Starting phenix.real_space_refine on Sat Jul 4 22:09:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lyp_23598/07_2026/7lyp_23598.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lyp_23598/07_2026/7lyp_23598.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lyp_23598/07_2026/7lyp_23598.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lyp_23598/07_2026/7lyp_23598.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7lyp_23598/07_2026/7lyp_23598.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lyp_23598/07_2026/7lyp_23598.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lyp_23598/07_2026/7lyp_23598.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lyp_23598/07_2026/7lyp_23598.map" } resolution = 4.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.034 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 102 5.16 5 C 15020 2.51 5 N 3878 2.21 5 O 4504 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23504 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7717 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 47, 'TRANS': 948} Chain breaks: 7 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 3, 'PHE:plan': 1, 'GLU:plan': 6, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 7712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7712 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 47, 'TRANS': 948} Chain breaks: 7 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'GLN:plan1': 4, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 7683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7683 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 47, 'TRANS': 945} Chain breaks: 7 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 5, 'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 50 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 5.57, per 1000 atoms: 0.24 Number of scatterers: 23504 At special positions: 0 Unit cell: (129.349, 137.901, 192.42, 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 102 16.00 O 4504 8.00 N 3878 7.00 C 15020 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 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=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 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=2.04 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.05 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 616 " " NAG A1302 " - " ASN A 657 " " NAG A1303 " - " ASN A 709 " " NAG A1304 " - " ASN A 717 " " NAG A1305 " - " ASN A 801 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A1098 " " NAG A1308 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 343 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B 717 " " NAG B1307 " - " ASN B 801 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B1098 " " NAG B1310 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C 717 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1098 " " NAG C1310 " - " ASN C1134 " Time building additional restraints: 1.89 Conformation dependent library (CDL) restraints added in 1.1 seconds 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5580 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 45 sheets defined 27.7% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.505A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.424A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.322A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 756 removed outlier: 3.673A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.868A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.695A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.890A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.597A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.998A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 4.006A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.767A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.941A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.276A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.149A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.603A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.508A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.715A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.820A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (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 966 removed outlier: 3.831A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.876A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.791A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1141 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.749A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.349A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.723A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 753 Processing helix chain 'C' and resid 754 through 757 removed outlier: 3.654A pdb=" N GLY C 757 " --> pdb=" O LEU C 754 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 754 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.995A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.250A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.521A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.577A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.524A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.714A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.696A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 10.866A pdb=" N PHE A 220 " --> pdb=" O PRO A 209 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ARG A 34 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N LEU A 223 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.606A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.582A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.011A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.422A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP A 578 " --> pdb=" O GLU A 583 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.074A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.713A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.097A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 5.553A pdb=" N VAL A1122 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N PHE A1089 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLY A1124 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.795A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.902A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 removed outlier: 4.339A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.343A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.620A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 357 through 358 removed outlier: 3.509A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.863A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.155A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.852A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.852A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1123 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.995A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.696A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 310 through 319 removed outlier: 5.462A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.025A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.416A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.025A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.416A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.821A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 656 removed outlier: 4.356A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.630A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.630A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 5.710A pdb=" N VAL C1122 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE C1089 " --> pdb=" O VAL C1122 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N GLY C1124 " --> pdb=" O ALA C1087 " (cutoff:3.500A) 1044 hydrogen bonds defined for protein. 2814 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.36 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6097 1.33 - 1.45: 4672 1.45 - 1.58: 13128 1.58 - 1.70: 0 1.70 - 1.82: 126 Bond restraints: 24023 Sorted by residual: bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C5 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C5 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C5 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C5 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.413 1.486 -0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 24018 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 23917 1.87 - 3.74: 7709 3.74 - 5.61: 965 5.61 - 7.48: 100 7.48 - 9.35: 10 Bond angle restraints: 32701 Sorted by residual: angle pdb=" CA PHE C 456 " pdb=" CB PHE C 456 " pdb=" CG PHE C 456 " ideal model delta sigma weight residual 113.80 119.86 -6.06 1.00e+00 1.00e+00 3.67e+01 angle pdb=" CA PHE A 456 " pdb=" CB PHE A 456 " pdb=" CG PHE A 456 " ideal model delta sigma weight residual 113.80 119.73 -5.93 1.00e+00 1.00e+00 3.52e+01 angle pdb=" CA ASP A 571 " pdb=" CB ASP A 571 " pdb=" CG ASP A 571 " ideal model delta sigma weight residual 112.60 118.40 -5.80 1.00e+00 1.00e+00 3.36e+01 angle pdb=" CA ASP B 427 " pdb=" CB ASP B 427 " pdb=" CG ASP B 427 " ideal model delta sigma weight residual 112.60 118.17 -5.57 1.00e+00 1.00e+00 3.11e+01 angle pdb=" N ASN C 709 " pdb=" CA ASN C 709 " pdb=" C ASN C 709 " ideal model delta sigma weight residual 112.87 119.33 -6.46 1.20e+00 6.94e-01 2.90e+01 ... (remaining 32696 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 12975 17.65 - 35.30: 872 35.30 - 52.94: 121 52.94 - 70.59: 46 70.59 - 88.24: 29 Dihedral angle restraints: 14043 sinusoidal: 5370 harmonic: 8673 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 164.50 -71.50 1 1.00e+01 1.00e-02 6.55e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 156.02 -63.02 1 1.00e+01 1.00e-02 5.25e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -143.28 57.28 1 1.00e+01 1.00e-02 4.41e+01 ... (remaining 14040 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2357 0.083 - 0.166: 1253 0.166 - 0.249: 186 0.249 - 0.332: 35 0.332 - 0.416: 7 Chirality restraints: 3838 Sorted by residual: chirality pdb=" CB THR C 523 " pdb=" CA THR C 523 " pdb=" OG1 THR C 523 " pdb=" CG2 THR C 523 " both_signs ideal model delta sigma weight residual False 2.55 2.14 0.42 2.00e-01 2.50e+01 4.32e+00 chirality pdb=" CA ASN A 710 " pdb=" N ASN A 710 " pdb=" C ASN A 710 " pdb=" CB ASN A 710 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" CA SER C 112 " pdb=" N SER C 112 " pdb=" C SER C 112 " pdb=" CB SER C 112 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.03e+00 ... (remaining 3835 not shown) Planarity restraints: 4209 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 707 " 0.240 2.00e-02 2.50e+03 1.33e-01 3.51e+02 pdb=" CG TYR C 707 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TYR C 707 " -0.099 2.00e-02 2.50e+03 pdb=" CD2 TYR C 707 " -0.118 2.00e-02 2.50e+03 pdb=" CE1 TYR C 707 " -0.085 2.00e-02 2.50e+03 pdb=" CE2 TYR C 707 " -0.073 2.00e-02 2.50e+03 pdb=" CZ TYR C 707 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR C 707 " 0.205 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " 0.138 2.00e-02 2.50e+03 1.49e-01 2.78e+02 pdb=" CG ASN B 331 " -0.073 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " -0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " -0.233 2.00e-02 2.50e+03 pdb=" C1 NAG B1302 " 0.180 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 709 " 0.143 2.00e-02 2.50e+03 1.47e-01 2.68e+02 pdb=" CG ASN C 709 " -0.091 2.00e-02 2.50e+03 pdb=" OD1 ASN C 709 " -0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN C 709 " -0.217 2.00e-02 2.50e+03 pdb=" C1 NAG C1306 " 0.178 2.00e-02 2.50e+03 ... (remaining 4206 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 12029 2.99 - 3.47: 24261 3.47 - 3.94: 39025 3.94 - 4.42: 43397 4.42 - 4.90: 71642 Nonbonded interactions: 190354 Sorted by model distance: nonbonded pdb=" OG1 THR A1116 " pdb=" OD1 ASP A1118 " model vdw 2.509 3.040 nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.513 3.040 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.522 3.040 nonbonded pdb=" OG1 THR C1116 " pdb=" OD1 ASP C1118 " model vdw 2.548 3.040 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.553 3.040 ... (remaining 190349 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 95 or (resid 96 through 97 and (name N or name CA or name C or name O or name \ CB )) or resid 98 through 109 or (resid 110 and (name N or name CA or name C or \ name O or name CB )) or resid 111 through 114 or (resid 115 and (name N or name \ CA or name C or name O or name CB )) or resid 116 through 131 or (resid 132 and \ (name N or name CA or name C or name O or name CB )) or resid 133 or (resid 134 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 143 or (resid 165 through 166 and (name N or name CA or name C or name \ O or name CB )) or resid 167 through 168 or (resid 169 and (name N or name CA o \ r name C or name O or name CB )) or resid 170 through 171 or (resid 172 and (nam \ e N or name CA or name C or name O or name CB )) or resid 186 through 190 or (re \ sid 191 and (name N or name CA or name C or name O or name CB )) or resid 192 th \ rough 196 or (resid 197 and (name N or name CA or name C or name O or name CB )) \ or resid 198 through 213 or (resid 214 and (name N or name CA or name C or name \ O or name CB )) or resid 215 through 217 or (resid 218 and (name N or name CA o \ r name C or name O or name CB )) or resid 219 through 238 or (resid 239 and (nam \ e N or name CA or name C or name O or name CB )) or resid 240 through 308 or (re \ sid 309 and (name N or name CA or name C or name O or name CB )) or resid 310 th \ rough 479 or (resid 480 and (name N or name CA or name C or name O or name CB )) \ or resid 481 through 527 or (resid 528 and (name N or name CA or name C or name \ O or name CB )) or resid 529 through 810 or (resid 811 and (name N or name CA o \ r name C or name O or name CB )) or resid 812 through 827 or resid 855 through 8 \ 66 or (resid 867 through 868 and (name N or name CA or name C or name O or name \ CB )) or resid 869 through 1141 or (resid 1142 and (name N or name CA or name C \ or name O or name CB )) or resid 1143 through 1144 or (resid 1145 through 1146 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1147 through 13 \ 08)) selection = (chain 'B' and (resid 27 through 66 or resid 82 through 87 or (resid 88 and (nam \ e N or name CA or name C or name O or name CB )) or resid 89 through 96 or (resi \ d 97 and (name N or name CA or name C or name O or name CB )) or resid 98 or (re \ sid 99 and (name N or name CA or name C or name O or name CB )) or resid 100 thr \ ough 109 or (resid 110 and (name N or name CA or name C or name O or name CB )) \ or resid 111 through 114 or (resid 115 and (name N or name CA or name C or name \ O or name CB )) or resid 116 through 134 or (resid 135 through 138 and (name N o \ r name CA or name C or name O or name CB )) or resid 139 through 164 or (resid 1 \ 66 and (name N or name CA or name C or name O or name CB )) or resid 167 through \ 168 or (resid 169 and (name N or name CA or name C or name O or name CB )) or r \ esid 170 through 190 or (resid 191 and (name N or name CA or name C or name O or \ name CB )) or resid 192 through 195 or (resid 196 through 197 and (name N or na \ me CA or name C or name O or name CB )) or resid 198 through 241 or (resid 242 t \ hrough 264 and (name N or name CA or name C or name O or name CB )) or resid 265 \ through 280 or (resid 281 and (name N or name CA or name C or name O or name CB \ )) or resid 282 through 479 or (resid 480 and (name N or name CA or name C or n \ ame O or name CB )) or resid 481 through 567 or (resid 568 and (name N or name C \ A or name C or name O or name CB )) or resid 569 through 582 or (resid 583 and ( \ name N or name CA or name C or name O or name CB )) or resid 584 through 585 or \ (resid 586 and (name N or name CA or name C or name O or name CB )) or resid 587 \ through 618 or (resid 619 and (name N or name CA or name C or name O or name CB \ )) or resid 620 through 676 or resid 690 through 744 or (resid 745 and (name N \ or name CA or name C or name O or name CB )) or resid 746 through 747 or (resid \ 748 and (name N or name CA or name C or name O or name CB )) or resid 749 throug \ h 810 or (resid 811 and (name N or name CA or name C or name O or name CB )) or \ resid 812 through 827 or resid 855 through 866 or (resid 867 through 868 and (na \ me N or name CA or name C or name O or name CB )) or resid 869 through 1091 or ( \ resid 1092 and (name N or name CA or name C or name O or name CB )) or resid 109 \ 3 through 1143 or (resid 1144 through 1146 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1147 through 1308)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 134 or (resid 135 through 138 and (name N or name CA or name C o \ r name O or name CB )) or resid 139 through 143 or (resid 165 through 166 and (n \ ame N or name CA or name C or name O or name CB )) or resid 167 through 195 or ( \ resid 196 through 197 and (name N or name CA or name C or name O or name CB )) o \ r resid 198 through 213 or (resid 214 and (name N or name CA or name C or name O \ or name CB )) or resid 215 through 217 or (resid 218 and (name N or name CA or \ name C or name O or name CB )) or resid 219 through 238 or (resid 239 and (name \ N or name CA or name C or name O or name CB )) or resid 240 through 308 or (resi \ d 309 and (name N or name CA or name C or name O or name CB )) or resid 310 thro \ ugh 527 or (resid 528 and (name N or name CA or name C or name O or name CB )) o \ r resid 529 through 567 or (resid 568 and (name N or name CA or name C or name O \ or name CB )) or resid 569 through 582 or (resid 583 and (name N or name CA or \ name C or name O or name CB )) or resid 584 through 585 or (resid 586 and (name \ N or name CA or name C or name O or name CB )) or resid 587 through 618 or (resi \ d 619 and (name N or name CA or name C or name O or name CB )) or resid 620 thro \ ugh 1091 or (resid 1092 and (name N or name CA or name C or name O or name CB )) \ or resid 1093 through 1141 or (resid 1142 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1143 or (resid 1144 through 1146 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1147 through 1308)) } 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: 2.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 24.980 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 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 : 0.013 0.075 24088 Z= 0.732 Angle : 1.743 9.347 32859 Z= 1.150 Chirality : 0.093 0.416 3838 Planarity : 0.015 0.150 4181 Dihedral : 13.096 88.242 8352 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.61 % Allowed : 6.67 % Favored : 92.71 % Rotamer: Outliers : 0.71 % Allowed : 2.04 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.14), residues: 2937 helix: -0.65 (0.17), residues: 686 sheet: 0.47 (0.24), residues: 417 loop : -1.21 (0.14), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG B 102 TYR 0.240 0.023 TYR C 707 PHE 0.088 0.013 PHE A1095 TRP 0.082 0.021 TRP A 436 HIS 0.023 0.004 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.01293 / 0.73 (24023) covalent geometry : angle 1.73157 / 1.15 (32701) SS BOND : bond 0.00950 / 0.54 ( 37) SS BOND : angle 1.77135 / 1.17 ( 74) hydrogen bonds : bond 0.14194 / 9.56 ( 1022) hydrogen bonds : angle 8.62606 / 6.03 ( 2814) link_NAG-ASN : bond 0.01119 / 0.67 ( 28) link_NAG-ASN : angle 4.35506 / 2.88 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 236 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 SER cc_start: 0.8929 (m) cc_final: 0.8709 (p) REVERT: A 417 ASN cc_start: 0.9355 (m-40) cc_final: 0.9093 (p0) REVERT: A 557 LYS cc_start: 0.7868 (mmtt) cc_final: 0.7289 (mmtm) REVERT: B 63 THR cc_start: 0.8506 (OUTLIER) cc_final: 0.7949 (p) REVERT: B 198 ASP cc_start: 0.9051 (m-30) cc_final: 0.8627 (p0) REVERT: B 238 PHE cc_start: 0.8800 (p90) cc_final: 0.8535 (p90) REVERT: B 365 TYR cc_start: 0.9333 (m-80) cc_final: 0.9101 (m-80) REVERT: B 427 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.7663 (m-30) REVERT: B 650 LEU cc_start: 0.9340 (tp) cc_final: 0.9028 (tt) REVERT: B 752 LEU cc_start: 0.9404 (mt) cc_final: 0.9064 (mp) REVERT: B 864 LEU cc_start: 0.8853 (tp) cc_final: 0.8440 (tp) REVERT: C 509 ARG cc_start: 0.7672 (mtt180) cc_final: 0.7418 (mtp85) REVERT: C 611 LEU cc_start: 0.9211 (tp) cc_final: 0.9006 (tt) REVERT: C 613 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8446 (mp10) REVERT: C 902 MET cc_start: 0.9568 (mmm) cc_final: 0.9365 (tpp) outliers start: 18 outliers final: 4 residues processed: 252 average time/residue: 0.1487 time to fit residues: 59.4648 Evaluate side-chains 116 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 109 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 ASN A 354 ASN A 710 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 481 ASN C 498 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C1048 HIS ** 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 = 0.3622 r_free = 0.3622 target = 0.072069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.052292 restraints weight = 123015.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.054189 restraints weight = 70428.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.054623 restraints weight = 40503.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.055001 restraints weight = 32282.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.055045 restraints weight = 29760.538| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 24088 Z= 0.168 Angle : 0.684 11.872 32859 Z= 0.362 Chirality : 0.047 0.294 3838 Planarity : 0.004 0.078 4181 Dihedral : 6.183 25.659 3188 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.98 % Favored : 95.85 % Rotamer: Outliers : 0.12 % Allowed : 1.72 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.15), residues: 2937 helix: 1.34 (0.20), residues: 662 sheet: 0.21 (0.21), residues: 542 loop : -0.83 (0.14), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 355 TYR 0.024 0.002 TYR A 396 PHE 0.026 0.002 PHE C 906 TRP 0.011 0.002 TRP B 64 HIS 0.006 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 (24023) covalent geometry : angle 0.66750 / 0.36 (32701) SS BOND : bond 0.00406 / 0.30 ( 37) SS BOND : angle 1.19620 / 0.73 ( 74) hydrogen bonds : bond 0.04833 / 3.13 ( 1022) hydrogen bonds : angle 6.30163 / 4.43 ( 2814) link_NAG-ASN : bond 0.00461 / 0.24 ( 28) link_NAG-ASN : angle 2.87446 / 1.87 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 167 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.9172 (mm) cc_final: 0.8511 (tp) REVERT: A 168 PHE cc_start: 0.8338 (t80) cc_final: 0.8001 (t80) REVERT: A 297 SER cc_start: 0.9007 (m) cc_final: 0.8667 (p) REVERT: A 417 ASN cc_start: 0.9544 (m-40) cc_final: 0.9049 (p0) REVERT: A 456 PHE cc_start: 0.8727 (p90) cc_final: 0.8487 (p90) REVERT: A 495 TYR cc_start: 0.7506 (m-10) cc_final: 0.7269 (m-80) REVERT: A 557 LYS cc_start: 0.7730 (mmtt) cc_final: 0.7234 (mmtm) REVERT: B 90 VAL cc_start: 0.9470 (t) cc_final: 0.8830 (m) REVERT: B 223 LEU cc_start: 0.8848 (mp) cc_final: 0.8466 (mp) REVERT: B 360 ASN cc_start: 0.8598 (p0) cc_final: 0.8295 (p0) REVERT: B 650 LEU cc_start: 0.9411 (tp) cc_final: 0.9128 (tt) REVERT: B 864 LEU cc_start: 0.8917 (tp) cc_final: 0.8618 (tp) REVERT: B 1002 GLN cc_start: 0.8671 (tm-30) cc_final: 0.8180 (tm-30) REVERT: C 395 VAL cc_start: 0.8179 (m) cc_final: 0.7825 (p) REVERT: C 417 ASN cc_start: 0.9476 (m110) cc_final: 0.9062 (p0) REVERT: C 509 ARG cc_start: 0.7993 (mtt180) cc_final: 0.7489 (mtp85) outliers start: 3 outliers final: 0 residues processed: 170 average time/residue: 0.1378 time to fit residues: 38.0210 Evaluate side-chains 93 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 147 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 21 optimal weight: 0.1980 chunk 236 optimal weight: 40.0000 chunk 259 optimal weight: 0.9980 chunk 112 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 250 optimal weight: 7.9990 chunk 175 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN A 675 GLN A1002 GLN B1119 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN C1002 GLN C1048 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.071920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.051894 restraints weight = 122395.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.053741 restraints weight = 67541.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.054599 restraints weight = 38056.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.054907 restraints weight = 28274.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.055002 restraints weight = 25656.004| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24088 Z= 0.122 Angle : 0.598 10.979 32859 Z= 0.313 Chirality : 0.045 0.324 3838 Planarity : 0.004 0.060 4181 Dihedral : 5.424 32.043 3188 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.36 % Favored : 95.47 % Rotamer: Outliers : 0.04 % Allowed : 1.68 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.15), residues: 2937 helix: 1.81 (0.21), residues: 659 sheet: -0.03 (0.20), residues: 596 loop : -0.69 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 408 TYR 0.040 0.002 TYR B 505 PHE 0.026 0.001 PHE C 559 TRP 0.022 0.002 TRP A 64 HIS 0.004 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (24023) covalent geometry : angle 0.58451 / 0.31 (32701) SS BOND : bond 0.00303 / 0.22 ( 37) SS BOND : angle 1.03805 / 0.66 ( 74) hydrogen bonds : bond 0.04149 / 2.69 ( 1022) hydrogen bonds : angle 5.82066 / 4.07 ( 2814) link_NAG-ASN : bond 0.00353 / 0.21 ( 28) link_NAG-ASN : angle 2.39083 / 1.63 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.8983 (mm) cc_final: 0.8292 (tp) REVERT: A 168 PHE cc_start: 0.8259 (t80) cc_final: 0.7882 (t80) REVERT: A 297 SER cc_start: 0.9035 (m) cc_final: 0.8658 (p) REVERT: A 417 ASN cc_start: 0.9521 (m-40) cc_final: 0.9067 (p0) REVERT: A 557 LYS cc_start: 0.7714 (mmtt) cc_final: 0.7218 (mmtm) REVERT: A 965 GLN cc_start: 0.9265 (mm-40) cc_final: 0.8958 (tp-100) REVERT: B 90 VAL cc_start: 0.9344 (t) cc_final: 0.8958 (t) REVERT: B 223 LEU cc_start: 0.8787 (mp) cc_final: 0.8440 (mp) REVERT: B 238 PHE cc_start: 0.8599 (p90) cc_final: 0.8094 (p90) REVERT: B 360 ASN cc_start: 0.8404 (p0) cc_final: 0.8117 (p0) REVERT: B 1002 GLN cc_start: 0.8552 (tm-30) cc_final: 0.8218 (tm-30) REVERT: C 395 VAL cc_start: 0.8135 (m) cc_final: 0.7840 (p) REVERT: C 417 ASN cc_start: 0.9420 (m110) cc_final: 0.9051 (p0) REVERT: C 509 ARG cc_start: 0.7946 (mtt180) cc_final: 0.7380 (mtp85) REVERT: C 613 GLN cc_start: 0.8775 (mp10) cc_final: 0.8557 (mp10) REVERT: C 697 MET cc_start: 0.8821 (ptp) cc_final: 0.8052 (ptp) REVERT: C 699 LEU cc_start: 0.8934 (mt) cc_final: 0.8711 (mp) outliers start: 1 outliers final: 0 residues processed: 149 average time/residue: 0.1447 time to fit residues: 35.0427 Evaluate side-chains 90 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 249 optimal weight: 7.9990 chunk 277 optimal weight: 5.9990 chunk 221 optimal weight: 5.9990 chunk 234 optimal weight: 30.0000 chunk 42 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 181 optimal weight: 0.0000 chunk 130 optimal weight: 20.0000 chunk 269 optimal weight: 2.9990 chunk 225 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 overall best weight: 3.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN C 762 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.070369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.050400 restraints weight = 124834.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.052116 restraints weight = 71498.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.052622 restraints weight = 41614.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.052911 restraints weight = 34426.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.052936 restraints weight = 31172.578| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 24088 Z= 0.224 Angle : 0.643 8.596 32859 Z= 0.332 Chirality : 0.045 0.289 3838 Planarity : 0.004 0.066 4181 Dihedral : 5.383 32.272 3188 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.60 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.15), residues: 2937 helix: 1.46 (0.20), residues: 675 sheet: 0.02 (0.20), residues: 608 loop : -0.77 (0.15), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 408 TYR 0.036 0.002 TYR A 369 PHE 0.026 0.002 PHE C 342 TRP 0.014 0.002 TRP A 64 HIS 0.005 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.22 (24023) covalent geometry : angle 0.63023 / 0.33 (32701) SS BOND : bond 0.00347 / 0.22 ( 37) SS BOND : angle 1.30937 / 0.83 ( 74) hydrogen bonds : bond 0.04317 / 2.80 ( 1022) hydrogen bonds : angle 5.89784 / 4.14 ( 2814) link_NAG-ASN : bond 0.00348 / 0.23 ( 28) link_NAG-ASN : angle 2.39973 / 1.52 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.673 Fit side-chains REVERT: A 168 PHE cc_start: 0.8263 (t80) cc_final: 0.8056 (t80) REVERT: A 297 SER cc_start: 0.9006 (m) cc_final: 0.8664 (p) REVERT: A 354 ASN cc_start: 0.8554 (m110) cc_final: 0.8273 (m-40) REVERT: A 417 ASN cc_start: 0.9602 (m-40) cc_final: 0.9190 (p0) REVERT: A 456 PHE cc_start: 0.8647 (p90) cc_final: 0.8364 (p90) REVERT: A 473 TYR cc_start: 0.6936 (t80) cc_final: 0.6537 (t80) REVERT: A 557 LYS cc_start: 0.7785 (mmtt) cc_final: 0.7286 (mmtm) REVERT: C 395 VAL cc_start: 0.7959 (m) cc_final: 0.7716 (p) REVERT: C 417 ASN cc_start: 0.9492 (m110) cc_final: 0.9090 (p0) REVERT: C 509 ARG cc_start: 0.8032 (mtt180) cc_final: 0.7303 (mtp85) REVERT: C 878 LEU cc_start: 0.9286 (tp) cc_final: 0.9070 (tt) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1409 time to fit residues: 26.3986 Evaluate side-chains 82 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 218 optimal weight: 0.8980 chunk 281 optimal weight: 5.9990 chunk 129 optimal weight: 20.0000 chunk 85 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 chunk 187 optimal weight: 8.9990 chunk 78 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 34 optimal weight: 20.0000 chunk 110 optimal weight: 20.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 926 GLN C 955 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.071908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.052546 restraints weight = 122658.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.054040 restraints weight = 71685.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.054628 restraints weight = 42100.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.055000 restraints weight = 33761.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.055020 restraints weight = 30565.223| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 24088 Z= 0.113 Angle : 0.558 13.962 32859 Z= 0.288 Chirality : 0.044 0.236 3838 Planarity : 0.004 0.061 4181 Dihedral : 4.976 30.164 3188 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.02 % Favored : 95.95 % Rotamer: Outliers : 0.04 % Allowed : 1.29 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.15), residues: 2937 helix: 1.84 (0.21), residues: 675 sheet: 0.02 (0.19), residues: 629 loop : -0.67 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 408 TYR 0.021 0.001 TYR A 369 PHE 0.025 0.001 PHE C 342 TRP 0.009 0.001 TRP A 436 HIS 0.003 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (24023) covalent geometry : angle 0.54715 / 0.29 (32701) SS BOND : bond 0.00485 / 0.37 ( 37) SS BOND : angle 1.02803 / 0.63 ( 74) hydrogen bonds : bond 0.03851 / 2.50 ( 1022) hydrogen bonds : angle 5.54180 / 3.88 ( 2814) link_NAG-ASN : bond 0.00325 / 0.18 ( 28) link_NAG-ASN : angle 2.07176 / 1.31 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 PHE cc_start: 0.8150 (t80) cc_final: 0.7915 (t80) REVERT: A 200 TYR cc_start: 0.8552 (m-10) cc_final: 0.8317 (m-10) REVERT: A 297 SER cc_start: 0.8952 (m) cc_final: 0.8602 (p) REVERT: A 417 ASN cc_start: 0.9560 (m-40) cc_final: 0.9163 (p0) REVERT: A 965 GLN cc_start: 0.9250 (mm-40) cc_final: 0.9029 (tp40) REVERT: B 52 GLN cc_start: 0.8785 (tm-30) cc_final: 0.8536 (tm-30) REVERT: B 56 LEU cc_start: 0.8863 (tp) cc_final: 0.8662 (tp) REVERT: B 90 VAL cc_start: 0.9444 (t) cc_final: 0.9132 (t) REVERT: B 91 TYR cc_start: 0.7895 (t80) cc_final: 0.7454 (t80) REVERT: B 238 PHE cc_start: 0.8750 (p90) cc_final: 0.8282 (p90) REVERT: B 864 LEU cc_start: 0.9020 (tp) cc_final: 0.8744 (tp) REVERT: C 238 PHE cc_start: 0.8336 (p90) cc_final: 0.8076 (p90) REVERT: C 297 SER cc_start: 0.9489 (m) cc_final: 0.9156 (p) REVERT: C 417 ASN cc_start: 0.9452 (m110) cc_final: 0.9055 (p0) REVERT: C 509 ARG cc_start: 0.7963 (mtt180) cc_final: 0.7233 (mtp85) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.1464 time to fit residues: 31.2361 Evaluate side-chains 80 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 138 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 39 optimal weight: 20.0000 chunk 150 optimal weight: 2.9990 chunk 199 optimal weight: 0.0770 chunk 191 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 229 optimal weight: 3.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.071170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.051675 restraints weight = 124835.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.052775 restraints weight = 77094.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.053604 restraints weight = 48119.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.053926 restraints weight = 35826.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.054016 restraints weight = 33122.640| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24088 Z= 0.146 Angle : 0.556 7.017 32859 Z= 0.287 Chirality : 0.044 0.237 3838 Planarity : 0.004 0.059 4181 Dihedral : 4.867 29.610 3188 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.49 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.15), residues: 2937 helix: 1.78 (0.20), residues: 669 sheet: 0.09 (0.20), residues: 607 loop : -0.67 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 328 TYR 0.023 0.001 TYR B 200 PHE 0.034 0.001 PHE C 329 TRP 0.009 0.001 TRP C 886 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (24023) covalent geometry : angle 0.54488 / 0.28 (32701) SS BOND : bond 0.00400 / 0.24 ( 37) SS BOND : angle 0.96019 / 0.59 ( 74) hydrogen bonds : bond 0.03857 / 2.52 ( 1022) hydrogen bonds : angle 5.51600 / 3.86 ( 2814) link_NAG-ASN : bond 0.00324 / 0.20 ( 28) link_NAG-ASN : angle 2.10348 / 1.34 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: A 168 PHE cc_start: 0.8188 (t80) cc_final: 0.7938 (t80) REVERT: A 200 TYR cc_start: 0.8573 (m-10) cc_final: 0.8369 (m-10) REVERT: A 297 SER cc_start: 0.8993 (m) cc_final: 0.8607 (p) REVERT: A 417 ASN cc_start: 0.9580 (m-40) cc_final: 0.9215 (p0) REVERT: A 473 TYR cc_start: 0.6622 (t80) cc_final: 0.6419 (t80) REVERT: A 979 ASP cc_start: 0.8986 (m-30) cc_final: 0.8572 (t0) REVERT: B 52 GLN cc_start: 0.8759 (tm-30) cc_final: 0.8507 (tm-30) REVERT: B 56 LEU cc_start: 0.8927 (tp) cc_final: 0.8722 (tp) REVERT: B 91 TYR cc_start: 0.7913 (t80) cc_final: 0.7496 (t80) REVERT: B 864 LEU cc_start: 0.9053 (tp) cc_final: 0.8738 (tp) REVERT: B 1002 GLN cc_start: 0.8517 (tm-30) cc_final: 0.7964 (tm-30) REVERT: C 297 SER cc_start: 0.9504 (m) cc_final: 0.9229 (p) REVERT: C 417 ASN cc_start: 0.9495 (m110) cc_final: 0.9109 (p0) REVERT: C 509 ARG cc_start: 0.7969 (mtt180) cc_final: 0.7225 (mtp85) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1286 time to fit residues: 25.0345 Evaluate side-chains 78 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 82 optimal weight: 0.0020 chunk 247 optimal weight: 5.9990 chunk 268 optimal weight: 3.9990 chunk 279 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 202 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 293 optimal weight: 4.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.071965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.052504 restraints weight = 121917.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.054223 restraints weight = 70198.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.054827 restraints weight = 42228.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.055179 restraints weight = 32161.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.055276 restraints weight = 28886.383| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 24088 Z= 0.100 Angle : 0.520 7.432 32859 Z= 0.268 Chirality : 0.043 0.236 3838 Planarity : 0.004 0.059 4181 Dihedral : 4.582 27.607 3188 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.78 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.15), residues: 2937 helix: 1.99 (0.21), residues: 667 sheet: 0.18 (0.20), residues: 608 loop : -0.56 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1000 TYR 0.018 0.001 TYR B 200 PHE 0.020 0.001 PHE C 342 TRP 0.009 0.001 TRP A 436 HIS 0.003 0.000 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (24023) covalent geometry : angle 0.50973 / 0.27 (32701) SS BOND : bond 0.00206 / 0.15 ( 37) SS BOND : angle 0.90115 / 0.57 ( 74) hydrogen bonds : bond 0.03575 / 2.32 ( 1022) hydrogen bonds : angle 5.29526 / 3.70 ( 2814) link_NAG-ASN : bond 0.00320 / 0.18 ( 28) link_NAG-ASN : angle 1.92988 / 1.23 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.803 Fit side-chains revert: symmetry clash REVERT: A 297 SER cc_start: 0.8939 (m) cc_final: 0.8569 (p) REVERT: A 965 GLN cc_start: 0.9177 (mm-40) cc_final: 0.8815 (tp-100) REVERT: A 979 ASP cc_start: 0.8940 (m-30) cc_final: 0.8635 (t0) REVERT: B 52 GLN cc_start: 0.8719 (tm-30) cc_final: 0.8517 (tm-30) REVERT: B 238 PHE cc_start: 0.8712 (p90) cc_final: 0.8349 (p90) REVERT: B 864 LEU cc_start: 0.8983 (tp) cc_final: 0.8752 (tp) REVERT: B 1002 GLN cc_start: 0.8449 (tm-30) cc_final: 0.7936 (tm-30) REVERT: C 55 PHE cc_start: 0.8663 (m-80) cc_final: 0.8264 (m-80) REVERT: C 297 SER cc_start: 0.9487 (m) cc_final: 0.9247 (p) REVERT: C 417 ASN cc_start: 0.9478 (m110) cc_final: 0.9118 (p0) REVERT: C 509 ARG cc_start: 0.7859 (mtt180) cc_final: 0.7077 (mtp85) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1380 time to fit residues: 28.2655 Evaluate side-chains 82 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 130 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 193 optimal weight: 7.9990 chunk 133 optimal weight: 0.6980 chunk 151 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 204 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 172 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.069861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.050074 restraints weight = 124680.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.051590 restraints weight = 73144.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.052107 restraints weight = 46552.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.052429 restraints weight = 34988.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.052643 restraints weight = 31246.538| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 24088 Z= 0.237 Angle : 0.629 8.024 32859 Z= 0.324 Chirality : 0.045 0.238 3838 Planarity : 0.004 0.061 4181 Dihedral : 4.910 28.628 3188 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.31 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.15), residues: 2937 helix: 1.56 (0.21), residues: 669 sheet: 0.06 (0.19), residues: 649 loop : -0.67 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 408 TYR 0.023 0.002 TYR B 200 PHE 0.024 0.002 PHE C 906 TRP 0.023 0.002 TRP C 886 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.24 (24023) covalent geometry : angle 0.61988 / 0.32 (32701) SS BOND : bond 0.00391 / 0.28 ( 37) SS BOND : angle 1.16203 / 0.73 ( 74) hydrogen bonds : bond 0.04140 / 2.72 ( 1022) hydrogen bonds : angle 5.66447 / 3.98 ( 2814) link_NAG-ASN : bond 0.00373 / 0.24 ( 28) link_NAG-ASN : angle 1.99997 / 1.23 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.589 Fit side-chains REVERT: A 168 PHE cc_start: 0.8100 (t80) cc_final: 0.7814 (t80) REVERT: A 297 SER cc_start: 0.9015 (m) cc_final: 0.8623 (p) REVERT: A 557 LYS cc_start: 0.7625 (mmtp) cc_final: 0.7275 (mmtm) REVERT: A 979 ASP cc_start: 0.8888 (m-30) cc_final: 0.8658 (t0) REVERT: B 864 LEU cc_start: 0.9045 (tp) cc_final: 0.8764 (tp) REVERT: C 297 SER cc_start: 0.9489 (m) cc_final: 0.9261 (p) REVERT: C 417 ASN cc_start: 0.9481 (m110) cc_final: 0.9106 (p0) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1290 time to fit residues: 22.9514 Evaluate side-chains 67 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 63 optimal weight: 0.6980 chunk 258 optimal weight: 0.9990 chunk 247 optimal weight: 7.9990 chunk 146 optimal weight: 8.9990 chunk 126 optimal weight: 20.0000 chunk 84 optimal weight: 0.9980 chunk 292 optimal weight: 0.0980 chunk 15 optimal weight: 9.9990 chunk 142 optimal weight: 0.9980 chunk 241 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 544 ASN A 901 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.071690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.052060 restraints weight = 122495.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.053769 restraints weight = 70360.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.054290 restraints weight = 42902.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.054642 restraints weight = 33471.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.054842 restraints weight = 29693.928| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 24088 Z= 0.102 Angle : 0.531 7.404 32859 Z= 0.274 Chirality : 0.044 0.229 3838 Planarity : 0.004 0.060 4181 Dihedral : 4.588 26.521 3188 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.95 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.16), residues: 2937 helix: 1.99 (0.21), residues: 656 sheet: 0.15 (0.20), residues: 650 loop : -0.53 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 408 TYR 0.034 0.001 TYR A 266 PHE 0.038 0.001 PHE A 559 TRP 0.029 0.001 TRP A 64 HIS 0.003 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (24023) covalent geometry : angle 0.52078 / 0.27 (32701) SS BOND : bond 0.00518 / 0.33 ( 37) SS BOND : angle 1.20997 / 0.78 ( 74) hydrogen bonds : bond 0.03597 / 2.35 ( 1022) hydrogen bonds : angle 5.33367 / 3.73 ( 2814) link_NAG-ASN : bond 0.00311 / 0.18 ( 28) link_NAG-ASN : angle 1.82027 / 1.14 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 PHE cc_start: 0.8083 (t80) cc_final: 0.7860 (t80) REVERT: A 297 SER cc_start: 0.8953 (m) cc_final: 0.8545 (p) REVERT: A 557 LYS cc_start: 0.7597 (mmtp) cc_final: 0.7167 (mmtm) REVERT: A 965 GLN cc_start: 0.9165 (mm-40) cc_final: 0.8764 (tp-100) REVERT: A 979 ASP cc_start: 0.8979 (m-30) cc_final: 0.8686 (t0) REVERT: B 52 GLN cc_start: 0.8778 (tm-30) cc_final: 0.8543 (tm-30) REVERT: B 119 ILE cc_start: 0.9208 (mp) cc_final: 0.8995 (mm) REVERT: B 238 PHE cc_start: 0.8863 (p90) cc_final: 0.8499 (p90) REVERT: B 1002 GLN cc_start: 0.8482 (tm-30) cc_final: 0.8081 (tm-30) REVERT: C 55 PHE cc_start: 0.8705 (m-80) cc_final: 0.8273 (m-80) REVERT: C 297 SER cc_start: 0.9517 (m) cc_final: 0.9261 (p) REVERT: C 417 ASN cc_start: 0.9467 (m110) cc_final: 0.9085 (p0) REVERT: C 509 ARG cc_start: 0.7837 (mtt180) cc_final: 0.6885 (mtt180) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1341 time to fit residues: 25.3066 Evaluate side-chains 82 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 69 optimal weight: 1.9990 chunk 241 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 262 optimal weight: 6.9990 chunk 148 optimal weight: 0.7980 chunk 49 optimal weight: 7.9990 chunk 203 optimal weight: 9.9990 chunk 195 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 162 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 540 ASN B1083 HIS ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.070661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.051157 restraints weight = 124040.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.052583 restraints weight = 73637.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.053131 restraints weight = 41951.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.053357 restraints weight = 36629.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.053436 restraints weight = 33168.583| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 24088 Z= 0.169 Angle : 0.562 7.344 32859 Z= 0.290 Chirality : 0.044 0.231 3838 Planarity : 0.004 0.061 4181 Dihedral : 4.636 26.899 3188 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.97 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.16), residues: 2937 helix: 1.80 (0.21), residues: 662 sheet: 0.14 (0.19), residues: 655 loop : -0.58 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 408 TYR 0.023 0.001 TYR A 266 PHE 0.036 0.002 PHE C 906 TRP 0.025 0.001 TRP A 64 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (24023) covalent geometry : angle 0.55237 / 0.29 (32701) SS BOND : bond 0.00325 / 0.24 ( 37) SS BOND : angle 1.23944 / 0.77 ( 74) hydrogen bonds : bond 0.03792 / 2.50 ( 1022) hydrogen bonds : angle 5.43271 / 3.81 ( 2814) link_NAG-ASN : bond 0.00281 / 0.18 ( 28) link_NAG-ASN : angle 1.82396 / 1.13 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 PHE cc_start: 0.8028 (t80) cc_final: 0.7780 (t80) REVERT: A 297 SER cc_start: 0.9013 (m) cc_final: 0.8609 (p) REVERT: A 557 LYS cc_start: 0.7592 (mmtp) cc_final: 0.7170 (mmtm) REVERT: A 979 ASP cc_start: 0.8918 (m-30) cc_final: 0.8693 (t0) REVERT: B 52 GLN cc_start: 0.8779 (tm-30) cc_final: 0.8556 (tm-30) REVERT: B 117 LEU cc_start: 0.9353 (mp) cc_final: 0.9124 (tp) REVERT: B 1002 GLN cc_start: 0.8518 (tm-30) cc_final: 0.7971 (tm-30) REVERT: C 55 PHE cc_start: 0.8716 (m-80) cc_final: 0.8411 (m-80) REVERT: C 297 SER cc_start: 0.9504 (m) cc_final: 0.9275 (p) REVERT: C 417 ASN cc_start: 0.9467 (m110) cc_final: 0.9083 (p0) REVERT: C 509 ARG cc_start: 0.7994 (mtt180) cc_final: 0.6977 (mtp85) REVERT: C 1029 MET cc_start: 0.9543 (tpp) cc_final: 0.9308 (tpp) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1531 time to fit residues: 27.2632 Evaluate side-chains 75 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 172 optimal weight: 0.9980 chunk 157 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 90 optimal weight: 0.9980 chunk 256 optimal weight: 6.9990 chunk 273 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 856 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.071784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.052158 restraints weight = 122814.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.053851 restraints weight = 72792.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.054500 restraints weight = 43250.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.054828 restraints weight = 32582.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.055024 restraints weight = 29063.695| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 24088 Z= 0.100 Angle : 0.515 6.872 32859 Z= 0.266 Chirality : 0.043 0.234 3838 Planarity : 0.004 0.060 4181 Dihedral : 4.421 24.729 3188 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.81 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.16), residues: 2937 helix: 2.03 (0.21), residues: 655 sheet: 0.28 (0.20), residues: 622 loop : -0.55 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 408 TYR 0.019 0.001 TYR A 473 PHE 0.031 0.001 PHE C 906 TRP 0.018 0.001 TRP A 64 HIS 0.003 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (24023) covalent geometry : angle 0.50594 / 0.26 (32701) SS BOND : bond 0.00255 / 0.19 ( 37) SS BOND : angle 1.04804 / 0.64 ( 74) hydrogen bonds : bond 0.03495 / 2.29 ( 1022) hydrogen bonds : angle 5.22419 / 3.65 ( 2814) link_NAG-ASN : bond 0.00302 / 0.18 ( 28) link_NAG-ASN : angle 1.71503 / 1.07 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3008.42 seconds wall clock time: 53 minutes 21.38 seconds (3201.38 seconds total)