle : 0.792 17.727 36857 Z= 0.404 Chirality : 0.050 0.512 4243 Planarity : 0.005 0.104 4704 Dihedral : 8.476 78.562 4340 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 0.07 % Allowed : 2.12 % Favored : 97.81 % 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: -3.11 (0.13), residues: 3258 helix: 0.25 (0.20), residues: 632 sheet: -2.19 (0.19), residues: 609 loop : -2.97 (0.12), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C1107 TYR 0.018 0.002 TYR C 313 PHE 0.032 0.002 PHE B 464 TRP 0.022 0.002 TRP A 64 HIS 0.014 0.002 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00613 (26957) covalent geometry : angle 0.75896 (36663) SS BOND : bond 0.00399 ( 40) SS BOND : angle 1.53206 ( 80) hydrogen bonds : bond 0.05370 ( 854) hydrogen bonds : angle 7.48907 ( 2379) link_NAG-ASN : bond 0.00897 ( 38) link_NAG-ASN : angle 3.98096 ( 114) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 187 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.9253 (mm-30) cc_final: 0.9022 (mm-30) REVERT: A 802 PHE cc_start: 0.8865 (m-10) cc_final: 0.8650 (m-10) REVERT: A 1050 MET cc_start: 0.9094 (pmm) cc_final: 0.8371 (pmm) REVERT: B 104 TRP cc_start: 0.7862 (m-90) cc_final: 0.7461 (m-90) REVERT: B 177 MET cc_start: 0.0409 (tpp) cc_final: -0.0350 (ttp) REVERT: B 471 GLU cc_start: 0.9074 (tt0) cc_final: 0.8864 (mm-30) REVERT: B 774 GLN cc_start: 0.9341 (mm-40) cc_final: 0.8998 (mm110) REVERT: B 1002 GLN cc_start: 0.8966 (tm-30) cc_final: 0.8386 (tm-30) REVERT: B 1050 MET cc_start: 0.8496 (ptt) cc_final: 0.8236 (ptt) REVERT: C 153 MET cc_start: 0.4654 (ptp) cc_final: 0.4300 (ppp) REVERT: C 237 ARG cc_start: 0.6892 (mtt180) cc_final: 0.6581 (mtm180) REVERT: C 353 TRP cc_start: 0.1957 (p90) cc_final: 0.1473 (p90) REVERT: C 731 MET cc_start: 0.8890 (ttp) cc_final: 0.8321 (ttp) REVERT: C 763 LEU cc_start: 0.9256 (mt) cc_final: 0.9014 (mt) REVERT: C 770 ILE cc_start: 0.9648 (mm) cc_final: 0.9109 (mm) REVERT: C 774 GLN cc_start: 0.9522 (mm-40) cc_final: 0.9078 (mm-40) REVERT: C 902 MET cc_start: 0.9504 (mmm) cc_final: 0.9292 (mmm) REVERT: C 1050 MET cc_start: 0.9032 (ptp) cc_final: 0.8694 (ptp) REVERT: D 12 VAL cc_start: 0.5076 (m) cc_final: 0.4639 (m) outliers start: 2 outliers final: 0 residues processed: 189 average time/residue: 0.1682 time to fit residues: 50.9028 Evaluate side-chains 123 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 271 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 chunk 198 optimal weight: 3.9990 chunk 242 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 196 optimal weight: 7.9990 chunk 226 optimal weight: 7.9990 chunk 259 optimal weight: 20.0000 chunk 269 optimal weight: 3.9990 chunk 109 optimal weight: 0.0980 chunk 11 optimal weight: 10.0000 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 925 ASN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 913 GLN B 957 GLN B1023 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 919 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.063886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.045610 restraints weight = 191801.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.046779 restraints weight = 113630.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.047548 restraints weight = 78654.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.048069 restraints weight = 61516.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.048390 restraints weight = 52222.364| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27035 Z= 0.162 Angle : 0.636 16.698 36857 Z= 0.319 Chirality : 0.047 0.477 4243 Planarity : 0.004 0.057 4704 Dihedral : 7.358 59.912 4340 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % 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: -2.73 (0.14), residues: 3258 helix: 0.79 (0.21), residues: 631 sheet: -1.98 (0.20), residues: 599 loop : -2.79 (0.12), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1019 TYR 0.022 0.001 TYR D 29 PHE 0.024 0.001 PHE B 464 TRP 0.044 0.002 TRP C 886 HIS 0.005 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00335 (26957) covalent geometry : angle 0.59646 (36663) SS BOND : bond 0.00274 ( 40) SS BOND : angle 1.44327 ( 80) hydrogen bonds : bond 0.04361 ( 854) hydrogen bonds : angle 6.74209 ( 2379) link_NAG-ASN : bond 0.00710 ( 38) link_NAG-ASN : angle 3.83476 ( 114) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.8503 (mp) cc_final: 0.8220 (tp) REVERT: A 763 LEU cc_start: 0.9518 (pp) cc_final: 0.9271 (pp) REVERT: A 764 ASN cc_start: 0.9466 (m-40) cc_final: 0.8772 (p0) REVERT: A 1050 MET cc_start: 0.9269 (pmm) cc_final: 0.8497 (pmm) REVERT: B 92 PHE cc_start: 0.9263 (t80) cc_final: 0.9031 (t80) REVERT: B 104 TRP cc_start: 0.7915 (m-90) cc_final: 0.7668 (m-90) REVERT: B 177 MET cc_start: 0.0595 (tpp) cc_final: -0.0335 (ttp) REVERT: B 387 LEU cc_start: 0.8763 (mt) cc_final: 0.8400 (mt) REVERT: B 389 ASP cc_start: 0.8467 (m-30) cc_final: 0.8138 (t0) REVERT: B 390 LEU cc_start: 0.8678 (tp) cc_final: 0.8438 (tt) REVERT: B 471 GLU cc_start: 0.9063 (tt0) cc_final: 0.8835 (mm-30) REVERT: B 774 GLN cc_start: 0.9391 (mm-40) cc_final: 0.9008 (mm110) REVERT: B 1002 GLN cc_start: 0.9047 (tm-30) cc_final: 0.8345 (tm-30) REVERT: C 153 MET cc_start: 0.4841 (ptp) cc_final: 0.4383 (ppp) REVERT: C 731 MET cc_start: 0.8884 (ttp) cc_final: 0.8361 (ttp) REVERT: C 763 LEU cc_start: 0.9423 (mt) cc_final: 0.9192 (mt) REVERT: C 770 ILE cc_start: 0.9598 (mm) cc_final: 0.8936 (mm) REVERT: C 774 GLN cc_start: 0.9509 (mm-40) cc_final: 0.8884 (mm-40) REVERT: C 869 MET cc_start: 0.9369 (mtp) cc_final: 0.8812 (mtp) REVERT: C 902 MET cc_start: 0.9528 (mmm) cc_final: 0.9235 (mmm) REVERT: C 966 LEU cc_start: 0.9629 (mt) cc_final: 0.9252 (mp) REVERT: C 1050 MET cc_start: 0.9026 (ptp) cc_final: 0.7885 (ptp) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.1625 time to fit residues: 51.8846 Evaluate side-chains 121 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 141 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 207 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 277 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 296 optimal weight: 5.9990 chunk 232 optimal weight: 9.9990 chunk 161 optimal weight: 20.0000 chunk 61 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 913 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 919 ASN C 957 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.061109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.042747 restraints weight = 181150.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.044007 restraints weight = 104275.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.044866 restraints weight = 70878.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.045438 restraints weight = 53984.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.045763 restraints weight = 44753.598| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 27035 Z= 0.237 Angle : 0.703 16.013 36857 Z= 0.356 Chirality : 0.048 0.450 4243 Planarity : 0.005 0.051 4704 Dihedral : 7.130 59.593 4340 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer: Outliers : 0.03 % Allowed : 2.50 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.14), residues: 3258 helix: 0.67 (0.20), residues: 634 sheet: -1.91 (0.20), residues: 573 loop : -2.69 (0.12), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1019 TYR 0.016 0.002 TYR D 29 PHE 0.033 0.002 PHE C 823 TRP 0.026 0.002 TRP C 886 HIS 0.009 0.002 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00491 (26957) covalent geometry : angle 0.66864 (36663) SS BOND : bond 0.00312 ( 40) SS BOND : angle 1.47251 ( 80) hydrogen bonds : bond 0.04386 ( 854) hydrogen bonds : angle 6.71549 ( 2379) link_NAG-ASN : bond 0.00731 ( 38) link_NAG-ASN : angle 3.82211 ( 114) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 PHE cc_start: 0.9174 (m-10) cc_final: 0.8418 (m-10) REVERT: A 1050 MET cc_start: 0.9256 (pmm) cc_final: 0.8396 (pmm) REVERT: B 92 PHE cc_start: 0.9154 (t80) cc_final: 0.8934 (t80) REVERT: B 177 MET cc_start: 0.0792 (tpp) cc_final: -0.0278 (ttp) REVERT: B 192 PHE cc_start: 0.8968 (m-80) cc_final: 0.8680 (m-10) REVERT: B 471 GLU cc_start: 0.9098 (tt0) cc_final: 0.8890 (mm-30) REVERT: B 774 GLN cc_start: 0.9330 (mm-40) cc_final: 0.8948 (mm110) REVERT: B 1002 GLN cc_start: 0.9090 (tm-30) cc_final: 0.8282 (tm-30) REVERT: C 153 MET cc_start: 0.4669 (ptp) cc_final: 0.4311 (ppp) REVERT: C 731 MET cc_start: 0.8952 (ttp) cc_final: 0.8482 (ttp) REVERT: C 763 LEU cc_start: 0.9436 (mt) cc_final: 0.9164 (mt) REVERT: C 770 ILE cc_start: 0.9603 (mm) cc_final: 0.8995 (mm) REVERT: C 774 GLN cc_start: 0.9515 (mm-40) cc_final: 0.8892 (mm-40) REVERT: C 869 MET cc_start: 0.9412 (mtp) cc_final: 0.8859 (mtp) REVERT: C 902 MET cc_start: 0.9546 (mmm) cc_final: 0.9267 (mmm) REVERT: C 933 LYS cc_start: 0.9389 (ptpp) cc_final: 0.9032 (pttm) REVERT: C 966 LEU cc_start: 0.9582 (mt) cc_final: 0.9148 (mp) outliers start: 1 outliers final: 0 residues processed: 161 average time/residue: 0.1561 time to fit residues: 41.6603 Evaluate side-chains 114 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 221 optimal weight: 6.9990 chunk 320 optimal weight: 40.0000 chunk 61 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 250 optimal weight: 20.0000 chunk 121 optimal weight: 0.9980 chunk 40 optimal weight: 40.0000 chunk 112 optimal weight: 9.9990 chunk 286 optimal weight: 4.9990 chunk 264 optimal weight: 2.9990 chunk 284 optimal weight: 6.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 895 GLN B 913 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN C 777 ASN C 901 GLN C 919 ASN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.063881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.045621 restraints weight = 190723.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.046828 restraints weight = 111615.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.047630 restraints weight = 76852.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.048127 restraints weight = 59852.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 67)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.048475 restraints weight = 50805.148| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27035 Z= 0.128 Angle : 0.602 15.949 36857 Z= 0.300 Chirality : 0.046 0.465 4243 Planarity : 0.004 0.061 4704 Dihedral : 6.635 59.914 4340 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.14), residues: 3258 helix: 0.97 (0.21), residues: 644 sheet: -1.79 (0.21), residues: 569 loop : -2.60 (0.12), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1107 TYR 0.022 0.001 TYR B 204 PHE 0.020 0.001 PHE B 464 TRP 0.015 0.001 TRP C 886 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00269 (26957) covalent geometry : angle 0.56372 (36663) SS BOND : bond 0.00356 ( 40) SS BOND : angle 1.34427 ( 80) hydrogen bonds : bond 0.03937 ( 854) hydrogen bonds : angle 6.20665 ( 2379) link_NAG-ASN : bond 0.00700 ( 38) link_NAG-ASN : angle 3.68912 ( 114) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.8498 (ttt) cc_final: 0.8185 (ttm) REVERT: A 763 LEU cc_start: 0.9537 (pp) cc_final: 0.9277 (pp) REVERT: A 764 ASN cc_start: 0.9496 (m-40) cc_final: 0.8744 (p0) REVERT: A 774 GLN cc_start: 0.9645 (mm-40) cc_final: 0.9270 (mm-40) REVERT: A 1050 MET cc_start: 0.9217 (pmm) cc_final: 0.8420 (pmm) REVERT: B 92 PHE cc_start: 0.9154 (t80) cc_final: 0.8858 (t80) REVERT: B 177 MET cc_start: 0.0682 (tpp) cc_final: -0.1572 (ptm) REVERT: B 192 PHE cc_start: 0.8962 (m-80) cc_final: 0.8544 (m-10) REVERT: B 347 PHE cc_start: 0.4143 (m-80) cc_final: 0.3906 (m-10) REVERT: B 387 LEU cc_start: 0.8727 (mt) cc_final: 0.8478 (mt) REVERT: B 471 GLU cc_start: 0.9061 (tt0) cc_final: 0.8824 (mm-30) REVERT: B 774 GLN cc_start: 0.9326 (mm-40) cc_final: 0.8945 (mm110) REVERT: B 869 MET cc_start: 0.9295 (mtp) cc_final: 0.9088 (mtp) REVERT: B 1002 GLN cc_start: 0.9088 (tm-30) cc_final: 0.8289 (tm-30) REVERT: C 153 MET cc_start: 0.4665 (ptp) cc_final: 0.4217 (ppp) REVERT: C 731 MET cc_start: 0.8931 (ttp) cc_final: 0.8403 (ttp) REVERT: C 763 LEU cc_start: 0.9415 (mt) cc_final: 0.9146 (mp) REVERT: C 774 GLN cc_start: 0.9488 (mm-40) cc_final: 0.9077 (mm-40) REVERT: C 869 MET cc_start: 0.9397 (mtp) cc_final: 0.8821 (mtp) REVERT: C 902 MET cc_start: 0.9445 (mmm) cc_final: 0.9104 (mmm) REVERT: C 966 LEU cc_start: 0.9562 (mt) cc_final: 0.9034 (mp) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1543 time to fit residues: 44.9880 Evaluate side-chains 115 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 326 optimal weight: 10.0000 chunk 149 optimal weight: 0.0970 chunk 281 optimal weight: 5.9990 chunk 30 optimal weight: 0.1980 chunk 145 optimal weight: 8.9990 chunk 298 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 156 optimal weight: 7.9990 chunk 309 optimal weight: 9.9990 chunk 301 optimal weight: 8.9990 overall best weight: 4.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 913 GLN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 919 ASN C 957 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.061745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.043396 restraints weight = 178469.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.044637 restraints weight = 102968.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.045491 restraints weight = 70466.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.046054 restraints weight = 54027.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.046410 restraints weight = 45009.209| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27035 Z= 0.183 Angle : 0.638 15.618 36857 Z= 0.319 Chirality : 0.047 0.452 4243 Planarity : 0.004 0.056 4704 Dihedral : 6.580 59.830 4340 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.14), residues: 3258 helix: 0.95 (0.20), residues: 643 sheet: -1.74 (0.21), residues: 561 loop : -2.55 (0.13), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1107 TYR 0.017 0.001 TYR B 204 PHE 0.036 0.002 PHE C 823 TRP 0.058 0.002 TRP C 886 HIS 0.007 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00379 (26957) covalent geometry : angle 0.60214 (36663) SS BOND : bond 0.00279 ( 40) SS BOND : angle 1.39584 ( 80) hydrogen bonds : bond 0.03998 ( 854) hydrogen bonds : angle 6.20890 ( 2379) link_NAG-ASN : bond 0.00705 ( 38) link_NAG-ASN : angle 3.66856 ( 114) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.8537 (ttt) cc_final: 0.8237 (ttm) REVERT: A 763 LEU cc_start: 0.9526 (pp) cc_final: 0.9242 (pp) REVERT: A 764 ASN cc_start: 0.9297 (m-40) cc_final: 0.8675 (p0) REVERT: A 802 PHE cc_start: 0.8935 (m-80) cc_final: 0.8594 (m-80) REVERT: A 1050 MET cc_start: 0.9246 (pmm) cc_final: 0.8402 (pmm) REVERT: B 177 MET cc_start: 0.0901 (tpp) cc_final: -0.1543 (ptm) REVERT: B 471 GLU cc_start: 0.9154 (tt0) cc_final: 0.8896 (mm-30) REVERT: B 774 GLN cc_start: 0.9329 (mm-40) cc_final: 0.8940 (mm110) REVERT: B 869 MET cc_start: 0.9274 (mtp) cc_final: 0.9000 (mtp) REVERT: B 1002 GLN cc_start: 0.9115 (tm-30) cc_final: 0.8250 (tm-30) REVERT: B 1062 PHE cc_start: 0.9441 (m-80) cc_final: 0.9112 (m-10) REVERT: C 153 MET cc_start: 0.4455 (ptp) cc_final: 0.4015 (ppp) REVERT: C 731 MET cc_start: 0.8954 (ttp) cc_final: 0.8726 (ttp) REVERT: C 762 GLN cc_start: 0.9173 (tm-30) cc_final: 0.8948 (tm-30) REVERT: C 763 LEU cc_start: 0.9472 (mt) cc_final: 0.9147 (mp) REVERT: C 774 GLN cc_start: 0.9513 (mm-40) cc_final: 0.9116 (mm-40) REVERT: C 869 MET cc_start: 0.9385 (mtp) cc_final: 0.8855 (mtp) REVERT: C 902 MET cc_start: 0.9506 (mmm) cc_final: 0.9068 (mmm) REVERT: C 966 LEU cc_start: 0.9570 (mt) cc_final: 0.9075 (mp) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.1502 time to fit residues: 37.3164 Evaluate side-chains 105 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 126 optimal weight: 0.0170 chunk 216 optimal weight: 2.9990 chunk 252 optimal weight: 0.1980 chunk 65 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 318 optimal weight: 30.0000 chunk 200 optimal weight: 0.0670 chunk 223 optimal weight: 0.0870 chunk 2 optimal weight: 8.9990 chunk 270 optimal weight: 3.9990 chunk 308 optimal weight: 10.0000 overall best weight: 0.6736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 901 GLN B 913 GLN C 125 ASN C 501 ASN C 901 GLN C 919 ASN C 957 GLN C1010 GLN C1023 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.064931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.046759 restraints weight = 188742.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.048328 restraints weight = 117665.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.048844 restraints weight = 73591.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.049081 restraints weight = 56778.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.049158 restraints weight = 60098.497| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 27035 Z= 0.096 Angle : 0.571 15.599 36857 Z= 0.281 Chirality : 0.046 0.461 4243 Planarity : 0.004 0.051 4704 Dihedral : 6.038 57.209 4340 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.14), residues: 3258 helix: 1.23 (0.21), residues: 648 sheet: -1.61 (0.22), residues: 551 loop : -2.41 (0.13), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1107 TYR 0.013 0.001 TYR C 904 PHE 0.025 0.001 PHE B 392 TRP 0.015 0.001 TRP B 104 HIS 0.003 0.001 HIS B 146 Details of bonding type rmsd covalent geometry : bond 0.00198 (26957) covalent geometry : angle 0.53372 (36663) SS BOND : bond 0.00262 ( 40) SS BOND : angle 1.37182 ( 80) hydrogen bonds : bond 0.03666 ( 854) hydrogen bonds : angle 5.67747 ( 2379) link_NAG-ASN : bond 0.00732 ( 38) link_NAG-ASN : angle 3.53620 ( 114) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 PHE cc_start: 0.8889 (m-10) cc_final: 0.7961 (m-10) REVERT: A 314 GLN cc_start: 0.8275 (tt0) cc_final: 0.7939 (tm-30) REVERT: A 664 ILE cc_start: 0.9277 (mp) cc_final: 0.8828 (mp) REVERT: A 774 GLN cc_start: 0.9572 (mm-40) cc_final: 0.9036 (mm-40) REVERT: A 777 ASN cc_start: 0.9259 (m110) cc_final: 0.9055 (m110) REVERT: A 952 VAL cc_start: 0.9131 (t) cc_final: 0.8913 (p) REVERT: A 1014 ARG cc_start: 0.8995 (mmt180) cc_final: 0.8742 (mmt180) REVERT: A 1050 MET cc_start: 0.9169 (pmm) cc_final: 0.8313 (pmm) REVERT: B 92 PHE cc_start: 0.9163 (t80) cc_final: 0.8790 (t80) REVERT: B 177 MET cc_start: 0.0944 (tpp) cc_final: -0.1459 (ptm) REVERT: B 192 PHE cc_start: 0.8979 (m-80) cc_final: 0.8492 (m-10) REVERT: B 471 GLU cc_start: 0.9045 (tt0) cc_final: 0.8806 (mm-30) REVERT: B 774 GLN cc_start: 0.9322 (mm-40) cc_final: 0.9055 (mm110) REVERT: B 1002 GLN cc_start: 0.9058 (tm-30) cc_final: 0.8191 (tm-30) REVERT: B 1062 PHE cc_start: 0.9485 (m-80) cc_final: 0.9186 (m-10) REVERT: B 1089 PHE cc_start: 0.8824 (m-80) cc_final: 0.8592 (m-10) REVERT: C 153 MET cc_start: 0.5110 (ptp) cc_final: 0.4568 (ppp) REVERT: C 774 GLN cc_start: 0.9430 (mm-40) cc_final: 0.9153 (mm-40) REVERT: C 869 MET cc_start: 0.9311 (mtp) cc_final: 0.8790 (mtp) REVERT: C 902 MET cc_start: 0.9429 (mmm) cc_final: 0.9046 (mmm) REVERT: C 966 LEU cc_start: 0.9526 (mt) cc_final: 0.9130 (pp) REVERT: C 1050 MET cc_start: 0.9023 (ptp) cc_final: 0.6901 (mtm) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.1523 time to fit residues: 46.2296 Evaluate side-chains 122 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 153 optimal weight: 20.0000 chunk 243 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 chunk 57 optimal weight: 0.0010 chunk 31 optimal weight: 8.9990 chunk 279 optimal weight: 7.9990 chunk 222 optimal weight: 1.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 1.9990 chunk 221 optimal weight: 5.9990 overall best weight: 1.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 913 GLN C 901 GLN C 919 ASN ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.064567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.046207 restraints weight = 189028.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.047393 restraints weight = 112079.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.048181 restraints weight = 77461.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.048714 restraints weight = 60009.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.049049 restraints weight = 50692.721| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 27035 Z= 0.105 Angle : 0.569 15.201 36857 Z= 0.281 Chirality : 0.046 0.455 4243 Planarity : 0.004 0.046 4704 Dihedral : 5.856 56.246 4340 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.14), residues: 3258 helix: 1.26 (0.21), residues: 647 sheet: -1.51 (0.21), residues: 569 loop : -2.33 (0.13), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 765 TYR 0.012 0.001 TYR C 904 PHE 0.029 0.001 PHE C 823 TRP 0.014 0.001 TRP B 104 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00225 (26957) covalent geometry : angle 0.53138 (36663) SS BOND : bond 0.00195 ( 40) SS BOND : angle 1.47183 ( 80) hydrogen bonds : bond 0.03580 ( 854) hydrogen bonds : angle 5.59365 ( 2379) link_NAG-ASN : bond 0.00712 ( 38) link_NAG-ASN : angle 3.51268 ( 114) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 PHE cc_start: 0.8872 (m-10) cc_final: 0.7907 (m-10) REVERT: A 314 GLN cc_start: 0.8295 (tt0) cc_final: 0.7847 (tm-30) REVERT: A 740 MET cc_start: 0.8281 (ttt) cc_final: 0.8049 (ttm) REVERT: A 777 ASN cc_start: 0.9300 (m110) cc_final: 0.8994 (m110) REVERT: A 1050 MET cc_start: 0.9135 (pmm) cc_final: 0.8196 (pmm) REVERT: B 92 PHE cc_start: 0.9166 (t80) cc_final: 0.8854 (t80) REVERT: B 177 MET cc_start: 0.0779 (tpp) cc_final: 0.0388 (mpp) REVERT: B 192 PHE cc_start: 0.8921 (m-80) cc_final: 0.8531 (m-10) REVERT: B 471 GLU cc_start: 0.9074 (tt0) cc_final: 0.8842 (mm-30) REVERT: B 774 GLN cc_start: 0.9304 (mm-40) cc_final: 0.9056 (mm110) REVERT: B 1002 GLN cc_start: 0.9056 (tm-30) cc_final: 0.8173 (tm-30) REVERT: C 153 MET cc_start: 0.4545 (ptp) cc_final: 0.3968 (ppp) REVERT: C 214 ARG cc_start: 0.9186 (ptt180) cc_final: 0.8790 (tpm170) REVERT: C 731 MET cc_start: 0.8531 (ttp) cc_final: 0.7602 (ptm) REVERT: C 762 GLN cc_start: 0.9175 (tm-30) cc_final: 0.8914 (tm-30) REVERT: C 763 LEU cc_start: 0.9343 (mt) cc_final: 0.8987 (mp) REVERT: C 869 MET cc_start: 0.9280 (mtp) cc_final: 0.8805 (mtp) REVERT: C 902 MET cc_start: 0.9445 (mmm) cc_final: 0.9172 (mmm) REVERT: C 966 LEU cc_start: 0.9505 (mt) cc_final: 0.9150 (pp) REVERT: C 1050 MET cc_start: 0.9013 (ptp) cc_final: 0.6654 (mtm) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1522 time to fit residues: 41.3508 Evaluate side-chains 115 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 259 optimal weight: 8.9990 chunk 182 optimal weight: 20.0000 chunk 144 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 150 optimal weight: 30.0000 chunk 241 optimal weight: 40.0000 chunk 163 optimal weight: 3.9990 chunk 171 optimal weight: 10.0000 chunk 126 optimal weight: 0.3980 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 895 GLN B 913 GLN C 787 GLN C 901 GLN C 919 ASN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.063639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.045252 restraints weight = 191550.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.046462 restraints weight = 112774.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.047262 restraints weight = 78374.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.047794 restraints weight = 60883.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.048052 restraints weight = 51441.774| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27035 Z= 0.138 Angle : 0.590 14.767 36857 Z= 0.292 Chirality : 0.046 0.451 4243 Planarity : 0.004 0.051 4704 Dihedral : 5.868 55.853 4340 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.03 % Allowed : 0.45 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.14), residues: 3258 helix: 1.26 (0.21), residues: 646 sheet: -1.41 (0.22), residues: 551 loop : -2.32 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 765 TYR 0.013 0.001 TYR C 904 PHE 0.020 0.001 PHE B 464 TRP 0.020 0.002 TRP B 886 HIS 0.006 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00291 (26957) covalent geometry : angle 0.55548 (36663) SS BOND : bond 0.00232 ( 40) SS BOND : angle 1.38152 ( 80) hydrogen bonds : bond 0.03646 ( 854) hydrogen bonds : angle 5.63696 ( 2379) link_NAG-ASN : bond 0.00685 ( 38) link_NAG-ASN : angle 3.44003 ( 114) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8244 (tt0) cc_final: 0.8016 (tm-30) REVERT: A 731 MET cc_start: 0.9502 (ptm) cc_final: 0.9211 (ppp) REVERT: A 740 MET cc_start: 0.8348 (ttt) cc_final: 0.8137 (ttm) REVERT: A 774 GLN cc_start: 0.9372 (mt0) cc_final: 0.8961 (mm-40) REVERT: A 777 ASN cc_start: 0.9154 (m110) cc_final: 0.8767 (m110) REVERT: A 802 PHE cc_start: 0.8886 (m-80) cc_final: 0.8645 (m-80) REVERT: A 964 LYS cc_start: 0.7716 (mttt) cc_final: 0.7010 (mttm) REVERT: A 1050 MET cc_start: 0.9254 (pmm) cc_final: 0.8333 (pmm) REVERT: B 177 MET cc_start: 0.0804 (tpp) cc_final: -0.1544 (ptm) REVERT: B 471 GLU cc_start: 0.9081 (tt0) cc_final: 0.8869 (mm-30) REVERT: B 774 GLN cc_start: 0.9322 (mm-40) cc_final: 0.9073 (mm110) REVERT: B 1002 GLN cc_start: 0.9091 (tm-30) cc_final: 0.8221 (tm-30) REVERT: B 1089 PHE cc_start: 0.8909 (m-80) cc_final: 0.8600 (m-10) REVERT: C 153 MET cc_start: 0.4600 (ptp) cc_final: 0.4119 (ppp) REVERT: C 763 LEU cc_start: 0.9349 (mt) cc_final: 0.9097 (mt) REVERT: C 774 GLN cc_start: 0.9388 (mm-40) cc_final: 0.9072 (mm-40) REVERT: C 869 MET cc_start: 0.9247 (mtp) cc_final: 0.8798 (mtp) REVERT: C 901 GLN cc_start: 0.9498 (tt0) cc_final: 0.9294 (tt0) REVERT: C 902 MET cc_start: 0.9491 (mmm) cc_final: 0.9170 (mmm) REVERT: C 966 LEU cc_start: 0.9580 (mt) cc_final: 0.9183 (pp) REVERT: C 1050 MET cc_start: 0.8998 (ptp) cc_final: 0.6557 (mtm) outliers start: 1 outliers final: 0 residues processed: 154 average time/residue: 0.1563 time to fit residues: 40.3289 Evaluate side-chains 109 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 220 optimal weight: 30.0000 chunk 218 optimal weight: 30.0000 chunk 252 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 227 optimal weight: 6.9990 chunk 241 optimal weight: 30.0000 chunk 81 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 45 optimal weight: 20.0000 chunk 277 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 901 GLN B 913 GLN ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN C 957 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.060073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.042066 restraints weight = 178012.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.043298 restraints weight = 103747.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.044123 restraints weight = 70914.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.044611 restraints weight = 54279.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.044994 restraints weight = 45537.556| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 27035 Z= 0.280 Angle : 0.749 14.271 36857 Z= 0.378 Chirality : 0.049 0.450 4243 Planarity : 0.005 0.060 4704 Dihedral : 6.622 54.998 4340 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: -2.30 (0.14), residues: 3258 helix: 0.68 (0.20), residues: 640 sheet: -1.46 (0.21), residues: 589 loop : -2.42 (0.13), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C1107 TYR 0.021 0.002 TYR C 789 PHE 0.023 0.002 PHE B 464 TRP 0.045 0.003 TRP B 886 HIS 0.010 0.002 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00580 (26957) covalent geometry : angle 0.71928 (36663) SS BOND : bond 0.00354 ( 40) SS BOND : angle 1.60855 ( 80) hydrogen bonds : bond 0.04373 ( 854) hydrogen bonds : angle 6.34980 ( 2379) link_NAG-ASN : bond 0.00732 ( 38) link_NAG-ASN : angle 3.64589 ( 114) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.9575 (ptm) cc_final: 0.9360 (ptm) REVERT: A 740 MET cc_start: 0.8209 (ttt) cc_final: 0.7927 (ttm) REVERT: A 759 PHE cc_start: 0.8517 (m-80) cc_final: 0.8113 (m-80) REVERT: A 763 LEU cc_start: 0.9516 (pp) cc_final: 0.9176 (pp) REVERT: A 764 ASN cc_start: 0.9421 (m-40) cc_final: 0.8795 (p0) REVERT: A 964 LYS cc_start: 0.7930 (mttt) cc_final: 0.7296 (mttp) REVERT: A 1050 MET cc_start: 0.9347 (pmm) cc_final: 0.8225 (pmm) REVERT: B 177 MET cc_start: 0.0970 (tpp) cc_final: -0.1502 (ptm) REVERT: B 731 MET cc_start: 0.8918 (ttm) cc_final: 0.8706 (ttm) REVERT: B 740 MET cc_start: 0.7600 (ttm) cc_final: 0.7395 (ttt) REVERT: B 774 GLN cc_start: 0.9326 (mm-40) cc_final: 0.8919 (mm110) REVERT: B 1002 GLN cc_start: 0.9194 (tm-30) cc_final: 0.8853 (tm-30) REVERT: C 582 LEU cc_start: 0.7919 (mt) cc_final: 0.7411 (tt) REVERT: C 763 LEU cc_start: 0.9367 (mt) cc_final: 0.9069 (mt) REVERT: C 869 MET cc_start: 0.9297 (mtp) cc_final: 0.8921 (mtp) REVERT: C 902 MET cc_start: 0.9563 (mmm) cc_final: 0.9323 (mmm) REVERT: C 966 LEU cc_start: 0.9625 (mt) cc_final: 0.9170 (mp) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1519 time to fit residues: 35.7501 Evaluate side-chains 96 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 291 optimal weight: 0.0870 chunk 219 optimal weight: 30.0000 chunk 176 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 256 optimal weight: 0.0010 chunk 104 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 253 optimal weight: 50.0000 chunk 126 optimal weight: 7.9990 overall best weight: 1.8170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS A 644 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 901 GLN B 913 GLN C 901 GLN C 919 ASN C 935 GLN C 957 GLN C1005 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.063562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.045195 restraints weight = 189979.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.046390 restraints weight = 112041.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.047114 restraints weight = 77594.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.047660 restraints weight = 61261.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.047958 restraints weight = 51998.102| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 27035 Z= 0.117 Angle : 0.593 14.711 36857 Z= 0.296 Chirality : 0.046 0.458 4243 Planarity : 0.004 0.053 4704 Dihedral : 6.076 55.783 4340 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.14), residues: 3258 helix: 1.19 (0.21), residues: 647 sheet: -1.37 (0.22), residues: 538 loop : -2.32 (0.13), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 765 TYR 0.013 0.001 TYR C 904 PHE 0.028 0.001 PHE C 823 TRP 0.018 0.001 TRP B 104 HIS 0.005 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00248 (26957) covalent geometry : angle 0.55789 (36663) SS BOND : bond 0.00213 ( 40) SS BOND : angle 1.36821 ( 80) hydrogen bonds : bond 0.03715 ( 854) hydrogen bonds : angle 5.74217 ( 2379) link_NAG-ASN : bond 0.00700 ( 38) link_NAG-ASN : angle 3.49567 ( 114) =============================================================================== Job complete usr+sys time: 4188.17 seconds wall clock time: 73 minutes 20.15 seconds (4400.15 seconds total)