Starting phenix.real_space_refine on Sun Jun 22 15:27:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xy3_33509/06_2025/7xy3_33509.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xy3_33509/06_2025/7xy3_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7xy3_33509/06_2025/7xy3_33509.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xy3_33509/06_2025/7xy3_33509.map" model { file = "/net/cci-nas-00/data/ceres_data/7xy3_33509/06_2025/7xy3_33509.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xy3_33509/06_2025/7xy3_33509.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 17.38, per 1000 atoms: 0.66 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: 6.68 Conformation dependent library (CDL) restraints added in 3.7 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: 4.10 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: 12.28 Time building geometry restraints manager: 8.01 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 1145 or resid 1201 thr \ ough 1211)) selection = (chain 'B' and (resid 14 through 331 or resid 334 through 525 or resid 530 throu \ gh 1145 or resid 1201 through 1211)) selection = (chain 'C' and (resid 14 through 331 or resid 334 through 1145 or resid 1201 thr \ ough 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: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.120 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 65.280 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.170 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (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 TRP 0.017 0.002 TRP B 886 HIS 0.008 0.002 HIS C 49 PHE 0.028 0.003 PHE B 823 TYR 0.022 0.002 TYR B 204 ARG 0.011 0.001 ARG C 815 Details of bonding type rmsd link_NAG-ASN : bond 0.04202 ( 38) link_NAG-ASN : angle 5.27686 ( 114) hydrogen bonds : bond 0.22063 ( 854) hydrogen bonds : angle 9.45296 ( 2379) SS BOND : bond 0.00354 ( 40) SS BOND : angle 1.18993 ( 80) covalent geometry : bond 0.00467 (26957) covalent geometry : angle 0.75293 (36663) *********************** 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 : 2.950 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: 0.9199 (ttm) REVERT: A 772 VAL cc_start: 0.9607 (t) cc_final: 0.9388 (p) REVERT: A 774 GLN cc_start: 0.9461 (mm-40) cc_final: 0.9248 (mm-40) REVERT: A 777 ASN cc_start: 0.9228 (m-40) cc_final: 0.8979 (m110) REVERT: A 781 VAL cc_start: 0.9641 (t) cc_final: 0.9078 (m) REVERT: A 802 PHE cc_start: 0.8697 (m-10) cc_final: 0.8441 (m-10) REVERT: A 953 ASN cc_start: 0.8362 (m-40) cc_final: 0.7970 (m110) REVERT: A 1029 MET cc_start: 0.8800 (mtt) cc_final: 0.8561 (tpp) REVERT: A 1065 VAL cc_start: 0.9397 (t) cc_final: 0.8920 (t) REVERT: B 92 PHE cc_start: 0.9276 (t80) cc_final: 0.9065 (t80) REVERT: B 177 MET cc_start: 0.0220 (tpp) cc_final: -0.0152 (ttp) REVERT: B 192 PHE cc_start: 0.8985 (m-10) cc_final: 0.8680 (m-10) REVERT: B 389 ASP cc_start: 0.8463 (m-30) cc_final: 0.8254 (t0) REVERT: B 424 LYS cc_start: 0.8050 (tttt) cc_final: 0.7669 (tptp) REVERT: B 471 GLU cc_start: 0.9089 (tt0) cc_final: 0.8868 (mm-30) REVERT: B 731 MET cc_start: 0.9251 (ttp) cc_final: 0.9002 (ttm) REVERT: B 740 MET cc_start: 0.7691 (ttt) cc_final: 0.7113 (ttt) REVERT: B 774 GLN cc_start: 0.9105 (mm-40) cc_final: 0.8696 (mm110) REVERT: B 1006 THR cc_start: 0.9206 (m) cc_final: 0.8898 (p) REVERT: B 1033 VAL cc_start: 0.9334 (t) cc_final: 0.9113 (t) REVERT: B 1062 PHE cc_start: 0.8921 (m-80) cc_final: 0.8245 (m-10) REVERT: C 153 MET cc_start: 0.4711 (ptp) cc_final: 0.4147 (ppp) REVERT: C 353 TRP cc_start: 0.2348 (p90) cc_final: 0.1766 (p90) REVERT: C 763 LEU cc_start: 0.9138 (mt) cc_final: 0.8816 (mt) REVERT: C 765 ARG cc_start: 0.8528 (ttp-170) cc_final: 0.8201 (ptm-80) REVERT: C 966 LEU cc_start: 0.9565 (mt) cc_final: 0.9102 (mp) REVERT: C 1050 MET cc_start: 0.9024 (ptp) cc_final: 0.8743 (ptp) REVERT: D 94 MET cc_start: 0.7521 (ttm) cc_final: 0.7217 (ptt) outliers start: 2 outliers final: 0 residues processed: 383 average time/residue: 0.4386 time to fit residues: 255.1700 Evaluate side-chains 172 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 3.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 277 optimal weight: 9.9990 chunk 249 optimal weight: 0.9990 chunk 138 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 168 optimal weight: 1.9990 chunk 133 optimal weight: 0.0270 chunk 257 optimal weight: 40.0000 chunk 99 optimal weight: 8.9990 chunk 156 optimal weight: 6.9990 chunk 191 optimal weight: 3.9990 chunk 298 optimal weight: 8.9990 overall best weight: 2.8046 ------------------------------------------------------------------------------- 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 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 B 14 GLN B 99 ASN B 115 GLN B 474 GLN B 655 HIS B 658 ASN ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 901 GLN B 965 GLN B1023 ASN B1083 HIS C 49 HIS C 487 ASN C 501 ASN C 710 ASN C 777 ASN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 907 ASN C 919 ASN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.065298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.046753 restraints weight = 188210.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.047969 restraints weight = 112463.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.048774 restraints weight = 78135.691| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27035 Z= 0.149 Angle : 0.647 17.154 36857 Z= 0.328 Chirality : 0.047 0.557 4243 Planarity : 0.005 0.104 4704 Dihedral : 8.155 79.800 4340 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.07 % Allowed : 1.53 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.13), residues: 3258 helix: 0.41 (0.20), residues: 637 sheet: -2.11 (0.20), residues: 571 loop : -2.95 (0.12), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 64 HIS 0.012 0.001 HIS B 655 PHE 0.028 0.001 PHE B 464 TYR 0.013 0.001 TYR D 63 ARG 0.007 0.001 ARG C 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00691 ( 38) link_NAG-ASN : angle 3.80518 ( 114) hydrogen bonds : bond 0.04809 ( 854) hydrogen bonds : angle 7.10240 ( 2379) SS BOND : bond 0.00362 ( 40) SS BOND : angle 1.45388 ( 80) covalent geometry : bond 0.00308 (26957) covalent geometry : angle 0.60907 (36663) *********************** 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 233 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 231 time to evaluate : 3.120 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 740 MET cc_start: 0.8381 (ttt) cc_final: 0.8073 (ttm) REVERT: A 777 ASN cc_start: 0.9397 (m-40) cc_final: 0.9082 (m110) REVERT: A 1050 MET cc_start: 0.8821 (pmm) cc_final: 0.8273 (pmm) REVERT: B 92 PHE cc_start: 0.9356 (t80) cc_final: 0.8972 (t80) REVERT: B 104 TRP cc_start: 0.7881 (m-90) cc_final: 0.7627 (m-90) REVERT: B 192 PHE cc_start: 0.9026 (m-10) cc_final: 0.8767 (m-10) REVERT: B 387 LEU cc_start: 0.8758 (mt) cc_final: 0.8382 (mt) REVERT: B 389 ASP cc_start: 0.8398 (m-30) cc_final: 0.8146 (t0) REVERT: B 471 GLU cc_start: 0.9153 (tt0) cc_final: 0.8894 (mm-30) REVERT: B 731 MET cc_start: 0.9059 (ttp) cc_final: 0.8740 (ttm) REVERT: B 774 GLN cc_start: 0.9350 (mm-40) cc_final: 0.8734 (mm-40) REVERT: B 957 GLN cc_start: 0.8491 (tp-100) cc_final: 0.8236 (tm-30) REVERT: B 1002 GLN cc_start: 0.8802 (tm-30) cc_final: 0.8297 (tm-30) REVERT: C 153 MET cc_start: 0.4776 (ptp) cc_final: 0.4252 (ppp) REVERT: C 583 GLU cc_start: 0.8733 (pt0) cc_final: 0.8132 (mp0) REVERT: C 869 MET cc_start: 0.9492 (mtm) cc_final: 0.8905 (mtp) REVERT: C 902 MET cc_start: 0.9427 (mmm) cc_final: 0.9187 (mmp) REVERT: C 966 LEU cc_start: 0.9570 (mt) cc_final: 0.9186 (mp) REVERT: C 1050 MET cc_start: 0.8969 (ptp) cc_final: 0.8332 (ptp) REVERT: D 12 VAL cc_start: 0.4614 (m) cc_final: 0.4301 (m) REVERT: D 96 MET cc_start: 0.6057 (ttt) cc_final: 0.5717 (tpt) outliers start: 2 outliers final: 0 residues processed: 233 average time/residue: 0.3887 time to fit residues: 145.4813 Evaluate side-chains 133 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 3.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 212 optimal weight: 0.0060 chunk 164 optimal weight: 10.0000 chunk 313 optimal weight: 9.9990 chunk 237 optimal weight: 20.0000 chunk 51 optimal weight: 6.9990 chunk 260 optimal weight: 40.0000 chunk 246 optimal weight: 5.9990 chunk 39 optimal weight: 0.0770 chunk 3 optimal weight: 3.9990 chunk 183 optimal weight: 0.6980 chunk 200 optimal weight: 10.0000 overall best weight: 2.1558 ------------------------------------------------------------------------------- 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 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B1071 GLN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 919 ASN ** C1010 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 = 0.3638 r_free = 0.3638 target = 0.065532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.047124 restraints weight = 187656.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.048371 restraints weight = 111027.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.049167 restraints weight = 76653.581| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 27035 Z= 0.120 Angle : 0.584 16.458 36857 Z= 0.292 Chirality : 0.046 0.484 4243 Planarity : 0.004 0.053 4704 Dihedral : 6.877 56.460 4340 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.07 % Allowed : 1.49 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.14), residues: 3258 helix: 0.78 (0.20), residues: 652 sheet: -1.99 (0.21), residues: 547 loop : -2.70 (0.12), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.004 0.001 HIS B 207 PHE 0.025 0.001 PHE B 464 TYR 0.021 0.001 TYR A 756 ARG 0.005 0.000 ARG A 815 Details of bonding type rmsd link_NAG-ASN : bond 0.00719 ( 38) link_NAG-ASN : angle 3.64489 ( 114) hydrogen bonds : bond 0.04117 ( 854) hydrogen bonds : angle 6.37190 ( 2379) SS BOND : bond 0.00255 ( 40) SS BOND : angle 1.38879 ( 80) covalent geometry : bond 0.00247 (26957) covalent geometry : angle 0.54515 (36663) *********************** 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 208 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 206 time to evaluate : 2.854 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: A 242 LEU cc_start: 0.8639 (mp) cc_final: 0.8336 (tp) REVERT: A 275 PHE cc_start: 0.8856 (m-10) cc_final: 0.8287 (m-10) REVERT: A 1019 ARG cc_start: 0.9121 (mtp-110) cc_final: 0.8724 (mtp-110) REVERT: A 1050 MET cc_start: 0.9104 (pmm) cc_final: 0.8260 (pmm) REVERT: B 104 TRP cc_start: 0.7967 (m-90) cc_final: 0.7750 (m-90) REVERT: B 177 MET cc_start: 0.0513 (mmt) cc_final: 0.0302 (mtt) REVERT: B 387 LEU cc_start: 0.8728 (mt) cc_final: 0.8335 (mt) REVERT: B 424 LYS cc_start: 0.7208 (tptp) cc_final: 0.6898 (tptp) REVERT: B 471 GLU cc_start: 0.9050 (tt0) cc_final: 0.8837 (mm-30) REVERT: B 774 GLN cc_start: 0.9377 (mm-40) cc_final: 0.9018 (mm110) REVERT: B 1002 GLN cc_start: 0.8964 (tm-30) cc_final: 0.8282 (tm-30) REVERT: C 153 MET cc_start: 0.4954 (ptp) cc_final: 0.4389 (ppp) REVERT: C 731 MET cc_start: 0.8796 (ttm) cc_final: 0.8494 (ttm) REVERT: C 869 MET cc_start: 0.9265 (mtm) cc_final: 0.8909 (mtp) REVERT: C 902 MET cc_start: 0.9447 (mmm) cc_final: 0.9165 (mmm) REVERT: C 966 LEU cc_start: 0.9583 (mt) cc_final: 0.9341 (mt) REVERT: D 96 MET cc_start: 0.6203 (ttt) cc_final: 0.5816 (tpt) outliers start: 2 outliers final: 0 residues processed: 208 average time/residue: 0.3788 time to fit residues: 127.1248 Evaluate side-chains 131 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 2.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 261 optimal weight: 0.6980 chunk 225 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 211 optimal weight: 50.0000 chunk 314 optimal weight: 20.0000 chunk 282 optimal weight: 0.9980 chunk 216 optimal weight: 30.0000 chunk 200 optimal weight: 7.9990 chunk 181 optimal weight: 10.0000 chunk 277 optimal weight: 5.9990 overall best weight: 4.9386 ------------------------------------------------------------------------------- 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 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 925 ASN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 66 HIS ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B 895 GLN B 913 GLN C 784 GLN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN ** C1010 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 = 0.3563 r_free = 0.3563 target = 0.062441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.043894 restraints weight = 180891.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.045203 restraints weight = 103738.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.046071 restraints weight = 70279.930| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 27035 Z= 0.202 Angle : 0.645 15.866 36857 Z= 0.325 Chirality : 0.047 0.466 4243 Planarity : 0.004 0.058 4704 Dihedral : 6.615 55.969 4340 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 0.03 % Allowed : 1.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.14), residues: 3258 helix: 0.80 (0.20), residues: 643 sheet: -1.86 (0.21), residues: 567 loop : -2.59 (0.12), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 886 HIS 0.008 0.002 HIS C1048 PHE 0.027 0.002 PHE C 823 TYR 0.012 0.001 TYR C 313 ARG 0.006 0.001 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00709 ( 38) link_NAG-ASN : angle 3.63375 ( 114) hydrogen bonds : bond 0.04144 ( 854) hydrogen bonds : angle 6.32790 ( 2379) SS BOND : bond 0.00660 ( 40) SS BOND : angle 1.34043 ( 80) covalent geometry : bond 0.00420 (26957) covalent geometry : angle 0.61141 (36663) *********************** 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 184 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 2.978 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: A 242 LEU cc_start: 0.8610 (mp) cc_final: 0.8370 (tp) REVERT: A 275 PHE cc_start: 0.9085 (m-10) cc_final: 0.8446 (m-10) REVERT: A 1050 MET cc_start: 0.9208 (pmm) cc_final: 0.8315 (pmm) REVERT: B 92 PHE cc_start: 0.9236 (t80) cc_final: 0.8840 (t80) REVERT: B 177 MET cc_start: 0.0306 (mmt) cc_final: -0.2403 (ttp) REVERT: B 192 PHE cc_start: 0.8846 (m-80) cc_final: 0.8468 (m-10) REVERT: B 387 LEU cc_start: 0.8669 (mt) cc_final: 0.8401 (mt) REVERT: B 471 GLU cc_start: 0.9075 (tt0) cc_final: 0.8869 (mm-30) REVERT: B 774 GLN cc_start: 0.9340 (mm-40) cc_final: 0.8950 (mm110) REVERT: B 867 ASP cc_start: 0.8902 (m-30) cc_final: 0.8591 (p0) REVERT: B 1002 GLN cc_start: 0.8970 (tm-30) cc_final: 0.8319 (tm-30) REVERT: C 153 MET cc_start: 0.4816 (ptp) cc_final: 0.4385 (ppp) REVERT: C 763 LEU cc_start: 0.9274 (mt) cc_final: 0.9060 (mt) REVERT: C 886 TRP cc_start: 0.7945 (p90) cc_final: 0.7622 (p90) REVERT: C 902 MET cc_start: 0.9507 (mmm) cc_final: 0.9169 (mmp) REVERT: D 96 MET cc_start: 0.6190 (ttt) cc_final: 0.5443 (tpp) outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.3817 time to fit residues: 113.7646 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 : 2.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 277 optimal weight: 4.9990 chunk 281 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 178 optimal weight: 0.0040 chunk 108 optimal weight: 10.0000 chunk 296 optimal weight: 0.9980 chunk 118 optimal weight: 8.9990 chunk 230 optimal weight: 10.0000 chunk 303 optimal weight: 6.9990 chunk 146 optimal weight: 0.0070 chunk 184 optimal weight: 1.9990 overall best weight: 0.8014 ------------------------------------------------------------------------------- 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 354 ASN A 501 ASN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 895 GLN B 913 GLN C 777 ASN C 919 ASN C 957 GLN C1010 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.065895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.047671 restraints weight = 188309.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.049285 restraints weight = 116624.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.049812 restraints weight = 71743.705| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.078 27035 Z= 0.096 Angle : 0.556 15.927 36857 Z= 0.275 Chirality : 0.046 0.470 4243 Planarity : 0.004 0.055 4704 Dihedral : 6.005 59.850 4340 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.14), residues: 3258 helix: 1.30 (0.21), residues: 639 sheet: -1.89 (0.21), residues: 545 loop : -2.40 (0.12), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 353 HIS 0.004 0.001 HIS B 207 PHE 0.020 0.001 PHE B 464 TYR 0.012 0.001 TYR C 380 ARG 0.005 0.000 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00729 ( 38) link_NAG-ASN : angle 3.47869 ( 114) hydrogen bonds : bond 0.03684 ( 854) hydrogen bonds : angle 5.72163 ( 2379) SS BOND : bond 0.00552 ( 40) SS BOND : angle 1.29155 ( 80) covalent geometry : bond 0.00203 (26957) covalent geometry : angle 0.51927 (36663) *********************** 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 200 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 3.216 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: A 275 PHE cc_start: 0.8851 (m-10) cc_final: 0.8110 (m-10) REVERT: A 664 ILE cc_start: 0.9325 (mp) cc_final: 0.8930 (mp) REVERT: A 736 VAL cc_start: 0.9454 (t) cc_final: 0.9126 (t) REVERT: A 763 LEU cc_start: 0.9534 (pp) cc_final: 0.9328 (pp) REVERT: A 764 ASN cc_start: 0.9381 (m-40) cc_final: 0.8746 (p0) REVERT: A 1050 MET cc_start: 0.9160 (pmm) cc_final: 0.8332 (pmm) REVERT: B 92 PHE cc_start: 0.9248 (t80) cc_final: 0.8885 (t80) REVERT: B 192 PHE cc_start: 0.8874 (m-80) cc_final: 0.8658 (m-10) REVERT: B 471 GLU cc_start: 0.9005 (tt0) cc_final: 0.8794 (mm-30) REVERT: B 774 GLN cc_start: 0.9386 (mm-40) cc_final: 0.9114 (mm110) REVERT: B 867 ASP cc_start: 0.8828 (m-30) cc_final: 0.8523 (p0) REVERT: B 1002 GLN cc_start: 0.8950 (tm-30) cc_final: 0.8183 (tm-30) REVERT: C 153 MET cc_start: 0.5291 (ptp) cc_final: 0.4742 (ppp) REVERT: C 214 ARG cc_start: 0.9165 (ptt180) cc_final: 0.8729 (tpm170) REVERT: C 731 MET cc_start: 0.8827 (ttp) cc_final: 0.8585 (ttp) REVERT: C 763 LEU cc_start: 0.9328 (mt) cc_final: 0.9094 (mt) REVERT: C 869 MET cc_start: 0.9315 (mtp) cc_final: 0.8676 (mtp) REVERT: C 902 MET cc_start: 0.9451 (mmm) cc_final: 0.9116 (mmp) REVERT: C 933 LYS cc_start: 0.9580 (mttt) cc_final: 0.9290 (mttp) REVERT: C 966 LEU cc_start: 0.9507 (mt) cc_final: 0.9070 (pp) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.3898 time to fit residues: 126.5597 Evaluate side-chains 131 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 3.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 195 optimal weight: 0.9990 chunk 235 optimal weight: 9.9990 chunk 163 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 chunk 275 optimal weight: 4.9990 chunk 105 optimal weight: 40.0000 chunk 9 optimal weight: 8.9990 chunk 115 optimal weight: 20.0000 chunk 227 optimal weight: 20.0000 chunk 145 optimal weight: 10.0000 chunk 307 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 501 ASN ** 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** A1064 HIS ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 913 GLN C 919 ASN C1010 GLN C1023 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.063470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.044948 restraints weight = 175354.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.046259 restraints weight = 100458.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.047150 restraints weight = 68041.472| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 27035 Z= 0.133 Angle : 0.572 15.375 36857 Z= 0.285 Chirality : 0.045 0.460 4243 Planarity : 0.004 0.070 4704 Dihedral : 5.939 59.287 4340 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.14), residues: 3258 helix: 1.27 (0.21), residues: 642 sheet: -1.78 (0.21), residues: 561 loop : -2.33 (0.13), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 353 HIS 0.007 0.001 HIS A1064 PHE 0.020 0.001 PHE C 823 TYR 0.010 0.001 TYR C 380 ARG 0.013 0.000 ARG A 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00689 ( 38) link_NAG-ASN : angle 3.42756 ( 114) hydrogen bonds : bond 0.03634 ( 854) hydrogen bonds : angle 5.70937 ( 2379) SS BOND : bond 0.00211 ( 40) SS BOND : angle 1.32192 ( 80) covalent geometry : bond 0.00279 (26957) covalent geometry : angle 0.53677 (36663) *********************** 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 174 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 2.769 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 736 VAL cc_start: 0.9555 (t) cc_final: 0.9209 (t) REVERT: A 763 LEU cc_start: 0.9494 (pp) cc_final: 0.9230 (pp) REVERT: A 764 ASN cc_start: 0.9443 (m-40) cc_final: 0.8797 (p0) REVERT: A 1050 MET cc_start: 0.9169 (pmm) cc_final: 0.8315 (pmm) REVERT: B 92 PHE cc_start: 0.9211 (t80) cc_final: 0.8903 (t80) REVERT: B 192 PHE cc_start: 0.8924 (m-80) cc_final: 0.8694 (m-10) REVERT: B 471 GLU cc_start: 0.9113 (tt0) cc_final: 0.8862 (mm-30) REVERT: B 774 GLN cc_start: 0.9378 (mm-40) cc_final: 0.9102 (mm110) REVERT: B 867 ASP cc_start: 0.8944 (m-30) cc_final: 0.8665 (p0) REVERT: B 1002 GLN cc_start: 0.9021 (tm-30) cc_final: 0.8243 (tm-30) REVERT: B 1089 PHE cc_start: 0.8880 (m-80) cc_final: 0.8635 (m-10) REVERT: C 153 MET cc_start: 0.4827 (ptp) cc_final: 0.4293 (ppp) REVERT: C 731 MET cc_start: 0.8961 (ttp) cc_final: 0.8697 (ttp) REVERT: C 763 LEU cc_start: 0.9327 (mt) cc_final: 0.9079 (mt) REVERT: C 869 MET cc_start: 0.9364 (mtp) cc_final: 0.8789 (mtp) REVERT: C 886 TRP cc_start: 0.8031 (p90) cc_final: 0.7703 (p90) REVERT: C 902 MET cc_start: 0.9410 (mmm) cc_final: 0.9104 (mmp) REVERT: C 933 LYS cc_start: 0.9604 (mttt) cc_final: 0.9317 (mttp) REVERT: C 963 VAL cc_start: 0.9728 (t) cc_final: 0.9457 (p) REVERT: C 966 LEU cc_start: 0.9526 (mt) cc_final: 0.9061 (pp) REVERT: D 96 MET cc_start: 0.6566 (ttt) cc_final: 0.6130 (tpt) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.3620 time to fit residues: 103.8377 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 : 3.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 8 optimal weight: 4.9990 chunk 277 optimal weight: 4.9990 chunk 223 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 185 optimal weight: 0.7980 chunk 282 optimal weight: 6.9990 chunk 48 optimal weight: 20.0000 chunk 209 optimal weight: 3.9990 chunk 35 optimal weight: 30.0000 chunk 85 optimal weight: 8.9990 chunk 307 optimal weight: 3.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 913 GLN ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN C1010 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.062848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.044430 restraints weight = 174228.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.045742 restraints weight = 100224.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.046611 restraints weight = 67718.906| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 27035 Z= 0.144 Angle : 0.581 15.036 36857 Z= 0.289 Chirality : 0.046 0.456 4243 Planarity : 0.004 0.056 4704 Dihedral : 5.905 56.106 4340 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.14), residues: 3258 helix: 1.29 (0.21), residues: 647 sheet: -1.62 (0.20), residues: 583 loop : -2.33 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 886 HIS 0.005 0.001 HIS C1048 PHE 0.029 0.001 PHE C 823 TYR 0.017 0.001 TYR B 904 ARG 0.009 0.000 ARG A 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00678 ( 38) link_NAG-ASN : angle 3.48753 ( 114) hydrogen bonds : bond 0.03660 ( 854) hydrogen bonds : angle 5.66968 ( 2379) SS BOND : bond 0.00205 ( 40) SS BOND : angle 1.34577 ( 80) covalent geometry : bond 0.00302 (26957) covalent geometry : angle 0.54500 (36663) *********************** 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 174 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 3.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 736 VAL cc_start: 0.9556 (t) cc_final: 0.9214 (t) REVERT: A 740 MET cc_start: 0.8463 (ttt) cc_final: 0.8245 (ttm) REVERT: A 763 LEU cc_start: 0.9478 (pp) cc_final: 0.9173 (pp) REVERT: A 764 ASN cc_start: 0.9407 (m-40) cc_final: 0.8722 (p0) REVERT: A 765 ARG cc_start: 0.8997 (tpt90) cc_final: 0.8699 (mmm160) REVERT: A 1050 MET cc_start: 0.9160 (pmm) cc_final: 0.8251 (pmm) REVERT: B 92 PHE cc_start: 0.9134 (t80) cc_final: 0.8878 (t80) REVERT: B 192 PHE cc_start: 0.8922 (m-80) cc_final: 0.8676 (m-10) REVERT: B 471 GLU cc_start: 0.9131 (tt0) cc_final: 0.8869 (mm-30) REVERT: B 774 GLN cc_start: 0.9358 (mm-40) cc_final: 0.9075 (mm110) REVERT: B 867 ASP cc_start: 0.8997 (m-30) cc_final: 0.8698 (p0) REVERT: B 1002 GLN cc_start: 0.9051 (tm-30) cc_final: 0.8346 (tm-30) REVERT: B 1089 PHE cc_start: 0.8879 (m-80) cc_final: 0.8592 (m-10) REVERT: C 153 MET cc_start: 0.4756 (ptp) cc_final: 0.4200 (ppp) REVERT: C 731 MET cc_start: 0.8980 (ttp) cc_final: 0.8768 (ttp) REVERT: C 763 LEU cc_start: 0.9326 (mt) cc_final: 0.9047 (mt) REVERT: C 869 MET cc_start: 0.9350 (mtp) cc_final: 0.8739 (mtp) REVERT: C 886 TRP cc_start: 0.8105 (p90) cc_final: 0.7724 (p90) REVERT: C 898 PHE cc_start: 0.8549 (t80) cc_final: 0.8181 (t80) REVERT: C 902 MET cc_start: 0.9394 (mmm) cc_final: 0.9101 (mmp) REVERT: C 933 LYS cc_start: 0.9606 (mttt) cc_final: 0.9325 (mttp) REVERT: C 966 LEU cc_start: 0.9543 (mt) cc_final: 0.9100 (pp) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.3668 time to fit residues: 106.0470 Evaluate side-chains 116 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 3.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 88 optimal weight: 30.0000 chunk 78 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 255 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 chunk 198 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 129 optimal weight: 10.0000 chunk 271 optimal weight: 5.9990 chunk 265 optimal weight: 10.0000 chunk 201 optimal weight: 0.7980 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.061884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.043590 restraints weight = 174994.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.044876 restraints weight = 101040.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.045725 restraints weight = 68376.576| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 27035 Z= 0.184 Angle : 0.630 14.589 36857 Z= 0.316 Chirality : 0.047 0.454 4243 Planarity : 0.004 0.048 4704 Dihedral : 6.150 55.755 4340 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.14), residues: 3258 helix: 1.21 (0.21), residues: 641 sheet: -1.53 (0.20), residues: 597 loop : -2.32 (0.13), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 886 HIS 0.007 0.001 HIS C1048 PHE 0.030 0.002 PHE C 823 TYR 0.012 0.001 TYR A 313 ARG 0.007 0.001 ARG A 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00678 ( 38) link_NAG-ASN : angle 3.44777 ( 114) hydrogen bonds : bond 0.03856 ( 854) hydrogen bonds : angle 5.86265 ( 2379) SS BOND : bond 0.00315 ( 40) SS BOND : angle 1.52676 ( 80) covalent geometry : bond 0.00383 (26957) covalent geometry : angle 0.59790 (36663) *********************** 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 161 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 2.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 736 VAL cc_start: 0.9590 (t) cc_final: 0.9266 (t) REVERT: A 740 MET cc_start: 0.8446 (ttt) cc_final: 0.8148 (ttm) REVERT: A 763 LEU cc_start: 0.9456 (pp) cc_final: 0.9211 (pp) REVERT: A 764 ASN cc_start: 0.9389 (m-40) cc_final: 0.8704 (p0) REVERT: A 765 ARG cc_start: 0.9045 (tpt90) cc_final: 0.8748 (mmm160) REVERT: A 802 PHE cc_start: 0.8904 (m-80) cc_final: 0.8607 (m-80) REVERT: A 1050 MET cc_start: 0.9202 (pmm) cc_final: 0.8204 (pmm) REVERT: B 92 PHE cc_start: 0.9119 (t80) cc_final: 0.8772 (t80) REVERT: B 192 PHE cc_start: 0.8942 (m-80) cc_final: 0.8517 (m-10) REVERT: B 774 GLN cc_start: 0.9312 (mm-40) cc_final: 0.8967 (mm110) REVERT: B 1002 GLN cc_start: 0.9069 (tm-30) cc_final: 0.8277 (tm-30) REVERT: C 153 MET cc_start: 0.4739 (ptp) cc_final: 0.4283 (ppp) REVERT: C 731 MET cc_start: 0.8992 (ttp) cc_final: 0.8765 (ttp) REVERT: C 763 LEU cc_start: 0.9362 (mt) cc_final: 0.9084 (mt) REVERT: C 869 MET cc_start: 0.9413 (mtp) cc_final: 0.8858 (mtp) REVERT: C 898 PHE cc_start: 0.8825 (t80) cc_final: 0.8467 (t80) REVERT: C 902 MET cc_start: 0.9464 (mmm) cc_final: 0.9176 (mmp) REVERT: C 966 LEU cc_start: 0.9573 (mt) cc_final: 0.9140 (mp) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.3612 time to fit residues: 96.3599 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 : 3.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 241 optimal weight: 40.0000 chunk 34 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 141 optimal weight: 20.0000 chunk 60 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 271 optimal weight: 7.9990 chunk 270 optimal weight: 6.9990 chunk 184 optimal weight: 5.9990 chunk 178 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 913 GLN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN C 965 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1048 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.060109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.042142 restraints weight = 179590.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.043343 restraints weight = 104085.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.044177 restraints weight = 71183.197| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 27035 Z= 0.290 Angle : 0.780 14.305 36857 Z= 0.394 Chirality : 0.050 0.456 4243 Planarity : 0.005 0.055 4704 Dihedral : 6.977 55.098 4340 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.14), residues: 3258 helix: 0.65 (0.20), residues: 632 sheet: -1.69 (0.21), residues: 565 loop : -2.46 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 886 HIS 0.011 0.002 HIS C1048 PHE 0.025 0.002 PHE B 800 TYR 0.026 0.002 TYR B 873 ARG 0.011 0.001 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00838 ( 38) link_NAG-ASN : angle 3.80513 ( 114) hydrogen bonds : bond 0.04518 ( 854) hydrogen bonds : angle 6.53302 ( 2379) SS BOND : bond 0.00408 ( 40) SS BOND : angle 1.71885 ( 80) covalent geometry : bond 0.00600 (26957) covalent geometry : angle 0.74850 (36663) *********************** 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 145 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 2.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.9187 (ttm) cc_final: 0.8986 (ttm) REVERT: A 740 MET cc_start: 0.8270 (ttt) cc_final: 0.7917 (ttm) REVERT: A 764 ASN cc_start: 0.9455 (m-40) cc_final: 0.8887 (p0) REVERT: A 765 ARG cc_start: 0.9099 (tpt90) cc_final: 0.8794 (mmm160) REVERT: A 777 ASN cc_start: 0.9395 (m110) cc_final: 0.9174 (m110) REVERT: A 779 GLN cc_start: 0.9242 (tp40) cc_final: 0.8948 (tm-30) REVERT: A 964 LYS cc_start: 0.7934 (mttt) cc_final: 0.7246 (mttp) REVERT: A 1050 MET cc_start: 0.9325 (pmm) cc_final: 0.8187 (pmm) REVERT: B 774 GLN cc_start: 0.9323 (mm-40) cc_final: 0.8946 (mm110) REVERT: B 1002 GLN cc_start: 0.9195 (tm-30) cc_final: 0.8897 (tm-30) REVERT: C 582 LEU cc_start: 0.7992 (mt) cc_final: 0.7455 (tt) REVERT: C 731 MET cc_start: 0.9002 (ttp) cc_final: 0.8666 (ttp) REVERT: C 763 LEU cc_start: 0.9367 (mt) cc_final: 0.9056 (mt) REVERT: C 869 MET cc_start: 0.9422 (mtp) cc_final: 0.8923 (mtp) REVERT: C 886 TRP cc_start: 0.8359 (p90) cc_final: 0.7955 (p90) REVERT: C 902 MET cc_start: 0.9544 (mmm) cc_final: 0.9316 (mmp) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.3722 time to fit residues: 88.0279 Evaluate side-chains 102 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 2.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 261 optimal weight: 20.0000 chunk 296 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 251 optimal weight: 8.9990 chunk 233 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 16 optimal weight: 20.0000 chunk 83 optimal weight: 4.9990 chunk 255 optimal weight: 0.0060 chunk 117 optimal weight: 9.9990 overall best weight: 3.8004 ------------------------------------------------------------------------------- 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 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 913 GLN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN C1005 GLN C1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.061511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.043227 restraints weight = 174791.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.044469 restraints weight = 100209.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.045366 restraints weight = 67791.857| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 27035 Z= 0.162 Angle : 0.635 14.570 36857 Z= 0.318 Chirality : 0.047 0.460 4243 Planarity : 0.004 0.060 4704 Dihedral : 6.465 55.399 4340 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.14), residues: 3258 helix: 0.97 (0.21), residues: 648 sheet: -1.57 (0.21), residues: 534 loop : -2.37 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 886 HIS 0.005 0.001 HIS C1064 PHE 0.033 0.002 PHE C 823 TYR 0.013 0.001 TYR B 873 ARG 0.008 0.001 ARG C1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00694 ( 38) link_NAG-ASN : angle 3.59010 ( 114) hydrogen bonds : bond 0.03972 ( 854) hydrogen bonds : angle 6.02179 ( 2379) SS BOND : bond 0.00248 ( 40) SS BOND : angle 1.47554 ( 80) covalent geometry : bond 0.00342 (26957) covalent geometry : angle 0.60090 (36663) ********************** 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 153 residues out of total 2878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 2.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.9223 (ttm) cc_final: 0.8828 (ttp) REVERT: A 740 MET cc_start: 0.8243 (ttt) cc_final: 0.7903 (ttm) REVERT: A 764 ASN cc_start: 0.9377 (m-40) cc_final: 0.8778 (p0) REVERT: A 765 ARG cc_start: 0.9052 (tpt90) cc_final: 0.8737 (mmm160) REVERT: A 777 ASN cc_start: 0.9253 (m110) cc_final: 0.9023 (m110) REVERT: A 779 GLN cc_start: 0.9193 (tp40) cc_final: 0.8886 (tm-30) REVERT: A 964 LYS cc_start: 0.7918 (mttt) cc_final: 0.7184 (mttm) REVERT: A 1050 MET cc_start: 0.9266 (pmm) cc_final: 0.8310 (pmm) REVERT: B 92 PHE cc_start: 0.9134 (t80) cc_final: 0.8612 (t80) REVERT: B 192 PHE cc_start: 0.8998 (m-10) cc_final: 0.8534 (m-10) REVERT: B 774 GLN cc_start: 0.9320 (mm-40) cc_final: 0.8950 (mm110) REVERT: C 582 LEU cc_start: 0.8022 (mt) cc_final: 0.7499 (tt) REVERT: C 731 MET cc_start: 0.9036 (ttp) cc_final: 0.8774 (ttp) REVERT: C 763 LEU cc_start: 0.9379 (mt) cc_final: 0.9102 (mt) REVERT: C 773 GLU cc_start: 0.9170 (mm-30) cc_final: 0.8958 (mm-30) REVERT: C 864 LEU cc_start: 0.8830 (tp) cc_final: 0.8469 (tp) REVERT: C 869 MET cc_start: 0.9308 (mtp) cc_final: 0.8721 (mtp) REVERT: C 886 TRP cc_start: 0.8329 (p90) cc_final: 0.7882 (p90) REVERT: C 898 PHE cc_start: 0.8974 (t80) cc_final: 0.8674 (t80) REVERT: C 902 MET cc_start: 0.9514 (mmm) cc_final: 0.9175 (mmp) REVERT: C 966 LEU cc_start: 0.9575 (mt) cc_final: 0.9128 (mp) REVERT: D 43 GLN cc_start: 0.9182 (tt0) cc_final: 0.8919 (pp30) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.3589 time to fit residues: 92.7231 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 : 2.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 104 optimal weight: 20.0000 chunk 88 optimal weight: 30.0000 chunk 178 optimal weight: 0.1980 chunk 40 optimal weight: 40.0000 chunk 315 optimal weight: 0.2980 chunk 81 optimal weight: 8.9990 chunk 241 optimal weight: 40.0000 chunk 68 optimal weight: 0.9990 chunk 153 optimal weight: 20.0000 chunk 232 optimal weight: 6.9990 chunk 191 optimal weight: 7.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- 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 185 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** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 913 GLN C 919 ASN C1010 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.061678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.043545 restraints weight = 174259.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.044821 restraints weight = 100439.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.045664 restraints weight = 68054.876| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27035 Z= 0.149 Angle : 0.613 14.454 36857 Z= 0.306 Chirality : 0.046 0.455 4243 Planarity : 0.004 0.054 4704 Dihedral : 6.202 55.323 4340 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.14), residues: 3258 helix: 1.09 (0.21), residues: 648 sheet: -1.53 (0.21), residues: 555 loop : -2.33 (0.13), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 886 HIS 0.005 0.001 HIS C1064 PHE 0.019 0.001 PHE B 464 TYR 0.024 0.001 TYR B 904 ARG 0.008 0.001 ARG C1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00690 ( 38) link_NAG-ASN : angle 3.51763 ( 114) hydrogen bonds : bond 0.03826 ( 854) hydrogen bonds : angle 5.86092 ( 2379) SS BOND : bond 0.00241 ( 40) SS BOND : angle 1.39618 ( 80) covalent geometry : bond 0.00314 (26957) covalent geometry : angle 0.57839 (36663) =============================================================================== Job complete usr+sys time: 8135.15 seconds wall clock time: 142 minutes 11.12 seconds (8531.12 seconds total)