Starting phenix.real_space_refine on Mon Sep 14 06:14:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wly_32594/09_2026/7wly_32594.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wly_32594/09_2026/7wly_32594.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wly_32594/09_2026/7wly_32594.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wly_32594/09_2026/7wly_32594.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7wly_32594/09_2026/7wly_32594.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wly_32594/09_2026/7wly_32594.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wly_32594/09_2026/7wly_32594.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wly_32594/09_2026/7wly_32594.map" } resolution = 3.4 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= -0.000 sd= 0.022 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 129 5.16 5 C 18219 2.51 5 N 4722 2.21 5 O 5480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 170 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28550 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8196 Classifications: {'peptide': 1051} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 57, 'TRANS': 993} Chain breaks: 7 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 8090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8090 Classifications: {'peptide': 1042} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 56, 'TRANS': 985} Chain breaks: 8 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASN:plan1': 3, 'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 4, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 42 Chain: "C" Number of atoms: 8225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8225 Classifications: {'peptide': 1058} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 56, 'TRANS': 1001} Chain breaks: 7 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 4, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "P" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 962 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 838 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 101} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain breaks: 1 Chain: "X" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 838 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 101} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 5.39, per 1000 atoms: 0.19 Number of scatterers: 28550 At special positions: 0 Unit cell: (132.834, 170.352, 202.8, 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 129 16.00 O 5480 8.00 N 4722 7.00 C 18219 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.02 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.02 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 93 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 96 " distance=2.04 Simple disulfide: pdb=" SG CYS X 23 " - pdb=" SG CYS X 93 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A1074 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 717 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A1098 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B 717 " " NAG B1305 " - " ASN B 801 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B1098 " " NAG B1309 " - " ASN B 331 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C 717 " " NAG C1306 " - " ASN C 801 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C1098 " " NAG C1309 " - " ASN C1134 " " NAG D 1 " - " ASN C 165 " " NAG E 1 " - " ASN C 234 " Time building additional restraints: 2.30 Conformation dependent library (CDL) restraints added in 1.2 seconds 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6770 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 64 sheets defined 22.8% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.807A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 542 through 546 removed outlier: 3.640A pdb=" N LEU A 546 " --> pdb=" O PHE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 removed outlier: 3.803A pdb=" N VAL A 622 " --> pdb=" O THR A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 639 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.762A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.298A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.426A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1034 removed outlier: 3.843A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.106A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 404 through 410 removed outlier: 4.130A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 633 through 639 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 4.079A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.524A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.531A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.936A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B1001 " --> pdb=" O ILE B 997 " (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 1140 through 1146 removed outlier: 3.667A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.231A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 388 Processing helix chain 'C' and resid 404 through 410 removed outlier: 4.176A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 747 through 754 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 836 through 841 removed outlier: 3.622A pdb=" N CYS C 840 " --> pdb=" O GLN C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 857 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 885 through 891 removed outlier: 3.951A pdb=" N PHE C 888 " --> pdb=" O GLY C 885 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.766A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'Y' and resid 28 through 32 removed outlier: 3.712A pdb=" N ASP Y 31 " --> pdb=" O THR Y 28 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N TYR Y 32 " --> pdb=" O PHE Y 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 28 through 32' Processing helix chain 'Y' and resid 87 through 91 removed outlier: 3.893A pdb=" N THR Y 91 " --> pdb=" O ALA Y 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.627A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.627A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.524A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.963A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.568A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 313 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 313 removed outlier: 3.773A pdb=" N THR A 645 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.235A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (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 538 through 540 removed outlier: 3.586A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.564A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.925A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 717 through 719 removed outlier: 6.604A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 722 through 728 Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.532A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1089 through 1090 Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.664A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.902A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.631A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 52 through 55 removed outlier: 3.901A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.583A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 312 Processing sheet with id=AC4, first strand: chain 'B' and resid 318 through 319 Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.528A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.184A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.844A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 712 through 713 Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 722 Processing sheet with id=AD4, first strand: chain 'B' and resid 725 through 728 Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.605A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER B 735 " --> pdb=" O THR B 859 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 788 through 789 removed outlier: 5.886A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.818A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1094 through 1097 removed outlier: 3.657A pdb=" N VAL B1094 " --> pdb=" O THR B1105 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AE1, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.707A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 65 through 66 removed outlier: 3.531A pdb=" N GLY C 268 " --> pdb=" O TYR C 91 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.506A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE C 106 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER C 116 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 134 through 135 Processing sheet with id=AE5, first strand: chain 'C' and resid 187 through 190 Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.676A pdb=" N PHE C 643 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 318 through 319 removed outlier: 4.265A pdb=" N PHE C 318 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'C' and resid 324 through 328 removed outlier: 3.967A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.541A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF2, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.586A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 565 through 567 removed outlier: 6.169A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.735A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 712 through 713 removed outlier: 3.918A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL C1094 " --> pdb=" O THR C1105 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR C1105 " --> pdb=" O VAL C1094 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 721 through 728 removed outlier: 6.682A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 721 through 728 Processing sheet with id=AF8, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.442A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AG1, first strand: chain 'C' and resid 1089 through 1090 Processing sheet with id=AG2, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AG3, first strand: chain 'P' and resid 45 through 51 removed outlier: 5.631A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'O' and resid 5 through 7 removed outlier: 3.598A pdb=" N ALA O 19 " --> pdb=" O ILE O 80 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'O' and resid 10 through 12 removed outlier: 3.506A pdb=" N LEU O 11 " --> pdb=" O LYS O 108 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASP O 110 " --> pdb=" O LEU O 11 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP O 40 " --> pdb=" O LEU O 52 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Y' and resid 3 through 7 Processing sheet with id=AG7, first strand: chain 'Y' and resid 11 through 12 Processing sheet with id=AG8, first strand: chain 'Y' and resid 45 through 51 removed outlier: 5.640A pdb=" N TRP Y 47 " --> pdb=" O ARG Y 38 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ARG Y 38 " --> pdb=" O TRP Y 47 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'X' and resid 5 through 7 Processing sheet with id=AH1, first strand: chain 'X' and resid 10 through 12 removed outlier: 3.572A pdb=" N LEU X 11 " --> pdb=" O LYS X 108 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP X 110 " --> pdb=" O LEU X 11 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP X 40 " --> pdb=" O LEU X 52 " (cutoff:3.500A) 1052 hydrogen bonds defined for protein. 2811 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.02 Time building geometry restraints manager: 3.07 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: 7373 1.33 - 1.45: 6212 1.45 - 1.58: 15464 1.58 - 1.70: 0 1.70 - 1.82: 165 Bond restraints: 29214 Sorted by residual: bond pdb=" N ILE A 805 " pdb=" CA ILE A 805 " ideal model delta sigma weight residual 1.452 1.495 -0.043 1.18e-02 7.18e+03 1.33e+01 bond pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" N VAL Y 100 " pdb=" CA VAL Y 100 " ideal model delta sigma weight residual 1.454 1.494 -0.040 1.19e-02 7.06e+03 1.14e+01 bond pdb=" N VAL B 445 " pdb=" CA VAL B 445 " ideal model delta sigma weight residual 1.460 1.499 -0.040 1.21e-02 6.83e+03 1.07e+01 bond pdb=" N ARG B 237 " pdb=" CA ARG B 237 " ideal model delta sigma weight residual 1.457 1.497 -0.041 1.24e-02 6.50e+03 1.07e+01 ... (remaining 29209 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 38800 2.53 - 5.06: 896 5.06 - 7.59: 56 7.59 - 10.12: 6 10.12 - 12.65: 1 Bond angle restraints: 39759 Sorted by residual: angle pdb=" N TYR C 449 " pdb=" CA TYR C 449 " pdb=" C TYR C 449 " ideal model delta sigma weight residual 113.61 105.41 8.20 1.50e+00 4.44e-01 2.99e+01 angle pdb=" N ASN A 907 " pdb=" CA ASN A 907 " pdb=" C ASN A 907 " ideal model delta sigma weight residual 112.89 106.42 6.47 1.24e+00 6.50e-01 2.72e+01 angle pdb=" C GLU B 702 " pdb=" CA GLU B 702 " pdb=" CB GLU B 702 " ideal model delta sigma weight residual 110.06 117.19 -7.13 1.39e+00 5.18e-01 2.63e+01 angle pdb=" N ALA A 163 " pdb=" CA ALA A 163 " pdb=" CB ALA A 163 " ideal model delta sigma weight residual 110.77 102.42 8.35 1.63e+00 3.76e-01 2.62e+01 angle pdb=" N LEU B 753 " pdb=" CA LEU B 753 " pdb=" C LEU B 753 " ideal model delta sigma weight residual 112.89 106.81 6.08 1.24e+00 6.50e-01 2.40e+01 ... (remaining 39754 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 15904 17.82 - 35.65: 982 35.65 - 53.47: 177 53.47 - 71.30: 45 71.30 - 89.12: 20 Dihedral angle restraints: 17128 sinusoidal: 6596 harmonic: 10532 Sorted by residual: dihedral pdb=" CB CYS C 743 " pdb=" SG CYS C 743 " pdb=" SG CYS C 749 " pdb=" CB CYS C 749 " ideal model delta sinusoidal sigma weight residual -86.00 -158.82 72.82 1 1.00e+01 1.00e-02 6.76e+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 93.00 162.17 -69.17 1 1.00e+01 1.00e-02 6.19e+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 -42.47 -43.53 1 1.00e+01 1.00e-02 2.64e+01 ... (remaining 17125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 4282 0.111 - 0.221: 280 0.221 - 0.332: 9 0.332 - 0.442: 3 0.442 - 0.553: 2 Chirality restraints: 4576 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.41e+01 chirality pdb=" C1 NAG B1308 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG B1308 " pdb=" O5 NAG B1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.64e+00 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.07e+00 ... (remaining 4573 not shown) Planarity restraints: 5137 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1305 " -0.342 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG A1305 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG A1305 " -0.090 2.00e-02 2.50e+03 pdb=" N2 NAG A1305 " 0.527 2.00e-02 2.50e+03 pdb=" O7 NAG A1305 " -0.175 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1301 " -0.342 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG C1301 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG C1301 " -0.094 2.00e-02 2.50e+03 pdb=" N2 NAG C1301 " 0.527 2.00e-02 2.50e+03 pdb=" O7 NAG C1301 " -0.172 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1308 " -0.342 2.00e-02 2.50e+03 2.95e-01 1.08e+03 pdb=" C7 NAG B1308 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG B1308 " -0.147 2.00e-02 2.50e+03 pdb=" N2 NAG B1308 " 0.524 2.00e-02 2.50e+03 pdb=" O7 NAG B1308 " -0.119 2.00e-02 2.50e+03 ... (remaining 5134 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3196 2.75 - 3.28: 29340 3.28 - 3.82: 45696 3.82 - 4.36: 54866 4.36 - 4.90: 94100 Nonbonded interactions: 227198 Sorted by model distance: nonbonded pdb=" O GLU B 309 " pdb=" OH TYR B 313 " model vdw 2.207 3.040 nonbonded pdb=" OG SER C 112 " pdb=" O PHE C 133 " model vdw 2.225 3.040 nonbonded pdb=" O TYR A 313 " pdb=" OG SER A 596 " model vdw 2.237 3.040 nonbonded pdb=" O THR C 676 " pdb=" OG1 THR C 676 " model vdw 2.264 3.040 nonbonded pdb=" OD1 ASP A 442 " pdb=" OH TYR A 451 " model vdw 2.269 3.040 ... (remaining 227193 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 66 or (resid 67 and (name N or name CA or name \ C or name O or name CB )) or resid 77 through 109 or (resid 110 through 111 and \ (name N or name CA or name C or name O or name CB )) or resid 112 or (resid 113 \ through 114 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 5 through 119 or (resid 120 through 121 and (name N or name CA or name C or name \ O or name CB )) or resid 122 through 136 or (resid 137 and (name N or name CA o \ r name C or name O or name CB )) or resid 138 through 158 or (resid 159 and (nam \ e N or name CA or name C or name O or name CB )) or resid 160 through 172 or (re \ sid 173 and (name N or name CA or name C or name O or name CB )) or resid 174 th \ rough 176 or (resid 177 through 178 and (name N or name CA or name C or name O o \ r name CB )) or resid 185 through 227 or (resid 228 through 229 and (name N or n \ ame CA or name C or name O or name CB )) or resid 230 through 269 or (resid 270 \ through 271 and (name N or name CA or name C or name O or name CB )) or resid 27 \ 2 through 334 or (resid 335 and (name N or name CA or name C or name O or name C \ B )) or resid 336 through 392 or (resid 393 through 394 and (name N or name CA o \ r name C or name O or name CB )) or resid 395 through 402 or (resid 403 and (nam \ e N or name CA or name C or name O or name CB )) or resid 404 through 461 or (re \ sid 462 and (name N or name CA or name C or name O or name CB )) or resid 463 th \ rough 502 or (resid 503 and (name N or name CA or name C or name O or name CB )) \ or resid 504 through 516 or (resid 517 through 518 and (name N or name CA or na \ me C or name O or name CB )) or resid 519 through 522 or (resid 523 and (name N \ or name CA or name C or name O or name CB )) or resid 524 through 527 or (resid \ 528 through 529 and (name N or name CA or name C or name O or name CB )) or resi \ d 530 through 532 or (resid 533 and (name N or name CA or name C or name O or na \ me CB )) or resid 534 through 550 or (resid 551 and (name N or name CA or name C \ or name O or name CB )) or resid 552 through 581 or (resid 582 through 583 and \ (name N or name CA or name C or name O or name CB )) or resid 584 through 622 or \ resid 632 through 827 or (resid 828 through 829 and (name N or name CA or name \ C or name O or name CB )) or resid 830 through 978 or (resid 979 and (name N or \ name CA or name C or name O or name CB )) or resid 980 through 984 or (resid 985 \ and (name N or name CA or name C or name O or name CB )) or resid 986 through 9 \ 87 or (resid 988 through 990 and (name N or name CA or name C or name O or name \ CB )) or resid 991 through 993 or (resid 994 and (name N or name CA or name C or \ name O or name CB )) or resid 995 through 1309)) selection = (chain 'B' and (resid 27 through 66 or (resid 67 and (name N or name CA or name \ C or name O or name CB )) or resid 77 through 109 or (resid 110 through 111 and \ (name N or name CA or name C or name O or name CB )) or resid 112 through 113 or \ (resid 114 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 5 through 119 or (resid 120 through 121 and (name N or name CA or name C or name \ O or name CB )) or resid 122 through 128 or (resid 129 and (name N or name CA o \ r name C or name O or name CB )) or resid 130 through 158 or (resid 159 and (nam \ e N or name CA or name C or name O or name CB )) or resid 160 through 205 or (re \ sid 206 and (name N or name CA or name C or name O or name CB )) or resid 207 th \ rough 270 or (resid 271 and (name N or name CA or name C or name O or name CB )) \ or resid 272 through 334 or (resid 335 and (name N or name CA or name C or name \ O or name CB )) or resid 336 through 345 or (resid 346 and (name N or name CA o \ r name C or name O or name CB )) or resid 347 through 356 or (resid 357 and (nam \ e N or name CA or name C or name O or name CB )) or resid 358 through 370 or (re \ sid 371 through 372 and (name N or name CA or name C or name O or name CB )) or \ resid 373 through 402 or (resid 403 and (name N or name CA or name C or name O o \ r name CB )) or resid 404 through 408 or (resid 409 and (name N or name CA or na \ me C or name O or name CB )) or resid 410 through 426 or (resid 427 and (name N \ or name CA or name C or name O or name CB )) or resid 428 through 454 or (resid \ 455 and (name N or name CA or name C or name O or name CB )) or resid 456 throug \ h 516 or (resid 517 through 518 and (name N or name CA or name C or name O or na \ me CB )) or resid 519 through 827 or (resid 828 through 829 and (name N or name \ CA or name C or name O or name CB )) or resid 830 through 984 or (resid 985 and \ (name N or name CA or name C or name O or name CB )) or resid 986 through 1126 o \ r (resid 1127 and (name N or name CA or name C or name O or name CB )) or resid \ 1128 through 1309)) selection = (chain 'C' and (resid 27 through 112 or (resid 113 through 114 and (name N or na \ me CA or name C or name O or name CB )) or resid 115 through 120 or (resid 121 a \ nd (name N or name CA or name C or name O or name CB )) or resid 122 through 136 \ or (resid 137 and (name N or name CA or name C or name O or name CB )) or resid \ 138 through 142 or (resid 158 through 159 and (name N or name CA or name C or n \ ame O or name CB )) or resid 160 through 172 or (resid 173 and (name N or name C \ A or name C or name O or name CB )) or resid 174 through 176 or (resid 177 throu \ gh 178 and (name N or name CA or name C or name O or name CB )) or resid 185 thr \ ough 205 or (resid 206 and (name N or name CA or name C or name O or name CB )) \ or resid 207 through 227 or (resid 228 through 229 and (name N or name CA or nam \ e C or name O or name CB )) or resid 230 through 269 or (resid 270 through 271 a \ nd (name N or name CA or name C or name O or name CB )) or resid 272 through 345 \ or (resid 346 and (name N or name CA or name C or name O or name CB )) or resid \ 347 through 356 or (resid 357 and (name N or name CA or name C or name O or nam \ e CB )) or resid 358 through 370 or (resid 371 through 372 and (name N or name C \ A or name C or name O or name CB )) or resid 373 through 408 or (resid 409 and ( \ name N or name CA or name C or name O or name CB )) or resid 410 through 426 or \ (resid 427 and (name N or name CA or name C or name O or name CB )) or resid 428 \ through 454 or (resid 455 and (name N or name CA or name C or name O or name CB \ )) or resid 456 through 517 or (resid 518 and (name N or name CA or name C or n \ ame O or name CB )) or resid 519 through 522 or (resid 523 and (name N or name C \ A or name C or name O or name CB )) or resid 524 through 532 or (resid 533 and ( \ name N or name CA or name C or name O or name CB )) or resid 534 through 550 or \ (resid 551 and (name N or name CA or name C or name O or name CB )) or resid 552 \ through 581 or (resid 582 through 583 and (name N or name CA or name C or name \ O or name CB )) or resid 584 through 622 or resid 632 through 836 or resid 848 t \ hrough 987 or (resid 988 through 990 and (name N or name CA or name C or name O \ or name CB )) or resid 991 through 993 or (resid 994 and (name N or name CA or n \ ame C or name O or name CB )) or resid 995 through 1309)) } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'O' selection = chain 'X' } ncs_group { reference = chain 'P' selection = (chain 'Y' and (resid 1 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 127 or (resid 128 and (name N or na \ me CA or name C or name O or name CB )) or resid 129 through 130)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 26.540 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 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 : 0.007 0.086 29288 Z= 0.419 Angle : 0.874 12.650 39938 Z= 0.551 Chirality : 0.058 0.553 4576 Planarity : 0.012 0.297 5108 Dihedral : 12.275 89.124 10229 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 0.97 % Allowed : 8.78 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.55 (0.13), residues: 3565 helix: -0.05 (0.19), residues: 730 sheet: -1.76 (0.18), residues: 856 loop : -2.37 (0.12), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 765 TYR 0.020 0.002 TYR C1067 PHE 0.036 0.002 PHE C 592 TRP 0.014 0.001 TRP B 886 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00712 / 0.42 (29214) covalent geometry : angle 0.85936 / 0.55 (39759) SS BOND : bond 0.00472 / 0.33 ( 43) SS BOND : angle 1.57205 / 1.02 ( 86) hydrogen bonds : bond 0.19833 / 13.35 ( 1020) hydrogen bonds : angle 9.24460 / 6.28 ( 2811) link_BETA1-4 : bond 0.00578 / 0.28 ( 2) link_BETA1-4 : angle 2.84123 / 1.80 ( 6) link_NAG-ASN : bond 0.00569 / 0.31 ( 29) link_NAG-ASN : angle 3.15982 / 2.20 ( 87) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 283 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.6817 (pmm-80) REVERT: A 49 HIS cc_start: 0.7629 (t70) cc_final: 0.7203 (t70) REVERT: A 464 PHE cc_start: 0.8663 (m-80) cc_final: 0.8275 (m-80) REVERT: A 498 ARG cc_start: 0.7991 (mtt-85) cc_final: 0.7629 (mmm-85) REVERT: A 934 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.7689 (mm) REVERT: B 977 LEU cc_start: 0.8052 (mp) cc_final: 0.7850 (mm) REVERT: B 981 PHE cc_start: 0.7665 (m-10) cc_final: 0.6985 (m-80) REVERT: C 54 LEU cc_start: 0.9069 (mp) cc_final: 0.8717 (mt) REVERT: C 198 ASP cc_start: 0.7899 (p0) cc_final: 0.7665 (p0) REVERT: C 342 PHE cc_start: 0.5887 (m-80) cc_final: 0.5116 (m-10) REVERT: C 508 TYR cc_start: 0.4255 (OUTLIER) cc_final: 0.2869 (t80) REVERT: C 547 LYS cc_start: 0.7226 (ptmt) cc_final: 0.6992 (ptmm) REVERT: P 36 TRP cc_start: 0.3059 (m100) cc_final: 0.2494 (m100) REVERT: X 29 LEU cc_start: -0.2832 (mt) cc_final: -0.3060 (tt) outliers start: 30 outliers final: 9 residues processed: 310 average time/residue: 0.1736 time to fit residues: 88.9558 Evaluate side-chains 183 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 171 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 40.0000 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 6.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 HIS A 87 ASN A 370 ASN A 448 ASN ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN A 836 GLN A1058 HIS A1106 GLN A1135 ASN B 218 GLN B 239 GLN B 314 GLN B 580 GLN B 751 ASN B 779 GLN B 804 GLN B 955 ASN B1101 HIS C 196 ASN C 360 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN C 450 ASN C 751 ASN C 901 GLN C 960 ASN C 965 GLN C1113 GLN C1135 ASN O 98 GLN Y 39 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.143840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.096712 restraints weight = 76496.658| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 3.86 r_work: 0.3211 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 29288 Z= 0.200 Angle : 0.697 24.123 39938 Z= 0.346 Chirality : 0.047 0.284 4576 Planarity : 0.004 0.061 5108 Dihedral : 5.255 57.294 3908 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.82 % Allowed : 10.92 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.13), residues: 3565 helix: 0.49 (0.19), residues: 728 sheet: -1.59 (0.17), residues: 895 loop : -2.09 (0.13), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 319 TYR 0.028 0.002 TYR B 796 PHE 0.023 0.002 PHE C1121 TRP 0.020 0.002 TRP C 353 HIS 0.006 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.20 (29214) covalent geometry : angle 0.66547 / 0.34 (39759) SS BOND : bond 0.00352 / 0.25 ( 43) SS BOND : angle 1.26539 / 0.83 ( 86) hydrogen bonds : bond 0.05100 / 3.34 ( 1020) hydrogen bonds : angle 6.61238 / 4.49 ( 2811) link_BETA1-4 : bond 0.00690 / 0.36 ( 2) link_BETA1-4 : angle 3.16083 / 1.84 ( 6) link_NAG-ASN : bond 0.00623 / 0.40 ( 29) link_NAG-ASN : angle 4.25367 / 3.28 ( 87) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 202 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7889 (t80) cc_final: 0.7580 (t80) REVERT: B 353 TRP cc_start: 0.2708 (p-90) cc_final: 0.1609 (p-90) REVERT: C 106 PHE cc_start: 0.8424 (m-80) cc_final: 0.8193 (m-80) REVERT: C 177 MET cc_start: 0.8880 (ttt) cc_final: 0.7904 (mmp) REVERT: C 198 ASP cc_start: 0.8237 (p0) cc_final: 0.8023 (p0) REVERT: C 353 TRP cc_start: 0.0291 (p-90) cc_final: -0.0299 (p-90) REVERT: P 86 LEU cc_start: 0.2077 (tt) cc_final: 0.1357 (pp) REVERT: O 54 TYR cc_start: 0.7564 (p90) cc_final: 0.7164 (p90) REVERT: Y 98 LYS cc_start: 0.6559 (OUTLIER) cc_final: 0.6244 (tppt) REVERT: X 4 MET cc_start: 0.2981 (mtm) cc_final: 0.2683 (mtm) outliers start: 87 outliers final: 41 residues processed: 278 average time/residue: 0.1722 time to fit residues: 80.7460 Evaluate side-chains 206 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 164 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain Y residue 98 LYS Chi-restraints excluded: chain Y residue 130 SER Chi-restraints excluded: chain X residue 30 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 188 optimal weight: 5.9990 chunk 307 optimal weight: 1.9990 chunk 263 optimal weight: 0.6980 chunk 180 optimal weight: 2.9990 chunk 316 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 201 optimal weight: 0.9980 chunk 231 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 108 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.143501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.096679 restraints weight = 76493.597| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 3.92 r_work: 0.3222 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 29288 Z= 0.156 Angle : 0.631 19.567 39938 Z= 0.312 Chirality : 0.046 0.325 4576 Planarity : 0.004 0.059 5108 Dihedral : 4.905 55.336 3899 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.30 % Allowed : 13.22 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.14), residues: 3565 helix: 0.81 (0.19), residues: 738 sheet: -1.42 (0.17), residues: 916 loop : -1.92 (0.13), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 319 TYR 0.022 0.001 TYR A 904 PHE 0.020 0.001 PHE B 175 TRP 0.013 0.001 TRP P 36 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (29214) covalent geometry : angle 0.60693 / 0.31 (39759) SS BOND : bond 0.00358 / 0.23 ( 43) SS BOND : angle 1.27213 / 0.85 ( 86) hydrogen bonds : bond 0.04506 / 2.94 ( 1020) hydrogen bonds : angle 6.05942 / 4.13 ( 2811) link_BETA1-4 : bond 0.00841 / 0.44 ( 2) link_BETA1-4 : angle 2.57411 / 1.40 ( 6) link_NAG-ASN : bond 0.00606 / 0.44 ( 29) link_NAG-ASN : angle 3.51461 / 2.69 ( 87) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 188 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.5963 (pmm-80) REVERT: A 983 ARG cc_start: 0.8525 (tmm-80) cc_final: 0.7835 (tmm-80) REVERT: B 904 TYR cc_start: 0.7841 (m-10) cc_final: 0.7320 (m-10) REVERT: B 981 PHE cc_start: 0.7707 (m-80) cc_final: 0.7486 (m-80) REVERT: C 106 PHE cc_start: 0.8466 (m-80) cc_final: 0.8168 (m-80) REVERT: C 177 MET cc_start: 0.8896 (ttt) cc_final: 0.7776 (mmp) REVERT: C 198 ASP cc_start: 0.8252 (p0) cc_final: 0.8039 (p0) REVERT: C 1107 ARG cc_start: 0.8089 (mtt180) cc_final: 0.7395 (mtt180) REVERT: Y 34 MET cc_start: 0.2290 (tpt) cc_final: 0.2003 (tpt) REVERT: Y 117 MET cc_start: 0.0710 (mpp) cc_final: -0.0131 (mtm) outliers start: 71 outliers final: 45 residues processed: 248 average time/residue: 0.1716 time to fit residues: 71.3567 Evaluate side-chains 212 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 166 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain Y residue 118 ASP Chi-restraints excluded: chain X residue 30 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 73 optimal weight: 1.9990 chunk 239 optimal weight: 0.8980 chunk 231 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 113 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 308 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 148 optimal weight: 7.9990 chunk 193 optimal weight: 6.9990 chunk 172 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 334 ASN A 580 GLN ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 35 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.143088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.097937 restraints weight = 75933.310| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 4.14 r_work: 0.3209 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 29288 Z= 0.132 Angle : 0.600 18.933 39938 Z= 0.294 Chirality : 0.045 0.280 4576 Planarity : 0.004 0.056 5108 Dihedral : 4.600 41.110 3895 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.56 % Allowed : 13.74 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % 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: -1.52 (0.14), residues: 3565 helix: 1.02 (0.20), residues: 733 sheet: -1.19 (0.17), residues: 903 loop : -1.76 (0.13), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 319 TYR 0.027 0.001 TYR Y 95 PHE 0.015 0.001 PHE C1121 TRP 0.024 0.002 TRP C 353 HIS 0.013 0.001 HIS P 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (29214) covalent geometry : angle 0.57645 / 0.29 (39759) SS BOND : bond 0.00253 / 0.17 ( 43) SS BOND : angle 1.05448 / 0.68 ( 86) hydrogen bonds : bond 0.04023 / 2.62 ( 1020) hydrogen bonds : angle 5.69204 / 3.89 ( 2811) link_BETA1-4 : bond 0.00681 / 0.36 ( 2) link_BETA1-4 : angle 2.61630 / 1.43 ( 6) link_NAG-ASN : bond 0.00585 / 0.43 ( 29) link_NAG-ASN : angle 3.40051 / 2.61 ( 87) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 184 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 316 SER cc_start: 0.9166 (t) cc_final: 0.8800 (m) REVERT: A 983 ARG cc_start: 0.8405 (tmm-80) cc_final: 0.7817 (tmm-80) REVERT: B 353 TRP cc_start: 0.2754 (p-90) cc_final: 0.1456 (p-90) REVERT: B 762 GLN cc_start: 0.8127 (mt0) cc_final: 0.7921 (mt0) REVERT: B 904 TYR cc_start: 0.7899 (m-10) cc_final: 0.7340 (m-10) REVERT: C 106 PHE cc_start: 0.8519 (m-80) cc_final: 0.8200 (m-80) REVERT: C 177 MET cc_start: 0.8913 (ttt) cc_final: 0.7750 (mmp) REVERT: C 353 TRP cc_start: 0.0522 (p-90) cc_final: -0.0392 (p-90) REVERT: C 1037 SER cc_start: 0.8846 (OUTLIER) cc_final: 0.8642 (p) REVERT: C 1107 ARG cc_start: 0.8240 (mtt180) cc_final: 0.7505 (mtt180) REVERT: P 83 MET cc_start: 0.3238 (OUTLIER) cc_final: 0.2704 (tmm) REVERT: Y 64 VAL cc_start: 0.3374 (t) cc_final: 0.2987 (m) REVERT: Y 98 LYS cc_start: 0.6708 (OUTLIER) cc_final: 0.6412 (tppt) REVERT: Y 117 MET cc_start: 0.0552 (mpp) cc_final: -0.0180 (mtm) outliers start: 79 outliers final: 48 residues processed: 249 average time/residue: 0.1661 time to fit residues: 70.1371 Evaluate side-chains 215 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 164 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain P residue 83 MET Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain Y residue 98 LYS Chi-restraints excluded: chain Y residue 118 ASP Chi-restraints excluded: chain X residue 30 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 343 optimal weight: 1.9990 chunk 279 optimal weight: 0.1980 chunk 88 optimal weight: 1.9990 chunk 206 optimal weight: 0.6980 chunk 215 optimal weight: 8.9990 chunk 335 optimal weight: 9.9990 chunk 321 optimal weight: 40.0000 chunk 178 optimal weight: 0.9980 chunk 191 optimal weight: 0.6980 chunk 288 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN P 39 GLN X 50 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.148150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.100555 restraints weight = 76663.905| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.41 r_work: 0.3245 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29288 Z= 0.117 Angle : 0.578 18.256 39938 Z= 0.284 Chirality : 0.044 0.270 4576 Planarity : 0.004 0.054 5108 Dihedral : 4.478 39.117 3895 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.69 % Allowed : 14.03 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.14), residues: 3565 helix: 1.17 (0.20), residues: 736 sheet: -1.00 (0.17), residues: 898 loop : -1.64 (0.13), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 237 TYR 0.024 0.001 TYR Y 95 PHE 0.024 0.001 PHE B 175 TRP 0.020 0.001 TRP O 40 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (29214) covalent geometry : angle 0.55599 / 0.28 (39759) SS BOND : bond 0.00383 / 0.22 ( 43) SS BOND : angle 1.17977 / 0.79 ( 86) hydrogen bonds : bond 0.03832 / 2.49 ( 1020) hydrogen bonds : angle 5.50704 / 3.77 ( 2811) link_BETA1-4 : bond 0.00715 / 0.37 ( 2) link_BETA1-4 : angle 2.32743 / 1.26 ( 6) link_NAG-ASN : bond 0.00573 / 0.43 ( 29) link_NAG-ASN : angle 3.23177 / 2.48 ( 87) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 183 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.5954 (pmm-80) REVERT: A 170 TYR cc_start: 0.7630 (t80) cc_final: 0.7370 (t80) REVERT: A 316 SER cc_start: 0.9086 (t) cc_final: 0.8733 (m) REVERT: A 498 ARG cc_start: 0.7331 (mmm-85) cc_final: 0.7043 (mmm-85) REVERT: B 353 TRP cc_start: 0.2789 (p-90) cc_final: 0.1425 (p-90) REVERT: B 981 PHE cc_start: 0.7682 (m-80) cc_final: 0.7476 (m-80) REVERT: C 106 PHE cc_start: 0.8449 (m-80) cc_final: 0.8191 (m-80) REVERT: C 177 MET cc_start: 0.8803 (ttt) cc_final: 0.7690 (mmp) REVERT: C 353 TRP cc_start: 0.0566 (p-90) cc_final: -0.0073 (p-90) REVERT: C 660 TYR cc_start: 0.8295 (OUTLIER) cc_final: 0.6263 (m-80) REVERT: Y 98 LYS cc_start: 0.6607 (OUTLIER) cc_final: 0.6098 (tppt) REVERT: Y 114 GLU cc_start: 0.2502 (tt0) cc_final: 0.1099 (pp20) REVERT: X 101 PHE cc_start: 0.7252 (m-10) cc_final: 0.5941 (m-10) outliers start: 83 outliers final: 55 residues processed: 255 average time/residue: 0.1604 time to fit residues: 70.4505 Evaluate side-chains 219 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 161 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain Y residue 98 LYS Chi-restraints excluded: chain Y residue 118 ASP Chi-restraints excluded: chain X residue 3 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 56 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 232 optimal weight: 7.9990 chunk 325 optimal weight: 50.0000 chunk 307 optimal weight: 0.3980 chunk 115 optimal weight: 0.0970 chunk 165 optimal weight: 5.9990 chunk 226 optimal weight: 4.9990 chunk 309 optimal weight: 8.9990 chunk 175 optimal weight: 3.9990 chunk 347 optimal weight: 8.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 GLN ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS B 271 GLN B 544 ASN C 134 GLN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN C 762 GLN O 31 HIS Y 35 HIS X 50 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.146879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.098839 restraints weight = 76664.281| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 3.42 r_work: 0.3194 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 29288 Z= 0.183 Angle : 0.620 18.221 39938 Z= 0.306 Chirality : 0.045 0.284 4576 Planarity : 0.004 0.052 5108 Dihedral : 4.600 37.712 3895 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.98 % Allowed : 14.61 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.32 (0.14), residues: 3565 helix: 1.10 (0.20), residues: 722 sheet: -0.94 (0.18), residues: 898 loop : -1.64 (0.13), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 457 TYR 0.022 0.001 TYR Y 95 PHE 0.023 0.001 PHE C1121 TRP 0.022 0.001 TRP O 40 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.18 (29214) covalent geometry : angle 0.59735 / 0.30 (39759) SS BOND : bond 0.00318 / 0.21 ( 43) SS BOND : angle 1.56019 / 1.19 ( 86) hydrogen bonds : bond 0.04165 / 2.72 ( 1020) hydrogen bonds : angle 5.58684 / 3.82 ( 2811) link_BETA1-4 : bond 0.00631 / 0.33 ( 2) link_BETA1-4 : angle 2.32074 / 1.26 ( 6) link_NAG-ASN : bond 0.00590 / 0.43 ( 29) link_NAG-ASN : angle 3.26548 / 2.50 ( 87) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 166 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.5932 (pmm-80) REVERT: A 170 TYR cc_start: 0.7697 (t80) cc_final: 0.7408 (t80) REVERT: A 197 ILE cc_start: 0.8843 (mm) cc_final: 0.8517 (pt) REVERT: A 316 SER cc_start: 0.9128 (t) cc_final: 0.8786 (m) REVERT: A 498 ARG cc_start: 0.7264 (mmm-85) cc_final: 0.7047 (mmm-85) REVERT: B 377 PHE cc_start: 0.5810 (OUTLIER) cc_final: 0.5208 (t80) REVERT: B 721 SER cc_start: 0.8892 (OUTLIER) cc_final: 0.8636 (p) REVERT: C 106 PHE cc_start: 0.8435 (m-80) cc_final: 0.8166 (m-80) REVERT: C 660 TYR cc_start: 0.8349 (OUTLIER) cc_final: 0.6280 (m-80) REVERT: Y 35 HIS cc_start: 0.3198 (m90) cc_final: 0.2514 (m-70) REVERT: Y 114 GLU cc_start: 0.2566 (tt0) cc_final: 0.1308 (pp20) REVERT: Y 117 MET cc_start: 0.0356 (mpp) cc_final: -0.0328 (mtm) REVERT: X 101 PHE cc_start: 0.7272 (m-10) cc_final: 0.5908 (m-10) outliers start: 92 outliers final: 67 residues processed: 243 average time/residue: 0.1582 time to fit residues: 67.1528 Evaluate side-chains 226 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 155 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 547 LYS Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain Y residue 118 ASP Chi-restraints excluded: chain X residue 3 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 143 optimal weight: 10.0000 chunk 208 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 300 optimal weight: 0.7980 chunk 357 optimal weight: 40.0000 chunk 13 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 24 optimal weight: 0.0030 chunk 197 optimal weight: 0.7980 chunk 173 optimal weight: 0.7980 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 GLN ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 HIS Y 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.148499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.100832 restraints weight = 76520.737| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 3.51 r_work: 0.3245 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29288 Z= 0.114 Angle : 0.575 17.595 39938 Z= 0.283 Chirality : 0.044 0.264 4576 Planarity : 0.004 0.049 5108 Dihedral : 4.431 38.346 3895 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.46 % Allowed : 15.58 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.14 (0.14), residues: 3565 helix: 1.27 (0.20), residues: 732 sheet: -0.82 (0.17), residues: 917 loop : -1.56 (0.14), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 38 TYR 0.023 0.001 TYR O 37 PHE 0.031 0.001 PHE P 68 TRP 0.047 0.002 TRP P 53 HIS 0.004 0.001 HIS O 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (29214) covalent geometry : angle 0.55500 / 0.28 (39759) SS BOND : bond 0.00230 / 0.15 ( 43) SS BOND : angle 1.19390 / 0.89 ( 86) hydrogen bonds : bond 0.03705 / 2.42 ( 1020) hydrogen bonds : angle 5.35729 / 3.67 ( 2811) link_BETA1-4 : bond 0.00610 / 0.32 ( 2) link_BETA1-4 : angle 2.21988 / 1.20 ( 6) link_NAG-ASN : bond 0.00566 / 0.43 ( 29) link_NAG-ASN : angle 3.07838 / 2.37 ( 87) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 175 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.5959 (pmm-80) REVERT: A 170 TYR cc_start: 0.7696 (t80) cc_final: 0.7374 (t80) REVERT: A 197 ILE cc_start: 0.8820 (mm) cc_final: 0.8516 (pt) REVERT: A 316 SER cc_start: 0.9093 (t) cc_final: 0.8767 (m) REVERT: A 498 ARG cc_start: 0.7370 (mmm-85) cc_final: 0.7126 (mmm-85) REVERT: A 983 ARG cc_start: 0.8471 (tmm-80) cc_final: 0.8267 (tmm-80) REVERT: B 353 TRP cc_start: 0.2688 (p-90) cc_final: 0.0987 (p-90) REVERT: B 377 PHE cc_start: 0.5847 (OUTLIER) cc_final: 0.5222 (t80) REVERT: B 721 SER cc_start: 0.8882 (OUTLIER) cc_final: 0.8627 (p) REVERT: C 134 GLN cc_start: 0.8039 (tp40) cc_final: 0.7639 (tp40) REVERT: C 353 TRP cc_start: 0.0738 (p-90) cc_final: -0.0427 (p-90) REVERT: C 660 TYR cc_start: 0.8297 (OUTLIER) cc_final: 0.6224 (m-80) REVERT: P 64 VAL cc_start: 0.3222 (p) cc_final: 0.2944 (t) REVERT: Y 35 HIS cc_start: 0.3304 (m90) cc_final: 0.2901 (m-70) REVERT: Y 98 LYS cc_start: 0.6629 (OUTLIER) cc_final: 0.6190 (tppt) REVERT: Y 117 MET cc_start: 0.0772 (mpp) cc_final: 0.0066 (mtm) outliers start: 76 outliers final: 54 residues processed: 237 average time/residue: 0.1632 time to fit residues: 66.9907 Evaluate side-chains 221 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 162 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 95 GLN Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 98 LYS Chi-restraints excluded: chain Y residue 118 ASP Chi-restraints excluded: chain X residue 3 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 132 optimal weight: 30.0000 chunk 235 optimal weight: 0.3980 chunk 305 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 chunk 326 optimal weight: 20.0000 chunk 266 optimal weight: 4.9990 chunk 275 optimal weight: 0.0980 chunk 224 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 268 optimal weight: 5.9990 chunk 218 optimal weight: 7.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B 317 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.147257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.100956 restraints weight = 76459.872| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 3.78 r_work: 0.3195 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29288 Z= 0.153 Angle : 0.597 17.598 39938 Z= 0.294 Chirality : 0.045 0.280 4576 Planarity : 0.004 0.049 5108 Dihedral : 4.498 36.830 3895 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.69 % Allowed : 15.55 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.15 (0.14), residues: 3565 helix: 1.21 (0.20), residues: 724 sheet: -0.81 (0.17), residues: 908 loop : -1.54 (0.14), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 905 TYR 0.019 0.001 TYR Y 95 PHE 0.035 0.001 PHE X 101 TRP 0.030 0.002 TRP P 53 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (29214) covalent geometry : angle 0.57690 / 0.29 (39759) SS BOND : bond 0.00251 / 0.17 ( 43) SS BOND : angle 1.29273 / 0.92 ( 86) hydrogen bonds : bond 0.03968 / 2.58 ( 1020) hydrogen bonds : angle 5.39054 / 3.69 ( 2811) link_BETA1-4 : bond 0.00627 / 0.33 ( 2) link_BETA1-4 : angle 2.25015 / 1.22 ( 6) link_NAG-ASN : bond 0.00563 / 0.42 ( 29) link_NAG-ASN : angle 3.10521 / 2.39 ( 87) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 163 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.5955 (pmm-80) REVERT: A 197 ILE cc_start: 0.8827 (mm) cc_final: 0.8514 (pt) REVERT: A 316 SER cc_start: 0.9158 (t) cc_final: 0.8826 (m) REVERT: A 390 LEU cc_start: 0.8590 (tp) cc_final: 0.8228 (tp) REVERT: A 498 ARG cc_start: 0.7369 (mmm-85) cc_final: 0.7139 (mmm-85) REVERT: A 1010 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.8120 (mp10) REVERT: B 377 PHE cc_start: 0.5902 (OUTLIER) cc_final: 0.5332 (t80) REVERT: B 721 SER cc_start: 0.8912 (OUTLIER) cc_final: 0.8638 (p) REVERT: C 106 PHE cc_start: 0.8476 (m-80) cc_final: 0.8205 (m-80) REVERT: C 134 GLN cc_start: 0.7932 (tp40) cc_final: 0.7552 (tp40) REVERT: C 353 TRP cc_start: 0.0830 (p-90) cc_final: -0.0356 (p-90) REVERT: C 660 TYR cc_start: 0.8339 (OUTLIER) cc_final: 0.6386 (m-80) REVERT: P 64 VAL cc_start: 0.3489 (p) cc_final: 0.3229 (t) REVERT: Y 114 GLU cc_start: 0.2335 (tt0) cc_final: 0.1094 (pp20) outliers start: 83 outliers final: 67 residues processed: 235 average time/residue: 0.1613 time to fit residues: 65.4782 Evaluate side-chains 227 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 155 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 95 GLN Chi-restraints excluded: chain Y residue 51 VAL Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 118 ASP Chi-restraints excluded: chain X residue 3 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 86 optimal weight: 0.9980 chunk 349 optimal weight: 0.0170 chunk 271 optimal weight: 0.6980 chunk 297 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 172 optimal weight: 0.9990 chunk 291 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 159 optimal weight: 0.0570 chunk 78 optimal weight: 0.7980 chunk 141 optimal weight: 20.0000 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN A1119 ASN B 321 GLN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 HIS O 95 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.148414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.103731 restraints weight = 76469.183| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 3.65 r_work: 0.3260 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 29288 Z= 0.102 Angle : 0.573 17.067 39938 Z= 0.281 Chirality : 0.044 0.268 4576 Planarity : 0.004 0.062 5108 Dihedral : 4.359 37.275 3895 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.33 % Allowed : 16.03 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.99 (0.14), residues: 3565 helix: 1.40 (0.20), residues: 721 sheet: -0.68 (0.17), residues: 920 loop : -1.48 (0.14), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 319 TYR 0.019 0.001 TYR Y 95 PHE 0.029 0.001 PHE X 101 TRP 0.026 0.001 TRP P 53 HIS 0.004 0.001 HIS Y 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (29214) covalent geometry : angle 0.55390 / 0.28 (39759) SS BOND : bond 0.00192 / 0.13 ( 43) SS BOND : angle 1.09004 / 0.78 ( 86) hydrogen bonds : bond 0.03624 / 2.36 ( 1020) hydrogen bonds : angle 5.23411 / 3.58 ( 2811) link_BETA1-4 : bond 0.00581 / 0.30 ( 2) link_BETA1-4 : angle 2.13458 / 1.16 ( 6) link_NAG-ASN : bond 0.00570 / 0.43 ( 29) link_NAG-ASN : angle 2.98125 / 2.30 ( 87) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 169 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.5935 (pmm-80) REVERT: A 197 ILE cc_start: 0.8821 (mm) cc_final: 0.8609 (pt) REVERT: A 316 SER cc_start: 0.9122 (t) cc_final: 0.8782 (m) REVERT: A 498 ARG cc_start: 0.7400 (mmm-85) cc_final: 0.7160 (mmm-85) REVERT: B 86 PHE cc_start: 0.4968 (t80) cc_final: 0.4583 (t80) REVERT: B 106 PHE cc_start: 0.7979 (m-80) cc_final: 0.7756 (m-80) REVERT: B 353 TRP cc_start: 0.2749 (p-90) cc_final: 0.0917 (p-90) REVERT: B 377 PHE cc_start: 0.5879 (OUTLIER) cc_final: 0.5296 (t80) REVERT: B 721 SER cc_start: 0.8878 (OUTLIER) cc_final: 0.8650 (p) REVERT: B 981 PHE cc_start: 0.7875 (m-80) cc_final: 0.7671 (m-80) REVERT: C 106 PHE cc_start: 0.8467 (m-80) cc_final: 0.8220 (m-80) REVERT: C 134 GLN cc_start: 0.7975 (tp40) cc_final: 0.7603 (tp40) REVERT: C 177 MET cc_start: 0.8730 (ttt) cc_final: 0.7619 (mmp) REVERT: C 353 TRP cc_start: 0.0826 (p-90) cc_final: -0.0287 (p-90) REVERT: C 495 TYR cc_start: 0.0500 (OUTLIER) cc_final: 0.0140 (m-10) REVERT: C 559 PHE cc_start: 0.6844 (OUTLIER) cc_final: 0.6142 (t80) REVERT: C 660 TYR cc_start: 0.8287 (OUTLIER) cc_final: 0.6332 (m-80) REVERT: P 64 VAL cc_start: 0.3235 (p) cc_final: 0.2927 (t) REVERT: P 117 MET cc_start: 0.4088 (tpt) cc_final: 0.3841 (tpp) REVERT: Y 114 GLU cc_start: 0.2283 (tt0) cc_final: 0.1082 (pp20) outliers start: 72 outliers final: 58 residues processed: 231 average time/residue: 0.1576 time to fit residues: 63.6026 Evaluate side-chains 222 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 158 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 118 ASP Chi-restraints excluded: chain X residue 3 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 297 optimal weight: 6.9990 chunk 150 optimal weight: 8.9990 chunk 296 optimal weight: 2.9990 chunk 250 optimal weight: 0.0970 chunk 31 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 359 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 chunk 167 optimal weight: 0.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN A1106 GLN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 98 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 = 0.4323 r_free = 0.4323 target = 0.143118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.097158 restraints weight = 75346.628| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 3.78 r_work: 0.3227 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29288 Z= 0.139 Angle : 0.589 17.217 39938 Z= 0.290 Chirality : 0.045 0.278 4576 Planarity : 0.004 0.058 5108 Dihedral : 4.387 36.276 3895 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.07 % Allowed : 16.33 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.02 (0.14), residues: 3565 helix: 1.24 (0.20), residues: 734 sheet: -0.66 (0.17), residues: 915 loop : -1.48 (0.14), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 319 TYR 0.018 0.001 TYR Y 95 PHE 0.027 0.001 PHE X 101 TRP 0.026 0.001 TRP P 36 HIS 0.003 0.001 HIS Y 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (29214) covalent geometry : angle 0.56982 / 0.29 (39759) SS BOND : bond 0.00240 / 0.17 ( 43) SS BOND : angle 1.16901 / 0.85 ( 86) hydrogen bonds : bond 0.03815 / 2.48 ( 1020) hydrogen bonds : angle 5.26156 / 3.60 ( 2811) link_BETA1-4 : bond 0.00620 / 0.32 ( 2) link_BETA1-4 : angle 2.17544 / 1.18 ( 6) link_NAG-ASN : bond 0.00551 / 0.42 ( 29) link_NAG-ASN : angle 2.99492 / 2.31 ( 87) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 160 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.5917 (pmm-80) REVERT: A 316 SER cc_start: 0.9133 (t) cc_final: 0.8799 (m) REVERT: A 498 ARG cc_start: 0.7388 (mmm-85) cc_final: 0.7158 (mmm-85) REVERT: B 86 PHE cc_start: 0.5043 (t80) cc_final: 0.4647 (t80) REVERT: B 106 PHE cc_start: 0.8012 (m-80) cc_final: 0.7732 (m-80) REVERT: B 353 TRP cc_start: 0.2695 (p-90) cc_final: 0.1045 (p-90) REVERT: B 377 PHE cc_start: 0.5927 (OUTLIER) cc_final: 0.5443 (t80) REVERT: B 721 SER cc_start: 0.8877 (OUTLIER) cc_final: 0.8674 (p) REVERT: B 981 PHE cc_start: 0.7856 (m-80) cc_final: 0.7652 (m-80) REVERT: C 106 PHE cc_start: 0.8460 (m-80) cc_final: 0.8206 (m-80) REVERT: C 177 MET cc_start: 0.8765 (ttt) cc_final: 0.7633 (mmp) REVERT: C 495 TYR cc_start: 0.0178 (OUTLIER) cc_final: -0.0137 (m-10) REVERT: C 559 PHE cc_start: 0.6969 (OUTLIER) cc_final: 0.6278 (t80) REVERT: C 660 TYR cc_start: 0.8296 (OUTLIER) cc_final: 0.6329 (m-80) REVERT: P 64 VAL cc_start: 0.3944 (p) cc_final: 0.3706 (t) REVERT: P 117 MET cc_start: 0.4190 (tpt) cc_final: 0.3676 (tpp) REVERT: Y 114 GLU cc_start: 0.2246 (tt0) cc_final: 0.0989 (pp20) outliers start: 64 outliers final: 57 residues processed: 215 average time/residue: 0.1536 time to fit residues: 57.8680 Evaluate side-chains 219 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 156 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain Y residue 51 VAL Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 118 ASP Chi-restraints excluded: chain X residue 3 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 243 optimal weight: 5.9990 chunk 162 optimal weight: 7.9990 chunk 272 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 123 optimal weight: 6.9990 chunk 220 optimal weight: 20.0000 chunk 260 optimal weight: 10.0000 chunk 275 optimal weight: 4.9990 chunk 186 optimal weight: 0.7980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.143188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.097574 restraints weight = 75759.859| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 3.89 r_work: 0.3206 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29288 Z= 0.127 Angle : 0.580 16.957 39938 Z= 0.285 Chirality : 0.045 0.273 4576 Planarity : 0.004 0.054 5108 Dihedral : 4.348 36.037 3895 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.30 % Allowed : 16.29 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.93 (0.14), residues: 3565 helix: 1.36 (0.20), residues: 727 sheet: -0.61 (0.18), residues: 914 loop : -1.43 (0.14), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 319 TYR 0.018 0.001 TYR Y 95 PHE 0.024 0.001 PHE X 101 TRP 0.035 0.002 TRP C 353 HIS 0.003 0.001 HIS Y 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (29214) covalent geometry : angle 0.56213 / 0.28 (39759) SS BOND : bond 0.00218 / 0.15 ( 43) SS BOND : angle 1.11366 / 0.81 ( 86) hydrogen bonds : bond 0.03725 / 2.42 ( 1020) hydrogen bonds : angle 5.20382 / 3.57 ( 2811) link_BETA1-4 : bond 0.00639 / 0.33 ( 2) link_BETA1-4 : angle 2.15686 / 1.16 ( 6) link_NAG-ASN : bond 0.00538 / 0.41 ( 29) link_NAG-ASN : angle 2.93601 / 2.28 ( 87) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8379.01 seconds wall clock time: 143 minutes 53.95 seconds (8633.95 seconds total)