Starting phenix.real_space_refine on Sat Jul 4 22:50:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lwj_23547/07_2026/7lwj_23547.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lwj_23547/07_2026/7lwj_23547.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lwj_23547/07_2026/7lwj_23547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lwj_23547/07_2026/7lwj_23547.map" model { file = "/net/cci-nas-00/data/ceres_data/7lwj_23547/07_2026/7lwj_23547.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lwj_23547/07_2026/7lwj_23547.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7lwj_23547/07_2026/7lwj_23547.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lwj_23547/07_2026/7lwj_23547.cif" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.057 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 98 5.16 5 C 15204 2.51 5 N 3924 2.21 5 O 4614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23840 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7807 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 47, 'TRANS': 953} Chain breaks: 7 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 7807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7807 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 47, 'TRANS': 953} Chain breaks: 7 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "C" Number of atoms: 7806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7806 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 47, 'TRANS': 953} Chain breaks: 7 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 5.73, per 1000 atoms: 0.24 Number of scatterers: 23840 At special positions: 0 Unit cell: (130.418, 136.832, 167.833, 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 98 16.00 O 4614 8.00 N 3924 7.00 C 15204 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.06 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 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=2.05 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.01 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 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 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 603 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A 165 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 61 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 122 " " NAG B1306 " - " ASN B 282 " " NAG B1307 " - " ASN B 165 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 165 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C 122 " Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.1 seconds 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5622 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 51 sheets defined 27.1% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.900A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.825A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.838A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 753 Processing helix chain 'A' and resid 754 through 757 Processing helix chain 'A' and resid 758 through 782 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 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 removed outlier: 3.953A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 196 through 200 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.735A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 4.014A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.540A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.610A pdb=" N ARG B 905 " --> pdb=" O GLN B 901 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.625A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 941 through 944 Processing helix chain 'B' and resid 945 through 965 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 982 removed outlier: 3.850A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 986 through 1033 Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.525A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.584A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 371 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.787A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.771A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 756 removed outlier: 4.510A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.538A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.064A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.719A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.683A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.558A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.989A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 986 through 1033 removed outlier: 3.792A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.047A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.021A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY A 89 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.625A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.194A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 317 removed outlier: 4.123A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.422A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 334 through 335 removed outlier: 6.711A pdb=" N ASN A 334 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 357 through 358 removed outlier: 4.718A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.829A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.349A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.322A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 4.423A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.531A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 65 through 66 removed outlier: 3.652A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.516A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.360A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 327 removed outlier: 6.937A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 357 through 358 removed outlier: 3.826A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.922A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 656 removed outlier: 5.860A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.569A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 722 removed outlier: 6.961A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 725 through 728 Processing sheet with id=AD7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 5.605A pdb=" N VAL B1122 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE B1089 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N GLY B1124 " --> pdb=" O ALA B1087 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.603A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.984A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.801A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.848A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 141 through 142 removed outlier: 6.083A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.517A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 318 through 319 Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.532A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.282A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 656 removed outlier: 4.632A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AF3, first strand: chain 'C' and resid 718 through 719 removed outlier: 6.892A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 722 through 728 removed outlier: 3.721A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 734 removed outlier: 4.430A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.367A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1011 hydrogen bonds defined for protein. 2718 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: 6.37 Time building geometry restraints manager: 3.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5580 1.33 - 1.45: 5229 1.45 - 1.58: 13428 1.58 - 1.70: 0 1.70 - 1.82: 122 Bond restraints: 24359 Sorted by residual: bond pdb=" CA PRO C 862 " pdb=" C PRO C 862 " ideal model delta sigma weight residual 1.514 1.536 -0.022 5.50e-03 3.31e+04 1.56e+01 bond pdb=" C5 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.413 1.492 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C5 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C5 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C5 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.41e+01 ... (remaining 24354 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 21828 1.69 - 3.38: 9038 3.38 - 5.06: 2020 5.06 - 6.75: 233 6.75 - 8.44: 18 Bond angle restraints: 33137 Sorted by residual: angle pdb=" CA PHE C 275 " pdb=" CB PHE C 275 " pdb=" CG PHE C 275 " ideal model delta sigma weight residual 113.80 120.63 -6.83 1.00e+00 1.00e+00 4.67e+01 angle pdb=" C GLY C 594 " pdb=" N VAL C 595 " pdb=" CA VAL C 595 " ideal model delta sigma weight residual 121.65 127.42 -5.77 9.40e-01 1.13e+00 3.76e+01 angle pdb=" CA PHE B 59 " pdb=" CB PHE B 59 " pdb=" CG PHE B 59 " ideal model delta sigma weight residual 113.80 119.66 -5.86 1.00e+00 1.00e+00 3.43e+01 angle pdb=" C GLY C 381 " pdb=" N VAL C 382 " pdb=" CA VAL C 382 " ideal model delta sigma weight residual 122.51 130.09 -7.58 1.31e+00 5.83e-01 3.35e+01 angle pdb=" CA PHE A 515 " pdb=" CB PHE A 515 " pdb=" CG PHE A 515 " ideal model delta sigma weight residual 113.80 119.49 -5.69 1.00e+00 1.00e+00 3.24e+01 ... (remaining 33132 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 13118 17.79 - 35.59: 921 35.59 - 53.38: 144 53.38 - 71.18: 43 71.18 - 88.97: 29 Dihedral angle restraints: 14255 sinusoidal: 5528 harmonic: 8727 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual 93.00 176.83 -83.83 1 1.00e+01 1.00e-02 8.57e+01 dihedral pdb=" CA THR B 95 " pdb=" C THR B 95 " pdb=" N GLU B 96 " pdb=" CA GLU B 96 " ideal model delta harmonic sigma weight residual -180.00 -149.97 -30.03 0 5.00e+00 4.00e-02 3.61e+01 dihedral pdb=" CA ASN C1135 " pdb=" C ASN C1135 " pdb=" N THR C1136 " pdb=" CA THR C1136 " ideal model delta harmonic sigma weight residual 180.00 150.02 29.98 0 5.00e+00 4.00e-02 3.60e+01 ... (remaining 14252 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 2548 0.097 - 0.193: 1184 0.193 - 0.290: 126 0.290 - 0.387: 16 0.387 - 0.483: 2 Chirality restraints: 3876 Sorted by residual: chirality pdb=" CA GLU A 773 " pdb=" N GLU A 773 " pdb=" C GLU A 773 " pdb=" CB GLU A 773 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.84e+00 chirality pdb=" CA GLU C 773 " pdb=" N GLU C 773 " pdb=" C GLU C 773 " pdb=" CB GLU C 773 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.21e+00 chirality pdb=" CA ASP B1041 " pdb=" N ASP B1041 " pdb=" C ASP B1041 " pdb=" CB ASP B1041 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.31e+00 ... (remaining 3873 not shown) Planarity restraints: 4281 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 917 " 0.224 2.00e-02 2.50e+03 1.29e-01 3.34e+02 pdb=" CG TYR C 917 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR C 917 " -0.084 2.00e-02 2.50e+03 pdb=" CD2 TYR C 917 " -0.140 2.00e-02 2.50e+03 pdb=" CE1 TYR C 917 " -0.104 2.00e-02 2.50e+03 pdb=" CE2 TYR C 917 " -0.063 2.00e-02 2.50e+03 pdb=" CZ TYR C 917 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 917 " 0.201 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 917 " 0.221 2.00e-02 2.50e+03 1.27e-01 3.22e+02 pdb=" CG TYR B 917 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR B 917 " -0.089 2.00e-02 2.50e+03 pdb=" CD2 TYR B 917 " -0.133 2.00e-02 2.50e+03 pdb=" CE1 TYR B 917 " -0.101 2.00e-02 2.50e+03 pdb=" CE2 TYR B 917 " -0.064 2.00e-02 2.50e+03 pdb=" CZ TYR B 917 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR B 917 " 0.197 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 917 " 0.203 2.00e-02 2.50e+03 1.18e-01 2.78e+02 pdb=" CG TYR A 917 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR A 917 " -0.070 2.00e-02 2.50e+03 pdb=" CD2 TYR A 917 " -0.124 2.00e-02 2.50e+03 pdb=" CE1 TYR A 917 " -0.100 2.00e-02 2.50e+03 pdb=" CE2 TYR A 917 " -0.056 2.00e-02 2.50e+03 pdb=" CZ TYR A 917 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 917 " 0.187 2.00e-02 2.50e+03 ... (remaining 4278 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.97: 10976 2.97 - 3.45: 23750 3.45 - 3.93: 40331 3.93 - 4.42: 45459 4.42 - 4.90: 76135 Nonbonded interactions: 196651 Sorted by model distance: nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.482 3.040 nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.485 3.040 nonbonded pdb=" OH TYR A 200 " pdb=" OE2 GLU C 516 " model vdw 2.519 3.040 nonbonded pdb=" OD1 ASP B 364 " pdb=" OG SER B 366 " model vdw 2.523 3.040 nonbonded pdb=" OG SER C 813 " pdb=" OE1 GLU C 868 " model vdw 2.530 3.040 ... (remaining 196646 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 479 or (resid 480 and (name N or name CA or nam \ e C or name O or name CB )) or resid 481 through 487 or (resid 488 and (name N o \ r name CA or name C or name O or name CB )) or resid 489 through 589 or (resid 5 \ 90 and (name N or name CA or name C or name O or name CB )) or resid 591 through \ 1310)) selection = (chain 'B' and (resid 27 through 360 or (resid 361 and (name N or name CA or nam \ e C or name O or name CB )) or resid 362 through 390 or (resid 391 and (name N o \ r name CA or name C or name O or name CB )) or resid 392 through 589 or (resid 5 \ 90 and (name N or name CA or name C or name O or name CB )) or resid 591 through \ 1310)) selection = (chain 'C' and (resid 27 through 360 or (resid 361 and (name N or name CA or nam \ e C or name O or name CB )) or resid 362 through 390 or (resid 391 and (name N o \ r name CA or name C or name O or name CB )) or resid 392 through 1310)) } 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: 2.240 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: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 25.740 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 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 : 0.014 0.079 24423 Z= 0.799 Angle : 1.841 9.848 33295 Z= 1.228 Chirality : 0.098 0.483 3876 Planarity : 0.015 0.174 4251 Dihedral : 13.550 88.970 8531 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 0.34 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.01 % Favored : 92.79 % Rotamer: Outliers : 0.84 % Allowed : 3.21 % Favored : 95.95 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.14), residues: 2955 helix: -1.30 (0.17), residues: 665 sheet: -0.34 (0.25), residues: 357 loop : -1.34 (0.13), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1019 TYR 0.224 0.026 TYR C 917 PHE 0.101 0.015 PHE A 718 TRP 0.178 0.026 TRP B 886 HIS 0.017 0.003 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.01369 / 0.80 (24359) covalent geometry : angle 1.82768 / 1.23 (33137) SS BOND : bond 0.01090 / 0.64 ( 34) SS BOND : angle 2.28498 / 1.55 ( 68) hydrogen bonds : bond 0.13814 / 9.32 ( 1009) hydrogen bonds : angle 8.83184 / 6.21 ( 2718) link_NAG-ASN : bond 0.01180 / 0.69 ( 30) link_NAG-ASN : angle 4.45901 / 3.00 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 358 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LEU cc_start: 0.7445 (tp) cc_final: 0.7123 (pp) REVERT: A 347 PHE cc_start: 0.1688 (OUTLIER) cc_final: 0.1018 (t80) REVERT: B 38 TYR cc_start: 0.3781 (m-80) cc_final: 0.2463 (m-80) REVERT: B 329 PHE cc_start: 0.7299 (m-10) cc_final: 0.6871 (m-80) REVERT: B 358 ILE cc_start: 0.7081 (mm) cc_final: 0.6838 (mp) REVERT: B 902 MET cc_start: 0.7419 (mmm) cc_final: 0.7216 (tpt) REVERT: C 740 MET cc_start: 0.5971 (tpt) cc_final: 0.5722 (tpt) REVERT: C 900 MET cc_start: 0.6799 (mtp) cc_final: 0.6217 (mtp) REVERT: C 902 MET cc_start: 0.8136 (mmm) cc_final: 0.7907 (tpt) REVERT: C 904 TYR cc_start: 0.7187 (m-80) cc_final: 0.6973 (m-10) outliers start: 22 outliers final: 9 residues processed: 375 average time/residue: 0.1696 time to fit residues: 100.3865 Evaluate side-chains 193 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 183 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 739 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.0270 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1088 HIS B 343 ASN B 360 ASN B1088 HIS C 314 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1113 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.192104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.161142 restraints weight = 45738.337| |-----------------------------------------------------------------------------| r_work (start): 0.4246 rms_B_bonded: 3.63 r_work: 0.3885 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 24423 Z= 0.182 Angle : 0.739 10.794 33295 Z= 0.385 Chirality : 0.048 0.220 3876 Planarity : 0.004 0.048 4251 Dihedral : 6.927 58.183 3217 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.91 % Allowed : 8.18 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.14), residues: 2955 helix: -0.06 (0.19), residues: 660 sheet: -0.63 (0.20), residues: 597 loop : -1.08 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 34 TYR 0.022 0.002 TYR B 369 PHE 0.024 0.002 PHE B 86 TRP 0.040 0.003 TRP C 64 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (24359) covalent geometry : angle 0.70674 / 0.38 (33137) SS BOND : bond 0.00557 / 0.34 ( 34) SS BOND : angle 1.99320 / 1.30 ( 68) hydrogen bonds : bond 0.05621 / 3.62 ( 1009) hydrogen bonds : angle 7.04311 / 4.98 ( 2718) link_NAG-ASN : bond 0.00352 / 0.19 ( 30) link_NAG-ASN : angle 3.89493 / 2.64 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 213 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8076 (mmtt) cc_final: 0.6964 (mtmm) REVERT: A 296 LEU cc_start: 0.7591 (tp) cc_final: 0.7319 (pp) REVERT: A 347 PHE cc_start: 0.1983 (OUTLIER) cc_final: 0.1163 (t80) REVERT: A 904 TYR cc_start: 0.5350 (m-10) cc_final: 0.4931 (m-80) REVERT: B 314 GLN cc_start: 0.7122 (mt0) cc_final: 0.6846 (mt0) REVERT: B 329 PHE cc_start: 0.7740 (m-10) cc_final: 0.7416 (m-80) REVERT: B 358 ILE cc_start: 0.7385 (mm) cc_final: 0.7143 (mp) REVERT: B 664 ILE cc_start: 0.7194 (OUTLIER) cc_final: 0.6665 (tp) REVERT: C 54 LEU cc_start: 0.6947 (tp) cc_final: 0.6720 (tt) REVERT: C 129 LYS cc_start: 0.8814 (mttm) cc_final: 0.8432 (tmmt) REVERT: C 619 GLU cc_start: 0.5813 (tp30) cc_final: 0.5543 (tp30) REVERT: C 697 MET cc_start: 0.7698 (ptm) cc_final: 0.7403 (ptm) REVERT: C 811 LYS cc_start: 0.6755 (OUTLIER) cc_final: 0.6473 (ttpt) REVERT: C 900 MET cc_start: 0.7179 (mtp) cc_final: 0.6226 (mtp) REVERT: C 904 TYR cc_start: 0.7817 (m-80) cc_final: 0.7181 (m-10) outliers start: 50 outliers final: 32 residues processed: 255 average time/residue: 0.1610 time to fit residues: 66.0525 Evaluate side-chains 183 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 148 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 948 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 275 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 270 optimal weight: 2.9990 chunk 125 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 256 optimal weight: 6.9990 chunk 272 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 246 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 ASN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1011 GLN C 317 ASN C 901 GLN C 935 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.190435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.159400 restraints weight = 45764.780| |-----------------------------------------------------------------------------| r_work (start): 0.4262 rms_B_bonded: 4.05 r_work: 0.3853 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 24423 Z= 0.197 Angle : 0.690 12.129 33295 Z= 0.356 Chirality : 0.047 0.208 3876 Planarity : 0.004 0.042 4251 Dihedral : 6.302 58.686 3215 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.29 % Allowed : 9.87 % Favored : 87.84 % 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: -1.05 (0.15), residues: 2955 helix: 0.05 (0.19), residues: 650 sheet: -0.60 (0.20), residues: 592 loop : -1.01 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 34 TYR 0.020 0.002 TYR C1067 PHE 0.049 0.002 PHE C 464 TRP 0.024 0.002 TRP C 64 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.20 (24359) covalent geometry : angle 0.66849 / 0.35 (33137) SS BOND : bond 0.00405 / 0.21 ( 34) SS BOND : angle 1.94676 / 1.25 ( 68) hydrogen bonds : bond 0.05117 / 3.31 ( 1009) hydrogen bonds : angle 6.70651 / 4.73 ( 2718) link_NAG-ASN : bond 0.00425 / 0.30 ( 30) link_NAG-ASN : angle 2.95444 / 2.02 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 175 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8235 (mmtt) cc_final: 0.7728 (mmmt) REVERT: A 97 LYS cc_start: 0.6349 (pttt) cc_final: 0.5955 (tppt) REVERT: A 296 LEU cc_start: 0.7654 (tp) cc_final: 0.7363 (pp) REVERT: A 347 PHE cc_start: 0.2545 (OUTLIER) cc_final: 0.1675 (t80) REVERT: A 735 SER cc_start: 0.8147 (t) cc_final: 0.7821 (m) REVERT: A 904 TYR cc_start: 0.5586 (m-10) cc_final: 0.5194 (m-10) REVERT: B 223 LEU cc_start: 0.5715 (mp) cc_final: 0.5463 (mp) REVERT: B 242 LEU cc_start: 0.6849 (mm) cc_final: 0.6497 (tp) REVERT: B 577 ARG cc_start: 0.7141 (ttp80) cc_final: 0.6285 (ptm160) REVERT: B 664 ILE cc_start: 0.7110 (OUTLIER) cc_final: 0.6586 (tp) REVERT: B 931 ILE cc_start: 0.6545 (OUTLIER) cc_final: 0.6323 (mm) REVERT: C 129 LYS cc_start: 0.8886 (mttm) cc_final: 0.8415 (tmmt) REVERT: C 242 LEU cc_start: 0.7373 (pt) cc_final: 0.7019 (pt) REVERT: C 332 ILE cc_start: 0.7994 (tp) cc_final: 0.7752 (tt) REVERT: C 619 GLU cc_start: 0.6024 (tp30) cc_final: 0.5622 (tp30) REVERT: C 759 PHE cc_start: 0.6882 (OUTLIER) cc_final: 0.5707 (m-10) REVERT: C 900 MET cc_start: 0.7357 (mtp) cc_final: 0.6477 (mtp) REVERT: C 902 MET cc_start: 0.8282 (tpp) cc_final: 0.7903 (tpt) REVERT: C 904 TYR cc_start: 0.7934 (m-80) cc_final: 0.7289 (m-10) REVERT: C 973 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7490 (mt) outliers start: 60 outliers final: 38 residues processed: 224 average time/residue: 0.1639 time to fit residues: 59.0454 Evaluate side-chains 187 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 144 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 3 optimal weight: 0.7980 chunk 211 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 40 optimal weight: 40.0000 chunk 202 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 chunk 173 optimal weight: 0.4980 chunk 90 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 655 HIS ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.189831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.158357 restraints weight = 45589.423| |-----------------------------------------------------------------------------| r_work (start): 0.4231 rms_B_bonded: 4.02 r_work: 0.3834 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 24423 Z= 0.198 Angle : 0.659 11.191 33295 Z= 0.339 Chirality : 0.047 0.230 3876 Planarity : 0.004 0.047 4251 Dihedral : 6.038 59.965 3213 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.94 % Allowed : 9.94 % Favored : 87.11 % 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: -1.02 (0.15), residues: 2955 helix: 0.07 (0.19), residues: 654 sheet: -0.63 (0.20), residues: 581 loop : -0.96 (0.14), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 34 TYR 0.021 0.002 TYR C1067 PHE 0.028 0.002 PHE C 464 TRP 0.022 0.002 TRP C 64 HIS 0.006 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.20 (24359) covalent geometry : angle 0.64037 / 0.33 (33137) SS BOND : bond 0.00439 / 0.31 ( 34) SS BOND : angle 1.94905 / 1.39 ( 68) hydrogen bonds : bond 0.04876 / 3.17 ( 1009) hydrogen bonds : angle 6.55920 / 4.63 ( 2718) link_NAG-ASN : bond 0.00308 / 0.21 ( 30) link_NAG-ASN : angle 2.57743 / 1.78 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 159 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.6337 (pttt) cc_final: 0.5987 (tppt) REVERT: A 296 LEU cc_start: 0.7663 (tp) cc_final: 0.7366 (pp) REVERT: A 298 GLU cc_start: 0.7163 (mm-30) cc_final: 0.6749 (mm-30) REVERT: A 347 PHE cc_start: 0.2701 (OUTLIER) cc_final: 0.1875 (t80) REVERT: A 759 PHE cc_start: 0.5773 (OUTLIER) cc_final: 0.5143 (m-80) REVERT: A 873 TYR cc_start: 0.7142 (OUTLIER) cc_final: 0.6486 (m-80) REVERT: B 129 LYS cc_start: 0.7679 (tppp) cc_final: 0.7444 (tppp) REVERT: B 223 LEU cc_start: 0.5951 (mp) cc_final: 0.5660 (mp) REVERT: B 242 LEU cc_start: 0.6887 (mm) cc_final: 0.6534 (tp) REVERT: B 365 TYR cc_start: 0.7041 (m-80) cc_final: 0.6715 (m-80) REVERT: B 577 ARG cc_start: 0.7081 (ttp80) cc_final: 0.6197 (ptm160) REVERT: B 873 TYR cc_start: 0.8288 (OUTLIER) cc_final: 0.7991 (m-10) REVERT: C 129 LYS cc_start: 0.8874 (mttm) cc_final: 0.8392 (tmmt) REVERT: C 169 GLU cc_start: 0.8357 (tp30) cc_final: 0.8095 (tp30) REVERT: C 213 VAL cc_start: 0.8458 (OUTLIER) cc_final: 0.7932 (t) REVERT: C 242 LEU cc_start: 0.7509 (pt) cc_final: 0.7235 (pt) REVERT: C 564 GLN cc_start: 0.6677 (mt0) cc_final: 0.6222 (mt0) REVERT: C 619 GLU cc_start: 0.6443 (tp30) cc_final: 0.6220 (tp30) REVERT: C 759 PHE cc_start: 0.6951 (OUTLIER) cc_final: 0.5811 (m-10) REVERT: C 823 PHE cc_start: 0.5416 (m-80) cc_final: 0.5211 (m-80) REVERT: C 900 MET cc_start: 0.7272 (mtp) cc_final: 0.6270 (mtp) REVERT: C 902 MET cc_start: 0.8346 (tpp) cc_final: 0.7983 (tpt) REVERT: C 904 TYR cc_start: 0.8002 (m-80) cc_final: 0.7360 (m-10) REVERT: C 973 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.7587 (mt) outliers start: 77 outliers final: 45 residues processed: 223 average time/residue: 0.1491 time to fit residues: 53.4913 Evaluate side-chains 199 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 147 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1032 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 0.9980 chunk 266 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 40 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 chunk 168 optimal weight: 3.9990 chunk 296 optimal weight: 3.9990 chunk 184 optimal weight: 0.9980 chunk 267 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 214 optimal weight: 0.7980 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1135 ASN B 245 HIS B1002 GLN C 196 ASN C 460 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.190941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.159411 restraints weight = 45314.929| |-----------------------------------------------------------------------------| r_work (start): 0.4261 rms_B_bonded: 3.92 r_work: 0.3877 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24423 Z= 0.162 Angle : 0.612 11.533 33295 Z= 0.314 Chirality : 0.045 0.163 3876 Planarity : 0.004 0.124 4251 Dihedral : 5.718 59.609 3213 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.06 % Allowed : 10.86 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.15), residues: 2955 helix: 0.33 (0.19), residues: 655 sheet: -0.63 (0.20), residues: 578 loop : -0.97 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 34 TYR 0.018 0.002 TYR C1067 PHE 0.018 0.001 PHE B 86 TRP 0.023 0.001 TRP C 64 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (24359) covalent geometry : angle 0.59714 / 0.31 (33137) SS BOND : bond 0.00234 / 0.15 ( 34) SS BOND : angle 1.64557 / 1.07 ( 68) hydrogen bonds : bond 0.04539 / 2.94 ( 1009) hydrogen bonds : angle 6.35147 / 4.47 ( 2718) link_NAG-ASN : bond 0.00229 / 0.15 ( 30) link_NAG-ASN : angle 2.26353 / 1.58 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 159 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.6280 (pttt) cc_final: 0.5988 (tppt) REVERT: A 296 LEU cc_start: 0.7735 (tp) cc_final: 0.7265 (pp) REVERT: A 318 PHE cc_start: 0.7112 (t80) cc_final: 0.6880 (t80) REVERT: A 347 PHE cc_start: 0.2741 (OUTLIER) cc_final: 0.1953 (t80) REVERT: A 759 PHE cc_start: 0.5767 (OUTLIER) cc_final: 0.5242 (m-80) REVERT: A 873 TYR cc_start: 0.6971 (OUTLIER) cc_final: 0.6250 (m-80) REVERT: A 902 MET cc_start: 0.7302 (tpt) cc_final: 0.7036 (mmt) REVERT: A 996 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8791 (tt) REVERT: B 223 LEU cc_start: 0.6165 (mp) cc_final: 0.5820 (mp) REVERT: B 242 LEU cc_start: 0.7042 (mm) cc_final: 0.6674 (tp) REVERT: B 360 ASN cc_start: 0.7257 (t0) cc_final: 0.7001 (t0) REVERT: B 365 TYR cc_start: 0.6970 (m-80) cc_final: 0.6662 (m-80) REVERT: B 577 ARG cc_start: 0.7038 (ttp80) cc_final: 0.6149 (ptm160) REVERT: B 873 TYR cc_start: 0.8224 (OUTLIER) cc_final: 0.7977 (m-10) REVERT: C 129 LYS cc_start: 0.8891 (mttm) cc_final: 0.8365 (tmmt) REVERT: C 169 GLU cc_start: 0.8304 (tp30) cc_final: 0.8057 (tp30) REVERT: C 242 LEU cc_start: 0.7352 (pt) cc_final: 0.7122 (pt) REVERT: C 564 GLN cc_start: 0.6617 (mt0) cc_final: 0.6057 (mt0) REVERT: C 740 MET cc_start: 0.6370 (tpp) cc_final: 0.5961 (tpp) REVERT: C 902 MET cc_start: 0.8287 (tpp) cc_final: 0.7971 (tpt) REVERT: C 904 TYR cc_start: 0.7925 (m-80) cc_final: 0.7298 (m-10) REVERT: C 973 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7589 (mt) outliers start: 80 outliers final: 53 residues processed: 227 average time/residue: 0.1514 time to fit residues: 56.8489 Evaluate side-chains 200 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 141 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1032 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 26 optimal weight: 2.9990 chunk 232 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 174 optimal weight: 3.9990 chunk 127 optimal weight: 20.0000 chunk 179 optimal weight: 0.6980 chunk 259 optimal weight: 1.9990 chunk 108 optimal weight: 20.0000 chunk 36 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 90 optimal weight: 0.0470 overall best weight: 1.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 GLN B1002 GLN C 196 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.190607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.159474 restraints weight = 45491.997| |-----------------------------------------------------------------------------| r_work (start): 0.4263 rms_B_bonded: 4.05 r_work: 0.3859 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 24423 Z= 0.177 Angle : 0.621 11.565 33295 Z= 0.318 Chirality : 0.045 0.160 3876 Planarity : 0.004 0.061 4251 Dihedral : 5.538 59.503 3209 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.83 % Allowed : 11.63 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.15), residues: 2955 helix: 0.38 (0.19), residues: 654 sheet: -0.54 (0.21), residues: 569 loop : -1.02 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 403 TYR 0.019 0.002 TYR C1067 PHE 0.018 0.002 PHE C 823 TRP 0.019 0.001 TRP C 64 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (24359) covalent geometry : angle 0.60508 / 0.31 (33137) SS BOND : bond 0.00277 / 0.18 ( 34) SS BOND : angle 2.07753 / 1.31 ( 68) hydrogen bonds : bond 0.04576 / 2.98 ( 1009) hydrogen bonds : angle 6.32612 / 4.45 ( 2718) link_NAG-ASN : bond 0.00226 / 0.14 ( 30) link_NAG-ASN : angle 2.13504 / 1.48 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 143 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.6252 (pttt) cc_final: 0.6005 (tppt) REVERT: A 296 LEU cc_start: 0.7629 (tp) cc_final: 0.7118 (pp) REVERT: A 318 PHE cc_start: 0.7128 (t80) cc_final: 0.6879 (t80) REVERT: A 347 PHE cc_start: 0.2784 (OUTLIER) cc_final: 0.2046 (t80) REVERT: A 759 PHE cc_start: 0.5663 (OUTLIER) cc_final: 0.5296 (m-80) REVERT: A 873 TYR cc_start: 0.7143 (OUTLIER) cc_final: 0.6336 (m-80) REVERT: B 129 LYS cc_start: 0.7682 (tppp) cc_final: 0.7363 (tppp) REVERT: B 242 LEU cc_start: 0.7035 (mm) cc_final: 0.6671 (tp) REVERT: B 360 ASN cc_start: 0.7212 (t0) cc_final: 0.6908 (t0) REVERT: B 365 TYR cc_start: 0.7034 (m-80) cc_final: 0.6714 (m-80) REVERT: B 577 ARG cc_start: 0.6906 (ttp80) cc_final: 0.6134 (ptm160) REVERT: B 873 TYR cc_start: 0.8295 (OUTLIER) cc_final: 0.8026 (m-10) REVERT: C 129 LYS cc_start: 0.8822 (mttm) cc_final: 0.8365 (tmmt) REVERT: C 169 GLU cc_start: 0.8295 (tp30) cc_final: 0.8030 (tp30) REVERT: C 564 GLN cc_start: 0.6663 (mt0) cc_final: 0.6121 (mt0) REVERT: C 740 MET cc_start: 0.6265 (tpp) cc_final: 0.5653 (tpp) REVERT: C 759 PHE cc_start: 0.7124 (OUTLIER) cc_final: 0.5871 (m-10) REVERT: C 902 MET cc_start: 0.8218 (tpp) cc_final: 0.7978 (tpt) REVERT: C 904 TYR cc_start: 0.8008 (m-80) cc_final: 0.7443 (m-10) REVERT: C 973 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7654 (mt) outliers start: 74 outliers final: 54 residues processed: 206 average time/residue: 0.1411 time to fit residues: 48.5993 Evaluate side-chains 197 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 137 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 167 optimal weight: 0.0970 chunk 129 optimal weight: 2.9990 chunk 289 optimal weight: 0.8980 chunk 288 optimal weight: 0.4980 chunk 116 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 260 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 232 optimal weight: 8.9990 chunk 270 optimal weight: 0.9990 chunk 198 optimal weight: 0.0170 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1002 GLN C 196 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.196675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.163379 restraints weight = 44318.802| |-----------------------------------------------------------------------------| r_work (start): 0.4257 rms_B_bonded: 3.12 r_work: 0.3960 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 24423 Z= 0.114 Angle : 0.580 14.555 33295 Z= 0.293 Chirality : 0.044 0.213 3876 Planarity : 0.004 0.072 4251 Dihedral : 5.155 59.225 3206 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.45 % Allowed : 12.35 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.15), residues: 2955 helix: 0.68 (0.20), residues: 654 sheet: -0.47 (0.21), residues: 553 loop : -0.86 (0.15), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 403 TYR 0.017 0.001 TYR B 266 PHE 0.019 0.001 PHE B 392 TRP 0.017 0.001 TRP C 64 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (24359) covalent geometry : angle 0.55819 / 0.29 (33137) SS BOND : bond 0.00200 / 0.12 ( 34) SS BOND : angle 1.62687 / 1.05 ( 68) hydrogen bonds : bond 0.04124 / 2.67 ( 1009) hydrogen bonds : angle 6.04948 / 4.25 ( 2718) link_NAG-ASN : bond 0.00364 / 0.25 ( 30) link_NAG-ASN : angle 2.81232 / 1.92 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 155 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.4665 (OUTLIER) cc_final: 0.4254 (p) REVERT: A 296 LEU cc_start: 0.7478 (tp) cc_final: 0.7012 (pp) REVERT: A 347 PHE cc_start: 0.2963 (OUTLIER) cc_final: 0.2161 (t80) REVERT: A 480 CYS cc_start: 0.2585 (OUTLIER) cc_final: 0.1030 (p) REVERT: A 759 PHE cc_start: 0.5747 (OUTLIER) cc_final: 0.5319 (m-80) REVERT: A 873 TYR cc_start: 0.6870 (OUTLIER) cc_final: 0.6107 (m-80) REVERT: B 129 LYS cc_start: 0.7674 (tppp) cc_final: 0.7307 (tppp) REVERT: B 242 LEU cc_start: 0.6959 (mm) cc_final: 0.6616 (tp) REVERT: B 360 ASN cc_start: 0.7092 (t0) cc_final: 0.6806 (t0) REVERT: B 365 TYR cc_start: 0.7041 (m-80) cc_final: 0.6734 (m-80) REVERT: B 577 ARG cc_start: 0.6828 (ttp80) cc_final: 0.6055 (ptm160) REVERT: B 873 TYR cc_start: 0.8084 (OUTLIER) cc_final: 0.7743 (m-10) REVERT: C 129 LYS cc_start: 0.8790 (mttm) cc_final: 0.8373 (tmmt) REVERT: C 169 GLU cc_start: 0.8284 (tp30) cc_final: 0.7996 (tp30) REVERT: C 564 GLN cc_start: 0.6399 (mt0) cc_final: 0.5844 (mt0) REVERT: C 740 MET cc_start: 0.6166 (tpp) cc_final: 0.5502 (tpp) REVERT: C 759 PHE cc_start: 0.6946 (OUTLIER) cc_final: 0.5739 (m-10) REVERT: C 904 TYR cc_start: 0.7800 (m-80) cc_final: 0.7291 (m-10) outliers start: 64 outliers final: 40 residues processed: 209 average time/residue: 0.1532 time to fit residues: 53.1568 Evaluate side-chains 186 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 139 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 1032 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 274 optimal weight: 1.9990 chunk 219 optimal weight: 0.9990 chunk 53 optimal weight: 0.0870 chunk 220 optimal weight: 6.9990 chunk 191 optimal weight: 1.9990 chunk 226 optimal weight: 20.0000 chunk 203 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 72 optimal weight: 0.6980 chunk 167 optimal weight: 0.6980 chunk 118 optimal weight: 10.0000 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B1002 GLN C 196 ASN ** C 755 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 = 0.4644 r_free = 0.4644 target = 0.192719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.162047 restraints weight = 45181.710| |-----------------------------------------------------------------------------| r_work (start): 0.4285 rms_B_bonded: 4.24 r_work: 0.3914 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 24423 Z= 0.130 Angle : 0.587 11.343 33295 Z= 0.295 Chirality : 0.045 0.249 3876 Planarity : 0.004 0.076 4251 Dihedral : 5.050 59.021 3206 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.26 % Allowed : 13.08 % Favored : 84.67 % 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: -0.63 (0.15), residues: 2955 helix: 0.67 (0.20), residues: 654 sheet: -0.51 (0.21), residues: 557 loop : -0.79 (0.15), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 403 TYR 0.018 0.001 TYR C 789 PHE 0.019 0.001 PHE C 823 TRP 0.015 0.001 TRP C 64 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (24359) covalent geometry : angle 0.56792 / 0.29 (33137) SS BOND : bond 0.00219 / 0.13 ( 34) SS BOND : angle 1.60786 / 1.04 ( 68) hydrogen bonds : bond 0.04125 / 2.70 ( 1009) hydrogen bonds : angle 6.00409 / 4.22 ( 2718) link_NAG-ASN : bond 0.00424 / 0.29 ( 30) link_NAG-ASN : angle 2.56867 / 1.86 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 148 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.4623 (OUTLIER) cc_final: 0.4202 (p) REVERT: A 85 PRO cc_start: 0.7684 (Cg_exo) cc_final: 0.7416 (Cg_endo) REVERT: A 296 LEU cc_start: 0.7607 (tp) cc_final: 0.7097 (pp) REVERT: A 347 PHE cc_start: 0.3089 (OUTLIER) cc_final: 0.2368 (t80) REVERT: A 480 CYS cc_start: 0.2804 (OUTLIER) cc_final: 0.1330 (p) REVERT: A 759 PHE cc_start: 0.5492 (OUTLIER) cc_final: 0.5140 (m-80) REVERT: A 873 TYR cc_start: 0.6943 (OUTLIER) cc_final: 0.6132 (m-80) REVERT: B 129 LYS cc_start: 0.7797 (tppp) cc_final: 0.7496 (tppp) REVERT: B 242 LEU cc_start: 0.7111 (mm) cc_final: 0.6783 (tp) REVERT: B 360 ASN cc_start: 0.7292 (t0) cc_final: 0.6995 (t0) REVERT: B 365 TYR cc_start: 0.7104 (m-80) cc_final: 0.6829 (m-80) REVERT: B 577 ARG cc_start: 0.6878 (ttp80) cc_final: 0.6059 (ptm160) REVERT: B 873 TYR cc_start: 0.8141 (OUTLIER) cc_final: 0.7926 (m-10) REVERT: C 64 TRP cc_start: 0.7532 (t60) cc_final: 0.7063 (t60) REVERT: C 129 LYS cc_start: 0.8813 (mttm) cc_final: 0.8405 (tmmt) REVERT: C 169 GLU cc_start: 0.8290 (tp30) cc_final: 0.8047 (tp30) REVERT: C 564 GLN cc_start: 0.6393 (mt0) cc_final: 0.5836 (mt0) REVERT: C 740 MET cc_start: 0.6316 (tpp) cc_final: 0.5660 (tpp) REVERT: C 759 PHE cc_start: 0.6970 (OUTLIER) cc_final: 0.5751 (m-10) REVERT: C 904 TYR cc_start: 0.7973 (m-80) cc_final: 0.7467 (m-10) outliers start: 59 outliers final: 43 residues processed: 199 average time/residue: 0.1248 time to fit residues: 41.0155 Evaluate side-chains 188 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 138 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 1032 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 116 optimal weight: 20.0000 chunk 190 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 172 optimal weight: 0.6980 chunk 215 optimal weight: 10.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 544 ASN B1002 GLN C 66 HIS C 196 ASN ** C 755 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 = 0.4624 r_free = 0.4624 target = 0.190740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.159938 restraints weight = 45595.200| |-----------------------------------------------------------------------------| r_work (start): 0.4267 rms_B_bonded: 4.31 r_work: 0.3861 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 24423 Z= 0.184 Angle : 0.627 11.081 33295 Z= 0.317 Chirality : 0.046 0.264 3876 Planarity : 0.004 0.067 4251 Dihedral : 5.150 59.148 3205 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.22 % Allowed : 13.19 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.15), residues: 2955 helix: 0.51 (0.20), residues: 653 sheet: -0.53 (0.21), residues: 565 loop : -0.86 (0.15), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 403 TYR 0.020 0.002 TYR C1067 PHE 0.023 0.002 PHE C 823 TRP 0.016 0.001 TRP C 64 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (24359) covalent geometry : angle 0.60923 / 0.31 (33137) SS BOND : bond 0.00266 / 0.18 ( 34) SS BOND : angle 1.75695 / 1.12 ( 68) hydrogen bonds : bond 0.04428 / 2.89 ( 1009) hydrogen bonds : angle 6.15284 / 4.32 ( 2718) link_NAG-ASN : bond 0.00470 / 0.33 ( 30) link_NAG-ASN : angle 2.54521 / 1.88 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 139 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.4756 (OUTLIER) cc_final: 0.4301 (p) REVERT: A 85 PRO cc_start: 0.7692 (Cg_exo) cc_final: 0.7424 (Cg_endo) REVERT: A 296 LEU cc_start: 0.7551 (tp) cc_final: 0.7017 (pp) REVERT: A 347 PHE cc_start: 0.3019 (OUTLIER) cc_final: 0.2280 (t80) REVERT: A 480 CYS cc_start: 0.2727 (OUTLIER) cc_final: 0.1147 (p) REVERT: A 759 PHE cc_start: 0.5554 (OUTLIER) cc_final: 0.5271 (m-80) REVERT: A 873 TYR cc_start: 0.7076 (OUTLIER) cc_final: 0.6218 (m-80) REVERT: B 242 LEU cc_start: 0.7070 (mm) cc_final: 0.6761 (tp) REVERT: B 360 ASN cc_start: 0.7305 (t0) cc_final: 0.7024 (t0) REVERT: B 365 TYR cc_start: 0.7178 (m-80) cc_final: 0.6903 (m-80) REVERT: B 577 ARG cc_start: 0.6866 (ttp80) cc_final: 0.6099 (ptm160) REVERT: B 873 TYR cc_start: 0.8241 (OUTLIER) cc_final: 0.7914 (m-10) REVERT: C 64 TRP cc_start: 0.7583 (t60) cc_final: 0.7081 (t60) REVERT: C 66 HIS cc_start: 0.4839 (m-70) cc_final: 0.4601 (m90) REVERT: C 129 LYS cc_start: 0.8834 (mttm) cc_final: 0.8428 (tmmt) REVERT: C 169 GLU cc_start: 0.8244 (tp30) cc_final: 0.7980 (tp30) REVERT: C 564 GLN cc_start: 0.6767 (mt0) cc_final: 0.6182 (mt0) REVERT: C 740 MET cc_start: 0.6418 (tpp) cc_final: 0.5783 (tpp) REVERT: C 759 PHE cc_start: 0.7121 (OUTLIER) cc_final: 0.5817 (m-10) REVERT: C 904 TYR cc_start: 0.7968 (m-80) cc_final: 0.7384 (m-10) outliers start: 58 outliers final: 43 residues processed: 191 average time/residue: 0.1357 time to fit residues: 42.9081 Evaluate side-chains 184 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 134 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 1032 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 156 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 227 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 46 optimal weight: 0.0980 chunk 151 optimal weight: 0.0370 chunk 245 optimal weight: 9.9990 chunk 291 optimal weight: 0.9980 chunk 246 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN C 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.193584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.164877 restraints weight = 45454.663| |-----------------------------------------------------------------------------| r_work (start): 0.4331 rms_B_bonded: 3.99 r_work: 0.3917 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24423 Z= 0.117 Angle : 0.573 10.894 33295 Z= 0.290 Chirality : 0.044 0.292 3876 Planarity : 0.004 0.061 4251 Dihedral : 4.861 59.336 3205 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.80 % Allowed : 13.65 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.15), residues: 2955 helix: 0.70 (0.20), residues: 654 sheet: -0.57 (0.21), residues: 576 loop : -0.70 (0.15), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 357 TYR 0.017 0.001 TYR C1067 PHE 0.017 0.001 PHE B 86 TRP 0.012 0.001 TRP C 64 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (24359) covalent geometry : angle 0.55907 / 0.29 (33137) SS BOND : bond 0.00194 / 0.13 ( 34) SS BOND : angle 1.50584 / 0.97 ( 68) hydrogen bonds : bond 0.03983 / 2.58 ( 1009) hydrogen bonds : angle 5.89278 / 4.13 ( 2718) link_NAG-ASN : bond 0.00348 / 0.23 ( 30) link_NAG-ASN : angle 2.20603 / 1.56 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 157 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 PRO cc_start: 0.7560 (Cg_exo) cc_final: 0.7350 (Cg_endo) REVERT: A 296 LEU cc_start: 0.7594 (tp) cc_final: 0.7056 (pp) REVERT: A 347 PHE cc_start: 0.2713 (OUTLIER) cc_final: 0.1979 (t80) REVERT: A 480 CYS cc_start: 0.2218 (OUTLIER) cc_final: 0.0629 (p) REVERT: A 759 PHE cc_start: 0.5549 (OUTLIER) cc_final: 0.5302 (m-80) REVERT: A 873 TYR cc_start: 0.6896 (OUTLIER) cc_final: 0.6108 (m-80) REVERT: B 223 LEU cc_start: 0.5947 (mp) cc_final: 0.5724 (mp) REVERT: B 242 LEU cc_start: 0.6802 (mm) cc_final: 0.6532 (tp) REVERT: B 353 TRP cc_start: 0.3302 (p-90) cc_final: 0.2342 (p-90) REVERT: B 360 ASN cc_start: 0.7321 (t0) cc_final: 0.6696 (p0) REVERT: B 365 TYR cc_start: 0.7093 (m-80) cc_final: 0.6812 (m-80) REVERT: B 577 ARG cc_start: 0.6812 (ttp80) cc_final: 0.6088 (ptm160) REVERT: C 64 TRP cc_start: 0.7603 (t60) cc_final: 0.7158 (t60) REVERT: C 66 HIS cc_start: 0.4874 (m-70) cc_final: 0.4641 (m90) REVERT: C 129 LYS cc_start: 0.8731 (mttm) cc_final: 0.8499 (tmmt) REVERT: C 564 GLN cc_start: 0.6488 (mt0) cc_final: 0.5959 (mt0) REVERT: C 649 CYS cc_start: 0.6093 (t) cc_final: 0.5839 (t) REVERT: C 740 MET cc_start: 0.6373 (tpp) cc_final: 0.5829 (tpp) REVERT: C 759 PHE cc_start: 0.6960 (OUTLIER) cc_final: 0.5697 (m-10) REVERT: C 904 TYR cc_start: 0.7849 (m-80) cc_final: 0.7140 (m-10) REVERT: C 1058 HIS cc_start: 0.7788 (m-70) cc_final: 0.7552 (m-70) outliers start: 47 outliers final: 37 residues processed: 196 average time/residue: 0.1353 time to fit residues: 43.5983 Evaluate side-chains 186 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 144 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 1032 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 255 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 265 optimal weight: 3.9990 chunk 179 optimal weight: 0.8980 chunk 133 optimal weight: 7.9990 chunk 250 optimal weight: 6.9990 chunk 225 optimal weight: 9.9990 chunk 218 optimal weight: 0.0870 chunk 292 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN C 196 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.193130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.163513 restraints weight = 45402.690| |-----------------------------------------------------------------------------| r_work (start): 0.4299 rms_B_bonded: 3.50 r_work: 0.3951 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24423 Z= 0.131 Angle : 0.583 15.227 33295 Z= 0.293 Chirality : 0.044 0.286 3876 Planarity : 0.004 0.061 4251 Dihedral : 4.830 59.381 3205 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.84 % Allowed : 14.03 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.15), residues: 2955 helix: 0.70 (0.20), residues: 655 sheet: -0.58 (0.20), residues: 588 loop : -0.67 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 357 TYR 0.018 0.001 TYR B 266 PHE 0.017 0.001 PHE B 86 TRP 0.012 0.001 TRP C 64 HIS 0.007 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (24359) covalent geometry : angle 0.57013 / 0.29 (33137) SS BOND : bond 0.00229 / 0.14 ( 34) SS BOND : angle 1.47470 / 0.96 ( 68) hydrogen bonds : bond 0.04017 / 2.61 ( 1009) hydrogen bonds : angle 5.88319 / 4.12 ( 2718) link_NAG-ASN : bond 0.00336 / 0.22 ( 30) link_NAG-ASN : angle 2.13711 / 1.51 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5936.51 seconds wall clock time: 102 minutes 36.80 seconds (6156.80 seconds total)