Starting phenix.real_space_refine on Sun Sep 13 20:15:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mao_63757/09_2026/9mao_63757.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mao_63757/09_2026/9mao_63757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mao_63757/09_2026/9mao_63757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mao_63757/09_2026/9mao_63757.map" model { file = "/net/cci-nas-00/data/ceres_data/9mao_63757/09_2026/9mao_63757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mao_63757/09_2026/9mao_63757.cif" } resolution = 3.09 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= -0.005 sd= 0.530 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 112 5.16 5 C 15756 2.51 5 N 4051 2.21 5 O 4822 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 156 residue(s): 0.03s 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: 24741 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 7922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 7922 Classifications: {'peptide': 1029} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 55, 'TRANS': 973} Chain breaks: 7 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 2, 'TYR:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'PHE:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 88 Chain: "B" Number of atoms: 8116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8116 Classifications: {'peptide': 1048} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 57, 'TRANS': 990} Chain breaks: 7 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'PHE:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 50 Chain: "A" Number of atoms: 7968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 7968 Classifications: {'peptide': 1027} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 55, 'TRANS': 971} Chain breaks: 7 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 5, 'GLN:plan1': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 189 Classifications: {'peptide': 26} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 25} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 5.57, per 1000 atoms: 0.23 Number of scatterers: 24741 At special positions: 0 Unit cell: (144.46, 138.868, 185.468, 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 112 16.00 O 4822 8.00 N 4051 7.00 C 15756 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 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=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 14 " - pdb=" SG CYS D 34 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A 717 " " NAG A1309 " - " ASN A 801 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A1098 " " NAG A1312 " - " ASN A1134 " " NAG B1301 " - " ASN B 165 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B 717 " " NAG B1310 " - " ASN B 801 " " NAG B1311 " - " ASN B1074 " " NAG B1312 " - " ASN B1098 " " NAG B1313 " - " ASN B1134 " " NAG B1314 " - " ASN B 17 " " NAG C1301 " - " ASN C 234 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C 717 " " NAG C1309 " - " ASN C 801 " " NAG C1310 " - " ASN C1074 " " NAG C1311 " - " ASN C1098 " " NAG C1312 " - " ASN C1134 " " NAG C1313 " - " ASN C 17 " Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 933.1 milliseconds 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5874 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 45 sheets defined 24.7% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.711A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 370' Processing helix chain 'C' and resid 383 through 388 removed outlier: 4.239A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.881A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.672A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 627 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 752 through 756 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 811 through 815 removed outlier: 3.583A pdb=" N LYS C 814 " --> pdb=" O LYS C 811 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG C 815 " --> pdb=" O PRO C 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 811 through 815' Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 850 through 855 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.938A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.529A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.006A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.567A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 384 through 390 removed outlier: 3.700A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.122A 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 502 through 506 removed outlier: 3.645A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 571 No H-bonds generated for 'chain 'B' and resid 569 through 571' Processing helix chain 'B' and resid 623 through 627 removed outlier: 3.645A pdb=" N ALA B 626 " --> pdb=" O ALA B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 752 through 757 removed outlier: 3.590A pdb=" N GLY B 757 " --> pdb=" O LEU B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 811 through 815 removed outlier: 3.620A pdb=" N LYS B 814 " --> pdb=" O LYS B 811 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 811 through 815' Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 850 through 856 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.902A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.014A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.540A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.846A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (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 1033 removed outlier: 4.921A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.934A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.739A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 404 through 408 removed outlier: 3.653A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.814A pdb=" N TYR A 505 " --> pdb=" O GLY A 502 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 502 through 506' Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 752 through 757 removed outlier: 3.941A pdb=" N GLY A 757 " --> pdb=" O LEU A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.821A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 850 through 855 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.881A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.954A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.765A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 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 984 Processing helix chain 'A' and resid 985 through 1033 Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 30 removed outlier: 6.604A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N TRP C 64 " --> pdb=" O ALA C 27 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 48 through 51 removed outlier: 3.805A pdb=" N VAL C 289 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.531A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 313 through 316 removed outlier: 7.222A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 357 through 358 removed outlier: 3.862A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 399 through 402 Processing sheet with id=AA7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'C' and resid 539 through 543 removed outlier: 3.625A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR C 572 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.003A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 702 through 703 Processing sheet with id=AB2, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AB3, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.052A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'C' and resid 787 through 790 Processing sheet with id=AB6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.857A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.042A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.921A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.123A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.560A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.560A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 313 through 314 Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.315A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.788A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR B 508 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 642 through 645 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.284A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 714 removed outlier: 3.505A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.335A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 788 through 790 removed outlier: 5.826A pdb=" N ILE B 788 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.138A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLY A 89 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.138A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLY A 89 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 106 through 107 Processing sheet with id=AD8, first strand: chain 'A' and resid 116 through 120 removed outlier: 3.877A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 313 through 314 removed outlier: 3.749A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.590A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AE3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'A' and resid 539 through 543 removed outlier: 3.602A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.097A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.221A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.221A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.541A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 1120 through 1122 871 hydrogen bonds defined for protein. 2421 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.17 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7921 1.34 - 1.46: 6045 1.46 - 1.58: 11189 1.58 - 1.70: 0 1.70 - 1.82: 136 Bond restraints: 25291 Sorted by residual: bond pdb=" C1 NAG A1305 " pdb=" O5 NAG A1305 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" C1 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.27e+00 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.20e+00 bond pdb=" C1 NAG C1313 " pdb=" O5 NAG C1313 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.18e+00 bond pdb=" C1 NAG B1311 " pdb=" O5 NAG B1311 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.14e+00 ... (remaining 25286 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 33571 1.34 - 2.69: 738 2.69 - 4.03: 143 4.03 - 5.37: 9 5.37 - 6.72: 5 Bond angle restraints: 34466 Sorted by residual: angle pdb=" C LEU B 18 " pdb=" N THR B 19 " pdb=" CA THR B 19 " ideal model delta sigma weight residual 121.54 126.31 -4.77 1.91e+00 2.74e-01 6.23e+00 angle pdb=" N GLY A 476 " pdb=" CA GLY A 476 " pdb=" C GLY A 476 " ideal model delta sigma weight residual 113.18 107.42 5.76 2.37e+00 1.78e-01 5.90e+00 angle pdb=" C GLN A 239 " pdb=" N THR A 240 " pdb=" CA THR A 240 " ideal model delta sigma weight residual 121.54 126.15 -4.61 1.91e+00 2.74e-01 5.83e+00 angle pdb=" C ALA B 123 " pdb=" N THR B 124 " pdb=" CA THR B 124 " ideal model delta sigma weight residual 121.54 125.95 -4.41 1.91e+00 2.74e-01 5.33e+00 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 113.26 -2.56 1.22e+00 6.72e-01 4.39e+00 ... (remaining 34461 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.28: 14821 14.28 - 28.56: 588 28.56 - 42.84: 134 42.84 - 57.13: 33 57.13 - 71.41: 7 Dihedral angle restraints: 15583 sinusoidal: 6471 harmonic: 9112 Sorted by residual: dihedral pdb=" CA GLY A 476 " pdb=" C GLY A 476 " pdb=" N SER A 477 " pdb=" CA SER A 477 " ideal model delta harmonic sigma weight residual -180.00 -157.20 -22.80 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -119.40 33.40 1 1.00e+01 1.00e-02 1.59e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 123.23 -30.23 1 1.00e+01 1.00e-02 1.31e+01 ... (remaining 15580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2530 0.029 - 0.058: 919 0.058 - 0.087: 266 0.087 - 0.116: 329 0.116 - 0.144: 26 Chirality restraints: 4070 Sorted by residual: chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" C1 NAG C1310 " pdb=" ND2 ASN C1074 " pdb=" C2 NAG C1310 " pdb=" O5 NAG C1310 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CB ILE C 233 " pdb=" CA ILE C 233 " pdb=" CG1 ILE C 233 " pdb=" CG2 ILE C 233 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 4067 not shown) Planarity restraints: 4464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 336 " 0.028 5.00e-02 4.00e+02 4.18e-02 2.80e+00 pdb=" N PRO A 337 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 337 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 337 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 898 " -0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO C 899 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 899 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 899 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 898 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO B 899 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 899 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 899 " -0.018 5.00e-02 4.00e+02 ... (remaining 4461 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4313 2.77 - 3.30: 23687 3.30 - 3.84: 39796 3.84 - 4.37: 45880 4.37 - 4.90: 80617 Nonbonded interactions: 194293 Sorted by model distance: nonbonded pdb=" OG SER B 975 " pdb=" OD2 ASP A 571 " model vdw 2.240 3.040 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.243 3.040 nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.250 3.040 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.251 3.040 nonbonded pdb=" OG SER C 884 " pdb=" OG1 THR C 887 " model vdw 2.254 3.040 ... (remaining 194288 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 29 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 65 or (resid 78 through 79 and (na \ me N or name CA or name C or name O or name CB )) or resid 80 through 128 or (re \ sid 129 and (name N or name CA or name C or name O or name CB )) or resid 130 th \ rough 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) \ or resid 133 through 157 or (resid 158 and (name N or name CA or name C or name \ O or name CB )) or resid 159 through 163 or (resid 164 through 165 and (name N \ or name CA or name C or name O or name CB )) or resid 166 through 172 or resid 1 \ 86 or (resid 187 and (name N or name CA or name C or name O or name CB )) or res \ id 188 through 196 or (resid 197 and (name N or name CA or name C or name O or n \ ame CB )) or resid 198 through 199 or (resid 200 and (name N or name CA or name \ C or name O or name CB )) or resid 201 through 339 or (resid 340 and (name N or \ name CA or name C or name O or name CB )) or resid 341 through 352 or (resid 353 \ and (name N or name CA or name C or name O or name CB )) or resid 354 or (resid \ 355 and (name N or name CA or name C or name O or name CB )) or resid 356 throu \ gh 364 or (resid 365 and (name N or name CA or name C or name O or name CB )) or \ resid 366 through 376 or (resid 377 through 378 and (name N or name CA or name \ C or name O or name CB )) or resid 379 through 440 or (resid 441 and (name N or \ name CA or name C or name O or name CB )) or resid 442 through 457 or (resid 458 \ and (name N or name CA or name C or name O or name CB )) or resid 459 through 4 \ 65 or (resid 466 through 468 and (name N or name CA or name C or name O or name \ CB )) or resid 469 through 518 or (resid 519 through 520 and (name N or name CA \ or name C or name O or name CB )) or resid 521 through 556 or (resid 557 through \ 560 and (name N or name CA or name C or name O or name CB )) or resid 561 throu \ gh 563 or (resid 564 and (name N or name CA or name C or name O or name CB )) or \ resid 565 through 582 or (resid 583 and (name N or name CA or name C or name O \ or name CB )) or resid 584 through 618 or (resid 619 and (name N or name CA or n \ ame C or name O or name CB )) or resid 620 through 628 or resid 640 through 676 \ or (resid 677 and (name N or name CA or name C or name O or name CB )) or resid \ 689 through 1091 or (resid 1092 and (name N or name CA or name C or name O or na \ me CB )) or resid 1093 through 1312)) selection = (chain 'B' and (resid 29 through 65 or resid 78 through 95 or resid 99 through 1 \ 04 or (resid 105 and (name N or name CA or name C or name O or name CB )) or res \ id 106 through 128 or (resid 129 and (name N or name CA or name C or name O or n \ ame CB )) or resid 130 through 131 or (resid 132 and (name N or name CA or name \ C or name O or name CB )) or resid 133 through 157 or (resid 158 and (name N or \ name CA or name C or name O or name CB )) or resid 159 through 163 or (resid 164 \ through 165 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 66 through 172 or resid 186 through 189 or (resid 190 and (name N or name CA or \ name C or name O or name CB )) or resid 191 through 196 or (resid 197 and (name \ N or name CA or name C or name O or name CB )) or resid 198 through 236 or (resi \ d 237 and (name N or name CA or name C or name O or name CB )) or resid 238 or ( \ resid 239 and (name N or name CA or name C or name O or name CB )) or resid 240 \ through 243 or resid 264 through 352 or (resid 353 and (name N or name CA or nam \ e C or name O or name CB )) or resid 354 or (resid 355 and (name N or name CA or \ name C or name O or name CB )) or resid 356 through 364 or (resid 365 and (name \ N or name CA or name C or name O or name CB )) or resid 366 through 376 or (res \ id 377 through 378 and (name N or name CA or name C or name O or name CB )) or r \ esid 379 through 414 or (resid 415 and (name N or name CA or name C or name O or \ name CB )) or resid 416 or (resid 417 and (name N or name CA or name C or name \ O or name CB )) or resid 418 through 440 or (resid 441 and (name N or name CA or \ name C or name O or name CB )) or resid 442 through 457 or (resid 458 and (name \ N or name CA or name C or name O or name CB )) or resid 459 through 465 or (res \ id 466 through 468 and (name N or name CA or name C or name O or name CB )) or r \ esid 469 through 473 or (resid 474 through 475 and (name N or name CA or name C \ or name O or name CB )) or resid 476 through 483 or (resid 484 and (name N or na \ me CA or name C or name O or name CB )) or resid 485 through 492 or (resid 493 a \ nd (name N or name CA or name C or name O or name CB )) or resid 494 through 557 \ or (resid 558 through 560 and (name N or name CA or name C or name O or name CB \ )) or resid 561 through 563 or (resid 564 and (name N or name CA or name C or n \ ame O or name CB )) or resid 565 through 582 or (resid 583 and (name N or name C \ A or name C or name O or name CB )) or resid 584 through 618 or (resid 619 and ( \ name N or name CA or name C or name O or name CB )) or resid 620 through 623 or \ (resid 624 and (name N or name CA or name C or name O or name CB )) or resid 625 \ through 1091 or (resid 1092 and (name N or name CA or name C or name O or name \ CB )) or resid 1093 through 1312)) selection = (chain 'C' and (resid 29 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 65 or (resid 78 through 79 and (na \ me N or name CA or name C or name O or name CB )) or resid 80 through 95 or resi \ d 99 through 104 or (resid 105 and (name N or name CA or name C or name O or nam \ e CB )) or resid 106 through 186 or (resid 187 and (name N or name CA or name C \ or name O or name CB )) or resid 188 through 189 or (resid 190 and (name N or na \ me CA or name C or name O or name CB )) or resid 191 through 199 or (resid 200 a \ nd (name N or name CA or name C or name O or name CB )) or resid 201 through 236 \ or (resid 237 and (name N or name CA or name C or name O or name CB )) or resid \ 238 or (resid 239 and (name N or name CA or name C or name O or name CB )) or r \ esid 240 through 339 or (resid 340 and (name N or name CA or name C or name O or \ name CB )) or resid 341 through 345 or (resid 346 and (name N or name CA or nam \ e C or name O or name CB )) or resid 347 through 377 or (resid 378 and (name N o \ r name CA or name C or name O or name CB )) or resid 379 through 402 or (resid 4 \ 03 and (name N or name CA or name C or name O or name CB )) or resid 404 through \ 414 or (resid 415 and (name N or name CA or name C or name O or name CB )) or r \ esid 416 or (resid 417 and (name N or name CA or name C or name O or name CB )) \ or resid 418 through 473 or (resid 474 through 475 and (name N or name CA or nam \ e C or name O or name CB )) or resid 476 through 483 or (resid 484 and (name N o \ r name CA or name C or name O or name CB )) or resid 485 through 492 or (resid 4 \ 93 and (name N or name CA or name C or name O or name CB )) or resid 494 through \ 518 or (resid 519 through 520 and (name N or name CA or name C or name O or nam \ e CB )) or resid 521 through 557 or (resid 558 through 560 and (name N or name C \ A or name C or name O or name CB )) or resid 561 through 623 or (resid 624 and ( \ name N or name CA or name C or name O or name CB )) or resid 625 through 676 or \ (resid 677 and (name N or name CA or name C or name O or name CB )) or resid 689 \ through 1312)) } 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: 3.460 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 24.780 Find NCS groups from input model: 0.680 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: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 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 : 0.002 0.031 25370 Z= 0.126 Angle : 0.461 6.718 34663 Z= 0.234 Chirality : 0.042 0.144 4070 Planarity : 0.003 0.042 4425 Dihedral : 8.120 71.407 9589 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 1.75 % Allowed : 5.28 % Favored : 92.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.13), residues: 3080 helix: 0.80 (0.20), residues: 619 sheet: -1.21 (0.21), residues: 541 loop : -2.78 (0.12), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1014 TYR 0.007 0.001 TYR A 904 PHE 0.016 0.001 PHE A 592 TRP 0.007 0.000 TRP A 436 HIS 0.003 0.000 HIS B 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.13 (25291) covalent geometry : angle 0.45853 / 0.23 (34466) SS BOND : bond 0.00139 / 0.09 ( 40) SS BOND : angle 0.55736 / 0.41 ( 80) hydrogen bonds : bond 0.19898 / 13.01 ( 846) hydrogen bonds : angle 7.92419 / 5.28 ( 2421) link_NAG-ASN : bond 0.00185 / 0.12 ( 39) link_NAG-ASN : angle 0.93329 / 0.64 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 552 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 99 ASN cc_start: 0.6911 (t0) cc_final: 0.6692 (t0) REVERT: C 206 LYS cc_start: 0.8435 (tppt) cc_final: 0.7333 (tppt) REVERT: C 370 ASN cc_start: 0.7314 (p0) cc_final: 0.7067 (p0) REVERT: B 54 LEU cc_start: 0.7926 (mp) cc_final: 0.7383 (mp) REVERT: B 265 TYR cc_start: 0.6647 (t80) cc_final: 0.6217 (t80) REVERT: B 456 PHE cc_start: 0.7156 (m-80) cc_final: 0.6809 (m-80) REVERT: B 515 PHE cc_start: 0.8488 (m-80) cc_final: 0.8200 (m-80) REVERT: A 551 VAL cc_start: 0.8549 (t) cc_final: 0.8328 (m) REVERT: A 559 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.8001 (m-80) REVERT: A 1010 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.6965 (mp10) REVERT: A 1138 TYR cc_start: 0.8395 (m-80) cc_final: 0.8102 (m-80) outliers start: 47 outliers final: 13 residues processed: 589 average time/residue: 0.1854 time to fit residues: 167.9460 Evaluate side-chains 388 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 373 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1010 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.1980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN C 677 GLN C 755 GLN C 853 GLN C 907 ASN C1011 GLN C1071 GLN B 52 GLN B 188 ASN B 271 GLN B 448 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B 556 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 628 GLN B 755 GLN B 762 GLN B 853 GLN B 913 GLN B 925 ASN B 957 GLN B1002 GLN B1011 GLN B1071 GLN A 196 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN A 506 GLN A 536 ASN A 563 GLN A 628 GLN A 641 ASN A 677 GLN A 755 GLN A 853 GLN A 969 ASN A1005 GLN A1071 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.089464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.063684 restraints weight = 66462.344| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.84 r_work: 0.2812 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 25370 Z= 0.226 Angle : 0.699 10.274 34663 Z= 0.360 Chirality : 0.048 0.225 4070 Planarity : 0.005 0.047 4425 Dihedral : 6.570 59.231 4179 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.75 % Allowed : 10.19 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.14), residues: 3080 helix: 1.72 (0.21), residues: 619 sheet: -0.57 (0.21), residues: 517 loop : -2.46 (0.12), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 328 TYR 0.030 0.002 TYR C 674 PHE 0.028 0.003 PHE B 559 TRP 0.021 0.002 TRP C 436 HIS 0.009 0.002 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.23 (25291) covalent geometry : angle 0.68700 / 0.36 (34466) SS BOND : bond 0.00907 / 0.43 ( 40) SS BOND : angle 2.02447 / 1.30 ( 80) hydrogen bonds : bond 0.05749 / 3.80 ( 846) hydrogen bonds : angle 5.95341 / 4.02 ( 2421) link_NAG-ASN : bond 0.00467 / 0.32 ( 39) link_NAG-ASN : angle 1.74010 / 1.15 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 392 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 52 GLN cc_start: 0.7987 (tp40) cc_final: 0.7769 (tm-30) REVERT: C 206 LYS cc_start: 0.8839 (tppt) cc_final: 0.8572 (tppp) REVERT: C 224 GLU cc_start: 0.8684 (mp0) cc_final: 0.8390 (pm20) REVERT: C 480 CYS cc_start: 0.6424 (OUTLIER) cc_final: 0.5621 (m) REVERT: C 573 THR cc_start: 0.8244 (OUTLIER) cc_final: 0.8039 (m) REVERT: B 237 ARG cc_start: 0.8123 (ttt180) cc_final: 0.7909 (ttp80) REVERT: B 265 TYR cc_start: 0.7429 (t80) cc_final: 0.7148 (t80) REVERT: B 269 TYR cc_start: 0.8763 (m-80) cc_final: 0.8466 (m-80) REVERT: B 309 GLU cc_start: 0.8680 (mp0) cc_final: 0.8449 (mp0) REVERT: B 453 TYR cc_start: 0.7489 (p90) cc_final: 0.6974 (p90) REVERT: B 565 PHE cc_start: 0.6298 (m-80) cc_final: 0.5982 (m-10) REVERT: B 823 PHE cc_start: 0.8512 (m-80) cc_final: 0.8175 (t80) REVERT: B 943 SER cc_start: 0.8089 (p) cc_final: 0.7812 (t) REVERT: A 80 ASP cc_start: 0.5851 (p0) cc_final: 0.5611 (p0) REVERT: A 456 PHE cc_start: 0.7932 (m-80) cc_final: 0.7294 (m-80) REVERT: A 460 ASN cc_start: 0.8548 (m-40) cc_final: 0.8270 (m-40) REVERT: A 1010 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7453 (mp10) outliers start: 74 outliers final: 37 residues processed: 446 average time/residue: 0.1729 time to fit residues: 122.8736 Evaluate side-chains 386 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 346 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1010 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 158 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 165 optimal weight: 0.5980 chunk 131 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 211 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 146 optimal weight: 7.9990 chunk 140 optimal weight: 0.0010 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN B 690 GLN B 755 GLN B 907 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.090313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.064534 restraints weight = 66521.431| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.90 r_work: 0.2841 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 25370 Z= 0.128 Angle : 0.599 8.545 34663 Z= 0.305 Chirality : 0.045 0.179 4070 Planarity : 0.004 0.043 4425 Dihedral : 5.964 59.218 4171 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.68 % Allowed : 11.75 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.14), residues: 3080 helix: 2.12 (0.21), residues: 607 sheet: -0.43 (0.21), residues: 541 loop : -2.32 (0.12), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 995 TYR 0.018 0.001 TYR B 473 PHE 0.028 0.001 PHE A 238 TRP 0.019 0.001 TRP C 436 HIS 0.007 0.001 HIS B 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (25291) covalent geometry : angle 0.58503 / 0.30 (34466) SS BOND : bond 0.00387 / 0.27 ( 40) SS BOND : angle 2.04189 / 1.44 ( 80) hydrogen bonds : bond 0.04634 / 3.08 ( 846) hydrogen bonds : angle 5.61246 / 3.79 ( 2421) link_NAG-ASN : bond 0.00266 / 0.19 ( 39) link_NAG-ASN : angle 1.63768 / 1.10 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 363 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 52 GLN cc_start: 0.7983 (tp40) cc_final: 0.7759 (tm-30) REVERT: C 121 ASN cc_start: 0.7910 (t0) cc_final: 0.7393 (p0) REVERT: C 357 ARG cc_start: 0.8169 (ttp80) cc_final: 0.7734 (ptm-80) REVERT: C 374 PHE cc_start: 0.8208 (m-10) cc_final: 0.7953 (m-80) REVERT: C 480 CYS cc_start: 0.6288 (OUTLIER) cc_final: 0.5364 (m) REVERT: C 592 PHE cc_start: 0.7618 (t80) cc_final: 0.6961 (t80) REVERT: B 269 TYR cc_start: 0.8719 (m-80) cc_final: 0.8424 (m-80) REVERT: B 341 VAL cc_start: 0.9076 (t) cc_final: 0.8828 (p) REVERT: B 405 ASP cc_start: 0.8394 (t0) cc_final: 0.8169 (t0) REVERT: B 465 GLU cc_start: 0.7861 (pt0) cc_final: 0.7651 (pt0) REVERT: B 565 PHE cc_start: 0.6332 (m-80) cc_final: 0.5837 (m-10) REVERT: B 943 SER cc_start: 0.8096 (p) cc_final: 0.7809 (t) REVERT: B 1094 VAL cc_start: 0.9031 (OUTLIER) cc_final: 0.8783 (m) REVERT: A 87 ASN cc_start: 0.8121 (m110) cc_final: 0.7757 (m110) REVERT: A 214 ARG cc_start: 0.6878 (mmp-170) cc_final: 0.6481 (mmp80) REVERT: A 460 ASN cc_start: 0.8606 (m-40) cc_final: 0.8311 (t0) REVERT: A 559 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.8391 (m-80) REVERT: A 1010 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7372 (mp10) outliers start: 72 outliers final: 46 residues processed: 416 average time/residue: 0.1707 time to fit residues: 112.5661 Evaluate side-chains 393 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 343 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain D residue 23 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 42 optimal weight: 0.0970 chunk 2 optimal weight: 0.0270 chunk 209 optimal weight: 5.9990 chunk 258 optimal weight: 3.9990 chunk 261 optimal weight: 0.0030 chunk 185 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 177 optimal weight: 3.9990 chunk 221 optimal weight: 0.0040 chunk 216 optimal weight: 6.9990 overall best weight: 0.2260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN B 755 GLN B1002 GLN B1135 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.091175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.065803 restraints weight = 66539.071| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.79 r_work: 0.2873 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 25370 Z= 0.112 Angle : 0.580 10.177 34663 Z= 0.292 Chirality : 0.044 0.180 4070 Planarity : 0.004 0.060 4425 Dihedral : 5.640 58.456 4171 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.64 % Allowed : 12.31 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.15), residues: 3080 helix: 2.16 (0.21), residues: 621 sheet: -0.35 (0.21), residues: 560 loop : -2.23 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 237 TYR 0.023 0.001 TYR B 473 PHE 0.035 0.001 PHE B 456 TRP 0.021 0.001 TRP C 436 HIS 0.007 0.001 HIS B 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (25291) covalent geometry : angle 0.56863 / 0.29 (34466) SS BOND : bond 0.00414 / 0.23 ( 40) SS BOND : angle 1.69891 / 1.16 ( 80) hydrogen bonds : bond 0.04055 / 2.72 ( 846) hydrogen bonds : angle 5.37842 / 3.62 ( 2421) link_NAG-ASN : bond 0.00253 / 0.17 ( 39) link_NAG-ASN : angle 1.56175 / 1.04 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 346 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 ASN cc_start: 0.7847 (t0) cc_final: 0.7471 (p0) REVERT: C 480 CYS cc_start: 0.6490 (OUTLIER) cc_final: 0.5770 (m) REVERT: C 592 PHE cc_start: 0.7533 (t80) cc_final: 0.7325 (t80) REVERT: B 265 TYR cc_start: 0.7218 (t80) cc_final: 0.7005 (t80) REVERT: B 269 TYR cc_start: 0.8745 (m-80) cc_final: 0.8365 (m-80) REVERT: B 405 ASP cc_start: 0.8377 (t0) cc_final: 0.8130 (t0) REVERT: B 420 ASP cc_start: 0.7669 (t0) cc_final: 0.7329 (t0) REVERT: B 421 TYR cc_start: 0.7763 (m-10) cc_final: 0.7510 (m-10) REVERT: B 462 LYS cc_start: 0.8976 (mtmm) cc_final: 0.8513 (mtmm) REVERT: B 465 GLU cc_start: 0.7756 (pt0) cc_final: 0.7354 (pt0) REVERT: B 565 PHE cc_start: 0.6329 (m-80) cc_final: 0.5860 (m-10) REVERT: B 943 SER cc_start: 0.8050 (p) cc_final: 0.7779 (t) REVERT: B 1094 VAL cc_start: 0.9023 (OUTLIER) cc_final: 0.8698 (m) REVERT: B 1136 THR cc_start: 0.9516 (OUTLIER) cc_final: 0.9292 (p) REVERT: B 1139 ASP cc_start: 0.8551 (t0) cc_final: 0.8311 (t0) REVERT: A 394 ASN cc_start: 0.8329 (p0) cc_final: 0.8046 (p0) REVERT: A 460 ASN cc_start: 0.8624 (m-40) cc_final: 0.8363 (t0) REVERT: A 559 PHE cc_start: 0.8761 (OUTLIER) cc_final: 0.8308 (m-80) REVERT: A 592 PHE cc_start: 0.7518 (p90) cc_final: 0.7253 (p90) REVERT: A 1010 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7299 (mp10) outliers start: 71 outliers final: 45 residues processed: 402 average time/residue: 0.1723 time to fit residues: 110.3363 Evaluate side-chains 381 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 331 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain D residue 23 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 70 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 233 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 chunk 300 optimal weight: 2.9990 chunk 296 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 269 optimal weight: 0.8980 chunk 156 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 30 ASN C 87 ASN C 211 ASN C 271 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 907 ASN B 969 ASN B1002 GLN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.085317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.059345 restraints weight = 65610.654| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 2.88 r_work: 0.2706 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 25370 Z= 0.255 Angle : 0.722 10.681 34663 Z= 0.373 Chirality : 0.049 0.194 4070 Planarity : 0.005 0.049 4425 Dihedral : 6.087 52.985 4171 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 3.46 % Allowed : 12.64 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.14), residues: 3080 helix: 1.70 (0.21), residues: 632 sheet: -0.26 (0.21), residues: 545 loop : -2.28 (0.13), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 273 TYR 0.033 0.002 TYR A 660 PHE 0.030 0.002 PHE A 238 TRP 0.018 0.002 TRP C 436 HIS 0.008 0.002 HIS C 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.26 (25291) covalent geometry : angle 0.70549 / 0.37 (34466) SS BOND : bond 0.00450 / 0.29 ( 40) SS BOND : angle 2.30788 / 1.66 ( 80) hydrogen bonds : bond 0.06004 / 3.95 ( 846) hydrogen bonds : angle 5.80118 / 3.93 ( 2421) link_NAG-ASN : bond 0.00499 / 0.32 ( 39) link_NAG-ASN : angle 2.02043 / 1.34 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 348 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 ASN cc_start: 0.7881 (t0) cc_final: 0.7559 (p0) REVERT: C 228 ASP cc_start: 0.7949 (m-30) cc_final: 0.7491 (t0) REVERT: C 374 PHE cc_start: 0.8221 (m-10) cc_final: 0.7838 (m-80) REVERT: C 480 CYS cc_start: 0.6211 (OUTLIER) cc_final: 0.5268 (m) REVERT: B 191 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7353 (tp30) REVERT: B 269 TYR cc_start: 0.8789 (m-80) cc_final: 0.8450 (m-80) REVERT: B 335 LEU cc_start: 0.6715 (OUTLIER) cc_final: 0.6451 (tp) REVERT: B 405 ASP cc_start: 0.8464 (t0) cc_final: 0.8252 (t0) REVERT: B 420 ASP cc_start: 0.7936 (t0) cc_final: 0.7400 (t0) REVERT: B 421 TYR cc_start: 0.7942 (m-10) cc_final: 0.7624 (m-10) REVERT: B 467 ASP cc_start: 0.7630 (p0) cc_final: 0.7035 (p0) REVERT: B 489 TYR cc_start: 0.6719 (m-80) cc_final: 0.6364 (m-80) REVERT: B 565 PHE cc_start: 0.6556 (m-80) cc_final: 0.6291 (m-10) REVERT: B 823 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.8198 (t80) REVERT: B 943 SER cc_start: 0.8224 (p) cc_final: 0.7960 (t) REVERT: B 1139 ASP cc_start: 0.8653 (t0) cc_final: 0.8416 (t0) REVERT: A 324 GLU cc_start: 0.8387 (pm20) cc_final: 0.8035 (pm20) REVERT: A 460 ASN cc_start: 0.8704 (m-40) cc_final: 0.8456 (t0) REVERT: A 461 LEU cc_start: 0.8626 (mm) cc_final: 0.8345 (mm) REVERT: A 1010 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7357 (mp10) REVERT: A 1139 ASP cc_start: 0.8797 (t0) cc_final: 0.8508 (t0) outliers start: 93 outliers final: 58 residues processed: 414 average time/residue: 0.1686 time to fit residues: 111.5054 Evaluate side-chains 379 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 317 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain D residue 23 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 56 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 chunk 217 optimal weight: 5.9990 chunk 102 optimal weight: 0.3980 chunk 179 optimal weight: 0.9990 chunk 302 optimal weight: 0.0770 chunk 17 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 238 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 75 optimal weight: 0.4980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C 955 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.087738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.062020 restraints weight = 65707.979| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 3.10 r_work: 0.2756 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 25370 Z= 0.129 Angle : 0.611 12.754 34663 Z= 0.310 Chirality : 0.045 0.197 4070 Planarity : 0.004 0.045 4425 Dihedral : 5.595 55.544 4167 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 2.53 % Allowed : 13.80 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.15), residues: 3080 helix: 2.08 (0.21), residues: 614 sheet: -0.28 (0.21), residues: 545 loop : -2.15 (0.13), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 995 TYR 0.025 0.001 TYR B 473 PHE 0.030 0.001 PHE A 238 TRP 0.024 0.001 TRP C 436 HIS 0.007 0.001 HIS B 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (25291) covalent geometry : angle 0.59685 / 0.31 (34466) SS BOND : bond 0.00463 / 0.31 ( 40) SS BOND : angle 1.91605 / 1.30 ( 80) hydrogen bonds : bond 0.04546 / 3.03 ( 846) hydrogen bonds : angle 5.48257 / 3.70 ( 2421) link_NAG-ASN : bond 0.00237 / 0.16 ( 39) link_NAG-ASN : angle 1.73012 / 1.15 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 323 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 ASN cc_start: 0.7699 (t0) cc_final: 0.7402 (p0) REVERT: C 128 ILE cc_start: 0.7851 (mp) cc_final: 0.7528 (mp) REVERT: C 480 CYS cc_start: 0.5824 (OUTLIER) cc_final: 0.4721 (m) REVERT: B 269 TYR cc_start: 0.8688 (m-80) cc_final: 0.8387 (m-80) REVERT: B 335 LEU cc_start: 0.6483 (OUTLIER) cc_final: 0.6252 (tp) REVERT: B 405 ASP cc_start: 0.8349 (t0) cc_final: 0.8100 (t0) REVERT: B 420 ASP cc_start: 0.7746 (t0) cc_final: 0.7291 (t0) REVERT: B 421 TYR cc_start: 0.7866 (m-10) cc_final: 0.7455 (m-10) REVERT: B 458 LYS cc_start: 0.9165 (ptpt) cc_final: 0.8821 (ptpp) REVERT: B 823 PHE cc_start: 0.8393 (m-80) cc_final: 0.8062 (t80) REVERT: B 943 SER cc_start: 0.8021 (p) cc_final: 0.7766 (t) REVERT: B 1139 ASP cc_start: 0.8410 (t0) cc_final: 0.8187 (t0) REVERT: A 394 ASN cc_start: 0.7952 (OUTLIER) cc_final: 0.7707 (p0) REVERT: A 460 ASN cc_start: 0.8549 (m-40) cc_final: 0.8305 (t0) REVERT: A 461 LEU cc_start: 0.8722 (mm) cc_final: 0.8514 (mm) REVERT: A 516 GLU cc_start: 0.8214 (pm20) cc_final: 0.7931 (pp20) REVERT: A 1010 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7171 (mp10) REVERT: A 1139 ASP cc_start: 0.8644 (t0) cc_final: 0.8345 (t0) outliers start: 68 outliers final: 46 residues processed: 369 average time/residue: 0.1724 time to fit residues: 100.7860 Evaluate side-chains 363 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 313 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain D residue 23 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 158 optimal weight: 0.8980 chunk 145 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 116 optimal weight: 8.9990 chunk 186 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 279 optimal weight: 4.9990 chunk 141 optimal weight: 7.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.085260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.059239 restraints weight = 65660.561| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 2.92 r_work: 0.2713 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 25370 Z= 0.211 Angle : 0.674 11.616 34663 Z= 0.346 Chirality : 0.047 0.231 4070 Planarity : 0.005 0.048 4425 Dihedral : 5.755 52.773 4167 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 2.79 % Allowed : 14.28 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.15), residues: 3080 helix: 1.82 (0.21), residues: 635 sheet: -0.25 (0.21), residues: 561 loop : -2.21 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 995 TYR 0.035 0.002 TYR B 473 PHE 0.031 0.002 PHE A 238 TRP 0.020 0.002 TRP C 436 HIS 0.007 0.001 HIS B 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.21 (25291) covalent geometry : angle 0.65868 / 0.34 (34466) SS BOND : bond 0.00396 / 0.23 ( 40) SS BOND : angle 2.11060 / 1.45 ( 80) hydrogen bonds : bond 0.05364 / 3.54 ( 846) hydrogen bonds : angle 5.58090 / 3.78 ( 2421) link_NAG-ASN : bond 0.00364 / 0.24 ( 39) link_NAG-ASN : angle 1.91576 / 1.27 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 332 time to evaluate : 1.101 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: C 121 ASN cc_start: 0.7893 (t0) cc_final: 0.7552 (p0) REVERT: C 128 ILE cc_start: 0.7975 (mp) cc_final: 0.7665 (mp) REVERT: C 319 ARG cc_start: 0.8442 (ttp80) cc_final: 0.8229 (ttp-170) REVERT: C 357 ARG cc_start: 0.8333 (ttp80) cc_final: 0.8028 (ttp80) REVERT: C 374 PHE cc_start: 0.8114 (m-10) cc_final: 0.7819 (m-80) REVERT: C 480 CYS cc_start: 0.6332 (OUTLIER) cc_final: 0.5443 (m) REVERT: B 191 GLU cc_start: 0.7562 (tp30) cc_final: 0.7273 (tp30) REVERT: B 269 TYR cc_start: 0.8815 (m-80) cc_final: 0.8563 (m-80) REVERT: B 335 LEU cc_start: 0.6852 (OUTLIER) cc_final: 0.6577 (tp) REVERT: B 405 ASP cc_start: 0.8460 (t0) cc_final: 0.8253 (t0) REVERT: B 420 ASP cc_start: 0.8035 (t0) cc_final: 0.7798 (t0) REVERT: B 458 LYS cc_start: 0.9130 (ptpt) cc_final: 0.8784 (ptpp) REVERT: B 462 LYS cc_start: 0.8952 (mtmm) cc_final: 0.8327 (mtmm) REVERT: B 473 TYR cc_start: 0.7751 (t80) cc_final: 0.7345 (t80) REVERT: B 565 PHE cc_start: 0.6622 (m-10) cc_final: 0.6391 (m-10) REVERT: B 823 PHE cc_start: 0.8512 (m-80) cc_final: 0.8184 (t80) REVERT: B 943 SER cc_start: 0.8298 (p) cc_final: 0.8046 (t) REVERT: A 269 TYR cc_start: 0.7532 (m-10) cc_final: 0.7257 (m-10) REVERT: A 460 ASN cc_start: 0.8692 (m-40) cc_final: 0.8441 (t0) REVERT: A 904 TYR cc_start: 0.7184 (m-10) cc_final: 0.6933 (m-10) REVERT: A 1010 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7311 (mp10) REVERT: A 1139 ASP cc_start: 0.8791 (t0) cc_final: 0.8474 (t0) outliers start: 75 outliers final: 48 residues processed: 385 average time/residue: 0.1610 time to fit residues: 98.9170 Evaluate side-chains 372 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 321 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain D residue 23 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 254 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 308 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 226 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 245 optimal weight: 7.9990 chunk 174 optimal weight: 0.2980 chunk 228 optimal weight: 0.0670 chunk 62 optimal weight: 0.9990 overall best weight: 1.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS B 23 GLN B 271 GLN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.085844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.060213 restraints weight = 65856.505| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 3.05 r_work: 0.2714 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 25370 Z= 0.166 Angle : 0.658 13.153 34663 Z= 0.335 Chirality : 0.046 0.229 4070 Planarity : 0.005 0.052 4425 Dihedral : 5.667 52.800 4167 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 2.49 % Allowed : 15.25 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.15), residues: 3080 helix: 1.98 (0.21), residues: 616 sheet: -0.29 (0.20), residues: 616 loop : -2.20 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 995 TYR 0.018 0.001 TYR B1067 PHE 0.031 0.002 PHE A 238 TRP 0.022 0.001 TRP C 436 HIS 0.007 0.001 HIS B 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (25291) covalent geometry : angle 0.64340 / 0.33 (34466) SS BOND : bond 0.00379 / 0.23 ( 40) SS BOND : angle 2.04624 / 1.44 ( 80) hydrogen bonds : bond 0.04935 / 3.27 ( 846) hydrogen bonds : angle 5.48364 / 3.71 ( 2421) link_NAG-ASN : bond 0.00243 / 0.16 ( 39) link_NAG-ASN : angle 1.82863 / 1.22 ( 117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 328 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 ASN cc_start: 0.7663 (t0) cc_final: 0.7363 (p0) REVERT: C 128 ILE cc_start: 0.7854 (mp) cc_final: 0.7569 (mp) REVERT: C 319 ARG cc_start: 0.8297 (ttp80) cc_final: 0.8084 (ttp-110) REVERT: C 357 ARG cc_start: 0.8280 (ttp80) cc_final: 0.7737 (ptm-80) REVERT: C 374 PHE cc_start: 0.8069 (m-10) cc_final: 0.7738 (m-80) REVERT: C 480 CYS cc_start: 0.5881 (OUTLIER) cc_final: 0.4798 (m) REVERT: C 592 PHE cc_start: 0.7822 (t80) cc_final: 0.7203 (t80) REVERT: B 191 GLU cc_start: 0.7458 (tp30) cc_final: 0.7199 (tp30) REVERT: B 237 ARG cc_start: 0.8028 (ttt180) cc_final: 0.7329 (ttt90) REVERT: B 335 LEU cc_start: 0.6770 (OUTLIER) cc_final: 0.6490 (tp) REVERT: B 410 ILE cc_start: 0.9216 (mm) cc_final: 0.8877 (tp) REVERT: B 421 TYR cc_start: 0.7893 (m-10) cc_final: 0.7616 (m-10) REVERT: B 823 PHE cc_start: 0.8415 (OUTLIER) cc_final: 0.8077 (t80) REVERT: B 943 SER cc_start: 0.8091 (p) cc_final: 0.7849 (t) REVERT: A 269 TYR cc_start: 0.7487 (m-10) cc_final: 0.7177 (m-10) REVERT: A 461 LEU cc_start: 0.8728 (mm) cc_final: 0.8084 (tp) REVERT: A 465 GLU cc_start: 0.7453 (pp20) cc_final: 0.7101 (pp20) REVERT: A 471 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8441 (mm-30) REVERT: A 1010 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7141 (mp10) REVERT: A 1139 ASP cc_start: 0.8643 (t0) cc_final: 0.8326 (t0) outliers start: 67 outliers final: 52 residues processed: 372 average time/residue: 0.1696 time to fit residues: 100.7218 Evaluate side-chains 370 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 314 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain D residue 23 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 276 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 118 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 209 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 183 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 195 optimal weight: 0.8980 chunk 217 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B1002 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.084474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.058908 restraints weight = 65780.166| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 3.01 r_work: 0.2677 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 25370 Z= 0.216 Angle : 0.710 12.569 34663 Z= 0.364 Chirality : 0.048 0.242 4070 Planarity : 0.005 0.053 4425 Dihedral : 5.834 52.658 4167 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 2.68 % Allowed : 15.28 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.15), residues: 3080 helix: 1.81 (0.21), residues: 628 sheet: -0.26 (0.21), residues: 603 loop : -2.20 (0.13), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 995 TYR 0.025 0.002 TYR C 660 PHE 0.032 0.002 PHE A 238 TRP 0.024 0.002 TRP C 436 HIS 0.007 0.001 HIS B 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.22 (25291) covalent geometry : angle 0.69391 / 0.36 (34466) SS BOND : bond 0.00384 / 0.23 ( 40) SS BOND : angle 2.33962 / 1.64 ( 80) hydrogen bonds : bond 0.05393 / 3.55 ( 846) hydrogen bonds : angle 5.59413 / 3.80 ( 2421) link_NAG-ASN : bond 0.00372 / 0.24 ( 39) link_NAG-ASN : angle 1.97184 / 1.31 ( 117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 318 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 ASN cc_start: 0.7658 (t0) cc_final: 0.7346 (p0) REVERT: C 128 ILE cc_start: 0.7966 (mp) cc_final: 0.7696 (mp) REVERT: C 319 ARG cc_start: 0.8318 (ttp80) cc_final: 0.8075 (ttp-170) REVERT: C 357 ARG cc_start: 0.8326 (ttp80) cc_final: 0.7806 (ptm-80) REVERT: C 480 CYS cc_start: 0.5777 (OUTLIER) cc_final: 0.4704 (m) REVERT: B 191 GLU cc_start: 0.7578 (tp30) cc_final: 0.7359 (mm-30) REVERT: B 269 TYR cc_start: 0.8661 (m-80) cc_final: 0.8341 (m-80) REVERT: B 410 ILE cc_start: 0.9229 (mm) cc_final: 0.8901 (tp) REVERT: B 823 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.8078 (t80) REVERT: B 943 SER cc_start: 0.8118 (p) cc_final: 0.7880 (t) REVERT: A 269 TYR cc_start: 0.7558 (m-10) cc_final: 0.7318 (m-10) REVERT: A 471 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8510 (mm-30) REVERT: A 1010 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7255 (mp10) REVERT: A 1139 ASP cc_start: 0.8659 (t0) cc_final: 0.8346 (t0) outliers start: 72 outliers final: 59 residues processed: 368 average time/residue: 0.1697 time to fit residues: 99.6239 Evaluate side-chains 371 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 309 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 164 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 280 optimal weight: 0.2980 chunk 271 optimal weight: 0.0270 chunk 222 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 184 optimal weight: 0.7980 chunk 191 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 178 optimal weight: 0.0980 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN B 414 GLN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 907 ASN B1002 GLN A 234 ASN A 394 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.086964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.061622 restraints weight = 65980.880| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.99 r_work: 0.2753 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 25370 Z= 0.130 Angle : 0.658 12.294 34663 Z= 0.334 Chirality : 0.045 0.290 4070 Planarity : 0.005 0.052 4425 Dihedral : 5.486 53.234 4167 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 2.27 % Allowed : 15.73 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.15), residues: 3080 helix: 2.01 (0.21), residues: 616 sheet: -0.30 (0.20), residues: 614 loop : -2.11 (0.13), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 995 TYR 0.017 0.001 TYR C 369 PHE 0.027 0.001 PHE A 238 TRP 0.043 0.002 TRP B 436 HIS 0.006 0.001 HIS B 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (25291) covalent geometry : angle 0.64675 / 0.33 (34466) SS BOND : bond 0.00320 / 0.18 ( 40) SS BOND : angle 1.79342 / 1.25 ( 80) hydrogen bonds : bond 0.04391 / 2.92 ( 846) hydrogen bonds : angle 5.42485 / 3.67 ( 2421) link_NAG-ASN : bond 0.00235 / 0.14 ( 39) link_NAG-ASN : angle 1.73747 / 1.15 ( 117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 331 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 ASN cc_start: 0.7631 (t0) cc_final: 0.7324 (p0) REVERT: C 128 ILE cc_start: 0.7852 (mp) cc_final: 0.7578 (mp) REVERT: C 319 ARG cc_start: 0.8279 (ttp80) cc_final: 0.8045 (ttp-170) REVERT: C 357 ARG cc_start: 0.8297 (ttp80) cc_final: 0.7793 (ptm-80) REVERT: C 985 ASP cc_start: 0.7607 (m-30) cc_final: 0.7125 (m-30) REVERT: B 237 ARG cc_start: 0.7980 (ttt180) cc_final: 0.7388 (tpt-90) REVERT: B 269 TYR cc_start: 0.8658 (m-80) cc_final: 0.8286 (m-80) REVERT: B 347 PHE cc_start: 0.6554 (m-10) cc_final: 0.6129 (m-10) REVERT: B 487 ASN cc_start: 0.7524 (t0) cc_final: 0.7131 (p0) REVERT: B 823 PHE cc_start: 0.8364 (m-80) cc_final: 0.8039 (t80) REVERT: B 943 SER cc_start: 0.8078 (p) cc_final: 0.7837 (t) REVERT: A 64 TRP cc_start: 0.6772 (t60) cc_final: 0.6495 (t60) REVERT: A 269 TYR cc_start: 0.7406 (m-10) cc_final: 0.7184 (m-10) REVERT: A 471 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8475 (mm-30) REVERT: A 1010 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7139 (mp10) REVERT: A 1139 ASP cc_start: 0.8626 (t0) cc_final: 0.8324 (t0) outliers start: 61 outliers final: 47 residues processed: 373 average time/residue: 0.1691 time to fit residues: 101.1175 Evaluate side-chains 367 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 319 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 1010 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 94 optimal weight: 4.9990 chunk 226 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 241 optimal weight: 2.9990 chunk 251 optimal weight: 0.9980 chunk 267 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 263 optimal weight: 0.8980 chunk 257 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 271 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN B 207 HIS ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 907 ASN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 ASN A 394 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.085070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.059271 restraints weight = 65979.515| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 2.86 r_work: 0.2717 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 25370 Z= 0.199 Angle : 0.707 12.180 34663 Z= 0.363 Chirality : 0.047 0.324 4070 Planarity : 0.005 0.051 4425 Dihedral : 5.634 52.779 4167 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 2.08 % Allowed : 15.81 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.15), residues: 3080 helix: 1.99 (0.21), residues: 616 sheet: -0.24 (0.20), residues: 623 loop : -2.16 (0.13), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 995 TYR 0.019 0.002 TYR B 265 PHE 0.040 0.002 PHE C 342 TRP 0.058 0.002 TRP B 436 HIS 0.006 0.001 HIS B 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 (25291) covalent geometry : angle 0.69245 / 0.36 (34466) SS BOND : bond 0.00459 / 0.27 ( 40) SS BOND : angle 2.21794 / 1.57 ( 80) hydrogen bonds : bond 0.05139 / 3.39 ( 846) hydrogen bonds : angle 5.57594 / 3.77 ( 2421) link_NAG-ASN : bond 0.00393 / 0.23 ( 39) link_NAG-ASN : angle 1.90744 / 1.26 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7572.15 seconds wall clock time: 130 minutes 7.36 seconds (7807.36 seconds total)