Starting phenix.real_space_refine on Sun Jul 5 20:56:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7k8x_22734/07_2026/7k8x_22734.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k8x_22734/07_2026/7k8x_22734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7k8x_22734/07_2026/7k8x_22734.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k8x_22734/07_2026/7k8x_22734.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k8x_22734/07_2026/7k8x_22734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k8x_22734/07_2026/7k8x_22734.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7k8x_22734/07_2026/7k8x_22734.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7k8x_22734/07_2026/7k8x_22734.cif" } resolution = 3.9 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3238 atoms to isotropic. 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 127 5.16 5 C 17436 2.51 5 N 4520 2.21 5 O 5316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 168 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: 27399 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "B" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "C" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'CIS': 1, 'PTRANS': 49, 'TRANS': 951} Chain breaks: 7 Chain: "D" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 991 Classifications: {'peptide': 128} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 121} Chain: "E" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 991 Classifications: {'peptide': 128} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 121} Chain: "F" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 778 Classifications: {'peptide': 108} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "G" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 778 Classifications: {'peptide': 108} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 6.11, per 1000 atoms: 0.22 Number of scatterers: 27399 At special positions: 0 Unit cell: (131.252, 149.644, 201.476, 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 127 16.00 O 5316 8.00 N 4520 7.00 C 17436 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, 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 343 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A 717 " " NAG A1309 " - " ASN A 801 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 234 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 717 " " NAG B1306 " - " ASN B 801 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B 331 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 165 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C 717 " " NAG C1309 " - " ASN C 801 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 1.1 seconds 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6462 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 59 sheets defined 22.2% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.805A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.344A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.632A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.019A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.599A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.278A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.336A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.596A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.141A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.616A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.050A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.571A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.930A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.669A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.554A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.324A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.052A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 405 through 410 removed outlier: 6.106A 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 502 through 505 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.697A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (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: 4.486A 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 985 through 1033 removed outlier: 4.428A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.994A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'G' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.908A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.355A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.091A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.963A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.246A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.242A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 314 through 319 removed outlier: 6.370A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.191A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.003A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASN A 437 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N PHE A 374 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.137A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.542A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.069A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 666 " --> pdb=" O ILE A 670 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.878A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 712 through 715 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.105A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.505A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.834A 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 1120 through 1125 removed outlier: 4.157A 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 31 removed outlier: 3.921A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.858A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.982A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.245A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.188A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.825A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.746A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.815A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.186A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 448 through 454 removed outlier: 5.718A pdb=" N TYR B 449 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N PHE B 497 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.437A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.182A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.536A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.536A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.530A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.131A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.266A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.144A 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: 5.822A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.632A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.892A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.420A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.838A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.977A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 712 through 728 removed outlier: 3.606A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 712 through 728 removed outlier: 3.606A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF5, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AF6, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.510A pdb=" N MET D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TRP D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.689A pdb=" N ASP D 118 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AF9, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.510A pdb=" N MET E 34 " --> pdb=" O TRP E 50 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TRP E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.689A pdb=" N ASP E 118 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 9 through 13 removed outlier: 3.650A pdb=" N THR F 105 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP F 35 " --> pdb=" O MET F 47 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 19 through 24 Processing sheet with id=AG4, first strand: chain 'G' and resid 9 through 13 removed outlier: 3.651A pdb=" N THR G 105 " --> pdb=" O VAL G 11 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP G 35 " --> pdb=" O MET G 47 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 19 through 24 1140 hydrogen bonds defined for protein. 3075 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.42 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8766 1.34 - 1.46: 6937 1.46 - 1.58: 12145 1.58 - 1.70: 0 1.70 - 1.82: 163 Bond restraints: 28011 Sorted by residual: bond pdb=" CA THR G 95A" pdb=" C THR G 95A" ideal model delta sigma weight residual 1.525 1.570 -0.045 2.10e-02 2.27e+03 4.63e+00 bond pdb=" N SER G 95 " pdb=" CA SER G 95 " ideal model delta sigma weight residual 1.456 1.483 -0.027 1.28e-02 6.10e+03 4.31e+00 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.60e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.93e+00 bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.63e+00 ... (remaining 28006 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 37515 2.12 - 4.25: 526 4.25 - 6.37: 50 6.37 - 8.50: 9 8.50 - 10.62: 5 Bond angle restraints: 38105 Sorted by residual: angle pdb=" N LEU E 107 " pdb=" CA LEU E 107 " pdb=" C LEU E 107 " ideal model delta sigma weight residual 113.55 104.67 8.88 1.26e+00 6.30e-01 4.96e+01 angle pdb=" N PHE G 98 " pdb=" CA PHE G 98 " pdb=" C PHE G 98 " ideal model delta sigma weight residual 108.07 117.57 -9.50 1.38e+00 5.25e-01 4.74e+01 angle pdb=" O SER G 94 " pdb=" C SER G 94 " pdb=" N SER G 95 " ideal model delta sigma weight residual 122.72 116.59 6.13 1.15e+00 7.56e-01 2.84e+01 angle pdb=" CA SER G 94 " pdb=" C SER G 94 " pdb=" N SER G 95 " ideal model delta sigma weight residual 116.18 122.29 -6.11 1.29e+00 6.01e-01 2.24e+01 angle pdb=" CA SER G 95 " pdb=" C SER G 95 " pdb=" N THR G 95A" ideal model delta sigma weight residual 116.06 121.19 -5.13 1.29e+00 6.01e-01 1.58e+01 ... (remaining 38100 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 15065 17.82 - 35.65: 1041 35.65 - 53.47: 221 53.47 - 71.30: 72 71.30 - 89.12: 22 Dihedral angle restraints: 16421 sinusoidal: 6346 harmonic: 10075 Sorted by residual: dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -173.22 87.22 1 1.00e+01 1.00e-02 9.13e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual -86.00 0.39 -86.39 1 1.00e+01 1.00e-02 9.00e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -169.68 83.68 1 1.00e+01 1.00e-02 8.54e+01 ... (remaining 16418 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.277: 4392 0.277 - 0.555: 7 0.555 - 0.832: 0 0.832 - 1.109: 2 1.109 - 1.386: 1 Chirality restraints: 4402 Sorted by residual: chirality pdb=" C1 NAG A1307 " pdb=" ND2 ASN A 709 " pdb=" C2 NAG A1307 " pdb=" O5 NAG A1307 " both_signs ideal model delta sigma weight residual False -2.40 -1.01 -1.39 2.00e-01 2.50e+01 4.81e+01 chirality pdb=" C1 NAG A1306 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG A1306 " pdb=" O5 NAG A1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.38 -1.02 2.00e-01 2.50e+01 2.58e+01 chirality pdb=" C1 NAG A1310 " pdb=" ND2 ASN A1074 " pdb=" C2 NAG A1310 " pdb=" O5 NAG A1310 " both_signs ideal model delta sigma weight residual False -2.40 -3.34 0.94 2.00e-01 2.50e+01 2.19e+01 ... (remaining 4399 not shown) Planarity restraints: 4915 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.063 2.00e-02 2.50e+03 6.29e-02 4.95e+01 pdb=" CG ASN A 331 " -0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.089 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " 0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1074 " 0.063 2.00e-02 2.50e+03 5.89e-02 4.33e+01 pdb=" CG ASN A1074 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN A1074 " -0.029 2.00e-02 2.50e+03 pdb=" ND2 ASN A1074 " -0.083 2.00e-02 2.50e+03 pdb=" C1 NAG A1310 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " 0.046 2.00e-02 2.50e+03 4.83e-02 2.92e+01 pdb=" CG ASN A 343 " -0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " -0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " -0.071 2.00e-02 2.50e+03 pdb=" C1 NAG A1305 " 0.062 2.00e-02 2.50e+03 ... (remaining 4912 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 161 2.47 - 3.07: 18392 3.07 - 3.68: 42161 3.68 - 4.29: 61494 4.29 - 4.90: 99780 Nonbonded interactions: 221988 Sorted by model distance: nonbonded pdb=" CB TYR F 87 " pdb=" CD1 PHE F 98 " model vdw 1.857 3.740 nonbonded pdb=" O ALA D 109 " pdb=" OH TYR D 114 " model vdw 1.865 3.040 nonbonded pdb=" CD2 TRP E 47 " pdb=" CG2 THR G 95A" model vdw 1.938 3.680 nonbonded pdb=" O ALA E 109 " pdb=" N ASP E 111 " model vdw 1.984 3.120 nonbonded pdb=" ND2 ASN A1134 " pdb=" C1 NAG A1311 " model vdw 2.034 3.550 ... (remaining 221983 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 1308) selection = chain 'B' selection = (chain 'C' and resid 27 through 1308) } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.650 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.820 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.301 28082 Z= 0.237 Angle : 0.706 25.704 38272 Z= 0.371 Chirality : 0.056 1.386 4402 Planarity : 0.004 0.075 4888 Dihedral : 13.155 89.124 9830 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.33 % Favored : 96.41 % Rotamer: Outliers : 2.49 % Allowed : 3.36 % Favored : 94.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.12), residues: 3422 helix: -0.98 (0.17), residues: 678 sheet: -0.89 (0.15), residues: 891 loop : -1.74 (0.12), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.000 ARG C 567 TYR 0.031 0.001 TYR E 115 PHE 0.021 0.001 PHE C 759 TRP 0.017 0.001 TRP D 36 HIS 0.004 0.000 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.16 (28011) covalent geometry : angle 0.61885 / 0.35 (38105) SS BOND : bond 0.00289 / 0.17 ( 43) SS BOND : angle 1.55540 / 1.05 ( 86) hydrogen bonds : bond 0.15433 / 10.01 ( 1114) hydrogen bonds : angle 7.35602 / 5.06 ( 3075) Misc. bond : bond 0.00157 / 0.08 ( 1) link_NAG-ASN : bond 0.11464 / 7.33 ( 27) link_NAG-ASN : angle 7.24419 / 4.59 ( 81) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 431 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7585 (p0) cc_final: 0.6773 (m-40) REVERT: A 110 LEU cc_start: 0.7899 (pp) cc_final: 0.7650 (mm) REVERT: A 189 LEU cc_start: 0.9573 (tp) cc_final: 0.9327 (tt) REVERT: A 360 ASN cc_start: 0.9052 (m-40) cc_final: 0.8379 (p0) REVERT: A 388 ASN cc_start: 0.7436 (m-40) cc_final: 0.5936 (p0) REVERT: A 402 ILE cc_start: 0.8318 (tp) cc_final: 0.8052 (tt) REVERT: A 614 ASP cc_start: 0.8468 (t0) cc_final: 0.8164 (t0) REVERT: A 646 ARG cc_start: 0.8557 (mtt180) cc_final: 0.8347 (tpm170) REVERT: A 711 SER cc_start: 0.8539 (m) cc_final: 0.8302 (p) REVERT: A 716 THR cc_start: 0.8878 (p) cc_final: 0.8671 (t) REVERT: A 726 ILE cc_start: 0.9453 (mt) cc_final: 0.8971 (tp) REVERT: A 740 MET cc_start: 0.9081 (ttt) cc_final: 0.8839 (ttp) REVERT: A 855 PHE cc_start: 0.7501 (m-80) cc_final: 0.7172 (m-80) REVERT: A 984 LEU cc_start: 0.7899 (tp) cc_final: 0.7641 (tp) REVERT: A 1114 ILE cc_start: 0.8268 (mm) cc_final: 0.8045 (pt) REVERT: B 223 LEU cc_start: 0.9066 (tp) cc_final: 0.8791 (tp) REVERT: B 773 GLU cc_start: 0.8418 (tp30) cc_final: 0.8187 (tp30) REVERT: B 869 MET cc_start: 0.9071 (mtt) cc_final: 0.8625 (mpp) REVERT: B 1119 ASN cc_start: 0.8412 (m-40) cc_final: 0.8123 (m-40) REVERT: B 1120 THR cc_start: 0.9043 (p) cc_final: 0.8788 (t) REVERT: B 1129 VAL cc_start: 0.6965 (t) cc_final: 0.6593 (m) REVERT: C 229 LEU cc_start: 0.8480 (tp) cc_final: 0.8105 (tp) REVERT: C 592 PHE cc_start: 0.7467 (p90) cc_final: 0.7229 (p90) REVERT: C 740 MET cc_start: 0.9072 (ttt) cc_final: 0.8845 (ttm) REVERT: C 773 GLU cc_start: 0.8491 (tp30) cc_final: 0.7758 (tm-30) REVERT: C 1129 VAL cc_start: 0.8215 (t) cc_final: 0.7937 (p) REVERT: D 47 TRP cc_start: 0.4118 (t60) cc_final: 0.3584 (t60) REVERT: D 73 ASP cc_start: 0.8769 (t0) cc_final: 0.8523 (t70) REVERT: D 93 VAL cc_start: 0.5692 (OUTLIER) cc_final: 0.5226 (t) REVERT: E 63 LYS cc_start: 0.8744 (mmtt) cc_final: 0.8134 (tptp) REVERT: E 80 TYR cc_start: 0.7997 (m-80) cc_final: 0.7495 (m-80) REVERT: F 32 LEU cc_start: 0.8355 (mp) cc_final: 0.8132 (tt) REVERT: F 34 SER cc_start: -0.0381 (OUTLIER) cc_final: -0.1356 (p) REVERT: F 49 TYR cc_start: 0.7710 (p90) cc_final: 0.7444 (p90) REVERT: F 59 SER cc_start: 0.4609 (OUTLIER) cc_final: 0.4406 (p) REVERT: F 63 SER cc_start: 0.5587 (OUTLIER) cc_final: 0.5135 (p) REVERT: F 67 SER cc_start: -0.0083 (OUTLIER) cc_final: -0.0377 (p) REVERT: G 34 SER cc_start: -0.1868 (OUTLIER) cc_final: -0.2228 (p) REVERT: G 42 LYS cc_start: 0.6771 (OUTLIER) cc_final: 0.5971 (ttpt) REVERT: G 48 ILE cc_start: 0.5672 (OUTLIER) cc_final: 0.4886 (mt) REVERT: G 54 ARG cc_start: 0.8291 (mtm-85) cc_final: 0.8040 (ttm110) REVERT: G 59 SER cc_start: 0.2454 (OUTLIER) cc_final: 0.1335 (p) REVERT: G 73 LEU cc_start: 0.7721 (tt) cc_final: 0.7287 (tt) REVERT: G 104 LEU cc_start: 0.7719 (tp) cc_final: 0.7282 (tt) REVERT: G 106 VAL cc_start: 0.6820 (OUTLIER) cc_final: 0.6408 (p) outliers start: 75 outliers final: 25 residues processed: 493 average time/residue: 0.1835 time to fit residues: 141.7832 Evaluate side-chains 213 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 42 LYS Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 42 LYS Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 89 CYS Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain G residue 106 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.0270 overall best weight: 3.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 125 ASN A 804 GLN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B 49 HIS B 218 GLN B 388 ASN B 675 GLN B 762 GLN B1142 GLN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 414 GLN C 655 HIS C 690 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 953 ASN C 957 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 ASN C1071 GLN C1074 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN F 17 GLN F 37 GLN F 38 GLN G 6 GLN G 17 GLN G 37 GLN G 60 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.072287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.050274 restraints weight = 150294.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.051775 restraints weight = 76666.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.052750 restraints weight = 48173.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.053402 restraints weight = 34415.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.053801 restraints weight = 27222.572| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 28082 Z= 0.229 Angle : 0.712 19.649 38272 Z= 0.357 Chirality : 0.048 0.325 4402 Planarity : 0.005 0.124 4888 Dihedral : 5.642 57.340 3775 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.62 % Favored : 96.32 % Rotamer: Outliers : 2.93 % Allowed : 11.10 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.13), residues: 3422 helix: 0.73 (0.19), residues: 667 sheet: -0.34 (0.16), residues: 890 loop : -1.13 (0.13), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C1107 TYR 0.034 0.002 TYR E 33 PHE 0.029 0.002 PHE D 102 TRP 0.026 0.003 TRP E 47 HIS 0.006 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.23 (28011) covalent geometry : angle 0.69815 / 0.35 (38105) SS BOND : bond 0.00463 / 0.30 ( 43) SS BOND : angle 1.76394 / 1.16 ( 86) hydrogen bonds : bond 0.04203 / 2.81 ( 1114) hydrogen bonds : angle 5.68539 / 3.88 ( 3075) Misc. bond : bond 0.00034 / 0.02 ( 1) link_NAG-ASN : bond 0.00548 / 0.31 ( 27) link_NAG-ASN : angle 2.58237 / 1.89 ( 81) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 198 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7518 (p0) cc_final: 0.7141 (m-40) REVERT: A 117 LEU cc_start: 0.9154 (mt) cc_final: 0.8796 (tp) REVERT: A 275 PHE cc_start: 0.8123 (m-10) cc_final: 0.7772 (m-10) REVERT: A 360 ASN cc_start: 0.8861 (m-40) cc_final: 0.8306 (p0) REVERT: A 512 VAL cc_start: 0.9661 (OUTLIER) cc_final: 0.9429 (m) REVERT: A 562 PHE cc_start: 0.7146 (p90) cc_final: 0.6399 (p90) REVERT: A 740 MET cc_start: 0.9022 (ttt) cc_final: 0.8704 (ttp) REVERT: A 984 LEU cc_start: 0.8207 (tp) cc_final: 0.7912 (tp) REVERT: A 1034 LEU cc_start: 0.9684 (OUTLIER) cc_final: 0.9427 (mm) REVERT: A 1081 ILE cc_start: 0.9544 (mt) cc_final: 0.9285 (tp) REVERT: B 613 GLN cc_start: 0.9300 (OUTLIER) cc_final: 0.8852 (mp10) REVERT: B 740 MET cc_start: 0.9406 (ttt) cc_final: 0.9151 (ttt) REVERT: B 762 GLN cc_start: 0.8549 (pt0) cc_final: 0.8288 (pt0) REVERT: B 869 MET cc_start: 0.9468 (mtt) cc_final: 0.8985 (mpp) REVERT: B 1029 MET cc_start: 0.8924 (tpp) cc_final: 0.8647 (tpp) REVERT: B 1119 ASN cc_start: 0.8679 (m-40) cc_final: 0.8363 (m-40) REVERT: B 1120 THR cc_start: 0.9372 (p) cc_final: 0.9085 (t) REVERT: B 1129 VAL cc_start: 0.9241 (t) cc_final: 0.9017 (m) REVERT: C 229 LEU cc_start: 0.8579 (tp) cc_final: 0.8201 (tp) REVERT: C 488 CYS cc_start: 0.2856 (OUTLIER) cc_final: 0.2325 (t) REVERT: C 740 MET cc_start: 0.9073 (ttt) cc_final: 0.8650 (ttm) REVERT: C 773 GLU cc_start: 0.8304 (tp30) cc_final: 0.8044 (tm-30) REVERT: D 47 TRP cc_start: 0.5130 (t60) cc_final: 0.4729 (t60) REVERT: D 48 MET cc_start: 0.4973 (ttp) cc_final: 0.4292 (ttp) REVERT: D 73 ASP cc_start: 0.8776 (t0) cc_final: 0.8486 (t70) REVERT: E 10 GLU cc_start: 0.7711 (tt0) cc_final: 0.7421 (tm-30) REVERT: E 63 LYS cc_start: 0.8719 (mmtt) cc_final: 0.8072 (tptp) REVERT: E 67 ARG cc_start: 0.5299 (ptm160) cc_final: 0.4875 (ptm160) REVERT: E 80 TYR cc_start: 0.8145 (m-80) cc_final: 0.7684 (m-80) REVERT: E 95 TYR cc_start: 0.6381 (m-80) cc_final: 0.6161 (m-10) REVERT: F 67 SER cc_start: -0.0752 (OUTLIER) cc_final: -0.1194 (p) REVERT: F 85 ASP cc_start: 0.5810 (p0) cc_final: 0.5308 (m-30) REVERT: G 33 VAL cc_start: 0.5610 (OUTLIER) cc_final: 0.5323 (p) REVERT: G 42 LYS cc_start: 0.7106 (mmtp) cc_final: 0.6416 (ttpt) REVERT: G 86 TYR cc_start: 0.7247 (m-10) cc_final: 0.6752 (m-10) REVERT: G 104 LEU cc_start: 0.7950 (tp) cc_final: 0.7396 (tt) outliers start: 88 outliers final: 44 residues processed: 269 average time/residue: 0.1757 time to fit residues: 76.3012 Evaluate side-chains 198 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 148 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 113 TYR Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 114 TYR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 89 CYS Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 95 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 53 optimal weight: 8.9990 chunk 323 optimal weight: 10.0000 chunk 233 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 237 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 ASN B 498 GLN B 762 GLN B 901 GLN B 907 ASN C 52 GLN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS C1119 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN E 1 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN G 38 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.069013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.046879 restraints weight = 151857.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.048286 restraints weight = 76125.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.049200 restraints weight = 47514.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.049777 restraints weight = 34157.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.050200 restraints weight = 27189.961| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 28082 Z= 0.248 Angle : 0.706 14.046 38272 Z= 0.355 Chirality : 0.048 0.326 4402 Planarity : 0.005 0.071 4888 Dihedral : 5.044 57.730 3736 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.03 % Favored : 95.91 % Rotamer: Outliers : 3.19 % Allowed : 14.46 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.14), residues: 3422 helix: 1.11 (0.20), residues: 661 sheet: -0.19 (0.16), residues: 933 loop : -0.95 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 509 TYR 0.028 0.002 TYR E 33 PHE 0.020 0.002 PHE C 347 TRP 0.020 0.002 TRP E 47 HIS 0.006 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.25 (28011) covalent geometry : angle 0.69016 / 0.35 (38105) SS BOND : bond 0.00490 / 0.33 ( 43) SS BOND : angle 1.94225 / 1.27 ( 86) hydrogen bonds : bond 0.04408 / 2.95 ( 1114) hydrogen bonds : angle 5.54361 / 3.78 ( 3075) Misc. bond : bond 0.00019 / 0.01 ( 1) link_NAG-ASN : bond 0.00528 / 0.30 ( 27) link_NAG-ASN : angle 2.72600 / 1.93 ( 81) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 149 time to evaluate : 0.845 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 81 ASN cc_start: 0.7490 (p0) cc_final: 0.7121 (m-40) REVERT: A 360 ASN cc_start: 0.8820 (m-40) cc_final: 0.8306 (p0) REVERT: A 562 PHE cc_start: 0.7351 (p90) cc_final: 0.6813 (p90) REVERT: A 577 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.7116 (mtm-85) REVERT: A 661 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8311 (tp30) REVERT: A 740 MET cc_start: 0.8985 (ttt) cc_final: 0.8723 (ttp) REVERT: A 869 MET cc_start: 0.9411 (mtm) cc_final: 0.9081 (ptp) REVERT: A 984 LEU cc_start: 0.8477 (tp) cc_final: 0.8120 (tp) REVERT: B 223 LEU cc_start: 0.9145 (tp) cc_final: 0.8890 (tp) REVERT: B 498 GLN cc_start: 0.6942 (OUTLIER) cc_final: 0.6739 (tp40) REVERT: B 1002 GLN cc_start: 0.9247 (OUTLIER) cc_final: 0.8856 (tm-30) REVERT: B 1029 MET cc_start: 0.9303 (tpp) cc_final: 0.8939 (tpp) REVERT: B 1041 ASP cc_start: 0.8276 (t0) cc_final: 0.8051 (t0) REVERT: C 229 LEU cc_start: 0.8689 (tp) cc_final: 0.8422 (tp) REVERT: C 488 CYS cc_start: 0.3022 (OUTLIER) cc_final: 0.2495 (t) REVERT: C 759 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.7698 (t80) REVERT: C 773 GLU cc_start: 0.8365 (tp30) cc_final: 0.8049 (tm-30) REVERT: C 1094 VAL cc_start: 0.9510 (OUTLIER) cc_final: 0.9298 (t) REVERT: D 47 TRP cc_start: 0.5336 (t60) cc_final: 0.4521 (t60) REVERT: D 48 MET cc_start: 0.4566 (ttp) cc_final: 0.3974 (ttm) REVERT: D 73 ASP cc_start: 0.8833 (t0) cc_final: 0.8544 (t70) REVERT: E 10 GLU cc_start: 0.7709 (tt0) cc_final: 0.7361 (tm-30) REVERT: E 33 TYR cc_start: 0.7548 (m-80) cc_final: 0.7257 (m-80) REVERT: E 80 TYR cc_start: 0.8246 (m-80) cc_final: 0.7817 (m-80) REVERT: E 81 MET cc_start: 0.6675 (tpp) cc_final: 0.5138 (tpp) REVERT: E 83 LEU cc_start: 0.8159 (tp) cc_final: 0.7951 (tp) REVERT: E 95 TYR cc_start: 0.6444 (m-80) cc_final: 0.6091 (m-10) REVERT: F 47 MET cc_start: 0.7545 (mtt) cc_final: 0.7321 (mpp) REVERT: F 85 ASP cc_start: 0.5975 (p0) cc_final: 0.5657 (m-30) REVERT: G 36 TYR cc_start: 0.7181 (m-80) cc_final: 0.6664 (m-80) REVERT: G 42 LYS cc_start: 0.6995 (mmtp) cc_final: 0.6397 (ttpt) REVERT: G 47 MET cc_start: 0.7248 (mmm) cc_final: 0.6318 (ptm) REVERT: G 73 LEU cc_start: 0.7687 (tt) cc_final: 0.7323 (tt) outliers start: 96 outliers final: 47 residues processed: 234 average time/residue: 0.1624 time to fit residues: 62.5576 Evaluate side-chains 175 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 122 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 113 TYR Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 67 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 307 optimal weight: 20.0000 chunk 93 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 247 optimal weight: 6.9990 chunk 277 optimal weight: 3.9990 chunk 336 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 329 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN B 762 GLN B 992 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.068820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.046455 restraints weight = 151766.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.047875 restraints weight = 75425.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.048795 restraints weight = 46874.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.049386 restraints weight = 33602.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.049774 restraints weight = 26800.469| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 28082 Z= 0.181 Angle : 0.620 10.710 38272 Z= 0.312 Chirality : 0.046 0.318 4402 Planarity : 0.004 0.068 4888 Dihedral : 4.683 54.237 3728 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.73 % Allowed : 15.99 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.14), residues: 3422 helix: 1.28 (0.20), residues: 663 sheet: -0.06 (0.16), residues: 890 loop : -0.85 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 577 TYR 0.015 0.001 TYR B 204 PHE 0.014 0.001 PHE A 562 TRP 0.014 0.002 TRP E 47 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (28011) covalent geometry : angle 0.60509 / 0.31 (38105) SS BOND : bond 0.00363 / 0.24 ( 43) SS BOND : angle 1.68963 / 1.10 ( 86) hydrogen bonds : bond 0.04005 / 2.68 ( 1114) hydrogen bonds : angle 5.36168 / 3.65 ( 3075) Misc. bond : bond 0.00007 / 0.00 ( 1) link_NAG-ASN : bond 0.00402 / 0.20 ( 27) link_NAG-ASN : angle 2.51106 / 1.84 ( 81) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 140 time to evaluate : 1.071 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 81 ASN cc_start: 0.7416 (p0) cc_final: 0.7212 (m-40) REVERT: A 360 ASN cc_start: 0.8791 (m-40) cc_final: 0.8292 (p0) REVERT: A 562 PHE cc_start: 0.7445 (p90) cc_final: 0.7157 (p90) REVERT: A 661 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8402 (tp30) REVERT: A 759 PHE cc_start: 0.8502 (OUTLIER) cc_final: 0.7940 (t80) REVERT: A 1005 GLN cc_start: 0.8986 (mt0) cc_final: 0.8618 (mm-40) REVERT: B 223 LEU cc_start: 0.9080 (tp) cc_final: 0.8850 (tp) REVERT: B 1029 MET cc_start: 0.9209 (tpp) cc_final: 0.8867 (tpp) REVERT: C 229 LEU cc_start: 0.8674 (tp) cc_final: 0.8399 (tp) REVERT: C 488 CYS cc_start: 0.3060 (OUTLIER) cc_final: 0.2545 (t) REVERT: C 773 GLU cc_start: 0.8284 (tp30) cc_final: 0.7968 (tm-30) REVERT: D 73 ASP cc_start: 0.8818 (t0) cc_final: 0.8538 (t70) REVERT: D 113 TYR cc_start: -0.0790 (OUTLIER) cc_final: -0.1193 (m-10) REVERT: E 10 GLU cc_start: 0.7669 (tt0) cc_final: 0.7394 (tm-30) REVERT: E 80 TYR cc_start: 0.8244 (m-80) cc_final: 0.7910 (m-80) REVERT: E 95 TYR cc_start: 0.6385 (m-80) cc_final: 0.6132 (m-80) REVERT: F 47 MET cc_start: 0.7701 (mtt) cc_final: 0.7470 (mtt) REVERT: F 85 ASP cc_start: 0.5939 (p0) cc_final: 0.5661 (m-30) REVERT: G 35 TRP cc_start: 0.6499 (m100) cc_final: 0.4521 (m100) REVERT: G 36 TYR cc_start: 0.7106 (m-80) cc_final: 0.6309 (m-80) REVERT: G 42 LYS cc_start: 0.7128 (mmtp) cc_final: 0.6389 (ttpt) REVERT: G 47 MET cc_start: 0.7661 (mmm) cc_final: 0.6294 (ptp) REVERT: G 73 LEU cc_start: 0.7840 (tt) cc_final: 0.4888 (tt) outliers start: 82 outliers final: 53 residues processed: 215 average time/residue: 0.1632 time to fit residues: 57.8162 Evaluate side-chains 173 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 117 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 734 THR 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 1027 THR Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 113 TYR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 67 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 30 optimal weight: 7.9990 chunk 314 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 224 optimal weight: 0.1980 chunk 217 optimal weight: 20.0000 chunk 118 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 239 optimal weight: 0.0870 chunk 246 optimal weight: 10.0000 chunk 210 optimal weight: 1.9990 chunk 333 optimal weight: 6.9990 overall best weight: 1.6362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 901 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 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 = 0.3605 r_free = 0.3605 target = 0.069242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.046960 restraints weight = 149857.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.048384 restraints weight = 73900.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.049321 restraints weight = 45720.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.049913 restraints weight = 32638.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.050322 restraints weight = 25926.285| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 28082 Z= 0.127 Angle : 0.581 10.409 38272 Z= 0.292 Chirality : 0.045 0.304 4402 Planarity : 0.004 0.067 4888 Dihedral : 4.474 53.414 3726 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.69 % Allowed : 16.69 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.14), residues: 3422 helix: 1.52 (0.21), residues: 660 sheet: -0.02 (0.16), residues: 893 loop : -0.76 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 577 TYR 0.015 0.001 TYR E 33 PHE 0.015 0.001 PHE A 562 TRP 0.019 0.002 TRP E 47 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (28011) covalent geometry : angle 0.56777 / 0.29 (38105) SS BOND : bond 0.00346 / 0.21 ( 43) SS BOND : angle 1.49046 / 0.96 ( 86) hydrogen bonds : bond 0.03798 / 2.52 ( 1114) hydrogen bonds : angle 5.16124 / 3.51 ( 3075) Misc. bond : bond 0.00004 / 0.00 ( 1) link_NAG-ASN : bond 0.00386 / 0.17 ( 27) link_NAG-ASN : angle 2.38677 / 1.76 ( 81) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 139 time to evaluate : 1.127 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 360 ASN cc_start: 0.8773 (m-40) cc_final: 0.8282 (p0) REVERT: A 492 LEU cc_start: 0.8696 (mp) cc_final: 0.8492 (mt) REVERT: A 562 PHE cc_start: 0.7536 (p90) cc_final: 0.7286 (p90) REVERT: A 577 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.7010 (ttm-80) REVERT: A 759 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.8062 (t80) REVERT: B 223 LEU cc_start: 0.9051 (tp) cc_final: 0.8759 (tp) REVERT: B 613 GLN cc_start: 0.9264 (OUTLIER) cc_final: 0.8971 (pm20) REVERT: B 740 MET cc_start: 0.9380 (ttt) cc_final: 0.9157 (ttt) REVERT: B 1002 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8908 (tm-30) REVERT: B 1029 MET cc_start: 0.9178 (tpp) cc_final: 0.8834 (tpp) REVERT: B 1119 ASN cc_start: 0.8603 (m-40) cc_final: 0.8371 (m-40) REVERT: C 488 CYS cc_start: 0.3009 (OUTLIER) cc_final: 0.2542 (t) REVERT: C 773 GLU cc_start: 0.8219 (tp30) cc_final: 0.7905 (tm-30) REVERT: D 73 ASP cc_start: 0.8840 (t0) cc_final: 0.8550 (t70) REVERT: D 81 MET cc_start: 0.6320 (ttt) cc_final: 0.5524 (ttm) REVERT: D 112 TYR cc_start: 0.2215 (OUTLIER) cc_final: 0.0522 (m-10) REVERT: D 113 TYR cc_start: -0.0588 (OUTLIER) cc_final: -0.0986 (m-10) REVERT: E 10 GLU cc_start: 0.7646 (tt0) cc_final: 0.7411 (tm-30) REVERT: E 80 TYR cc_start: 0.8251 (m-80) cc_final: 0.7846 (m-80) REVERT: E 83 LEU cc_start: 0.8055 (tp) cc_final: 0.7587 (tp) REVERT: E 95 TYR cc_start: 0.6286 (m-80) cc_final: 0.6063 (m-80) REVERT: F 47 MET cc_start: 0.7843 (mtt) cc_final: 0.7635 (mtt) REVERT: F 85 ASP cc_start: 0.5902 (p0) cc_final: 0.5646 (m-30) REVERT: G 35 TRP cc_start: 0.6383 (m100) cc_final: 0.4626 (m100) REVERT: G 36 TYR cc_start: 0.7063 (m-80) cc_final: 0.6329 (m-80) REVERT: G 42 LYS cc_start: 0.7177 (mmtp) cc_final: 0.6410 (ttpt) REVERT: G 47 MET cc_start: 0.7908 (mmm) cc_final: 0.6341 (ptp) REVERT: G 73 LEU cc_start: 0.7793 (tt) cc_final: 0.5209 (tt) REVERT: G 86 TYR cc_start: 0.7175 (m-10) cc_final: 0.6337 (m-10) outliers start: 81 outliers final: 48 residues processed: 215 average time/residue: 0.1625 time to fit residues: 58.8276 Evaluate side-chains 172 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 117 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 112 TYR Chi-restraints excluded: chain D residue 113 TYR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 65 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 46 optimal weight: 10.0000 chunk 315 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 chunk 257 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 302 optimal weight: 10.0000 chunk 166 optimal weight: 0.0980 chunk 41 optimal weight: 6.9990 chunk 176 optimal weight: 8.9990 overall best weight: 4.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN A 804 GLN A 935 GLN B 498 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1002 GLN B1088 HIS C 644 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN C1101 HIS ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.067330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.044398 restraints weight = 147445.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.045699 restraints weight = 75182.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.046545 restraints weight = 47839.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.047108 restraints weight = 34998.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.047443 restraints weight = 28230.847| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.5318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 28082 Z= 0.281 Angle : 0.701 11.452 38272 Z= 0.354 Chirality : 0.047 0.324 4402 Planarity : 0.004 0.068 4888 Dihedral : 4.915 57.995 3726 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.49 % Allowed : 16.92 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.14), residues: 3422 helix: 1.25 (0.20), residues: 655 sheet: -0.04 (0.16), residues: 919 loop : -0.81 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 577 TYR 0.014 0.002 TYR D 94 PHE 0.017 0.002 PHE A 562 TRP 0.021 0.002 TRP E 47 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.28 (28011) covalent geometry : angle 0.68502 / 0.35 (38105) SS BOND : bond 0.00456 / 0.30 ( 43) SS BOND : angle 1.81682 / 1.18 ( 86) hydrogen bonds : bond 0.04337 / 2.90 ( 1114) hydrogen bonds : angle 5.52797 / 3.74 ( 3075) Misc. bond : bond 0.00010 / 0.01 ( 1) link_NAG-ASN : bond 0.00488 / 0.29 ( 27) link_NAG-ASN : angle 2.76106 / 1.97 ( 81) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 118 time to evaluate : 0.921 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 360 ASN cc_start: 0.8825 (m-40) cc_final: 0.8341 (p0) REVERT: A 394 ASN cc_start: 0.8393 (OUTLIER) cc_final: 0.8097 (t0) REVERT: A 759 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.8232 (t80) REVERT: B 740 MET cc_start: 0.9371 (ttt) cc_final: 0.9148 (ttt) REVERT: B 1002 GLN cc_start: 0.9284 (OUTLIER) cc_final: 0.8882 (tm-30) REVERT: B 1029 MET cc_start: 0.9322 (tpp) cc_final: 0.8859 (tpp) REVERT: C 488 CYS cc_start: 0.2722 (OUTLIER) cc_final: 0.2203 (t) REVERT: C 567 ARG cc_start: 0.7208 (mtm180) cc_final: 0.5025 (mmm-85) REVERT: C 773 GLU cc_start: 0.8420 (tp30) cc_final: 0.8065 (tm-30) REVERT: C 1101 HIS cc_start: 0.6384 (OUTLIER) cc_final: 0.5707 (m-70) REVERT: D 34 MET cc_start: 0.6007 (mmm) cc_final: 0.5106 (mmm) REVERT: D 73 ASP cc_start: 0.8908 (t0) cc_final: 0.8644 (t70) REVERT: D 112 TYR cc_start: 0.2210 (OUTLIER) cc_final: 0.1016 (m-10) REVERT: E 3 GLN cc_start: 0.7443 (mp10) cc_final: 0.7156 (mp10) REVERT: E 122 GLN cc_start: 0.7551 (tm-30) cc_final: 0.7336 (tm-30) REVERT: F 85 ASP cc_start: 0.6029 (p0) cc_final: 0.5754 (m-30) REVERT: G 35 TRP cc_start: 0.6766 (m100) cc_final: 0.5545 (m100) REVERT: G 36 TYR cc_start: 0.7024 (m-80) cc_final: 0.6393 (m-80) REVERT: G 42 LYS cc_start: 0.7055 (mmtp) cc_final: 0.6302 (ttpt) REVERT: G 73 LEU cc_start: 0.7964 (tt) cc_final: 0.6243 (tt) outliers start: 105 outliers final: 75 residues processed: 217 average time/residue: 0.1567 time to fit residues: 57.6879 Evaluate side-chains 188 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 107 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1039 ARG Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 112 TYR Chi-restraints excluded: chain D residue 113 TYR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 67 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 118 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 291 optimal weight: 0.9980 chunk 201 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 310 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 306 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN A 394 ASN B 901 GLN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 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 = 0.3564 r_free = 0.3564 target = 0.067671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.045693 restraints weight = 148409.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.047073 restraints weight = 73856.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.047963 restraints weight = 45913.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.048542 restraints weight = 32916.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.048847 restraints weight = 26236.986| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.5350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 28082 Z= 0.138 Angle : 0.606 11.493 38272 Z= 0.302 Chirality : 0.046 0.310 4402 Planarity : 0.004 0.064 4888 Dihedral : 4.690 59.416 3726 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.99 % Allowed : 17.65 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.14), residues: 3422 helix: 1.43 (0.21), residues: 662 sheet: 0.02 (0.17), residues: 891 loop : -0.74 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 577 TYR 0.015 0.001 TYR E 112 PHE 0.027 0.001 PHE A 562 TRP 0.023 0.002 TRP D 47 HIS 0.006 0.001 HIS C1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (28011) covalent geometry : angle 0.59184 / 0.30 (38105) SS BOND : bond 0.00317 / 0.21 ( 43) SS BOND : angle 1.53956 / 1.01 ( 86) hydrogen bonds : bond 0.03958 / 2.64 ( 1114) hydrogen bonds : angle 5.29233 / 3.59 ( 3075) Misc. bond : bond 0.00004 / 0.00 ( 1) link_NAG-ASN : bond 0.00385 / 0.17 ( 27) link_NAG-ASN : angle 2.49110 / 1.82 ( 81) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 118 time to evaluate : 1.117 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 360 ASN cc_start: 0.8792 (m-40) cc_final: 0.8332 (p0) REVERT: A 759 PHE cc_start: 0.8561 (OUTLIER) cc_final: 0.8122 (t80) REVERT: B 223 LEU cc_start: 0.8972 (tp) cc_final: 0.8652 (tp) REVERT: B 613 GLN cc_start: 0.9264 (OUTLIER) cc_final: 0.8982 (pm20) REVERT: B 740 MET cc_start: 0.9352 (ttt) cc_final: 0.8761 (ttt) REVERT: B 1002 GLN cc_start: 0.9477 (OUTLIER) cc_final: 0.9219 (tm-30) REVERT: B 1029 MET cc_start: 0.9229 (tpp) cc_final: 0.8770 (tpp) REVERT: C 488 CYS cc_start: 0.3240 (OUTLIER) cc_final: 0.2745 (t) REVERT: C 567 ARG cc_start: 0.7032 (mtm180) cc_final: 0.5003 (mmm-85) REVERT: C 759 PHE cc_start: 0.8396 (m-80) cc_final: 0.7881 (t80) REVERT: C 773 GLU cc_start: 0.8259 (tp30) cc_final: 0.7941 (tm-30) REVERT: D 34 MET cc_start: 0.6024 (mmm) cc_final: 0.5093 (mmm) REVERT: D 73 ASP cc_start: 0.8899 (t0) cc_final: 0.8604 (t70) REVERT: D 112 TYR cc_start: 0.1833 (OUTLIER) cc_final: 0.0861 (m-10) REVERT: E 3 GLN cc_start: 0.7431 (mp10) cc_final: 0.7125 (mp10) REVERT: E 48 MET cc_start: 0.6978 (mmt) cc_final: 0.6738 (mmt) REVERT: E 86 LEU cc_start: 0.6724 (mm) cc_final: 0.5971 (mt) REVERT: E 122 GLN cc_start: 0.7533 (tm-30) cc_final: 0.7291 (tm-30) REVERT: F 47 MET cc_start: 0.7419 (mtt) cc_final: 0.7186 (mpp) REVERT: F 85 ASP cc_start: 0.5928 (p0) cc_final: 0.5728 (m-30) REVERT: G 35 TRP cc_start: 0.6525 (m100) cc_final: 0.6257 (m100) REVERT: G 36 TYR cc_start: 0.7110 (m-80) cc_final: 0.6788 (m-80) REVERT: G 42 LYS cc_start: 0.7024 (mmtp) cc_final: 0.6025 (ttpt) REVERT: G 47 MET cc_start: 0.7874 (mmm) cc_final: 0.6518 (ptp) REVERT: G 86 TYR cc_start: 0.6998 (m-10) cc_final: 0.6787 (m-10) outliers start: 90 outliers final: 66 residues processed: 203 average time/residue: 0.1579 time to fit residues: 54.2943 Evaluate side-chains 181 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 110 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 112 TYR Chi-restraints excluded: chain D residue 113 TYR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 65 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 262 optimal weight: 0.9990 chunk 282 optimal weight: 7.9990 chunk 199 optimal weight: 6.9990 chunk 38 optimal weight: 30.0000 chunk 223 optimal weight: 8.9990 chunk 162 optimal weight: 0.9990 chunk 339 optimal weight: 8.9990 chunk 228 optimal weight: 10.0000 chunk 176 optimal weight: 0.9980 chunk 258 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 901 GLN B1002 GLN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 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 = 0.3578 r_free = 0.3578 target = 0.068273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.046257 restraints weight = 150501.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.047653 restraints weight = 73956.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.048567 restraints weight = 45785.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.049120 restraints weight = 32724.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.049536 restraints weight = 26078.332| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.5453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 28082 Z= 0.120 Angle : 0.591 11.798 38272 Z= 0.293 Chirality : 0.045 0.299 4402 Planarity : 0.004 0.080 4888 Dihedral : 4.483 58.002 3726 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.63 % Allowed : 17.89 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.14), residues: 3422 helix: 1.63 (0.21), residues: 654 sheet: -0.02 (0.17), residues: 906 loop : -0.71 (0.15), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 357 TYR 0.012 0.001 TYR A 351 PHE 0.026 0.001 PHE A 562 TRP 0.038 0.002 TRP A 353 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (28011) covalent geometry : angle 0.57753 / 0.29 (38105) SS BOND : bond 0.00272 / 0.18 ( 43) SS BOND : angle 1.41356 / 0.92 ( 86) hydrogen bonds : bond 0.03759 / 2.50 ( 1114) hydrogen bonds : angle 5.13766 / 3.49 ( 3075) Misc. bond : bond 0.00006 / 0.00 ( 1) link_NAG-ASN : bond 0.00413 / 0.19 ( 27) link_NAG-ASN : angle 2.44610 / 1.79 ( 81) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 120 time to evaluate : 1.029 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 360 ASN cc_start: 0.8784 (m-40) cc_final: 0.8317 (p0) REVERT: A 740 MET cc_start: 0.8975 (ttt) cc_final: 0.8314 (tmm) REVERT: A 759 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.8100 (t80) REVERT: B 223 LEU cc_start: 0.8957 (tp) cc_final: 0.8632 (tp) REVERT: B 357 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7729 (ttm-80) REVERT: B 740 MET cc_start: 0.9357 (ttt) cc_final: 0.8768 (ttt) REVERT: B 1002 GLN cc_start: 0.9357 (OUTLIER) cc_final: 0.8958 (tm-30) REVERT: B 1029 MET cc_start: 0.9227 (tpp) cc_final: 0.8820 (tpp) REVERT: B 1039 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8106 (mtp180) REVERT: C 488 CYS cc_start: 0.3155 (OUTLIER) cc_final: 0.2692 (t) REVERT: C 567 ARG cc_start: 0.7014 (mtm180) cc_final: 0.5061 (mmm-85) REVERT: C 759 PHE cc_start: 0.8372 (m-80) cc_final: 0.7487 (t80) REVERT: C 773 GLU cc_start: 0.8247 (tp30) cc_final: 0.7917 (tm-30) REVERT: D 34 MET cc_start: 0.6086 (mmm) cc_final: 0.5126 (mmm) REVERT: D 73 ASP cc_start: 0.8897 (t0) cc_final: 0.8615 (t70) REVERT: E 3 GLN cc_start: 0.7412 (mp10) cc_final: 0.7087 (mp10) REVERT: E 48 MET cc_start: 0.6929 (mmt) cc_final: 0.6721 (mmt) REVERT: E 86 LEU cc_start: 0.6762 (mm) cc_final: 0.6066 (mt) REVERT: E 122 GLN cc_start: 0.7539 (tm-30) cc_final: 0.7291 (tm-30) REVERT: F 31 ASN cc_start: 0.8211 (p0) cc_final: 0.7919 (p0) REVERT: F 85 ASP cc_start: 0.5908 (p0) cc_final: 0.5705 (m-30) REVERT: G 35 TRP cc_start: 0.6426 (m100) cc_final: 0.6221 (m100) REVERT: G 36 TYR cc_start: 0.7097 (m-80) cc_final: 0.6805 (m-80) REVERT: G 42 LYS cc_start: 0.6898 (mmtp) cc_final: 0.6082 (ttpt) REVERT: G 47 MET cc_start: 0.7842 (mmm) cc_final: 0.6453 (ptp) REVERT: G 86 TYR cc_start: 0.6990 (m-10) cc_final: 0.6755 (m-10) outliers start: 79 outliers final: 65 residues processed: 193 average time/residue: 0.1561 time to fit residues: 51.2161 Evaluate side-chains 182 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 112 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1039 ARG Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 113 TYR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 26 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 126 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 213 optimal weight: 2.9990 chunk 242 optimal weight: 30.0000 chunk 143 optimal weight: 5.9990 chunk 202 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 276 optimal weight: 1.9990 chunk 272 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 chunk 274 optimal weight: 3.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.068076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.046038 restraints weight = 150679.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.047435 restraints weight = 73966.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.048330 restraints weight = 45667.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.048915 restraints weight = 32718.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.049262 restraints weight = 26053.809| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.5563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 28082 Z= 0.128 Angle : 0.590 12.353 38272 Z= 0.292 Chirality : 0.045 0.302 4402 Planarity : 0.004 0.063 4888 Dihedral : 4.428 55.975 3726 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.76 % Allowed : 17.99 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.14), residues: 3422 helix: 1.62 (0.21), residues: 660 sheet: -0.02 (0.17), residues: 906 loop : -0.69 (0.15), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 357 TYR 0.012 0.001 TYR D 115 PHE 0.025 0.001 PHE A 562 TRP 0.027 0.001 TRP D 47 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (28011) covalent geometry : angle 0.57713 / 0.29 (38105) SS BOND : bond 0.00347 / 0.22 ( 43) SS BOND : angle 1.39354 / 0.92 ( 86) hydrogen bonds : bond 0.03740 / 2.49 ( 1114) hydrogen bonds : angle 5.12849 / 3.48 ( 3075) Misc. bond : bond 0.00001 / 0.00 ( 1) link_NAG-ASN : bond 0.00371 / 0.16 ( 27) link_NAG-ASN : angle 2.39006 / 1.75 ( 81) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 116 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 ASN cc_start: 0.8791 (m-40) cc_final: 0.8308 (p0) REVERT: A 740 MET cc_start: 0.8953 (ttt) cc_final: 0.8296 (tmm) REVERT: A 759 PHE cc_start: 0.8560 (OUTLIER) cc_final: 0.8153 (t80) REVERT: B 223 LEU cc_start: 0.8948 (tp) cc_final: 0.8595 (tp) REVERT: B 357 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7753 (ttm-80) REVERT: B 613 GLN cc_start: 0.9266 (OUTLIER) cc_final: 0.8915 (pm20) REVERT: B 740 MET cc_start: 0.9353 (ttt) cc_final: 0.8764 (ttt) REVERT: B 1002 GLN cc_start: 0.9471 (OUTLIER) cc_final: 0.9264 (tm-30) REVERT: B 1029 MET cc_start: 0.9230 (tpp) cc_final: 0.8807 (tpp) REVERT: B 1039 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8115 (mtp180) REVERT: C 488 CYS cc_start: 0.3174 (OUTLIER) cc_final: 0.2687 (t) REVERT: C 567 ARG cc_start: 0.7016 (mtm180) cc_final: 0.5087 (mmm-85) REVERT: C 740 MET cc_start: 0.8895 (ttm) cc_final: 0.8218 (tmm) REVERT: C 773 GLU cc_start: 0.8270 (tp30) cc_final: 0.7915 (tm-30) REVERT: D 73 ASP cc_start: 0.8933 (t0) cc_final: 0.8660 (t70) REVERT: E 3 GLN cc_start: 0.7390 (mp10) cc_final: 0.7064 (mp10) REVERT: E 48 MET cc_start: 0.7003 (mmt) cc_final: 0.6774 (mmt) REVERT: E 86 LEU cc_start: 0.6796 (mm) cc_final: 0.6106 (mt) REVERT: E 122 GLN cc_start: 0.7529 (tm-30) cc_final: 0.7284 (tm-30) REVERT: F 85 ASP cc_start: 0.5894 (p0) cc_final: 0.5685 (m-30) REVERT: G 35 TRP cc_start: 0.6478 (m100) cc_final: 0.6260 (m100) REVERT: G 36 TYR cc_start: 0.7154 (m-80) cc_final: 0.6875 (m-80) REVERT: G 42 LYS cc_start: 0.6896 (mmtp) cc_final: 0.6127 (ttpt) REVERT: G 47 MET cc_start: 0.7825 (mmm) cc_final: 0.6438 (ptp) REVERT: G 86 TYR cc_start: 0.7018 (m-10) cc_final: 0.6793 (m-10) outliers start: 83 outliers final: 67 residues processed: 195 average time/residue: 0.1574 time to fit residues: 51.4346 Evaluate side-chains 185 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 112 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1039 ARG Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 113 TYR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 65 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 99 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 186 optimal weight: 1.9990 chunk 181 optimal weight: 6.9990 chunk 332 optimal weight: 7.9990 chunk 158 optimal weight: 0.0040 chunk 207 optimal weight: 5.9990 chunk 132 optimal weight: 0.0000 chunk 171 optimal weight: 0.5980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS B 777 ASN B 935 GLN B1002 GLN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 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 = 0.3593 r_free = 0.3593 target = 0.068781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.046830 restraints weight = 146496.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.048251 restraints weight = 72350.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.049185 restraints weight = 44680.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.049778 restraints weight = 31743.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.050191 restraints weight = 25114.669| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.5590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 28082 Z= 0.099 Angle : 0.583 12.016 38272 Z= 0.287 Chirality : 0.045 0.295 4402 Planarity : 0.004 0.062 4888 Dihedral : 4.301 54.654 3726 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.26 % Allowed : 18.58 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.15), residues: 3422 helix: 1.74 (0.21), residues: 655 sheet: 0.04 (0.17), residues: 881 loop : -0.63 (0.15), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 357 TYR 0.012 0.001 TYR A1067 PHE 0.023 0.001 PHE A 562 TRP 0.029 0.001 TRP D 47 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (28011) covalent geometry : angle 0.57202 / 0.28 (38105) SS BOND : bond 0.00259 / 0.17 ( 43) SS BOND : angle 1.30673 / 0.86 ( 86) hydrogen bonds : bond 0.03580 / 2.36 ( 1114) hydrogen bonds : angle 5.00583 / 3.41 ( 3075) Misc. bond : bond 0.00005 / 0.00 ( 1) link_NAG-ASN : bond 0.00411 / 0.17 ( 27) link_NAG-ASN : angle 2.25698 / 1.67 ( 81) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 125 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 ASN cc_start: 0.8761 (m-40) cc_final: 0.8259 (p0) REVERT: A 740 MET cc_start: 0.8905 (ttt) cc_final: 0.8266 (tmm) REVERT: A 759 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.8090 (t80) REVERT: B 223 LEU cc_start: 0.8930 (tp) cc_final: 0.8594 (tp) REVERT: B 357 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7736 (ttm-80) REVERT: B 613 GLN cc_start: 0.9178 (OUTLIER) cc_final: 0.8944 (pm20) REVERT: B 740 MET cc_start: 0.9365 (ttt) cc_final: 0.8828 (ttt) REVERT: B 1002 GLN cc_start: 0.9309 (OUTLIER) cc_final: 0.9075 (tm-30) REVERT: C 488 CYS cc_start: 0.3520 (OUTLIER) cc_final: 0.3077 (t) REVERT: C 567 ARG cc_start: 0.6952 (mtm180) cc_final: 0.5130 (mmm-85) REVERT: C 740 MET cc_start: 0.8810 (ttm) cc_final: 0.8123 (tmm) REVERT: C 773 GLU cc_start: 0.8252 (tp30) cc_final: 0.7878 (tm-30) REVERT: D 34 MET cc_start: 0.6136 (mmm) cc_final: 0.5124 (mmm) REVERT: D 73 ASP cc_start: 0.8930 (t0) cc_final: 0.8644 (t70) REVERT: D 81 MET cc_start: 0.5792 (ttt) cc_final: 0.5448 (tmm) REVERT: E 3 GLN cc_start: 0.7412 (mp10) cc_final: 0.6870 (mp10) REVERT: E 10 GLU cc_start: 0.7319 (tt0) cc_final: 0.7069 (tm-30) REVERT: E 48 MET cc_start: 0.6949 (mmt) cc_final: 0.6714 (mmt) REVERT: E 80 TYR cc_start: 0.8427 (m-80) cc_final: 0.8016 (m-80) REVERT: E 86 LEU cc_start: 0.6820 (mm) cc_final: 0.6113 (mt) REVERT: E 95 TYR cc_start: 0.6552 (m-80) cc_final: 0.6236 (m-10) REVERT: F 85 ASP cc_start: 0.5859 (p0) cc_final: 0.5658 (m-30) REVERT: G 35 TRP cc_start: 0.6420 (m100) cc_final: 0.6217 (m100) REVERT: G 36 TYR cc_start: 0.7205 (m-80) cc_final: 0.6934 (m-80) REVERT: G 42 LYS cc_start: 0.6845 (mmtp) cc_final: 0.6078 (ttpt) REVERT: G 47 MET cc_start: 0.7722 (mmm) cc_final: 0.6411 (ptp) REVERT: G 86 TYR cc_start: 0.7029 (m-10) cc_final: 0.6819 (m-10) outliers start: 68 outliers final: 55 residues processed: 187 average time/residue: 0.1648 time to fit residues: 52.1307 Evaluate side-chains 173 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 113 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 113 TYR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 65 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 175 optimal weight: 7.9990 chunk 250 optimal weight: 3.9990 chunk 270 optimal weight: 7.9990 chunk 285 optimal weight: 0.9980 chunk 108 optimal weight: 9.9990 chunk 323 optimal weight: 5.9990 chunk 69 optimal weight: 20.0000 chunk 214 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 162 optimal weight: 6.9990 chunk 326 optimal weight: 40.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 784 GLN B 498 GLN B 777 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS D 1 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.066754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.044182 restraints weight = 147574.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.045498 restraints weight = 74570.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.046344 restraints weight = 46994.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.046895 restraints weight = 34103.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.047215 restraints weight = 27484.947| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.6012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 28082 Z= 0.257 Angle : 0.690 12.427 38272 Z= 0.347 Chirality : 0.047 0.306 4402 Planarity : 0.004 0.064 4888 Dihedral : 4.703 48.882 3726 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.56 % Allowed : 18.38 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.14), residues: 3422 helix: 1.45 (0.21), residues: 655 sheet: -0.03 (0.17), residues: 914 loop : -0.70 (0.15), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1107 TYR 0.015 0.002 TYR C1067 PHE 0.031 0.002 PHE A 562 TRP 0.027 0.002 TRP D 47 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.26 (28011) covalent geometry : angle 0.67597 / 0.34 (38105) SS BOND : bond 0.00477 / 0.31 ( 43) SS BOND : angle 1.55122 / 1.03 ( 86) hydrogen bonds : bond 0.04202 / 2.78 ( 1114) hydrogen bonds : angle 5.32590 / 3.61 ( 3075) Misc. bond : bond 0.00018 / 0.01 ( 1) link_NAG-ASN : bond 0.00456 / 0.26 ( 27) link_NAG-ASN : angle 2.70363 / 1.95 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5102.45 seconds wall clock time: 89 minutes 7.35 seconds (5347.35 seconds total)