Starting phenix.real_space_refine on Fri Mar 6 06:38:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n9t_24262/03_2026/7n9t_24262.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n9t_24262/03_2026/7n9t_24262.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7n9t_24262/03_2026/7n9t_24262.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n9t_24262/03_2026/7n9t_24262.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n9t_24262/03_2026/7n9t_24262.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n9t_24262/03_2026/7n9t_24262.map" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 18345 2.51 5 N 4848 2.21 5 O 5556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28884 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1123, 8747 Classifications: {'peptide': 1123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 55, 'TRANS': 1067} Chain: "D" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 881 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 114} Restraints were copied for chains: B, C, E, F Residues with excluded nonbonded symmetry interactions: 357 residue: pdb=" N HIS D 1 " occ=0.00 ... (8 atoms not shown) pdb=" NE2 HIS D 1 " occ=0.00 residue: pdb=" N VAL D 2 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL D 2 " occ=0.00 residue: pdb=" N GLN D 3 " occ=0.00 ... (7 atoms not shown) pdb=" NE2 GLN D 3 " occ=0.00 residue: pdb=" N LEU D 4 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU D 4 " occ=0.00 residue: pdb=" N VAL D 5 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL D 5 " occ=0.00 residue: pdb=" N GLU D 6 " occ=0.00 ... (7 atoms not shown) pdb=" OE2 GLU D 6 " occ=0.00 residue: pdb=" N SER D 7 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER D 7 " occ=0.00 residue: pdb=" N GLY D 8 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY D 8 " occ=0.00 residue: pdb=" N GLY D 9 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY D 9 " occ=0.00 residue: pdb=" N GLY D 10 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY D 10 " occ=0.00 residue: pdb=" N LEU D 11 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU D 11 " occ=0.00 residue: pdb=" N VAL D 12 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL D 12 " occ=0.00 ... (remaining 345 not shown) Time building chain proxies: 10.40, per 1000 atoms: 0.36 Number of scatterers: 28884 At special positions: 0 Unit cell: (159.43, 158.36, 197.95, 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 135 16.00 O 5556 8.00 N 4848 7.00 C 18345 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, 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=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " 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 C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 1.1 seconds 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6924 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 60 sheets defined 21.6% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.349A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.763A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.482A pdb=" N GLN A 409 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.660A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 783 removed outlier: 4.048A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 849 through 854 removed outlier: 3.827A pdb=" N GLN A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 887 through 891 removed outlier: 3.554A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.941A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 941 removed outlier: 3.608A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.959A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.879A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.350A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.764A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.483A pdb=" N GLN B 409 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.661A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 783 removed outlier: 4.048A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 849 through 854 removed outlier: 3.827A pdb=" N GLN B 853 " --> pdb=" O LEU B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 887 through 891 removed outlier: 3.555A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.941A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 3.607A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.959A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.879A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.925A 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 337 through 343 removed outlier: 4.350A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 368 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.765A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.483A pdb=" N GLN C 409 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.660A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 783 removed outlier: 4.048A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 849 through 854 removed outlier: 3.827A pdb=" N GLN C 853 " --> pdb=" O LEU C 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 887 through 891 removed outlier: 3.554A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.941A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 941 removed outlier: 3.606A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.958A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.880A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 88 Processing helix chain 'E' and resid 84 through 88 Processing helix chain 'F' and resid 84 through 88 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.218A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.491A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 52 removed outlier: 3.815A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 225 through 229 removed outlier: 7.851A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE A 192 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A 92 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 101 through 106 removed outlier: 6.052A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 118 through 122 Processing sheet with id=AA7, first strand: chain 'A' and resid 312 through 314 removed outlier: 3.636A pdb=" N TYR A 313 " --> pdb=" O VAL A 597 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 376 through 379 removed outlier: 3.682A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 539 through 543 Processing sheet with id=AB3, first strand: chain 'A' and resid 575 through 577 removed outlier: 3.589A pdb=" N VAL A 576 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.672A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.191A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 712 through 719 removed outlier: 6.020A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 712 through 719 removed outlier: 6.020A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB9, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.219A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.492A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 52 removed outlier: 3.814A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 225 through 229 removed outlier: 7.851A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 197 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE B 192 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE B 92 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.051A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 118 through 122 Processing sheet with id=AC8, first strand: chain 'B' and resid 312 through 314 removed outlier: 3.636A pdb=" N TYR B 313 " --> pdb=" O VAL B 597 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 376 through 379 removed outlier: 3.683A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 453 through 454 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 539 through 543 Processing sheet with id=AD4, first strand: chain 'B' and resid 575 through 577 removed outlier: 3.588A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.671A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 712 through 719 removed outlier: 6.019A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 712 through 719 removed outlier: 6.019A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD9, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AE1, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.218A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.492A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 48 through 52 removed outlier: 3.815A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 225 through 229 removed outlier: 7.852A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE C 197 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ARG C 190 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE C 192 " --> pdb=" O PHE C 92 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE C 92 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.053A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 118 through 122 Processing sheet with id=AE8, first strand: chain 'C' and resid 312 through 314 removed outlier: 3.636A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 376 through 379 removed outlier: 3.683A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 453 through 454 Processing sheet with id=AF2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF3, first strand: chain 'C' and resid 539 through 543 Processing sheet with id=AF4, first strand: chain 'C' and resid 575 through 577 removed outlier: 3.589A pdb=" N VAL C 576 " --> pdb=" O LEU C 585 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.671A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 712 through 719 removed outlier: 6.019A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 712 through 719 removed outlier: 6.019A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AF9, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AG1, first strand: chain 'D' and resid 57 through 59 removed outlier: 7.203A pdb=" N ARG D 45 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N ALA D 40 " --> pdb=" O ARG D 45 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ARG D 38 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 67 through 72 Processing sheet with id=AG3, first strand: chain 'E' and resid 57 through 59 removed outlier: 7.204A pdb=" N ARG E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N ALA E 40 " --> pdb=" O ARG E 45 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ARG E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 67 through 72 Processing sheet with id=AG5, first strand: chain 'F' and resid 57 through 59 removed outlier: 7.204A pdb=" N ARG F 45 " --> pdb=" O ALA F 40 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N ALA F 40 " --> pdb=" O ARG F 45 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ARG F 38 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 67 through 72 872 hydrogen bonds defined for protein. 2364 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.13 Time building geometry restraints manager: 3.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 9423 1.35 - 1.46: 7255 1.46 - 1.58: 12710 1.58 - 1.70: 0 1.70 - 1.82: 177 Bond restraints: 29565 Sorted by residual: bond pdb=" CA PHE B 186 " pdb=" CB PHE B 186 " ideal model delta sigma weight residual 1.524 1.560 -0.036 1.62e-02 3.81e+03 4.95e+00 bond pdb=" CA PHE C 186 " pdb=" CB PHE C 186 " ideal model delta sigma weight residual 1.524 1.560 -0.036 1.62e-02 3.81e+03 4.91e+00 bond pdb=" CA PHE A 186 " pdb=" CB PHE A 186 " ideal model delta sigma weight residual 1.524 1.559 -0.036 1.62e-02 3.81e+03 4.82e+00 bond pdb=" CB MET B 153 " pdb=" CG MET B 153 " ideal model delta sigma weight residual 1.520 1.579 -0.059 3.00e-02 1.11e+03 3.92e+00 bond pdb=" CB MET A 153 " pdb=" CG MET A 153 " ideal model delta sigma weight residual 1.520 1.579 -0.059 3.00e-02 1.11e+03 3.85e+00 ... (remaining 29560 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.60: 40005 4.60 - 9.20: 180 9.20 - 13.80: 44 13.80 - 18.40: 7 18.40 - 23.00: 15 Bond angle restraints: 40251 Sorted by residual: angle pdb=" C HIS C 245 " pdb=" N ARG C 246 " pdb=" CA ARG C 246 " ideal model delta sigma weight residual 120.60 143.48 -22.88 1.60e+00 3.91e-01 2.04e+02 angle pdb=" C HIS B 245 " pdb=" N ARG B 246 " pdb=" CA ARG B 246 " ideal model delta sigma weight residual 120.60 143.47 -22.87 1.60e+00 3.91e-01 2.04e+02 angle pdb=" C HIS A 245 " pdb=" N ARG A 246 " pdb=" CA ARG A 246 " ideal model delta sigma weight residual 120.60 143.44 -22.84 1.60e+00 3.91e-01 2.04e+02 angle pdb=" C GLY B 842 " pdb=" N ASP B 843 " pdb=" CA ASP B 843 " ideal model delta sigma weight residual 122.74 142.67 -19.93 1.44e+00 4.82e-01 1.92e+02 angle pdb=" C GLY A 842 " pdb=" N ASP A 843 " pdb=" CA ASP A 843 " ideal model delta sigma weight residual 122.74 142.66 -19.92 1.44e+00 4.82e-01 1.91e+02 ... (remaining 40246 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 16278 17.29 - 34.59: 967 34.59 - 51.88: 250 51.88 - 69.18: 52 69.18 - 86.47: 21 Dihedral angle restraints: 17568 sinusoidal: 6753 harmonic: 10815 Sorted by residual: dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sinusoidal sigma weight residual 93.00 135.01 -42.01 1 1.00e+01 1.00e-02 2.47e+01 dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual 93.00 134.99 -41.99 1 1.00e+01 1.00e-02 2.47e+01 dihedral pdb=" CB CYS C 131 " pdb=" SG CYS C 131 " pdb=" SG CYS C 166 " pdb=" CB CYS C 166 " ideal model delta sinusoidal sigma weight residual 93.00 134.98 -41.98 1 1.00e+01 1.00e-02 2.46e+01 ... (remaining 17565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.343: 4427 0.343 - 0.685: 67 0.685 - 1.028: 12 1.028 - 1.371: 3 1.371 - 1.713: 9 Chirality restraints: 4518 Sorted by residual: chirality pdb=" CG LEU C 629 " pdb=" CB LEU C 629 " pdb=" CD1 LEU C 629 " pdb=" CD2 LEU C 629 " both_signs ideal model delta sigma weight residual False -2.59 -0.88 -1.71 2.00e-01 2.50e+01 7.34e+01 chirality pdb=" CG LEU B 629 " pdb=" CB LEU B 629 " pdb=" CD1 LEU B 629 " pdb=" CD2 LEU B 629 " both_signs ideal model delta sigma weight residual False -2.59 -0.88 -1.71 2.00e-01 2.50e+01 7.33e+01 chirality pdb=" CG LEU A 629 " pdb=" CB LEU A 629 " pdb=" CD1 LEU A 629 " pdb=" CD2 LEU A 629 " both_signs ideal model delta sigma weight residual False -2.59 -0.88 -1.71 2.00e-01 2.50e+01 7.33e+01 ... (remaining 4515 not shown) Planarity restraints: 5250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 792 " -0.040 5.00e-02 4.00e+02 6.05e-02 5.85e+00 pdb=" N PRO B 793 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 793 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 793 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 792 " -0.040 5.00e-02 4.00e+02 6.05e-02 5.85e+00 pdb=" N PRO A 793 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 793 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 793 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 792 " -0.040 5.00e-02 4.00e+02 6.03e-02 5.82e+00 pdb=" N PRO C 793 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO C 793 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 793 " -0.034 5.00e-02 4.00e+02 ... (remaining 5247 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 308 2.61 - 3.18: 25313 3.18 - 3.75: 40237 3.75 - 4.33: 53804 4.33 - 4.90: 89377 Nonbonded interactions: 209039 Sorted by model distance: nonbonded pdb=" OG1 THR B 645 " pdb=" O GLY B 648 " model vdw 2.032 3.040 nonbonded pdb=" OG1 THR C 645 " pdb=" O GLY C 648 " model vdw 2.032 3.040 nonbonded pdb=" OG1 THR A 645 " pdb=" O GLY A 648 " model vdw 2.033 3.040 nonbonded pdb=" OD1 ASP C 294 " pdb=" OG SER C 297 " model vdw 2.067 3.040 nonbonded pdb=" OD1 ASP A 294 " pdb=" OG SER A 297 " model vdw 2.067 3.040 ... (remaining 209034 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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=0.00 max=1.00 mean=0.91 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 30.110 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 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 : 0.003 0.059 29598 Z= 0.142 Angle : 0.951 23.001 40317 Z= 0.544 Chirality : 0.116 1.713 4518 Planarity : 0.003 0.060 5250 Dihedral : 12.538 86.470 10545 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.77 % Favored : 96.15 % Rotamer: Outliers : 2.91 % Allowed : 1.78 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.14), residues: 3714 helix: 2.29 (0.21), residues: 672 sheet: 0.25 (0.20), residues: 708 loop : -0.65 (0.13), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1014 TYR 0.005 0.000 TYR B 873 PHE 0.011 0.001 PHE B 927 TRP 0.006 0.000 TRP F 36 HIS 0.002 0.000 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00286 (29565) covalent geometry : angle 0.95200 (40251) SS BOND : bond 0.00095 ( 33) SS BOND : angle 0.54363 ( 66) hydrogen bonds : bond 0.18139 ( 857) hydrogen bonds : angle 7.12658 ( 2364) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 375 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.6647 (mmt-90) cc_final: 0.5751 (mtt180) REVERT: A 805 ILE cc_start: 0.5616 (OUTLIER) cc_final: 0.5340 (tt) REVERT: A 844 MET cc_start: 0.2160 (mpp) cc_final: 0.1739 (mpp) REVERT: A 1104 VAL cc_start: 0.6541 (p) cc_final: 0.5630 (m) REVERT: B 55 PHE cc_start: 0.5125 (m-10) cc_final: 0.4599 (m-10) REVERT: B 92 PHE cc_start: 0.7839 (t80) cc_final: 0.6929 (m-80) REVERT: B 153 MET cc_start: -0.1803 (OUTLIER) cc_final: -0.2484 (ppp) REVERT: B 567 ARG cc_start: 0.6990 (OUTLIER) cc_final: 0.6697 (mmt-90) REVERT: B 568 ASP cc_start: 0.6761 (t0) cc_final: 0.6415 (t0) REVERT: B 844 MET cc_start: 0.3263 (mpp) cc_final: 0.2811 (mpp) REVERT: B 974 SER cc_start: 0.8065 (t) cc_final: 0.7830 (p) REVERT: C 153 MET cc_start: -0.0302 (OUTLIER) cc_final: -0.0732 (mtm) REVERT: C 195 LYS cc_start: 0.7926 (pttt) cc_final: 0.7246 (ptmt) REVERT: C 560 LEU cc_start: 0.1726 (mm) cc_final: 0.1405 (mt) REVERT: C 835 MET cc_start: 0.0349 (mmp) cc_final: -0.0244 (ptp) REVERT: C 844 MET cc_start: 0.3047 (mpp) cc_final: 0.2603 (mpp) REVERT: C 931 ILE cc_start: 0.6939 (mm) cc_final: 0.6447 (mm) REVERT: C 1084 ASP cc_start: 0.6146 (OUTLIER) cc_final: 0.5567 (p0) REVERT: D 34 MET cc_start: -0.0604 (tmm) cc_final: -0.1209 (tmm) REVERT: E 34 MET cc_start: 0.0674 (tmm) cc_final: 0.0016 (tmm) REVERT: E 61 ASP cc_start: 0.1453 (m-30) cc_final: 0.1043 (p0) REVERT: F 118 SER cc_start: 0.1542 (t) cc_final: 0.1182 (p) outliers start: 93 outliers final: 19 residues processed: 434 average time/residue: 0.1785 time to fit residues: 123.8144 Evaluate side-chains 225 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 201 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1014 ARG Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 40.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 0.0070 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 overall best weight: 2.1204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 606 ASN A 613 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN B 613 GLN B 644 GLN B 690 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN C 52 GLN C 87 ASN C 644 GLN C 690 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 969 ASN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.180489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.126863 restraints weight = 61189.235| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 3.81 r_work: 0.3571 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 29598 Z= 0.239 Angle : 0.688 9.264 40317 Z= 0.362 Chirality : 0.049 0.223 4518 Planarity : 0.005 0.054 5250 Dihedral : 4.695 53.666 4075 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.72 % Allowed : 6.54 % Favored : 91.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.14), residues: 3714 helix: 1.95 (0.20), residues: 621 sheet: 0.26 (0.19), residues: 741 loop : -0.91 (0.13), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1014 TYR 0.034 0.002 TYR C 904 PHE 0.037 0.002 PHE B1089 TRP 0.011 0.001 TRP C1102 HIS 0.005 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00551 (29565) covalent geometry : angle 0.68544 (40251) SS BOND : bond 0.00507 ( 33) SS BOND : angle 1.69450 ( 66) hydrogen bonds : bond 0.05073 ( 857) hydrogen bonds : angle 5.50070 ( 2364) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 207 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.6915 (mmt-90) cc_final: 0.5839 (mtt180) REVERT: A 160 TYR cc_start: 0.6026 (p90) cc_final: 0.5823 (p90) REVERT: A 195 LYS cc_start: 0.7089 (pttt) cc_final: 0.6492 (pttp) REVERT: A 238 PHE cc_start: 0.3858 (OUTLIER) cc_final: 0.3275 (p90) REVERT: A 322 PRO cc_start: 0.5764 (Cg_exo) cc_final: 0.5415 (Cg_endo) REVERT: A 835 MET cc_start: 0.1768 (OUTLIER) cc_final: -0.1412 (mmm) REVERT: A 844 MET cc_start: 0.3100 (mpp) cc_final: 0.2823 (mpp) REVERT: A 953 ASN cc_start: 0.8188 (m-40) cc_final: 0.7981 (m-40) REVERT: A 979 ASP cc_start: 0.8286 (m-30) cc_final: 0.7957 (t0) REVERT: B 153 MET cc_start: -0.3684 (pmm) cc_final: -0.3970 (ptt) REVERT: B 160 TYR cc_start: 0.5225 (p90) cc_final: 0.4934 (p90) REVERT: B 612 TYR cc_start: 0.8795 (m-10) cc_final: 0.8588 (m-10) REVERT: B 759 PHE cc_start: 0.6457 (OUTLIER) cc_final: 0.5571 (t80) REVERT: B 817 PHE cc_start: 0.6427 (t80) cc_final: 0.6128 (t80) REVERT: B 844 MET cc_start: 0.4130 (mpp) cc_final: 0.3444 (mpp) REVERT: B 904 TYR cc_start: 0.8891 (m-10) cc_final: 0.8678 (m-10) REVERT: B 998 THR cc_start: 0.8752 (OUTLIER) cc_final: 0.8534 (p) REVERT: C 105 ILE cc_start: 0.6001 (mt) cc_final: 0.5764 (mm) REVERT: C 195 LYS cc_start: 0.7927 (pttt) cc_final: 0.7663 (pttt) REVERT: C 675 GLN cc_start: 0.8454 (pt0) cc_final: 0.8245 (pp30) REVERT: C 817 PHE cc_start: 0.7646 (m-10) cc_final: 0.7421 (m-80) REVERT: C 844 MET cc_start: 0.3476 (mpp) cc_final: 0.2882 (mpp) outliers start: 55 outliers final: 26 residues processed: 245 average time/residue: 0.1637 time to fit residues: 67.5139 Evaluate side-chains 189 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 188 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 142 optimal weight: 10.0000 chunk 197 optimal weight: 0.6980 chunk 328 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 343 optimal weight: 8.9990 chunk 41 optimal weight: 30.0000 chunk 75 optimal weight: 0.9980 chunk 183 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 134 GLN A 690 GLN A 901 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1142 GLN B 644 GLN B 777 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 751 ASN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN C1098 ASN C1135 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.177363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.123281 restraints weight = 60521.290| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 3.18 r_work: 0.3549 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 29598 Z= 0.175 Angle : 0.557 9.363 40317 Z= 0.292 Chirality : 0.044 0.142 4518 Planarity : 0.004 0.069 5250 Dihedral : 4.021 55.622 4036 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.60 % Allowed : 8.76 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.14), residues: 3714 helix: 1.99 (0.20), residues: 642 sheet: 0.46 (0.18), residues: 729 loop : -1.01 (0.13), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 815 TYR 0.016 0.001 TYR A 789 PHE 0.032 0.002 PHE C1121 TRP 0.010 0.001 TRP B1102 HIS 0.005 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00404 (29565) covalent geometry : angle 0.55145 (40251) SS BOND : bond 0.00430 ( 33) SS BOND : angle 2.04444 ( 66) hydrogen bonds : bond 0.04565 ( 857) hydrogen bonds : angle 5.09621 ( 2364) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 185 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.6276 (p90) cc_final: 0.5991 (p90) REVERT: A 195 LYS cc_start: 0.7473 (pttt) cc_final: 0.6871 (pttp) REVERT: A 238 PHE cc_start: 0.4001 (OUTLIER) cc_final: 0.3367 (p90) REVERT: A 568 ASP cc_start: 0.7549 (t0) cc_final: 0.6904 (p0) REVERT: A 592 PHE cc_start: 0.7322 (t80) cc_final: 0.6871 (t80) REVERT: A 817 PHE cc_start: 0.6823 (t80) cc_final: 0.6558 (t80) REVERT: A 835 MET cc_start: 0.1751 (OUTLIER) cc_final: -0.1389 (mmm) REVERT: A 844 MET cc_start: 0.2982 (mpp) cc_final: 0.2712 (mpp) REVERT: A 983 ARG cc_start: 0.8119 (mtm110) cc_final: 0.7535 (mtm110) REVERT: A 1031 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.7283 (mp0) REVERT: B 153 MET cc_start: -0.3797 (pmm) cc_final: -0.4055 (ptt) REVERT: B 160 TYR cc_start: 0.5280 (p90) cc_final: 0.4989 (p90) REVERT: B 195 LYS cc_start: 0.7732 (pttt) cc_final: 0.7519 (tttt) REVERT: B 568 ASP cc_start: 0.7945 (t0) cc_final: 0.7714 (t0) REVERT: B 740 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7914 (ttt) REVERT: B 808 ASP cc_start: 0.8011 (m-30) cc_final: 0.7145 (t70) REVERT: B 856 ASN cc_start: 0.7353 (t0) cc_final: 0.7043 (t0) REVERT: C 105 ILE cc_start: 0.6467 (mt) cc_final: 0.6211 (mm) REVERT: C 195 LYS cc_start: 0.7625 (pttt) cc_final: 0.7061 (pttm) REVERT: C 241 LEU cc_start: 0.7296 (mt) cc_final: 0.7046 (mt) REVERT: C 612 TYR cc_start: 0.8780 (m-10) cc_final: 0.8332 (m-10) REVERT: C 614 ASP cc_start: 0.8208 (t0) cc_final: 0.7891 (t0) REVERT: C 844 MET cc_start: 0.3258 (mpp) cc_final: 0.2366 (mpp) REVERT: C 1005 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8500 (tp40) outliers start: 51 outliers final: 23 residues processed: 217 average time/residue: 0.1594 time to fit residues: 58.1376 Evaluate side-chains 173 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain F residue 118 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 232 optimal weight: 7.9990 chunk 214 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 240 optimal weight: 9.9990 chunk 254 optimal weight: 7.9990 chunk 213 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 222 optimal weight: 3.9990 chunk 253 optimal weight: 3.9990 chunk 291 optimal weight: 0.7980 chunk 234 optimal weight: 7.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 641 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 644 GLN B 901 GLN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN C 969 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.177364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.123229 restraints weight = 60610.256| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 3.59 r_work: 0.3519 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 29598 Z= 0.137 Angle : 0.521 8.729 40317 Z= 0.272 Chirality : 0.043 0.166 4518 Planarity : 0.004 0.056 5250 Dihedral : 3.733 21.438 4032 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.53 % Allowed : 10.02 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.14), residues: 3714 helix: 2.00 (0.20), residues: 642 sheet: 0.44 (0.19), residues: 729 loop : -1.00 (0.13), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 815 TYR 0.011 0.001 TYR A 789 PHE 0.021 0.001 PHE A 592 TRP 0.007 0.001 TRP B1102 HIS 0.003 0.000 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00314 (29565) covalent geometry : angle 0.51825 (40251) SS BOND : bond 0.00330 ( 33) SS BOND : angle 1.49763 ( 66) hydrogen bonds : bond 0.04108 ( 857) hydrogen bonds : angle 4.88494 ( 2364) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 161 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.6669 (OUTLIER) cc_final: 0.5359 (m-80) REVERT: A 160 TYR cc_start: 0.6172 (p90) cc_final: 0.5676 (p90) REVERT: A 238 PHE cc_start: 0.4213 (OUTLIER) cc_final: 0.3497 (p90) REVERT: A 568 ASP cc_start: 0.7604 (t0) cc_final: 0.6872 (p0) REVERT: A 817 PHE cc_start: 0.7011 (t80) cc_final: 0.6733 (t80) REVERT: A 835 MET cc_start: 0.1923 (OUTLIER) cc_final: -0.1645 (mmm) REVERT: A 844 MET cc_start: 0.2946 (mpp) cc_final: 0.2697 (mpp) REVERT: A 988 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7785 (tm-30) REVERT: A 1031 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.7335 (mp0) REVERT: B 153 MET cc_start: -0.3184 (pmm) cc_final: -0.3443 (ptt) REVERT: B 160 TYR cc_start: 0.5353 (p90) cc_final: 0.4940 (p90) REVERT: B 856 ASN cc_start: 0.7478 (t0) cc_final: 0.7148 (t0) REVERT: C 105 ILE cc_start: 0.6427 (mt) cc_final: 0.6213 (mm) REVERT: C 195 LYS cc_start: 0.7581 (pttt) cc_final: 0.7207 (ptmt) REVERT: C 241 LEU cc_start: 0.7228 (mt) cc_final: 0.7018 (mt) REVERT: C 612 TYR cc_start: 0.8709 (m-10) cc_final: 0.8263 (m-10) REVERT: C 614 ASP cc_start: 0.8223 (t0) cc_final: 0.7676 (t0) REVERT: C 699 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.7991 (mp) REVERT: C 740 MET cc_start: 0.7281 (ttt) cc_final: 0.7038 (ttt) REVERT: C 844 MET cc_start: 0.3098 (mpp) cc_final: 0.1961 (mpp) outliers start: 49 outliers final: 28 residues processed: 197 average time/residue: 0.1558 time to fit residues: 52.9092 Evaluate side-chains 172 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain F residue 118 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 54 optimal weight: 7.9990 chunk 111 optimal weight: 0.7980 chunk 61 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 204 optimal weight: 0.8980 chunk 214 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 chunk 357 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN B 804 GLN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.174693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.119616 restraints weight = 60055.625| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 3.66 r_work: 0.3454 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.5463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 29598 Z= 0.154 Angle : 0.531 7.360 40317 Z= 0.279 Chirality : 0.044 0.168 4518 Planarity : 0.004 0.052 5250 Dihedral : 3.814 21.805 4032 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.10 % Allowed : 10.17 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.14), residues: 3714 helix: 1.86 (0.20), residues: 645 sheet: 0.32 (0.19), residues: 729 loop : -1.07 (0.13), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 983 TYR 0.014 0.001 TYR A 38 PHE 0.028 0.001 PHE C 817 TRP 0.010 0.001 TRP B1102 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00358 (29565) covalent geometry : angle 0.52730 (40251) SS BOND : bond 0.00437 ( 33) SS BOND : angle 1.63969 ( 66) hydrogen bonds : bond 0.04247 ( 857) hydrogen bonds : angle 4.87004 ( 2364) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 149 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.6829 (OUTLIER) cc_final: 0.5774 (m-80) REVERT: A 160 TYR cc_start: 0.6158 (p90) cc_final: 0.5711 (p90) REVERT: A 238 PHE cc_start: 0.4315 (OUTLIER) cc_final: 0.3539 (p90) REVERT: A 568 ASP cc_start: 0.7700 (t0) cc_final: 0.7317 (p0) REVERT: A 569 ILE cc_start: 0.7852 (mm) cc_final: 0.7574 (mp) REVERT: A 740 MET cc_start: 0.8606 (mmm) cc_final: 0.8365 (mmm) REVERT: A 821 LEU cc_start: 0.7456 (mm) cc_final: 0.7065 (mm) REVERT: A 835 MET cc_start: 0.1746 (OUTLIER) cc_final: -0.1236 (mmm) REVERT: A 988 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7651 (tm-30) REVERT: A 1031 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: B 160 TYR cc_start: 0.5260 (p90) cc_final: 0.4874 (p90) REVERT: B 223 LEU cc_start: 0.5557 (mp) cc_final: 0.5324 (mp) REVERT: C 105 ILE cc_start: 0.6629 (mt) cc_final: 0.6371 (mm) REVERT: C 195 LYS cc_start: 0.7812 (pttt) cc_final: 0.7221 (pttm) REVERT: C 614 ASP cc_start: 0.8166 (t0) cc_final: 0.7604 (t0) REVERT: C 740 MET cc_start: 0.7982 (ttt) cc_final: 0.7669 (ttt) REVERT: C 844 MET cc_start: 0.3069 (mpp) cc_final: 0.1850 (mpp) outliers start: 67 outliers final: 40 residues processed: 199 average time/residue: 0.1577 time to fit residues: 54.4520 Evaluate side-chains 180 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 136 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain F residue 118 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 266 optimal weight: 4.9990 chunk 331 optimal weight: 0.9990 chunk 205 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 323 optimal weight: 3.9990 chunk 367 optimal weight: 8.9990 chunk 140 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 154 optimal weight: 7.9990 chunk 247 optimal weight: 50.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 87 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN B 641 ASN B 804 GLN ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** 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 = 0.4452 r_free = 0.4452 target = 0.166628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.110312 restraints weight = 59846.379| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 3.09 r_work: 0.3350 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.6829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.112 29598 Z= 0.311 Angle : 0.697 9.355 40317 Z= 0.370 Chirality : 0.048 0.375 4518 Planarity : 0.005 0.055 5250 Dihedral : 4.878 26.895 4030 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.07 % Allowed : 11.52 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.13), residues: 3714 helix: 1.34 (0.20), residues: 636 sheet: 0.03 (0.19), residues: 693 loop : -1.47 (0.12), residues: 2385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 577 TYR 0.033 0.002 TYR A 38 PHE 0.027 0.002 PHE C 559 TRP 0.017 0.002 TRP C1102 HIS 0.004 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00723 (29565) covalent geometry : angle 0.68811 (40251) SS BOND : bond 0.00519 ( 33) SS BOND : angle 2.76747 ( 66) hydrogen bonds : bond 0.05808 ( 857) hydrogen bonds : angle 5.54302 ( 2364) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 157 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.6553 (p90) cc_final: 0.6119 (p90) REVERT: A 238 PHE cc_start: 0.4453 (OUTLIER) cc_final: 0.3658 (p90) REVERT: A 568 ASP cc_start: 0.7883 (t0) cc_final: 0.7521 (p0) REVERT: A 569 ILE cc_start: 0.8249 (mm) cc_final: 0.7985 (mp) REVERT: A 817 PHE cc_start: 0.7512 (t80) cc_final: 0.7234 (t80) REVERT: A 835 MET cc_start: 0.1618 (OUTLIER) cc_final: -0.1650 (mmm) REVERT: A 1031 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.7340 (mp0) REVERT: B 160 TYR cc_start: 0.6054 (p90) cc_final: 0.5764 (p90) REVERT: B 844 MET cc_start: 0.4079 (mpp) cc_final: 0.3156 (mpp) REVERT: B 955 ASN cc_start: 0.8566 (m110) cc_final: 0.8308 (m-40) REVERT: C 195 LYS cc_start: 0.7869 (pttt) cc_final: 0.7375 (ptmt) REVERT: C 269 TYR cc_start: 0.6703 (m-80) cc_final: 0.6400 (m-80) REVERT: C 614 ASP cc_start: 0.8072 (t0) cc_final: 0.7631 (t0) outliers start: 66 outliers final: 42 residues processed: 205 average time/residue: 0.1521 time to fit residues: 53.5170 Evaluate side-chains 177 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 132 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 118 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 294 optimal weight: 0.7980 chunk 349 optimal weight: 0.1980 chunk 138 optimal weight: 1.9990 chunk 332 optimal weight: 0.5980 chunk 298 optimal weight: 1.9990 chunk 222 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 45 optimal weight: 0.1980 chunk 101 optimal weight: 0.8980 chunk 226 optimal weight: 9.9990 chunk 254 optimal weight: 8.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN B 804 GLN B 856 ASN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B 955 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C 955 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.172248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.116861 restraints weight = 59582.282| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 3.13 r_work: 0.3463 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.6657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 29598 Z= 0.108 Angle : 0.530 9.188 40317 Z= 0.275 Chirality : 0.043 0.152 4518 Planarity : 0.004 0.051 5250 Dihedral : 4.068 22.752 4030 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.53 % Allowed : 12.55 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.13), residues: 3714 helix: 1.76 (0.20), residues: 636 sheet: 0.08 (0.19), residues: 732 loop : -1.28 (0.12), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 328 TYR 0.013 0.001 TYR B1067 PHE 0.038 0.001 PHE A 592 TRP 0.012 0.001 TRP A 64 HIS 0.002 0.000 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00237 (29565) covalent geometry : angle 0.52701 (40251) SS BOND : bond 0.00379 ( 33) SS BOND : angle 1.57598 ( 66) hydrogen bonds : bond 0.03885 ( 857) hydrogen bonds : angle 4.79523 ( 2364) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 144 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.6420 (p90) cc_final: 0.5991 (p90) REVERT: A 238 PHE cc_start: 0.4340 (OUTLIER) cc_final: 0.3775 (p90) REVERT: A 569 ILE cc_start: 0.8343 (mm) cc_final: 0.7997 (mp) REVERT: A 835 MET cc_start: 0.1790 (OUTLIER) cc_final: -0.1285 (mmm) REVERT: A 844 MET cc_start: 0.3117 (mpp) cc_final: 0.2853 (mpp) REVERT: A 988 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7586 (tm-30) REVERT: A 1031 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.7162 (mp0) REVERT: B 160 TYR cc_start: 0.6295 (p90) cc_final: 0.5919 (p90) REVERT: C 195 LYS cc_start: 0.7972 (pttt) cc_final: 0.7641 (ptmt) REVERT: C 614 ASP cc_start: 0.7811 (t0) cc_final: 0.7199 (t0) REVERT: C 740 MET cc_start: 0.8253 (ttp) cc_final: 0.8043 (ttt) REVERT: C 1017 GLU cc_start: 0.8631 (tp30) cc_final: 0.8325 (tp30) outliers start: 49 outliers final: 25 residues processed: 184 average time/residue: 0.1456 time to fit residues: 47.1373 Evaluate side-chains 155 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain D residue 119 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 157 optimal weight: 10.0000 chunk 196 optimal weight: 2.9990 chunk 268 optimal weight: 8.9990 chunk 328 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 chunk 207 optimal weight: 0.9980 chunk 129 optimal weight: 0.2980 chunk 69 optimal weight: 0.6980 chunk 159 optimal weight: 30.0000 chunk 270 optimal weight: 7.9990 chunk 192 optimal weight: 8.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 87 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 804 GLN B 913 GLN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.168242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.111885 restraints weight = 59322.059| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 3.10 r_work: 0.3461 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.7076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 29598 Z= 0.210 Angle : 0.593 11.320 40317 Z= 0.310 Chirality : 0.045 0.220 4518 Planarity : 0.004 0.057 5250 Dihedral : 4.337 23.646 4030 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.88 % Allowed : 12.61 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.13), residues: 3714 helix: 1.67 (0.20), residues: 639 sheet: -0.00 (0.19), residues: 729 loop : -1.42 (0.12), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 995 TYR 0.020 0.001 TYR A 38 PHE 0.019 0.002 PHE C 559 TRP 0.012 0.001 TRP C1102 HIS 0.004 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00492 (29565) covalent geometry : angle 0.58813 (40251) SS BOND : bond 0.00413 ( 33) SS BOND : angle 2.04836 ( 66) hydrogen bonds : bond 0.04745 ( 857) hydrogen bonds : angle 5.01949 ( 2364) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 143 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7423 (tt) cc_final: 0.6811 (mm) REVERT: A 160 TYR cc_start: 0.6025 (p90) cc_final: 0.5664 (p90) REVERT: A 238 PHE cc_start: 0.4747 (OUTLIER) cc_final: 0.3890 (p90) REVERT: A 740 MET cc_start: 0.9134 (mmm) cc_final: 0.8599 (mmm) REVERT: A 835 MET cc_start: 0.2007 (OUTLIER) cc_final: -0.1757 (mmm) REVERT: A 856 ASN cc_start: 0.8457 (t0) cc_final: 0.7875 (t0) REVERT: A 1031 GLU cc_start: 0.9148 (OUTLIER) cc_final: 0.7498 (mp0) REVERT: B 160 TYR cc_start: 0.6271 (p90) cc_final: 0.6014 (p90) REVERT: B 223 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6934 (mt) REVERT: B 568 ASP cc_start: 0.8365 (t0) cc_final: 0.7644 (p0) REVERT: B 856 ASN cc_start: 0.8361 (t0) cc_final: 0.7853 (t0) REVERT: C 58 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.8267 (m-10) REVERT: C 614 ASP cc_start: 0.8279 (t0) cc_final: 0.7680 (t0) REVERT: C 740 MET cc_start: 0.8735 (ttp) cc_final: 0.7781 (tmm) outliers start: 60 outliers final: 39 residues processed: 190 average time/residue: 0.1542 time to fit residues: 50.6771 Evaluate side-chains 177 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 133 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain F residue 68 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 136 optimal weight: 5.9990 chunk 112 optimal weight: 10.0000 chunk 292 optimal weight: 0.5980 chunk 342 optimal weight: 2.9990 chunk 355 optimal weight: 30.0000 chunk 109 optimal weight: 1.9990 chunk 32 optimal weight: 30.0000 chunk 220 optimal weight: 0.6980 chunk 12 optimal weight: 8.9990 chunk 358 optimal weight: 20.0000 chunk 291 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN B 777 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.169483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.113872 restraints weight = 59064.975| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 3.66 r_work: 0.3393 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.7299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 29598 Z= 0.174 Angle : 0.566 11.471 40317 Z= 0.293 Chirality : 0.044 0.171 4518 Planarity : 0.004 0.054 5250 Dihedral : 4.200 21.617 4030 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.53 % Allowed : 13.02 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.13), residues: 3714 helix: 1.72 (0.20), residues: 639 sheet: -0.09 (0.19), residues: 747 loop : -1.36 (0.12), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1019 TYR 0.016 0.001 TYR A 269 PHE 0.032 0.001 PHE C 855 TRP 0.013 0.001 TRP B 64 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00406 (29565) covalent geometry : angle 0.56159 (40251) SS BOND : bond 0.00505 ( 33) SS BOND : angle 1.84354 ( 66) hydrogen bonds : bond 0.04238 ( 857) hydrogen bonds : angle 4.83034 ( 2364) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 142 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7481 (tt) cc_final: 0.7027 (mm) REVERT: A 160 TYR cc_start: 0.6469 (p90) cc_final: 0.6083 (p90) REVERT: A 238 PHE cc_start: 0.5162 (OUTLIER) cc_final: 0.4434 (p90) REVERT: A 740 MET cc_start: 0.8926 (mmm) cc_final: 0.8692 (mmm) REVERT: A 804 GLN cc_start: 0.9084 (OUTLIER) cc_final: 0.8859 (tp40) REVERT: A 835 MET cc_start: 0.1795 (OUTLIER) cc_final: -0.1171 (mmm) REVERT: A 856 ASN cc_start: 0.8090 (t0) cc_final: 0.7478 (t0) REVERT: A 988 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7560 (tm-30) REVERT: A 1031 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: B 160 TYR cc_start: 0.6639 (p90) cc_final: 0.6184 (p90) REVERT: B 568 ASP cc_start: 0.8229 (t0) cc_final: 0.7762 (p0) REVERT: B 856 ASN cc_start: 0.8092 (t0) cc_final: 0.7761 (t0) REVERT: C 614 ASP cc_start: 0.7829 (t0) cc_final: 0.7216 (t0) REVERT: C 740 MET cc_start: 0.8540 (ttp) cc_final: 0.8193 (ttt) outliers start: 49 outliers final: 38 residues processed: 178 average time/residue: 0.1439 time to fit residues: 45.4522 Evaluate side-chains 181 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 139 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 118 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 44 optimal weight: 30.0000 chunk 6 optimal weight: 5.9990 chunk 164 optimal weight: 0.5980 chunk 117 optimal weight: 5.9990 chunk 241 optimal weight: 0.3980 chunk 288 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 246 optimal weight: 6.9990 chunk 300 optimal weight: 0.6980 chunk 41 optimal weight: 20.0000 chunk 158 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.171167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.115974 restraints weight = 59284.301| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 3.50 r_work: 0.3422 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.7242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29598 Z= 0.105 Angle : 0.529 13.978 40317 Z= 0.270 Chirality : 0.043 0.260 4518 Planarity : 0.004 0.056 5250 Dihedral : 3.921 24.262 4030 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.25 % Allowed : 13.27 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.14), residues: 3714 helix: 1.98 (0.20), residues: 636 sheet: 0.08 (0.19), residues: 687 loop : -1.24 (0.12), residues: 2391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1019 TYR 0.013 0.001 TYR B1067 PHE 0.019 0.001 PHE C 238 TRP 0.010 0.001 TRP B 104 HIS 0.002 0.000 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00239 (29565) covalent geometry : angle 0.52541 (40251) SS BOND : bond 0.00341 ( 33) SS BOND : angle 1.55607 ( 66) hydrogen bonds : bond 0.03637 ( 857) hydrogen bonds : angle 4.63510 ( 2364) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 148 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7879 (tt) cc_final: 0.7341 (mm) REVERT: A 160 TYR cc_start: 0.6371 (p90) cc_final: 0.5946 (p90) REVERT: A 195 LYS cc_start: 0.7833 (pttt) cc_final: 0.7523 (pttt) REVERT: A 238 PHE cc_start: 0.4954 (OUTLIER) cc_final: 0.4595 (p90) REVERT: A 592 PHE cc_start: 0.6142 (m-10) cc_final: 0.5887 (m-10) REVERT: A 740 MET cc_start: 0.8677 (mmm) cc_final: 0.8398 (mmm) REVERT: A 835 MET cc_start: 0.1801 (OUTLIER) cc_final: -0.1100 (mmm) REVERT: A 856 ASN cc_start: 0.7808 (t0) cc_final: 0.7238 (t0) REVERT: A 988 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7572 (tm-30) REVERT: A 1031 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.7285 (mp0) REVERT: B 160 TYR cc_start: 0.6579 (p90) cc_final: 0.6183 (p90) REVERT: B 568 ASP cc_start: 0.8086 (t0) cc_final: 0.7744 (p0) REVERT: C 614 ASP cc_start: 0.7708 (t0) cc_final: 0.7043 (t0) REVERT: C 740 MET cc_start: 0.7841 (ttp) cc_final: 0.7554 (ttt) outliers start: 40 outliers final: 34 residues processed: 179 average time/residue: 0.1482 time to fit residues: 46.8496 Evaluate side-chains 180 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain F residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 193 optimal weight: 0.3980 chunk 141 optimal weight: 5.9990 chunk 235 optimal weight: 0.2980 chunk 270 optimal weight: 9.9990 chunk 240 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 285 optimal weight: 10.0000 chunk 231 optimal weight: 0.0570 chunk 26 optimal weight: 1.9990 chunk 133 optimal weight: 10.0000 overall best weight: 1.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.170449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.114121 restraints weight = 60075.297| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 3.14 r_work: 0.3383 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.7583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 29598 Z= 0.187 Angle : 0.585 11.149 40317 Z= 0.303 Chirality : 0.045 0.187 4518 Planarity : 0.004 0.056 5250 Dihedral : 4.210 22.525 4030 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.50 % Allowed : 13.33 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.14), residues: 3714 helix: 1.78 (0.21), residues: 636 sheet: -0.02 (0.19), residues: 738 loop : -1.29 (0.12), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 995 TYR 0.015 0.001 TYR B1067 PHE 0.017 0.002 PHE C 592 TRP 0.010 0.001 TRP C1102 HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00442 (29565) covalent geometry : angle 0.57894 (40251) SS BOND : bond 0.00353 ( 33) SS BOND : angle 2.19780 ( 66) hydrogen bonds : bond 0.04382 ( 857) hydrogen bonds : angle 4.86676 ( 2364) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8351.36 seconds wall clock time: 142 minutes 47.40 seconds (8567.40 seconds total)