Starting phenix.real_space_refine on Thu Mar 5 14:18:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fb0_31511/03_2026/7fb0_31511.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fb0_31511/03_2026/7fb0_31511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7fb0_31511/03_2026/7fb0_31511.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fb0_31511/03_2026/7fb0_31511.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7fb0_31511/03_2026/7fb0_31511.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fb0_31511/03_2026/7fb0_31511.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.079 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 99 5.16 5 C 14624 2.51 5 N 3796 2.21 5 O 4357 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 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: 22876 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 976, 7628 Classifications: {'peptide': 976} Link IDs: {'PTRANS': 49, 'TRANS': 926} Chain breaks: 10 Chain: "B" Number of atoms: 7624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 975, 7624 Classifications: {'peptide': 975} Link IDs: {'PTRANS': 49, 'TRANS': 925} Chain breaks: 11 Chain: "C" Number of atoms: 7624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 975, 7624 Classifications: {'peptide': 975} Link IDs: {'PTRANS': 49, 'TRANS': 925} Chain breaks: 11 Time building chain proxies: 4.76, per 1000 atoms: 0.21 Number of scatterers: 22876 At special positions: 0 Unit cell: (138.72, 130.56, 171.36, 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 99 16.00 O 4357 8.00 N 3796 7.00 C 14624 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 779.4 milliseconds 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5502 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 62 sheets defined 25.6% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.010A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.912A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 5.313A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.604A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.981A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.662A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.119A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.668A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.970A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.715A 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 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.661A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 756 through 759 Processing helix chain 'B' and resid 760 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.678A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.884A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.925A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.784A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.889A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.607A 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: 3.565A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.006A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.887A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 421 removed outlier: 4.018A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.501A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.527A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.124A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.311A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' 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 removed outlier: 4.027A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.947A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.674A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.798A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.957A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.942A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 9.534A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.957A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.942A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 9.534A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 50 removed outlier: 3.889A pdb=" N LEU A 277 " --> pdb=" O HIS A 49 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 54 through 55 removed outlier: 3.627A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 65 through 66 removed outlier: 3.939A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.105A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA9, first strand: chain 'A' and resid 118 through 121 removed outlier: 3.763A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 311 through 317 removed outlier: 6.789A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.725A pdb=" N ILE A 326 " --> pdb=" O ASN A 540 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 354 through 356 removed outlier: 3.610A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 391 through 392 removed outlier: 3.813A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 452 through 453 removed outlier: 3.697A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 576 through 577 Processing sheet with id=AB7, first strand: chain 'A' and resid 664 through 665 removed outlier: 3.840A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 712 through 713 Processing sheet with id=AB9, first strand: chain 'A' and resid 717 through 720 removed outlier: 6.365A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 725 through 728 removed outlier: 3.534A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AC3, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.588A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AC5, first strand: chain 'A' and resid 1089 through 1090 Processing sheet with id=AC6, first strand: chain 'A' and resid 1095 through 1097 Processing sheet with id=AC7, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.568A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.779A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.556A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE B 92 " --> pdb=" O PHE B 192 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.779A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.556A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.530A pdb=" N HIS B 49 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU B 277 " --> pdb=" O HIS B 49 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AD3, first strand: chain 'B' and resid 65 through 66 removed outlier: 4.040A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AD5, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.346A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.360A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.927A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.927A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 354 through 356 removed outlier: 3.563A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 391 through 392 removed outlier: 3.572A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.149A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 712 through 713 Processing sheet with id=AE4, first strand: chain 'B' and resid 717 through 720 removed outlier: 6.397A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 723 through 728 removed outlier: 3.603A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 1088 through 1090 Processing sheet with id=AE7, first strand: chain 'B' and resid 1095 through 1097 Processing sheet with id=AE8, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.719A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AF1, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AF2, first strand: chain 'C' and resid 95 through 96 removed outlier: 3.643A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 95 through 96 removed outlier: 3.643A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 275 through 279 removed outlier: 3.697A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.600A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 324 through 328 removed outlier: 3.693A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 354 through 356 removed outlier: 3.709A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 391 through 392 removed outlier: 3.654A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 452 through 453 removed outlier: 3.696A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 575 through 577 removed outlier: 3.631A pdb=" N LEU C 585 " --> pdb=" O VAL C 576 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.185A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 712 through 713 Processing sheet with id=AG4, first strand: chain 'C' and resid 718 through 722 Processing sheet with id=AG5, first strand: chain 'C' and resid 725 through 728 Processing sheet with id=AG6, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AG7, first strand: chain 'C' and resid 1089 through 1090 Processing sheet with id=AG8, first strand: chain 'C' and resid 1094 through 1097 803 hydrogen bonds defined for protein. 2187 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: 5.09 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7393 1.34 - 1.47: 5837 1.47 - 1.59: 10031 1.59 - 1.72: 0 1.72 - 1.84: 123 Bond restraints: 23384 Sorted by residual: bond pdb=" C PHE B 565 " pdb=" N GLY B 566 " ideal model delta sigma weight residual 1.336 1.298 0.038 1.01e-02 9.80e+03 1.39e+01 bond pdb=" C LYS A 790 " pdb=" N THR A 791 " ideal model delta sigma weight residual 1.331 1.235 0.095 3.12e-02 1.03e+03 9.34e+00 bond pdb=" C PHE C 565 " pdb=" N GLY C 566 " ideal model delta sigma weight residual 1.333 1.303 0.030 1.11e-02 8.12e+03 7.33e+00 bond pdb=" C ALA C1078 " pdb=" N PRO C1079 " ideal model delta sigma weight residual 1.334 1.312 0.022 8.40e-03 1.42e+04 6.72e+00 bond pdb=" CA ARG A 190 " pdb=" CB ARG A 190 " ideal model delta sigma weight residual 1.527 1.471 0.056 2.48e-02 1.63e+03 5.18e+00 ... (remaining 23379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 31011 2.38 - 4.75: 727 4.75 - 7.13: 68 7.13 - 9.51: 4 9.51 - 11.88: 4 Bond angle restraints: 31814 Sorted by residual: angle pdb=" N SER A 205 " pdb=" CA SER A 205 " pdb=" C SER A 205 " ideal model delta sigma weight residual 107.88 113.78 -5.90 1.41e+00 5.03e-01 1.75e+01 angle pdb=" C PHE C 92 " pdb=" N ALA C 93 " pdb=" CA ALA C 93 " ideal model delta sigma weight residual 122.32 115.11 7.21 1.76e+00 3.23e-01 1.68e+01 angle pdb=" N CYS B 432 " pdb=" CA CYS B 432 " pdb=" C CYS B 432 " ideal model delta sigma weight residual 108.38 113.52 -5.14 1.35e+00 5.49e-01 1.45e+01 angle pdb=" CA GLY C 416 " pdb=" C GLY C 416 " pdb=" N LYS C 417 " ideal model delta sigma weight residual 114.23 117.34 -3.11 8.80e-01 1.29e+00 1.25e+01 angle pdb=" N CYS C 432 " pdb=" CA CYS C 432 " pdb=" C CYS C 432 " ideal model delta sigma weight residual 108.14 113.44 -5.30 1.52e+00 4.33e-01 1.21e+01 ... (remaining 31809 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 12372 17.48 - 34.96: 1337 34.96 - 52.44: 190 52.44 - 69.92: 37 69.92 - 87.40: 13 Dihedral angle restraints: 13949 sinusoidal: 5430 harmonic: 8519 Sorted by residual: dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual -86.00 -8.14 -77.86 1 1.00e+01 1.00e-02 7.58e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual 93.00 155.26 -62.26 1 1.00e+01 1.00e-02 5.13e+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 -86.00 -29.30 -56.70 1 1.00e+01 1.00e-02 4.33e+01 ... (remaining 13946 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2225 0.042 - 0.085: 1030 0.085 - 0.127: 338 0.127 - 0.170: 46 0.170 - 0.212: 6 Chirality restraints: 3645 Sorted by residual: chirality pdb=" CB ILE B 312 " pdb=" CA ILE B 312 " pdb=" CG1 ILE B 312 " pdb=" CG2 ILE B 312 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CB ILE C 312 " pdb=" CA ILE C 312 " pdb=" CG1 ILE C 312 " pdb=" CG2 ILE C 312 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.00e-01 chirality pdb=" CA CYS A 291 " pdb=" N CYS A 291 " pdb=" C CYS A 291 " pdb=" CB CYS A 291 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.82e-01 ... (remaining 3642 not shown) Planarity restraints: 4115 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 192 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.95e+00 pdb=" C PHE A 192 " -0.042 2.00e-02 2.50e+03 pdb=" O PHE A 192 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL A 193 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 84 " 0.037 5.00e-02 4.00e+02 5.63e-02 5.07e+00 pdb=" N PRO A 85 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 85 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 85 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 329 " -0.037 5.00e-02 4.00e+02 5.58e-02 4.98e+00 pdb=" N PRO A 330 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 330 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 330 " -0.031 5.00e-02 4.00e+02 ... (remaining 4112 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 312 2.52 - 3.12: 19238 3.12 - 3.71: 34058 3.71 - 4.31: 47643 4.31 - 4.90: 79360 Nonbonded interactions: 180611 Sorted by model distance: nonbonded pdb=" O ASP B 290 " pdb=" OG SER B 297 " model vdw 1.931 3.040 nonbonded pdb=" O ASP C 290 " pdb=" OG SER C 297 " model vdw 2.004 3.040 nonbonded pdb=" OH TYR A 91 " pdb=" OE1 GLU A 191 " model vdw 2.010 3.040 nonbonded pdb=" O GLU A 661 " pdb=" OH TYR A 695 " model vdw 2.095 3.040 nonbonded pdb=" OH TYR A 200 " pdb=" ND2 ASN C 394 " model vdw 2.113 3.120 ... (remaining 180606 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 501 or resid 503 through 1147)) selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 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: 0.210 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 20.190 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 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 : 0.010 0.103 23420 Z= 0.460 Angle : 0.880 11.883 31886 Z= 0.496 Chirality : 0.052 0.212 3645 Planarity : 0.005 0.056 4115 Dihedral : 14.092 87.398 8339 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Rotamer: Outliers : 0.47 % Allowed : 10.29 % Favored : 89.24 % 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: -4.69 (0.13), residues: 2856 helix: -1.49 (0.17), residues: 662 sheet: -3.84 (0.16), residues: 657 loop : -3.60 (0.13), residues: 1537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1107 TYR 0.029 0.002 TYR C1067 PHE 0.031 0.003 PHE B 906 TRP 0.022 0.003 TRP B 64 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.01043 (23384) covalent geometry : angle 0.87571 (31814) SS BOND : bond 0.00716 ( 36) SS BOND : angle 2.10525 ( 72) hydrogen bonds : bond 0.21847 ( 789) hydrogen bonds : angle 9.30965 ( 2187) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.8221 (tp30) cc_final: 0.8019 (tm-30) REVERT: A 380 TYR cc_start: 0.8335 (m-80) cc_final: 0.7932 (m-80) REVERT: A 759 PHE cc_start: 0.8406 (m-80) cc_final: 0.8045 (m-80) REVERT: A 773 GLU cc_start: 0.8554 (pt0) cc_final: 0.8306 (pt0) REVERT: A 1002 GLN cc_start: 0.9012 (tt0) cc_final: 0.8459 (tp40) REVERT: A 1029 MET cc_start: 0.8426 (tpp) cc_final: 0.7697 (ttm) REVERT: B 1089 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.8018 (m-80) REVERT: C 55 PHE cc_start: 0.8472 (m-80) cc_final: 0.7856 (m-80) REVERT: C 277 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7160 (pp) REVERT: C 900 MET cc_start: 0.8149 (mtp) cc_final: 0.7513 (mtm) REVERT: C 904 TYR cc_start: 0.7982 (m-10) cc_final: 0.7550 (m-10) REVERT: C 964 LYS cc_start: 0.9433 (tmtt) cc_final: 0.9119 (tptp) REVERT: C 1002 GLN cc_start: 0.8970 (tt0) cc_final: 0.8531 (tm-30) outliers start: 12 outliers final: 8 residues processed: 163 average time/residue: 0.1426 time to fit residues: 37.1022 Evaluate side-chains 115 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 40.0000 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 331 ASN ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN A 437 ASN A 501 ASN A 506 GLN A 655 HIS A 675 GLN A 926 GLN A 928 ASN A 965 GLN A1005 GLN B 121 ASN B 196 ASN B 331 ASN B 388 ASN B 448 ASN B 501 ASN B 655 HIS B 675 GLN B 690 GLN B 919 ASN B 953 ASN B 954 GLN B 957 GLN B 965 GLN B1002 GLN B1088 HIS C 448 ASN C 655 HIS C 690 GLN C 965 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.127996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.082752 restraints weight = 47296.449| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 4.01 r_work: 0.3085 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23420 Z= 0.132 Angle : 0.588 8.142 31886 Z= 0.311 Chirality : 0.045 0.175 3645 Planarity : 0.005 0.050 4115 Dihedral : 5.385 49.218 3128 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.64 % Allowed : 12.24 % Favored : 86.12 % 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: -3.01 (0.14), residues: 2856 helix: 0.71 (0.20), residues: 645 sheet: -3.00 (0.17), residues: 638 loop : -2.83 (0.13), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 357 TYR 0.016 0.001 TYR C1067 PHE 0.018 0.001 PHE C 800 TRP 0.014 0.001 TRP C 436 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00299 (23384) covalent geometry : angle 0.58411 (31814) SS BOND : bond 0.00542 ( 36) SS BOND : angle 1.60146 ( 72) hydrogen bonds : bond 0.04404 ( 789) hydrogen bonds : angle 6.22384 ( 2187) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 154 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8257 (t70) cc_final: 0.7947 (t70) REVERT: A 309 GLU cc_start: 0.8664 (tp30) cc_final: 0.8132 (tm-30) REVERT: A 329 PHE cc_start: 0.7374 (m-80) cc_final: 0.7044 (m-80) REVERT: A 380 TYR cc_start: 0.8555 (m-80) cc_final: 0.7944 (m-80) REVERT: A 759 PHE cc_start: 0.8364 (m-80) cc_final: 0.8050 (m-80) REVERT: A 773 GLU cc_start: 0.8939 (pt0) cc_final: 0.8692 (pt0) REVERT: A 954 GLN cc_start: 0.9245 (mt0) cc_final: 0.8892 (mt0) REVERT: A 988 GLU cc_start: 0.7830 (mp0) cc_final: 0.7413 (mp0) REVERT: A 1002 GLN cc_start: 0.9175 (tt0) cc_final: 0.8673 (tp40) REVERT: A 1029 MET cc_start: 0.8233 (tpp) cc_final: 0.7996 (ttm) REVERT: B 95 THR cc_start: 0.8470 (OUTLIER) cc_final: 0.8120 (t) REVERT: B 297 SER cc_start: 0.8521 (OUTLIER) cc_final: 0.8193 (t) REVERT: B 329 PHE cc_start: 0.7552 (m-80) cc_final: 0.6832 (m-10) REVERT: B 432 CYS cc_start: 0.5012 (p) cc_final: 0.4701 (p) REVERT: B 436 TRP cc_start: 0.8006 (p90) cc_final: 0.6026 (p90) REVERT: B 437 ASN cc_start: 0.8941 (p0) cc_final: 0.8554 (t0) REVERT: B 873 TYR cc_start: 0.8947 (OUTLIER) cc_final: 0.8718 (m-10) REVERT: B 902 MET cc_start: 0.8503 (tpp) cc_final: 0.8028 (tpt) REVERT: C 55 PHE cc_start: 0.8290 (m-80) cc_final: 0.7311 (m-80) REVERT: C 277 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.6733 (pp) REVERT: C 436 TRP cc_start: 0.7752 (p90) cc_final: 0.6650 (p90) REVERT: C 725 GLU cc_start: 0.8471 (tt0) cc_final: 0.7901 (mt-10) REVERT: C 740 MET cc_start: 0.8850 (tpt) cc_final: 0.8279 (tpt) REVERT: C 759 PHE cc_start: 0.8864 (m-80) cc_final: 0.8410 (m-80) REVERT: C 900 MET cc_start: 0.8321 (mtp) cc_final: 0.8023 (mtm) REVERT: C 902 MET cc_start: 0.8503 (tpp) cc_final: 0.8282 (tpt) REVERT: C 964 LYS cc_start: 0.9508 (tmtt) cc_final: 0.9209 (tptp) outliers start: 42 outliers final: 16 residues processed: 190 average time/residue: 0.1194 time to fit residues: 38.8910 Evaluate side-chains 138 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 873 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 70 optimal weight: 4.9990 chunk 281 optimal weight: 5.9990 chunk 171 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 247 optimal weight: 4.9990 chunk 36 optimal weight: 0.1980 chunk 186 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 227 optimal weight: 7.9990 chunk 197 optimal weight: 7.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN A 926 GLN A 953 ASN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.128708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.083163 restraints weight = 47424.274| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 3.88 r_work: 0.3102 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 23420 Z= 0.238 Angle : 0.631 10.238 31886 Z= 0.331 Chirality : 0.046 0.165 3645 Planarity : 0.005 0.054 4115 Dihedral : 5.224 39.988 3116 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 2.57 % Allowed : 15.20 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.14), residues: 2856 helix: 0.91 (0.20), residues: 662 sheet: -2.73 (0.17), residues: 670 loop : -2.56 (0.14), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 357 TYR 0.026 0.001 TYR C 91 PHE 0.024 0.002 PHE B1121 TRP 0.014 0.002 TRP B 64 HIS 0.006 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00555 (23384) covalent geometry : angle 0.62541 (31814) SS BOND : bond 0.00651 ( 36) SS BOND : angle 1.81786 ( 72) hydrogen bonds : bond 0.04678 ( 789) hydrogen bonds : angle 6.18256 ( 2187) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 119 time to evaluate : 0.854 Fit side-chains REVERT: A 53 ASP cc_start: 0.8323 (t70) cc_final: 0.7973 (t70) REVERT: A 309 GLU cc_start: 0.8738 (tp30) cc_final: 0.8229 (tm-30) REVERT: A 329 PHE cc_start: 0.7397 (m-80) cc_final: 0.7095 (m-80) REVERT: A 380 TYR cc_start: 0.8514 (m-80) cc_final: 0.7971 (m-80) REVERT: A 759 PHE cc_start: 0.8296 (m-80) cc_final: 0.7948 (m-80) REVERT: A 773 GLU cc_start: 0.8932 (pt0) cc_final: 0.8648 (pt0) REVERT: A 913 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7804 (pm20) REVERT: A 954 GLN cc_start: 0.9225 (mt0) cc_final: 0.8888 (mt0) REVERT: A 988 GLU cc_start: 0.7927 (mp0) cc_final: 0.7467 (mp0) REVERT: A 1002 GLN cc_start: 0.9188 (tt0) cc_final: 0.8762 (tp40) REVERT: A 1029 MET cc_start: 0.8487 (tpp) cc_final: 0.8215 (ttm) REVERT: B 95 THR cc_start: 0.8600 (OUTLIER) cc_final: 0.8259 (t) REVERT: B 297 SER cc_start: 0.8701 (OUTLIER) cc_final: 0.8498 (t) REVERT: B 329 PHE cc_start: 0.7502 (m-80) cc_final: 0.6956 (m-10) REVERT: B 356 LYS cc_start: 0.8126 (pttt) cc_final: 0.7821 (ptmt) REVERT: B 432 CYS cc_start: 0.5037 (p) cc_final: 0.4803 (p) REVERT: B 436 TRP cc_start: 0.7953 (p90) cc_final: 0.6248 (p90) REVERT: B 437 ASN cc_start: 0.8974 (p0) cc_final: 0.8653 (t0) REVERT: B 988 GLU cc_start: 0.8357 (mp0) cc_final: 0.7894 (mp0) REVERT: C 55 PHE cc_start: 0.8474 (m-80) cc_final: 0.7567 (m-80) REVERT: C 273 ARG cc_start: 0.8746 (mmt90) cc_final: 0.8394 (ttm-80) REVERT: C 277 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7090 (pp) REVERT: C 332 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7741 (tp) REVERT: C 436 TRP cc_start: 0.7761 (p90) cc_final: 0.6085 (p90) REVERT: C 740 MET cc_start: 0.8831 (tpt) cc_final: 0.8591 (tpt) REVERT: C 759 PHE cc_start: 0.8751 (m-80) cc_final: 0.8218 (m-10) REVERT: C 902 MET cc_start: 0.8679 (tpp) cc_final: 0.8165 (tpt) REVERT: C 904 TYR cc_start: 0.8101 (m-10) cc_final: 0.7894 (m-10) REVERT: C 964 LYS cc_start: 0.9527 (tmtt) cc_final: 0.9250 (tptp) REVERT: C 1002 GLN cc_start: 0.9216 (tt0) cc_final: 0.8951 (tp-100) outliers start: 66 outliers final: 37 residues processed: 176 average time/residue: 0.1155 time to fit residues: 35.2693 Evaluate side-chains 148 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 106 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 800 PHE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1066 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 117 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 230 optimal weight: 40.0000 chunk 245 optimal weight: 0.0050 chunk 157 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 243 optimal weight: 0.7980 chunk 204 optimal weight: 2.9990 chunk 213 optimal weight: 0.2980 overall best weight: 1.2198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.131391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.086184 restraints weight = 47091.403| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 3.88 r_work: 0.3159 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23420 Z= 0.134 Angle : 0.546 7.334 31886 Z= 0.285 Chirality : 0.044 0.156 3645 Planarity : 0.004 0.052 4115 Dihedral : 4.726 40.303 3116 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.50 % Allowed : 16.10 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.15), residues: 2856 helix: 1.48 (0.21), residues: 654 sheet: -2.28 (0.19), residues: 633 loop : -2.27 (0.14), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 357 TYR 0.016 0.001 TYR C1067 PHE 0.022 0.001 PHE C 201 TRP 0.012 0.001 TRP B 104 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00312 (23384) covalent geometry : angle 0.54171 (31814) SS BOND : bond 0.00544 ( 36) SS BOND : angle 1.61234 ( 72) hydrogen bonds : bond 0.03969 ( 789) hydrogen bonds : angle 5.67392 ( 2187) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 130 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8320 (t70) cc_final: 0.7958 (t70) REVERT: A 309 GLU cc_start: 0.8735 (tp30) cc_final: 0.8232 (tm-30) REVERT: A 380 TYR cc_start: 0.8341 (m-80) cc_final: 0.7821 (m-10) REVERT: A 574 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7615 (t0) REVERT: A 725 GLU cc_start: 0.8659 (tt0) cc_final: 0.8412 (mt-10) REVERT: A 759 PHE cc_start: 0.8304 (m-80) cc_final: 0.8000 (m-80) REVERT: A 773 GLU cc_start: 0.8838 (pt0) cc_final: 0.8592 (pt0) REVERT: A 913 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7773 (pm20) REVERT: A 954 GLN cc_start: 0.9220 (mt0) cc_final: 0.8844 (mt0) REVERT: A 988 GLU cc_start: 0.8006 (mp0) cc_final: 0.7609 (mp0) REVERT: A 1002 GLN cc_start: 0.9123 (tt0) cc_final: 0.8682 (tp40) REVERT: A 1029 MET cc_start: 0.8363 (tpp) cc_final: 0.8088 (ttm) REVERT: B 95 THR cc_start: 0.8260 (OUTLIER) cc_final: 0.7822 (t) REVERT: B 329 PHE cc_start: 0.7471 (m-80) cc_final: 0.6879 (m-10) REVERT: B 356 LYS cc_start: 0.8221 (pttt) cc_final: 0.7979 (ptmt) REVERT: B 432 CYS cc_start: 0.5155 (p) cc_final: 0.4705 (p) REVERT: B 436 TRP cc_start: 0.7897 (p90) cc_final: 0.6267 (p90) REVERT: B 437 ASN cc_start: 0.8907 (p0) cc_final: 0.8650 (t0) REVERT: B 574 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7126 (t0) REVERT: B 988 GLU cc_start: 0.8342 (mp0) cc_final: 0.7941 (mp0) REVERT: C 55 PHE cc_start: 0.8390 (m-80) cc_final: 0.7516 (m-80) REVERT: C 273 ARG cc_start: 0.8704 (mmt90) cc_final: 0.8395 (ttm-80) REVERT: C 277 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7511 (pp) REVERT: C 332 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7744 (tp) REVERT: C 436 TRP cc_start: 0.7838 (p90) cc_final: 0.6916 (p90) REVERT: C 574 ASP cc_start: 0.7311 (OUTLIER) cc_final: 0.6507 (t70) REVERT: C 755 GLN cc_start: 0.8315 (mt0) cc_final: 0.7995 (mm110) REVERT: C 900 MET cc_start: 0.8344 (mtp) cc_final: 0.8072 (mtm) REVERT: C 902 MET cc_start: 0.8572 (tpp) cc_final: 0.8317 (tpt) REVERT: C 904 TYR cc_start: 0.8029 (m-10) cc_final: 0.7805 (m-10) REVERT: C 954 GLN cc_start: 0.9263 (mt0) cc_final: 0.9039 (mt0) REVERT: C 964 LYS cc_start: 0.9489 (tmtt) cc_final: 0.9206 (tptp) REVERT: C 988 GLU cc_start: 0.8183 (mp0) cc_final: 0.7776 (mp0) REVERT: C 1002 GLN cc_start: 0.9192 (tt0) cc_final: 0.8885 (tp40) outliers start: 64 outliers final: 38 residues processed: 189 average time/residue: 0.1191 time to fit residues: 39.1060 Evaluate side-chains 162 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 117 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 116 optimal weight: 5.9990 chunk 274 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 273 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 255 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 214 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.128459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.082772 restraints weight = 46026.185| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 3.84 r_work: 0.3089 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 23420 Z= 0.261 Angle : 0.624 9.196 31886 Z= 0.329 Chirality : 0.046 0.157 3645 Planarity : 0.005 0.053 4115 Dihedral : 5.083 42.877 3116 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 3.27 % Allowed : 17.27 % Favored : 79.45 % 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: -2.07 (0.15), residues: 2856 helix: 1.16 (0.21), residues: 654 sheet: -2.31 (0.19), residues: 644 loop : -2.13 (0.14), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 357 TYR 0.029 0.002 TYR B 91 PHE 0.025 0.002 PHE B1121 TRP 0.012 0.002 TRP B 64 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00608 (23384) covalent geometry : angle 0.61930 (31814) SS BOND : bond 0.00656 ( 36) SS BOND : angle 1.80195 ( 72) hydrogen bonds : bond 0.04563 ( 789) hydrogen bonds : angle 5.91502 ( 2187) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 116 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8384 (t70) cc_final: 0.7985 (t70) REVERT: A 309 GLU cc_start: 0.8734 (tp30) cc_final: 0.8260 (tm-30) REVERT: A 329 PHE cc_start: 0.7390 (m-80) cc_final: 0.7186 (m-80) REVERT: A 380 TYR cc_start: 0.8365 (m-80) cc_final: 0.7815 (m-80) REVERT: A 725 GLU cc_start: 0.8719 (tt0) cc_final: 0.8329 (mt-10) REVERT: A 759 PHE cc_start: 0.8261 (m-80) cc_final: 0.7822 (m-80) REVERT: A 773 GLU cc_start: 0.8914 (pt0) cc_final: 0.8631 (pt0) REVERT: A 913 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7807 (pm20) REVERT: A 954 GLN cc_start: 0.9246 (mt0) cc_final: 0.8886 (mt0) REVERT: A 988 GLU cc_start: 0.8071 (mp0) cc_final: 0.7657 (mp0) REVERT: A 1002 GLN cc_start: 0.9151 (tt0) cc_final: 0.8745 (tp40) REVERT: A 1029 MET cc_start: 0.8483 (tpp) cc_final: 0.8226 (ttm) REVERT: B 95 THR cc_start: 0.8532 (OUTLIER) cc_final: 0.7920 (t) REVERT: B 356 LYS cc_start: 0.8251 (pttt) cc_final: 0.7993 (ptmt) REVERT: B 432 CYS cc_start: 0.5177 (p) cc_final: 0.4956 (p) REVERT: B 436 TRP cc_start: 0.7989 (p90) cc_final: 0.6023 (p90) REVERT: B 437 ASN cc_start: 0.8909 (p0) cc_final: 0.8619 (t0) REVERT: B 574 ASP cc_start: 0.8069 (OUTLIER) cc_final: 0.7093 (t0) REVERT: B 759 PHE cc_start: 0.8601 (OUTLIER) cc_final: 0.8258 (t80) REVERT: B 988 GLU cc_start: 0.8366 (mp0) cc_final: 0.7974 (mp0) REVERT: C 55 PHE cc_start: 0.8664 (m-80) cc_final: 0.7827 (m-80) REVERT: C 273 ARG cc_start: 0.8715 (mmt90) cc_final: 0.8317 (ttm-80) REVERT: C 277 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7257 (pp) REVERT: C 332 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7780 (tp) REVERT: C 436 TRP cc_start: 0.7766 (p90) cc_final: 0.6855 (p90) REVERT: C 755 GLN cc_start: 0.8305 (mt0) cc_final: 0.8027 (mm110) REVERT: C 855 PHE cc_start: 0.7226 (m-80) cc_final: 0.6931 (m-80) REVERT: C 902 MET cc_start: 0.8676 (tpp) cc_final: 0.8285 (tpt) REVERT: C 904 TYR cc_start: 0.8064 (m-10) cc_final: 0.7728 (m-10) REVERT: C 954 GLN cc_start: 0.9257 (mt0) cc_final: 0.9041 (mt0) REVERT: C 964 LYS cc_start: 0.9527 (tmtt) cc_final: 0.9244 (tptp) REVERT: C 988 GLU cc_start: 0.8189 (mp0) cc_final: 0.7757 (mp0) REVERT: C 1050 MET cc_start: 0.8643 (ptp) cc_final: 0.8434 (ptp) outliers start: 84 outliers final: 57 residues processed: 191 average time/residue: 0.1166 time to fit residues: 38.6621 Evaluate side-chains 174 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 111 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 800 PHE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 10 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 64 optimal weight: 0.0060 chunk 206 optimal weight: 2.9990 chunk 273 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 146 optimal weight: 0.8980 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 GLN A 755 GLN A1002 GLN B 655 HIS ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.128298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.082538 restraints weight = 47358.697| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 4.04 r_work: 0.3078 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23420 Z= 0.131 Angle : 0.542 7.286 31886 Z= 0.282 Chirality : 0.044 0.279 3645 Planarity : 0.004 0.051 4115 Dihedral : 4.633 42.231 3116 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.04 % Allowed : 18.01 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.15), residues: 2856 helix: 1.60 (0.21), residues: 655 sheet: -1.98 (0.19), residues: 656 loop : -1.91 (0.14), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 237 TYR 0.016 0.001 TYR C1067 PHE 0.019 0.001 PHE C 201 TRP 0.015 0.001 TRP C 353 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00305 (23384) covalent geometry : angle 0.53721 (31814) SS BOND : bond 0.00522 ( 36) SS BOND : angle 1.64005 ( 72) hydrogen bonds : bond 0.03902 ( 789) hydrogen bonds : angle 5.47731 ( 2187) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 126 time to evaluate : 0.833 Fit side-chains REVERT: A 309 GLU cc_start: 0.8738 (tp30) cc_final: 0.8210 (tm-30) REVERT: A 574 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7549 (t0) REVERT: A 725 GLU cc_start: 0.8664 (tt0) cc_final: 0.8411 (mt-10) REVERT: A 759 PHE cc_start: 0.8604 (m-80) cc_final: 0.8224 (m-80) REVERT: A 773 GLU cc_start: 0.8869 (pt0) cc_final: 0.8517 (pt0) REVERT: A 913 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7812 (pm20) REVERT: A 954 GLN cc_start: 0.9225 (mt0) cc_final: 0.8823 (mt0) REVERT: A 988 GLU cc_start: 0.8114 (mp0) cc_final: 0.7695 (mp0) REVERT: A 1002 GLN cc_start: 0.9079 (tt0) cc_final: 0.8698 (tp40) REVERT: A 1029 MET cc_start: 0.8415 (tpp) cc_final: 0.8149 (ttm) REVERT: B 356 LYS cc_start: 0.8244 (pttt) cc_final: 0.7985 (ptmt) REVERT: B 432 CYS cc_start: 0.5203 (p) cc_final: 0.4911 (p) REVERT: B 436 TRP cc_start: 0.7971 (p90) cc_final: 0.6054 (p90) REVERT: B 437 ASN cc_start: 0.8922 (p0) cc_final: 0.8700 (t0) REVERT: B 574 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.6985 (t0) REVERT: B 759 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.8003 (t80) REVERT: B 873 TYR cc_start: 0.8965 (OUTLIER) cc_final: 0.8705 (m-10) REVERT: B 902 MET cc_start: 0.8736 (tpt) cc_final: 0.7964 (tpt) REVERT: B 988 GLU cc_start: 0.8397 (mp0) cc_final: 0.7999 (mp0) REVERT: C 55 PHE cc_start: 0.8373 (m-80) cc_final: 0.7579 (m-80) REVERT: C 273 ARG cc_start: 0.8651 (mmt90) cc_final: 0.8311 (ttm-80) REVERT: C 277 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7442 (pp) REVERT: C 303 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7818 (tp) REVERT: C 332 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7792 (tp) REVERT: C 436 TRP cc_start: 0.7845 (p90) cc_final: 0.6795 (p90) REVERT: C 574 ASP cc_start: 0.7339 (OUTLIER) cc_final: 0.6551 (t70) REVERT: C 725 GLU cc_start: 0.8499 (tt0) cc_final: 0.8073 (mt-10) REVERT: C 755 GLN cc_start: 0.8302 (mt0) cc_final: 0.8018 (mm110) REVERT: C 900 MET cc_start: 0.8364 (mtp) cc_final: 0.7787 (mtm) REVERT: C 902 MET cc_start: 0.8572 (tpp) cc_final: 0.8276 (tpt) REVERT: C 904 TYR cc_start: 0.8028 (m-10) cc_final: 0.7784 (m-10) REVERT: C 954 GLN cc_start: 0.9278 (mt0) cc_final: 0.9032 (mt0) REVERT: C 964 LYS cc_start: 0.9510 (tmtt) cc_final: 0.9232 (tptp) REVERT: C 988 GLU cc_start: 0.8226 (mp0) cc_final: 0.7797 (mp0) outliers start: 78 outliers final: 51 residues processed: 195 average time/residue: 0.1166 time to fit residues: 39.6749 Evaluate side-chains 178 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 118 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 259 optimal weight: 2.9990 chunk 187 optimal weight: 0.7980 chunk 141 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 251 optimal weight: 0.8980 chunk 209 optimal weight: 4.9990 chunk 27 optimal weight: 30.0000 chunk 245 optimal weight: 10.0000 chunk 202 optimal weight: 8.9990 chunk 182 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 GLN ** C 437 ASN ** 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 = 0.3942 r_free = 0.3942 target = 0.126714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.080547 restraints weight = 47396.108| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 4.03 r_work: 0.3037 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 23420 Z= 0.197 Angle : 0.579 8.093 31886 Z= 0.302 Chirality : 0.045 0.214 3645 Planarity : 0.004 0.053 4115 Dihedral : 4.767 43.534 3116 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.08 % Allowed : 18.01 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.15), residues: 2856 helix: 1.57 (0.21), residues: 640 sheet: -1.94 (0.20), residues: 624 loop : -1.87 (0.14), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 237 TYR 0.021 0.001 TYR C 91 PHE 0.026 0.001 PHE C 201 TRP 0.016 0.002 TRP C 353 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00458 (23384) covalent geometry : angle 0.57384 (31814) SS BOND : bond 0.00545 ( 36) SS BOND : angle 1.76436 ( 72) hydrogen bonds : bond 0.04190 ( 789) hydrogen bonds : angle 5.60732 ( 2187) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 119 time to evaluate : 0.683 Fit side-chains revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8078 (t70) cc_final: 0.7607 (t70) REVERT: A 298 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7911 (mt-10) REVERT: A 309 GLU cc_start: 0.8740 (tp30) cc_final: 0.8211 (tm-30) REVERT: A 574 ASP cc_start: 0.8156 (OUTLIER) cc_final: 0.7680 (t0) REVERT: A 725 GLU cc_start: 0.8730 (tt0) cc_final: 0.8481 (mt-10) REVERT: A 759 PHE cc_start: 0.8420 (m-80) cc_final: 0.8081 (m-80) REVERT: A 773 GLU cc_start: 0.8930 (pt0) cc_final: 0.8650 (pt0) REVERT: A 913 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7769 (pm20) REVERT: A 954 GLN cc_start: 0.9248 (mt0) cc_final: 0.8867 (mt0) REVERT: A 988 GLU cc_start: 0.8106 (mp0) cc_final: 0.7719 (mp0) REVERT: A 1002 GLN cc_start: 0.9109 (tt0) cc_final: 0.8733 (tp40) REVERT: A 1029 MET cc_start: 0.8436 (tpp) cc_final: 0.8080 (ttm) REVERT: B 55 PHE cc_start: 0.8121 (m-80) cc_final: 0.7680 (m-80) REVERT: B 356 LYS cc_start: 0.8235 (pttt) cc_final: 0.7998 (ptmt) REVERT: B 436 TRP cc_start: 0.7963 (p90) cc_final: 0.6100 (p90) REVERT: B 574 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7120 (t0) REVERT: B 759 PHE cc_start: 0.8598 (OUTLIER) cc_final: 0.8132 (t80) REVERT: B 873 TYR cc_start: 0.8989 (OUTLIER) cc_final: 0.8763 (m-10) REVERT: B 988 GLU cc_start: 0.8357 (mp0) cc_final: 0.7939 (mp0) REVERT: C 55 PHE cc_start: 0.8590 (m-80) cc_final: 0.7740 (m-80) REVERT: C 273 ARG cc_start: 0.8698 (mmt90) cc_final: 0.8346 (ttm-80) REVERT: C 277 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7494 (pp) REVERT: C 332 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7754 (tp) REVERT: C 436 TRP cc_start: 0.7652 (p90) cc_final: 0.6549 (p90) REVERT: C 574 ASP cc_start: 0.7408 (OUTLIER) cc_final: 0.6428 (t70) REVERT: C 755 GLN cc_start: 0.8301 (mt0) cc_final: 0.8016 (mm110) REVERT: C 900 MET cc_start: 0.8456 (mtp) cc_final: 0.7875 (mtm) REVERT: C 902 MET cc_start: 0.8707 (tpp) cc_final: 0.8479 (tpt) REVERT: C 904 TYR cc_start: 0.8091 (m-10) cc_final: 0.7798 (m-10) REVERT: C 954 GLN cc_start: 0.9293 (mt0) cc_final: 0.9055 (mt0) REVERT: C 964 LYS cc_start: 0.9527 (tmtt) cc_final: 0.9247 (tptp) REVERT: C 988 GLU cc_start: 0.8255 (mp0) cc_final: 0.7829 (mp0) outliers start: 79 outliers final: 60 residues processed: 193 average time/residue: 0.1130 time to fit residues: 37.9707 Evaluate side-chains 177 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 108 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 113 optimal weight: 0.3980 chunk 119 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 223 optimal weight: 0.0870 chunk 266 optimal weight: 0.8980 chunk 280 optimal weight: 2.9990 chunk 239 optimal weight: 0.7980 chunk 228 optimal weight: 9.9990 chunk 138 optimal weight: 6.9990 chunk 146 optimal weight: 0.9980 chunk 256 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 GLN B 317 ASN B 437 ASN C 437 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.130195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.084629 restraints weight = 46621.395| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 4.04 r_work: 0.3118 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 23420 Z= 0.105 Angle : 0.524 8.297 31886 Z= 0.269 Chirality : 0.043 0.272 3645 Planarity : 0.004 0.049 4115 Dihedral : 4.351 42.576 3116 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.65 % Allowed : 18.60 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.16), residues: 2856 helix: 1.87 (0.21), residues: 663 sheet: -1.67 (0.20), residues: 636 loop : -1.71 (0.15), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 237 TYR 0.015 0.001 TYR C1067 PHE 0.028 0.001 PHE C 201 TRP 0.017 0.001 TRP C 353 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00241 (23384) covalent geometry : angle 0.51767 (31814) SS BOND : bond 0.00413 ( 36) SS BOND : angle 1.80591 ( 72) hydrogen bonds : bond 0.03620 ( 789) hydrogen bonds : angle 5.18670 ( 2187) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 134 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8086 (t70) cc_final: 0.7518 (t70) REVERT: A 104 TRP cc_start: 0.7228 (m-90) cc_final: 0.6310 (m-90) REVERT: A 298 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7884 (mt-10) REVERT: A 309 GLU cc_start: 0.8648 (tp30) cc_final: 0.8112 (tm-30) REVERT: A 574 ASP cc_start: 0.7411 (OUTLIER) cc_final: 0.7070 (t70) REVERT: A 725 GLU cc_start: 0.8641 (tt0) cc_final: 0.8122 (mt-10) REVERT: A 759 PHE cc_start: 0.8525 (m-80) cc_final: 0.8209 (m-80) REVERT: A 773 GLU cc_start: 0.8920 (pt0) cc_final: 0.8266 (pt0) REVERT: A 777 ASN cc_start: 0.8618 (m-40) cc_final: 0.8233 (m110) REVERT: A 954 GLN cc_start: 0.9249 (mt0) cc_final: 0.8817 (mt0) REVERT: A 988 GLU cc_start: 0.8185 (mp0) cc_final: 0.7730 (mp0) REVERT: A 1002 GLN cc_start: 0.9050 (tt0) cc_final: 0.8795 (tp40) REVERT: A 1029 MET cc_start: 0.8282 (tpp) cc_final: 0.8073 (ttm) REVERT: B 55 PHE cc_start: 0.7819 (m-80) cc_final: 0.7489 (m-80) REVERT: B 238 PHE cc_start: 0.6193 (p90) cc_final: 0.5826 (p90) REVERT: B 356 LYS cc_start: 0.8223 (pttt) cc_final: 0.7976 (ptmt) REVERT: B 436 TRP cc_start: 0.7942 (p90) cc_final: 0.6134 (p90) REVERT: B 574 ASP cc_start: 0.7800 (OUTLIER) cc_final: 0.6837 (t0) REVERT: B 759 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.8175 (t80) REVERT: B 873 TYR cc_start: 0.8912 (OUTLIER) cc_final: 0.8680 (m-10) REVERT: B 988 GLU cc_start: 0.8358 (mp0) cc_final: 0.7979 (mp0) REVERT: C 55 PHE cc_start: 0.8353 (m-80) cc_final: 0.7514 (m-80) REVERT: C 273 ARG cc_start: 0.8501 (mmt90) cc_final: 0.8183 (ttm-80) REVERT: C 277 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7275 (pp) REVERT: C 332 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7776 (tp) REVERT: C 436 TRP cc_start: 0.7625 (p90) cc_final: 0.6462 (p90) REVERT: C 574 ASP cc_start: 0.6836 (OUTLIER) cc_final: 0.6138 (t70) REVERT: C 725 GLU cc_start: 0.8494 (tt0) cc_final: 0.8010 (mt-10) REVERT: C 755 GLN cc_start: 0.8226 (mt0) cc_final: 0.7944 (mm110) REVERT: C 902 MET cc_start: 0.8543 (tpp) cc_final: 0.8255 (tpt) REVERT: C 904 TYR cc_start: 0.7999 (m-10) cc_final: 0.7783 (m-10) REVERT: C 954 GLN cc_start: 0.9283 (mt0) cc_final: 0.9031 (mt0) REVERT: C 964 LYS cc_start: 0.9557 (tmtt) cc_final: 0.9273 (tptp) REVERT: C 988 GLU cc_start: 0.8212 (mp0) cc_final: 0.7771 (mp0) outliers start: 68 outliers final: 46 residues processed: 195 average time/residue: 0.1141 time to fit residues: 38.6138 Evaluate side-chains 177 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 123 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 283 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 246 optimal weight: 7.9990 chunk 248 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 134 optimal weight: 30.0000 chunk 58 optimal weight: 3.9990 chunk 190 optimal weight: 0.6980 chunk 131 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 chunk 156 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.129765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.084126 restraints weight = 46852.852| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 4.04 r_work: 0.3105 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23420 Z= 0.116 Angle : 0.526 7.819 31886 Z= 0.270 Chirality : 0.043 0.210 3645 Planarity : 0.004 0.058 4115 Dihedral : 4.327 43.343 3116 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.53 % Allowed : 19.06 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.16), residues: 2856 helix: 1.89 (0.21), residues: 662 sheet: -1.50 (0.19), residues: 656 loop : -1.58 (0.15), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 237 TYR 0.016 0.001 TYR C1067 PHE 0.025 0.001 PHE C 201 TRP 0.017 0.001 TRP C 353 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00268 (23384) covalent geometry : angle 0.51951 (31814) SS BOND : bond 0.00489 ( 36) SS BOND : angle 1.77756 ( 72) hydrogen bonds : bond 0.03630 ( 789) hydrogen bonds : angle 5.16886 ( 2187) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 129 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8108 (t70) cc_final: 0.7755 (t70) REVERT: A 104 TRP cc_start: 0.7390 (m-90) cc_final: 0.6665 (m-90) REVERT: A 298 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7932 (mt-10) REVERT: A 309 GLU cc_start: 0.8693 (tp30) cc_final: 0.8169 (tm-30) REVERT: A 574 ASP cc_start: 0.7590 (OUTLIER) cc_final: 0.7087 (t0) REVERT: A 725 GLU cc_start: 0.8623 (tt0) cc_final: 0.8168 (mt-10) REVERT: A 759 PHE cc_start: 0.8545 (m-80) cc_final: 0.8281 (m-80) REVERT: A 773 GLU cc_start: 0.8930 (pt0) cc_final: 0.8305 (pt0) REVERT: A 777 ASN cc_start: 0.8579 (m-40) cc_final: 0.8239 (m110) REVERT: A 954 GLN cc_start: 0.9254 (mt0) cc_final: 0.8919 (mt0) REVERT: A 988 GLU cc_start: 0.8197 (mp0) cc_final: 0.7740 (mp0) REVERT: A 994 ASP cc_start: 0.9296 (t0) cc_final: 0.9060 (t0) REVERT: A 1002 GLN cc_start: 0.9177 (tt0) cc_final: 0.8823 (tp40) REVERT: A 1029 MET cc_start: 0.8391 (tpp) cc_final: 0.8128 (ttm) REVERT: B 55 PHE cc_start: 0.7946 (m-80) cc_final: 0.7614 (m-80) REVERT: B 356 LYS cc_start: 0.8262 (pttt) cc_final: 0.7989 (ptmt) REVERT: B 436 TRP cc_start: 0.7962 (p90) cc_final: 0.6175 (p90) REVERT: B 574 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.6820 (t0) REVERT: B 759 PHE cc_start: 0.8578 (OUTLIER) cc_final: 0.8129 (t80) REVERT: B 873 TYR cc_start: 0.8954 (OUTLIER) cc_final: 0.8719 (m-10) REVERT: B 988 GLU cc_start: 0.8382 (mp0) cc_final: 0.8036 (mp0) REVERT: C 55 PHE cc_start: 0.8390 (m-80) cc_final: 0.7574 (m-80) REVERT: C 273 ARG cc_start: 0.8581 (mmt90) cc_final: 0.8280 (ttm-80) REVERT: C 277 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7497 (pp) REVERT: C 332 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7730 (tp) REVERT: C 436 TRP cc_start: 0.7629 (p90) cc_final: 0.6003 (p90) REVERT: C 574 ASP cc_start: 0.7065 (OUTLIER) cc_final: 0.6246 (t70) REVERT: C 725 GLU cc_start: 0.8492 (tt0) cc_final: 0.8077 (mt-10) REVERT: C 755 GLN cc_start: 0.8245 (mt0) cc_final: 0.7975 (mm110) REVERT: C 900 MET cc_start: 0.8359 (mtp) cc_final: 0.8066 (mtm) REVERT: C 902 MET cc_start: 0.8568 (tpp) cc_final: 0.8316 (tpt) REVERT: C 904 TYR cc_start: 0.8047 (m-10) cc_final: 0.7829 (m-10) REVERT: C 954 GLN cc_start: 0.9292 (mt0) cc_final: 0.9028 (mt0) REVERT: C 964 LYS cc_start: 0.9574 (tmtt) cc_final: 0.9292 (tptp) REVERT: C 988 GLU cc_start: 0.8234 (mp0) cc_final: 0.7770 (mp0) outliers start: 65 outliers final: 49 residues processed: 188 average time/residue: 0.1164 time to fit residues: 38.4238 Evaluate side-chains 172 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 115 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 183 optimal weight: 0.6980 chunk 127 optimal weight: 9.9990 chunk 197 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 238 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 280 optimal weight: 0.3980 chunk 226 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 107 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.130298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.084545 restraints weight = 46753.672| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 4.06 r_work: 0.3117 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23420 Z= 0.111 Angle : 0.521 7.683 31886 Z= 0.268 Chirality : 0.043 0.169 3645 Planarity : 0.004 0.050 4115 Dihedral : 4.259 43.107 3116 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.38 % Allowed : 19.45 % Favored : 78.17 % 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: -0.95 (0.16), residues: 2856 helix: 2.04 (0.21), residues: 652 sheet: -1.39 (0.20), residues: 658 loop : -1.50 (0.15), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 237 TYR 0.014 0.001 TYR C1067 PHE 0.025 0.001 PHE C 201 TRP 0.015 0.001 TRP C 353 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00256 (23384) covalent geometry : angle 0.51586 (31814) SS BOND : bond 0.00458 ( 36) SS BOND : angle 1.67493 ( 72) hydrogen bonds : bond 0.03557 ( 789) hydrogen bonds : angle 5.08986 ( 2187) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 124 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8090 (t70) cc_final: 0.7722 (t70) REVERT: A 104 TRP cc_start: 0.7417 (m-90) cc_final: 0.6733 (m-90) REVERT: A 298 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7855 (mt-10) REVERT: A 309 GLU cc_start: 0.8631 (tp30) cc_final: 0.8097 (mm-30) REVERT: A 574 ASP cc_start: 0.7483 (OUTLIER) cc_final: 0.6961 (t0) REVERT: A 725 GLU cc_start: 0.8617 (tt0) cc_final: 0.8089 (mt-10) REVERT: A 745 ASP cc_start: 0.8201 (m-30) cc_final: 0.7803 (t0) REVERT: A 759 PHE cc_start: 0.8522 (m-80) cc_final: 0.8255 (m-80) REVERT: A 773 GLU cc_start: 0.8912 (pt0) cc_final: 0.8294 (pt0) REVERT: A 777 ASN cc_start: 0.8482 (m-40) cc_final: 0.8186 (m110) REVERT: A 954 GLN cc_start: 0.9271 (mt0) cc_final: 0.8919 (mt0) REVERT: A 988 GLU cc_start: 0.8151 (mp0) cc_final: 0.7679 (mp0) REVERT: A 994 ASP cc_start: 0.9299 (t0) cc_final: 0.9063 (t0) REVERT: A 1002 GLN cc_start: 0.9186 (tt0) cc_final: 0.8808 (tp40) REVERT: A 1029 MET cc_start: 0.8313 (tpp) cc_final: 0.8077 (ttm) REVERT: B 55 PHE cc_start: 0.7916 (m-80) cc_final: 0.7563 (m-80) REVERT: B 329 PHE cc_start: 0.7427 (m-80) cc_final: 0.7127 (m-10) REVERT: B 356 LYS cc_start: 0.8223 (pttt) cc_final: 0.7963 (ptmt) REVERT: B 436 TRP cc_start: 0.7837 (p90) cc_final: 0.6193 (p90) REVERT: B 574 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.6777 (t0) REVERT: B 759 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.8176 (t80) REVERT: B 873 TYR cc_start: 0.8903 (OUTLIER) cc_final: 0.8677 (m-10) REVERT: B 988 GLU cc_start: 0.8472 (mp0) cc_final: 0.8170 (mp0) REVERT: C 55 PHE cc_start: 0.8351 (m-80) cc_final: 0.7547 (m-80) REVERT: C 273 ARG cc_start: 0.8502 (mmt90) cc_final: 0.8179 (ttm-80) REVERT: C 277 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7371 (pp) REVERT: C 332 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7554 (tp) REVERT: C 436 TRP cc_start: 0.7610 (p90) cc_final: 0.5934 (p90) REVERT: C 574 ASP cc_start: 0.6748 (OUTLIER) cc_final: 0.5968 (t70) REVERT: C 725 GLU cc_start: 0.8486 (tt0) cc_final: 0.8008 (mt-10) REVERT: C 755 GLN cc_start: 0.8185 (mt0) cc_final: 0.7895 (mm110) REVERT: C 900 MET cc_start: 0.8279 (mtp) cc_final: 0.7982 (mtm) REVERT: C 902 MET cc_start: 0.8522 (tpp) cc_final: 0.8222 (tpt) REVERT: C 954 GLN cc_start: 0.9295 (mt0) cc_final: 0.9014 (mt0) REVERT: C 964 LYS cc_start: 0.9567 (tmtt) cc_final: 0.9286 (tptp) REVERT: C 984 LEU cc_start: 0.8541 (mt) cc_final: 0.8146 (tp) REVERT: C 988 GLU cc_start: 0.8187 (mp0) cc_final: 0.7906 (mp0) REVERT: C 1050 MET cc_start: 0.8469 (ptp) cc_final: 0.8157 (ptm) outliers start: 61 outliers final: 48 residues processed: 180 average time/residue: 0.1122 time to fit residues: 35.1900 Evaluate side-chains 174 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 118 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 263 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 145 optimal weight: 0.2980 chunk 31 optimal weight: 30.0000 chunk 167 optimal weight: 1.9990 chunk 128 optimal weight: 30.0000 chunk 193 optimal weight: 0.5980 chunk 135 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 GLN B1142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.128892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.083042 restraints weight = 46921.150| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 4.04 r_work: 0.3082 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23420 Z= 0.143 Angle : 0.541 9.178 31886 Z= 0.278 Chirality : 0.044 0.176 3645 Planarity : 0.004 0.049 4115 Dihedral : 4.375 43.924 3116 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.50 % Allowed : 19.49 % Favored : 78.01 % 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: -0.95 (0.16), residues: 2856 helix: 1.99 (0.21), residues: 648 sheet: -1.38 (0.20), residues: 638 loop : -1.47 (0.15), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 319 TYR 0.016 0.001 TYR C 91 PHE 0.025 0.001 PHE B 238 TRP 0.014 0.001 TRP C 353 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00332 (23384) covalent geometry : angle 0.53545 (31814) SS BOND : bond 0.00455 ( 36) SS BOND : angle 1.67534 ( 72) hydrogen bonds : bond 0.03796 ( 789) hydrogen bonds : angle 5.17437 ( 2187) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6259.52 seconds wall clock time: 107 minutes 35.24 seconds (6455.24 seconds total)